annotate dataset.py @ 231:38beb81f4e8b

Automated merge with ssh://projects@lgcm.iro.umontreal.ca/hg/pylearn
author Frederic Bastien <bastienf@iro.umontreal.ca>
date Tue, 27 May 2008 13:46:03 -0400
parents 17c5d080964b 6f55e301c687
children a70f2c973ea5 ddb88a8e9fd2
rev   line source
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
1
12
ff4e551490f1 Added LookupList type in lookup_list.py and used it to keep order
bengioy@esprit.iro.umontreal.ca
parents: 11
diff changeset
2 from lookup_list import LookupList
ff4e551490f1 Added LookupList type in lookup_list.py and used it to keep order
bengioy@esprit.iro.umontreal.ca
parents: 11
diff changeset
3 Example = LookupList
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
4 from misc import unique_elements_list_intersection
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
5 from string import join
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
6 from sys import maxint
171
895b4b60f5e8 bugfix. Otherwise the example was writed over and not a new one was returned
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 167
diff changeset
7 import numpy, copy
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
8
166
ee11ed427ba8 Created exceptions.py
Joseph Turian <turian@gmail.com>
parents: 163
diff changeset
9 from exceptions import *
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
10
110
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
11 class AttributesHolder(object):
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
12 def __init__(self): pass
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
13
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
14 def attributeNames(self):
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
15 raise AbstractFunction()
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
16
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
17 def setAttributes(self,attribute_names,attribute_values,make_copies=False):
134
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 132
diff changeset
18 """
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 132
diff changeset
19 Allow the attribute_values to not be a list (but a single value) if the attribute_names is of length 1.
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 132
diff changeset
20 """
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 132
diff changeset
21 if len(attribute_names)==1 and not (isinstance(attribute_values,list) or isinstance(attribute_values,tuple) ):
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 132
diff changeset
22 attribute_values = [attribute_values]
110
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
23 if make_copies:
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
24 for name,value in zip(attribute_names,attribute_values):
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
25 self.__setattr__(name,copy.deepcopy(value))
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
26 else:
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
27 for name,value in zip(attribute_names,attribute_values):
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
28 self.__setattr__(name,value)
193
cb6b945acf5a Complete redesign of learner...
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 188
diff changeset
29
cb6b945acf5a Complete redesign of learner...
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 188
diff changeset
30 def getAttributes(self,attribute_names=None, return_copy=False):
cb6b945acf5a Complete redesign of learner...
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 188
diff changeset
31 """
cb6b945acf5a Complete redesign of learner...
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 188
diff changeset
32 Return all (if attribute_names=None, in the order of attributeNames()) or a specified subset of attributes.
cb6b945acf5a Complete redesign of learner...
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 188
diff changeset
33 """
cb6b945acf5a Complete redesign of learner...
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 188
diff changeset
34 if attribute_names is None:
cb6b945acf5a Complete redesign of learner...
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 188
diff changeset
35 attribute_names = self.attributeNames()
cb6b945acf5a Complete redesign of learner...
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 188
diff changeset
36 if return_copy:
cb6b945acf5a Complete redesign of learner...
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 188
diff changeset
37 return [copy.copy(self.__getattribute__(name)) for name in attribute_names]
cb6b945acf5a Complete redesign of learner...
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 188
diff changeset
38 else:
cb6b945acf5a Complete redesign of learner...
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 188
diff changeset
39 return [self.__getattribute__(name) for name in attribute_names]
110
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
40
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
41
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression
bengioy@bengiomac.local
parents: 105
diff changeset
42 class DataSet(AttributesHolder):
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
43 """A virtual base class for datasets.
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
44
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
45 A DataSet can be seen as a generalization of a matrix, meant to be used in conjunction
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
46 with learning algorithms (for training and testing them): rows/records are called examples, and
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
47 columns/attributes are called fields. The field value for a particular example can be an arbitrary
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
48 python object, which depends on the particular dataset.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
49
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
50 We call a DataSet a 'stream' when its length is unbounded (otherwise its __len__ method
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
51 should return sys.maxint).
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
52
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
53 A DataSet is a generator of iterators; these iterators can run through the
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
54 examples or the fields in a variety of ways. A DataSet need not necessarily have a finite
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
55 or known length, so this class can be used to interface to a 'stream' which
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
56 feeds on-line learning (however, as noted below, some operations are not
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
57 feasible or not recommanded on streams).
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
58
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
59 To iterate over examples, there are several possibilities:
90
a289b8bed64c corrected comment
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 88
diff changeset
60 - for example in dataset:
a289b8bed64c corrected comment
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 88
diff changeset
61 - for val1,val2,... in dataset:
a289b8bed64c corrected comment
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 88
diff changeset
62 - for example in dataset(field1, field2,field3, ...):
a289b8bed64c corrected comment
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 88
diff changeset
63 - for val1,val2,val3 in dataset(field1, field2,field3):
72
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
64 - for minibatch in dataset.minibatches([field1, field2, ...],minibatch_size=N):
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
65 - for mini1,mini2,mini3 in dataset.minibatches([field1, field2, field3], minibatch_size=N):
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
66 Each of these is documented below. All of these iterators are expected
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
67 to provide, in addition to the usual 'next()' method, a 'next_index()' method
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
68 which returns a non-negative integer pointing to the position of the next
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
69 example that will be returned by 'next()' (or of the first example in the
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
70 next minibatch returned). This is important because these iterators
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
71 can wrap around the dataset in order to do multiple passes through it,
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
72 in possibly unregular ways if the minibatch size is not a divisor of the
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
73 dataset length.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
74
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
75 To iterate over fields, one can do
72
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
76 - for field in dataset.fields():
46
c5b07e87b0cb comments modif made by Yoshua
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 45
diff changeset
77 for field_value in field: # iterate over the values associated to that field for all the dataset examples
72
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
78 - for field in dataset(field1,field2,...).fields() to select a subset of fields
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
79 - for field in dataset.fields(field1,field2,...) to select a subset of fields
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
80 and each of these fields is iterable over the examples:
72
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
81 - for field_examples in dataset.fields():
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
82 for example_value in field_examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
83 ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
84 but when the dataset is a stream (unbounded length), it is not recommanded to do
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
85 such things because the underlying dataset may refuse to access the different fields in
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
86 an unsynchronized ways. Hence the fields() method is illegal for streams, by default.
132
f6505ec32dc3 Updated documentation slightly
Joseph Turian <turian@gmail.com>
parents: 128
diff changeset
87 The result of fields() is a L{DataSetFields} object, which iterates over fields,
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
88 and whose elements are iterable over examples. A DataSetFields object can
72
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
89 be turned back into a DataSet with its examples() method::
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
90 dataset2 = dataset1.fields().examples()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
91 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1).
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
92
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
93 Note: Fields are not mutually exclusive, i.e. two fields can overlap in their actual content.
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
94
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
95 Note: The content of a field can be of any type. Field values can also be 'missing'
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
96 (e.g. to handle semi-supervised learning), and in the case of numeric (numpy array)
46
c5b07e87b0cb comments modif made by Yoshua
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 45
diff changeset
97 fields (i.e. an ArrayFieldsDataSet), NaN plays the role of a missing value.
c5b07e87b0cb comments modif made by Yoshua
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 45
diff changeset
98 What about non-numeric values? None.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
99
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
100 Dataset elements can be indexed and sub-datasets (with a subset
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
101 of examples) can be extracted. These operations are not supported
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
102 by default in the case of streams.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
103
72
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
104 - dataset[:n] returns a dataset with the n first examples.
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
105
72
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
106 - dataset[i1:i2:s] returns a dataset with the examples i1,i1+s,...i2-s.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
107
72
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
108 - dataset[i] returns an Example.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
109
72
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
110 - dataset[[i1,i2,...in]] returns a dataset with examples i1,i2,...in.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
111
72
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
112 - dataset[fieldname] an iterable over the values of the field fieldname across
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
113 the dataset (the iterable is obtained by default by calling valuesVStack
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
114 over the values for individual examples).
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
115
72
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
116 - dataset.<property> returns the value of a property associated with
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
117 the name <property>. The following properties should be supported:
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
118 - 'description': a textual description or name for the dataset
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
119 - 'fieldtypes': a list of types (one per field)
78
3499918faa9d In the middle of designing TLearner
bengioy@bengiomac.local
parents: 77
diff changeset
120 A DataSet may have other attributes that it makes visible to other objects. These are
3499918faa9d In the middle of designing TLearner
bengioy@bengiomac.local
parents: 77
diff changeset
121 used to store information that is not example-wise but global to the dataset.
3499918faa9d In the middle of designing TLearner
bengioy@bengiomac.local
parents: 77
diff changeset
122 The list of names of these attributes is given by the attribute_names() method.
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
123
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
124 Datasets can be concatenated either vertically (increasing the length) or
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
125 horizontally (augmenting the set of fields), if they are compatible, using
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
126 the following operations (with the same basic semantics as numpy.hstack
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
127 and numpy.vstack):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
128
72
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
129 - dataset1 | dataset2 | dataset3 == dataset.hstack([dataset1,dataset2,dataset3])
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
130
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
131 creates a new dataset whose list of fields is the concatenation of the list of
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
132 fields of the argument datasets. This only works if they all have the same length.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
133
72
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
134 - dataset1 & dataset2 & dataset3 == dataset.vstack([dataset1,dataset2,dataset3])
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
135
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
136 creates a new dataset that concatenates the examples from the argument datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
137 (and whose length is the sum of the length of the argument datasets). This only
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
138 works if they all have the same fields.
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
139
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
140 According to the same logic, and viewing a DataSetFields object associated to
46
c5b07e87b0cb comments modif made by Yoshua
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 45
diff changeset
141 a DataSet as a kind of transpose of it, fields1 & fields2 concatenates fields of
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
142 a DataSetFields fields1 and fields2, and fields1 | fields2 concatenates their
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
143 examples.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
144
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
145 A dataset can hold arbitrary key-value pairs that may be used to access meta-data
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
146 or other properties of the dataset or associated with the dataset or the result
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
147 of a computation stored in a dataset. These can be accessed through the [key] syntax
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
148 when key is a string (or more specifically, neither an integer, a slice, nor a list).
78
3499918faa9d In the middle of designing TLearner
bengioy@bengiomac.local
parents: 77
diff changeset
149
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
150 A DataSet sub-class should always redefine the following methods:
72
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
151 - __len__ if it is not a stream
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
152 - fieldNames
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
153 - minibatches_nowrap (called by DataSet.minibatches())
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
154 - valuesHStack
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
155 - valuesVStack
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
156 For efficiency of implementation, a sub-class might also want to redefine
72
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
157 - hasFields
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
158 - __getitem__ may not be feasible with some streams
2b6656b2ef52 Changed docs slightly
Joseph Turian <turian@iro.umontreal.ca>
parents: 66
diff changeset
159 - __iter__
78
3499918faa9d In the middle of designing TLearner
bengioy@bengiomac.local
parents: 77
diff changeset
160 A sub-class should also append attributes to self._attribute_names
3499918faa9d In the middle of designing TLearner
bengioy@bengiomac.local
parents: 77
diff changeset
161 (the default value returned by attributeNames()).
3499918faa9d In the middle of designing TLearner
bengioy@bengiomac.local
parents: 77
diff changeset
162 By convention, attributes not in attributeNames() should have a name
3499918faa9d In the middle of designing TLearner
bengioy@bengiomac.local
parents: 77
diff changeset
163 starting with an underscore.
3499918faa9d In the middle of designing TLearner
bengioy@bengiomac.local
parents: 77
diff changeset
164 @todo enforce/test that convention!
2
3fddb1c8f955 Rewrote DataSet interface and created FiniteDataSet interface.
bengioy@bengiomac.local
parents: 1
diff changeset
165 """
1
2cd82666b9a7 Added statscollector and started writing dataset and learner.
bengioy@esprit.iro.umontreal.ca
parents: 0
diff changeset
166
83
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 82
diff changeset
167 numpy_vstack = lambda fieldname,values: numpy.vstack(values)
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 82
diff changeset
168 numpy_hstack = lambda fieldnames,values: numpy.hstack(values)
77
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
169
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
170 def __init__(self,description=None,fieldtypes=None):
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
171 if description is None:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
172 # by default return "<DataSetType>(<SuperClass1>,<SuperClass2>,...)"
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
173 description = type(self).__name__ + " ( " + join([x.__name__ for x in type(self).__bases__]) + " )"
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
174 self.description=description
60
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 57
diff changeset
175 self.fieldtypes=fieldtypes
78
3499918faa9d In the middle of designing TLearner
bengioy@bengiomac.local
parents: 77
diff changeset
176 self._attribute_names = ["description"]
3499918faa9d In the middle of designing TLearner
bengioy@bengiomac.local
parents: 77
diff changeset
177 if fieldtypes:
3499918faa9d In the middle of designing TLearner
bengioy@bengiomac.local
parents: 77
diff changeset
178 self._attribute_names.append("fieldtypes")
3499918faa9d In the middle of designing TLearner
bengioy@bengiomac.local
parents: 77
diff changeset
179
3499918faa9d In the middle of designing TLearner
bengioy@bengiomac.local
parents: 77
diff changeset
180 def attributeNames(self): return self._attribute_names
3499918faa9d In the middle of designing TLearner
bengioy@bengiomac.local
parents: 77
diff changeset
181
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
182 class MinibatchToSingleExampleIterator(object):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
183 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
184 Converts the result of minibatch iterator with minibatch_size==1 into
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
185 single-example values in the result. Therefore the result of
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
186 iterating on the dataset itself gives a sequence of single examples
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
187 (whereas the result of iterating over minibatches gives in each
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
188 Example field an iterable object over the individual examples in
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
189 the minibatch).
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
190 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
191 def __init__(self, minibatch_iterator):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
192 self.minibatch_iterator = minibatch_iterator
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
193 self.minibatch = None
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
194 def __iter__(self): #makes for loop work
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
195 return self
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
196 def next(self):
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
197 size1_minibatch = self.minibatch_iterator.next()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
198 if not self.minibatch:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
199 self.minibatch = Example(size1_minibatch.keys(),[value[0] for value in size1_minibatch.values()])
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
200 else:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
201 self.minibatch._values = [value[0] for value in size1_minibatch.values()]
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
202 return self.minibatch
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
203
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
204 def next_index(self):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
205 return self.minibatch_iterator.next_index()
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
206
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
207 def __iter__(self):
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
208 """Supports the syntax "for i in dataset: ..."
1
2cd82666b9a7 Added statscollector and started writing dataset and learner.
bengioy@esprit.iro.umontreal.ca
parents: 0
diff changeset
209
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
210 Using this syntax, "i" will be an Example instance (or equivalent) with
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
211 all the fields of DataSet self. Every field of "i" will give access to
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
212 a field of a single example. Fields should be accessible via
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
213 i["fielname"] or i[3] (in the order defined by the elements of the
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
214 Example returned by this iterator), but the derived class is free
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
215 to accept any type of identifier, and add extra functionality to the iterator.
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
216
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
217 The default implementation calls the minibatches iterator and extracts the first example of each field.
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
218 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
219 return DataSet.MinibatchToSingleExampleIterator(self.minibatches(None, minibatch_size = 1))
2
3fddb1c8f955 Rewrote DataSet interface and created FiniteDataSet interface.
bengioy@bengiomac.local
parents: 1
diff changeset
220
188
f01ac276c6fb added __contains__ to Dataset, added parent constructor call to ArrayDataSet
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 171
diff changeset
221 def __contains__(self, fieldname):
f01ac276c6fb added __contains__ to Dataset, added parent constructor call to ArrayDataSet
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 171
diff changeset
222 return (fieldname in self.fieldNames()) \
f01ac276c6fb added __contains__ to Dataset, added parent constructor call to ArrayDataSet
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 171
diff changeset
223 or (fieldname in self.attributeNames())
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
224
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
225 class MinibatchWrapAroundIterator(object):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
226 """
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
227 An iterator for minibatches that handles the case where we need to wrap around the
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
228 dataset because n_batches*minibatch_size > len(dataset). It is constructed from
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
229 a dataset that provides a minibatch iterator that does not need to handle that problem.
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
230 This class is a utility for dataset subclass writers, so that they do not have to handle
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
231 this issue multiple times, nor check that fieldnames are valid, nor handle the
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
232 empty fieldnames (meaning 'use all the fields').
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
233 """
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
234 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
235 self.dataset=dataset
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
236 self.fieldnames=fieldnames
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
237 self.minibatch_size=minibatch_size
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
238 self.n_batches=n_batches
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
239 self.n_batches_done=0
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
240 self.next_row=offset
98
7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 95
diff changeset
241 self.offset=offset
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
242 self.L=len(dataset)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
243 assert offset+minibatch_size<=self.L
98
7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 95
diff changeset
244 ds_nbatches = (self.L-self.next_row)/self.minibatch_size
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
245 if n_batches is not None:
98
7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 95
diff changeset
246 ds_nbatches = min(n_batches,ds_nbatches)
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
247 if fieldnames:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
248 assert dataset.hasFields(*fieldnames)
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
249 else:
98
7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 95
diff changeset
250 self.fieldnames=dataset.fieldNames()
7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 95
diff changeset
251 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size,
7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 95
diff changeset
252 ds_nbatches,self.next_row)
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
253
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
254 def __iter__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
255 return self
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
256
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
257 def next_index(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
258 return self.next_row
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
259
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
260 def next(self):
43
e92244f30116 Corrected iterator logic errors
bengioy@grenat.iro.umontreal.ca
parents: 42
diff changeset
261 if self.n_batches and self.n_batches_done==self.n_batches:
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
262 raise StopIteration
101
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 99
diff changeset
263 elif not self.n_batches and self.next_row ==self.L:
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 99
diff changeset
264 raise StopIteration
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
265 upper = self.next_row+self.minibatch_size
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
266 if upper <=self.L:
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
267 minibatch = self.iterator.next()
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
268 else:
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
269 if not self.n_batches:
101
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 99
diff changeset
270 upper=min(upper, self.L)
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 99
diff changeset
271 # if their is not a fixed number of batch, we continue to the end of the dataset.
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 99
diff changeset
272 # this can create a minibatch that is smaller then the minibatch_size
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 99
diff changeset
273 assert (self.L-self.next_row)<=self.minibatch_size
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 99
diff changeset
274 minibatch = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next()
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 99
diff changeset
275 else:
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 99
diff changeset
276 # we must concatenate (vstack) the bottom and top parts of our minibatch
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 99
diff changeset
277 # first get the beginning of our minibatch (top of dataset)
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 99
diff changeset
278 first_part = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next()
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 99
diff changeset
279 second_part = self.dataset.minibatches_nowrap(self.fieldnames,upper-self.L,1,0).next()
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 99
diff changeset
280 minibatch = Example(self.fieldnames,
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 99
diff changeset
281 [self.dataset.valuesVStack(name,[first_part[name],second_part[name]])
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 99
diff changeset
282 for name in self.fieldnames])
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
283 self.next_row=upper
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
284 self.n_batches_done+=1
43
e92244f30116 Corrected iterator logic errors
bengioy@grenat.iro.umontreal.ca
parents: 42
diff changeset
285 if upper >= self.L and self.n_batches:
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
286 self.next_row -= self.L
98
7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 95
diff changeset
287 ds_nbatches = (self.L-self.next_row)/self.minibatch_size
7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 95
diff changeset
288 if self.n_batches is not None:
7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 95
diff changeset
289 ds_nbatches = min(self.n_batches,ds_nbatches)
7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 95
diff changeset
290 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size,
7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 95
diff changeset
291 ds_nbatches,self.next_row)
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
292 return DataSetFields(MinibatchDataSet(minibatch,self.dataset.valuesVStack,
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
293 self.dataset.valuesHStack),
74
b4159cbdc06b Fixed errors raised by test_dataset
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 73
diff changeset
294 minibatch.keys())
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
295
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
296
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
297 minibatches_fieldnames = None
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
298 minibatches_minibatch_size = 1
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
299 minibatches_n_batches = None
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
300 def minibatches(self,
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
301 fieldnames = minibatches_fieldnames,
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
302 minibatch_size = minibatches_minibatch_size,
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
303 n_batches = minibatches_n_batches,
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
304 offset = 0):
6
d5738b79089a Removed MinibatchIterator and instead made minibatch_size a field of all DataSets,
bengioy@bengiomac.local
parents: 5
diff changeset
305 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
306 Return an iterator that supports three forms of syntax:
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
307
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
308 for i in dataset.minibatches(None,**kwargs): ...
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
309
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
310 for i in dataset.minibatches([f1, f2, f3],**kwargs): ...
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
311
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
312 for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ...
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
313
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
314 Using the first two syntaxes, "i" will be an indexable object, such as a list,
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
315 tuple, or Example instance. In both cases, i[k] is a list-like container
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
316 of a batch of current examples. In the second case, i[0] is
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
317 list-like container of the f1 field of a batch current examples, i[1] is
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
318 a list-like container of the f2 field, etc.
2
3fddb1c8f955 Rewrote DataSet interface and created FiniteDataSet interface.
bengioy@bengiomac.local
parents: 1
diff changeset
319
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
320 Using the first syntax, all the fields will be returned in "i".
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
321 Using the third syntax, i1, i2, i3 will be list-like containers of the
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
322 f1, f2, and f3 fields of a batch of examples on each loop iteration.
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
323
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
324 The minibatches iterator is expected to return upon each call to next()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
325 a DataSetFields object, which is a LookupList (indexed by the field names) whose
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
326 elements are iterable and indexable over the minibatch examples, and which keeps a pointer to
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
327 a sub-dataset that can be used to iterate over the individual examples
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
328 in the minibatch. Hence a minibatch can be converted back to a regular
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
329 dataset or its fields can be looked at individually (and possibly iterated over).
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
330
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
331 PARAMETERS
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
332 - fieldnames (list of any type, default None):
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
333 The loop variables i1, i2, i3 (in the example above) should contain the
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
334 f1, f2, and f3 fields of the current batch of examples. If None, the
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
335 derived class can choose a default, e.g. all fields.
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
336
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
337 - minibatch_size (integer, default 1)
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
338 On every iteration, the variables i1, i2, i3 will have
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
339 exactly minibatch_size elements. e.g. len(i1) == minibatch_size
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
340
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
341 - n_batches (integer, default None)
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
342 The iterator will loop exactly this many times, and then stop. If None,
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
343 the derived class can choose a default. If (-1), then the returned
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
344 iterator should support looping indefinitely.
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
345
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
346 - offset (integer, default 0)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
347 The iterator will start at example 'offset' in the dataset, rather than the default.
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
348
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
349 Note: A list-like container is something like a tuple, list, numpy.ndarray or
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
350 any other object that supports integer indexing and slicing.
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
351
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
352 """
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
353 return DataSet.MinibatchWrapAroundIterator(self,fieldnames,minibatch_size,n_batches,offset)
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
354
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
355 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
356 """
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
357 This is the minibatches iterator generator that sub-classes must define.
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
358 It does not need to worry about wrapping around multiple times across the dataset,
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
359 as this is handled by MinibatchWrapAroundIterator when DataSet.minibatches() is called.
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
360 The next() method of the returned iterator does not even need to worry about
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
361 the termination condition (as StopIteration will be raised by DataSet.minibatches
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
362 before an improper call to minibatches_nowrap's next() is made).
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
363 That next() method can assert that its next row will always be within [0,len(dataset)).
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
364 The iterator returned by minibatches_nowrap does not need to implement
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
365 a next_index() method either, as this will be provided by MinibatchWrapAroundIterator.
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
366 """
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
367 raise AbstractFunction()
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
368
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
369 def __len__(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
370 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
371 len(dataset) returns the number of examples in the dataset.
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
372 By default, a DataSet is a 'stream', i.e. it has an unbounded length (sys.maxint).
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
373 Sub-classes which implement finite-length datasets should redefine this method.
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
374 Some methods only make sense for finite-length datasets.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
375 """
123
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 110
diff changeset
376 return maxint
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
377
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
378 def is_unbounded(self):
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
379 """
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
380 Tests whether a dataset is unbounded (e.g. a stream).
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
381 """
123
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 110
diff changeset
382 return len(self)==maxint
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
383
26
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
bengioy@grenat.iro.umontreal.ca
parents: 23
diff changeset
384 def hasFields(self,*fieldnames):
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
385 """
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
386 Return true if the given field name (or field names, if multiple arguments are
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
387 given) is recognized by the DataSet (i.e. can be used as a field name in one
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
388 of the iterators).
29
46c5c90019c2 Changed apply_function so that it propagates methods of the source.
bengioy@grenat.iro.umontreal.ca
parents: 28
diff changeset
389
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
390 The default implementation may be inefficient (O(# fields in dataset)), as it calls the fieldNames()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
391 method. Many datasets may store their field names in a dictionary, which would allow more efficiency.
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
392 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
393 return len(unique_elements_list_intersection(fieldnames,self.fieldNames()))>0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
394
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
395 def fieldNames(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
396 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
397 Return the list of field names that are supported by the iterators,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
398 and for which hasFields(fieldname) would return True.
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
399 """
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
400 raise AbstractFunction()
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
401
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
402 def __call__(self,*fieldnames):
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
403 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
404 Return a dataset that sees only the fields whose name are specified.
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
405 """
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
406 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
407 return self.fields(*fieldnames).examples()
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
408
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
409 def fields(self,*fieldnames):
29
46c5c90019c2 Changed apply_function so that it propagates methods of the source.
bengioy@grenat.iro.umontreal.ca
parents: 28
diff changeset
410 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
411 Return a DataSetFields object associated with this dataset.
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
412 """
74
b4159cbdc06b Fixed errors raised by test_dataset
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 73
diff changeset
413 return DataSetFields(self,fieldnames)
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
414
2
3fddb1c8f955 Rewrote DataSet interface and created FiniteDataSet interface.
bengioy@bengiomac.local
parents: 1
diff changeset
415 def __getitem__(self,i):
28
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
416 """
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
417 dataset[i] returns the (i+1)-th example of the dataset.
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
418 dataset[i:j] returns the subdataset with examples i,i+1,...,j-1.
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
419 dataset[i:j:s] returns the subdataset with examples i,i+2,i+4...,j-2.
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
420 dataset[[i1,i2,..,in]] returns the subdataset with examples i1,i2,...,in.
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
421 dataset['key'] returns a property associated with the given 'key' string.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
422 If 'key' is a fieldname, then the VStacked field values (iterable over
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
423 field values) for that field is returned. Other keys may be supported
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
424 by different dataset subclasses. The following key names are encouraged:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
425 - 'description': a textual description or name for the dataset
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
426 - '<fieldname>.type': a type name or value for a given <fieldname>
1
2cd82666b9a7 Added statscollector and started writing dataset and learner.
bengioy@esprit.iro.umontreal.ca
parents: 0
diff changeset
427
39
c682c6e9bf93 Minor edits
bengioy@esprit.iro.umontreal.ca
parents: 38
diff changeset
428 Note that some stream datasets may be unable to implement random access, i.e.
c682c6e9bf93 Minor edits
bengioy@esprit.iro.umontreal.ca
parents: 38
diff changeset
429 arbitrary slicing/indexing
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
430 because they can only iterate through examples one or a minibatch at a time
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
431 and do not actually store or keep past (or future) examples.
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
432
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
433 The default implementation of getitem uses the minibatches iterator
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
434 to obtain one example, one slice, or a list of examples. It may not
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
435 always be the most efficient way to obtain the result, especially if
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
436 the data are actually stored in a memory array.
28
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
437 """
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
438 # check for an index
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
439 if type(i) is int:
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
440 return DataSet.MinibatchToSingleExampleIterator(
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
441 self.minibatches(minibatch_size=1,n_batches=1,offset=i)).next()
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
442 rows=None
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
443 # or a slice
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
444 if type(i) is slice:
211
bd728c83faff in __get__, problem if the i.stop was None, i being the slice, added one line replacing None by the len(self)
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 203
diff changeset
445 #print 'i=',i
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
446 if not i.start: i=slice(0,i.stop,i.step)
211
bd728c83faff in __get__, problem if the i.stop was None, i being the slice, added one line replacing None by the len(self)
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 203
diff changeset
447 if not i.stop: i=slice(i.start,len(self),i.step)
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
448 if not i.step: i=slice(i.start,i.stop,1)
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
449 if i.step is 1:
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
450 return self.minibatches(minibatch_size=i.stop-i.start,n_batches=1,offset=i.start).next().examples()
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
451 rows = range(i.start,i.stop,i.step)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
452 # or a list of indices
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
453 elif type(i) is list:
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
454 rows = i
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
455 if rows is not None:
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
456 examples = [self[row] for row in rows]
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
457 fields_values = zip(*examples)
45
a5c70dc42972 Test functions for dataset.py
bengioy@grenat.iro.umontreal.ca
parents: 44
diff changeset
458 return MinibatchDataSet(
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
459 Example(self.fieldNames(),[ self.valuesVStack(fieldname,field_values)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
460 for fieldname,field_values
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
461 in zip(self.fieldNames(),fields_values)]),
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
462 self.valuesVStack,self.valuesHStack)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
463 # else check for a fieldname
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
464 if self.hasFields(i):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
465 return self.minibatches(fieldnames=[i],minibatch_size=len(self),n_batches=1,offset=0).next()[0]
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
466 # else we are trying to access a property of the dataset
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
467 assert i in self.__dict__ # else it means we are trying to access a non-existing property
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
468 return self.__dict__[i]
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
469
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
470 def valuesHStack(self,fieldnames,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
471 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
472 Return a value that corresponds to concatenating (horizontally) several field values.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
473 This can be useful to merge some fields. The implementation of this operation is likely
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
474 to involve a copy of the original values. When the values are numpy arrays, the
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
475 result should be numpy.hstack(values). If it makes sense, this operation should
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
476 work as well when each value corresponds to multiple examples in a minibatch
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
477 e.g. if each value is a Ni-vector and a minibatch of length L is a LxNi matrix,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
478 then the result should be a Lx(N1+N2+..) matrix equal to numpy.hstack(values).
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
479 The default is to use numpy.hstack for numpy.ndarray values, and a list
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
480 pointing to the original values for other data types.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
481 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
482 all_numpy=True
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
483 for value in fieldvalues:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
484 if not type(value) is numpy.ndarray:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
485 all_numpy=False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
486 if all_numpy:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
487 return numpy.hstack(fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
488 # the default implementation of horizontal stacking is to put values in a list
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
489 return fieldvalues
26
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
bengioy@grenat.iro.umontreal.ca
parents: 23
diff changeset
490
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
bengioy@grenat.iro.umontreal.ca
parents: 23
diff changeset
491
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
492 def valuesVStack(self,fieldname,values):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
493 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
494 Return a value that corresponds to concatenating (vertically) several values of the
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
495 same field. This can be important to build a minibatch out of individual examples. This
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
496 is likely to involve a copy of the original values. When the values are numpy arrays, the
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
497 result should be numpy.vstack(values).
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
498 The default is to use numpy.vstack for numpy.ndarray values, and a list
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
499 pointing to the original values for other data types.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
500 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
501 all_numpy=True
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
502 for value in values:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
503 if not type(value) is numpy.ndarray:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
504 all_numpy=False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
505 if all_numpy:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
506 return numpy.vstack(values)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
507 # the default implementation of vertical stacking is to put values in a list
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
508 return values
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
509
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
510 def __or__(self,other):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
511 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
512 dataset1 | dataset2 returns a dataset whose list of fields is the concatenation of the list of
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
513 fields of the argument datasets. This only works if they all have the same length.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
514 """
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
515 return HStackedDataSet([self,other])
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
516
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
517 def __and__(self,other):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
518 """
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
519 dataset1 & dataset2 is a dataset that concatenates the examples from the argument datasets
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
520 (and whose length is the sum of the length of the argument datasets). This only
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
521 works if they all have the same fields.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
522 """
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
523 return VStackedDataSet([self,other])
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
524
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
525 def hstack(datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
526 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
527 hstack(dataset1,dataset2,...) returns dataset1 | datataset2 | ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
528 which is a dataset whose fields list is the concatenation of the fields
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
529 of the individual datasets.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
530 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
531 assert len(datasets)>0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
532 if len(datasets)==1:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
533 return datasets[0]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
534 return HStackedDataSet(datasets)
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
535
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
536 def vstack(datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
537 """
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
538 vstack(dataset1,dataset2,...) returns dataset1 & datataset2 & ...
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
539 which is a dataset which iterates first over the examples of dataset1, then
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
540 over those of dataset2, etc.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
541 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
542 assert len(datasets)>0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
543 if len(datasets)==1:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
544 return datasets[0]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
545 return VStackedDataSet(datasets)
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
546
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
547 class FieldsSubsetDataSet(DataSet):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
548 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
549 A sub-class of L{DataSet} that selects a subset of the fields.
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
550 """
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
551 def __init__(self,src,fieldnames):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
552 self.src=src
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
553 self.fieldnames=fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
554 assert src.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
555 self.valuesHStack = src.valuesHStack
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
556 self.valuesVStack = src.valuesVStack
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
557
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
558 def __len__(self): return len(self.src)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
559
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
560 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
561 return self.fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
562
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
563 def __iter__(self):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
564 class FieldsSubsetIterator(object):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
565 def __init__(self,ds):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
566 self.ds=ds
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
567 self.src_iter=ds.src.__iter__()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
568 self.example=None
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
569 def __iter__(self): return self
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
570 def next(self):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
571 complete_example = self.src_iter.next()
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
572 if self.example:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
573 self.example._values=[complete_example[field]
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
574 for field in self.ds.fieldnames]
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
575 else:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
576 self.example=Example(self.ds.fieldnames,
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
577 [complete_example[field] for field in self.ds.fieldnames])
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
578 return self.example
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
579 return FieldsSubsetIterator(self)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
580
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
581 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
582 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
583 return self.src.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
584 def __getitem__(self,i):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
585 return FieldsSubsetDataSet(self.src[i],self.fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
586
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
587
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
588 class DataSetFields(LookupList):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
589 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
590 Although a L{DataSet} iterates over examples (like rows of a matrix), an associated
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
591 DataSetFields iterates over fields (like columns of a matrix), and can be understood
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
592 as a transpose of the associated dataset.
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
593
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
594 To iterate over fields, one can do
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
595 * for fields in dataset.fields()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
596 * for fields in dataset(field1,field2,...).fields() to select a subset of fields
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
597 * for fields in dataset.fields(field1,field2,...) to select a subset of fields
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
598 and each of these fields is iterable over the examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
599 * for field_examples in dataset.fields():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
600 for example_value in field_examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
601 ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
602 but when the dataset is a stream (unbounded length), it is not recommanded to do
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
603 such things because the underlying dataset may refuse to access the different fields in
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
604 an unsynchronized ways. Hence the fields() method is illegal for streams, by default.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
605 The result of fields() is a DataSetFields object, which iterates over fields,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
606 and whose elements are iterable over examples. A DataSetFields object can
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
607 be turned back into a DataSet with its examples() method:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
608 dataset2 = dataset1.fields().examples()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
609 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1).
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
610
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
611 DataSetFields can be concatenated vertically or horizontally. To be consistent with
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
612 the syntax used for DataSets, the | concatenates the fields and the & concatenates
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
613 the examples.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
614 """
74
b4159cbdc06b Fixed errors raised by test_dataset
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 73
diff changeset
615 def __init__(self,dataset,fieldnames):
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
616 original_dataset=dataset
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
617 if not fieldnames:
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
618 fieldnames=dataset.fieldNames()
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
619 elif not fieldnames==dataset.fieldNames():
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
620 dataset = FieldsSubsetDataSet(dataset,fieldnames)
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
621 assert dataset.hasFields(*fieldnames)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
622 self.dataset=dataset
66
dde1fb1b63ba fixed test and removed print
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 65
diff changeset
623
64
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
624 if isinstance(dataset,MinibatchDataSet):
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
625 LookupList.__init__(self,fieldnames,list(dataset._fields))
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
626 elif isinstance(original_dataset,MinibatchDataSet):
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
627 LookupList.__init__(self,fieldnames,
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
628 [original_dataset._fields[field]
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
629 for field in fieldnames])
64
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
630 else:
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
631 minibatch_iterator = dataset.minibatches(fieldnames,
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
632 minibatch_size=len(dataset),
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
633 n_batches=1)
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
634 minibatch=minibatch_iterator.next()
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
635 LookupList.__init__(self,fieldnames,minibatch)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
636
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
637 def examples(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
638 return self.dataset
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
639
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
640 def __or__(self,other):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
641 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
642 fields1 | fields2 is a DataSetFields that whose list of examples is the concatenation
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
643 of the list of examples of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
644 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
645 return (self.examples() + other.examples()).fields()
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
646
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
647 def __and__(self,other):
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
648 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
649 fields1 + fields2 is a DataSetFields that whose list of fields is the concatenation
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
650 of the fields of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
651 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
652 return (self.examples() | other.examples()).fields()
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
653
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
654
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
655 class MinibatchDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
656 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
657 Turn a L{LookupList} of same-length (iterable) fields into an example-iterable dataset.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
658 Each element of the lookup-list should be an iterable and sliceable, all of the same length.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
659 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
660 def __init__(self,fields_lookuplist,values_vstack=DataSet().valuesVStack,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
661 values_hstack=DataSet().valuesHStack):
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
662 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
663 The user can (and generally should) also provide values_vstack(fieldname,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
664 and a values_hstack(fieldnames,fieldvalues) functions behaving with the same
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
665 semantics as the DataSet methods of the same name (but without the self argument).
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
666 """
211
bd728c83faff in __get__, problem if the i.stop was None, i being the slice, added one line replacing None by the len(self)
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 203
diff changeset
667
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
668 self._fields=fields_lookuplist
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
669 assert len(fields_lookuplist)>0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
670 self.length=len(fields_lookuplist[0])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
671 for field in fields_lookuplist[1:]:
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
672 if self.length != len(field) :
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
673 print 'self.length = ',self.length
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
674 print 'len(field) = ', len(field)
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
675 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
676 print 'field=',field
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
677 assert self.length==len(field)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
678 self.values_vstack=values_vstack
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
679 self.values_hstack=values_hstack
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
680
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
681 def __len__(self):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
682 return self.length
28
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
683
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
684 def __getitem__(self,i):
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
685 if type(i) in (slice,list):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
686 return DataSetFields(MinibatchDataSet(
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
687 Example(self._fields.keys(),[field[i] for field in self._fields])),self.fieldNames())
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
688 if type(i) is int:
85
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 83
diff changeset
689 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
690 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
691 return self._fields[i]
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
692 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
693 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
694
29
46c5c90019c2 Changed apply_function so that it propagates methods of the source.
bengioy@grenat.iro.umontreal.ca
parents: 28
diff changeset
695 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
696 return self._fields.keys()
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
697
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
698 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
699 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
700 if fieldname not in self._fields.keys():
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
701 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
702 return True
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
703
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
704 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
705 #@TODO bug somewhere here, fieldnames doesnt seem to be well handled
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
706 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
707 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
708 # 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
709 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
710 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
711
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
712 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
713 self.next_example=offset
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
714 assert minibatch_size > 0
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
715 if offset+minibatch_size > ds.length:
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
716 raise NotImplementedError()
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
717 def __iter__(self):
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
718 return self
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
719 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
720 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
721 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
722 #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
723 # [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
724 # 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
725 # 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
726 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
727 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
728 #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
729 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
730 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
731 #print minibatch
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
732 self.next_example+=minibatch_size
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
733 return minibatch
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
734
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
735 # 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
736 return Iterator(self,fieldnames)
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
737
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
738 def valuesVStack(self,fieldname,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
739 return self.values_vstack(fieldname,fieldvalues)
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
740
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
741 def valuesHStack(self,fieldnames,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
742 return self.values_hstack(fieldnames,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
743
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
744 class HStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
745 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
746 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
747 i.e. whose list of fields is the concatenation of their lists of fields.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
748
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
749 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
750 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
751 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
752
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
753 @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
754 """
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
755 def __init__(self,datasets,accept_nonunique_names=False,description=None,field_types=None):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
756 DataSet.__init__(self,description,field_types)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
757 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
758 self.accept_nonunique_names=accept_nonunique_names
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
759 self.fieldname2dataset={}
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
760
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
761 def rename_field(fieldname,dataset,i):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
762 if hasattr(dataset,"__name__"):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
763 return dataset.__name__ + "." + fieldname
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
764 return fieldname+"."+str(i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
765
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
766 # make sure all datasets have the same length and unique field names
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
767 self.length=None
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
768 names_to_change=[]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
769 for i in xrange(len(datasets)):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
770 dataset = datasets[i]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
771 length=len(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
772 if self.length:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
773 assert self.length==length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
774 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
775 self.length=length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
776 for fieldname in dataset.fieldNames():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
777 if fieldname in self.fieldname2dataset: # name conflict!
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
778 if accept_nonunique_names:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
779 fieldname=rename_field(fieldname,dataset,i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
780 names2change.append((fieldname,i))
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
781 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
782 raise ValueError("Incompatible datasets: non-unique field name = "+fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
783 self.fieldname2dataset[fieldname]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
784 for fieldname,i in names_to_change:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
785 del self.fieldname2dataset[fieldname]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
786 self.fieldname2dataset[rename_field(fieldname,self.datasets[i],i)]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
787
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
788 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
789 for fieldname in fieldnames:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
790 if not fieldname in self.fieldname2dataset:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
791 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
792 return True
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
793
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
794 def fieldNames(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
795 return self.fieldname2dataset.keys()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
796
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
797 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
798
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
799 class HStackedIterator(object):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
800 def __init__(self,hsds,iterators):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
801 self.hsds=hsds
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
802 self.iterators=iterators
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
803 def __iter__(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
804 return self
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
805 def next(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
806 # concatenate all the fields of the minibatches
140
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
807 l=LookupList()
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
808 for iter in self.iterators:
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
809 l.append_lookuplist(iter.next())
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
810 return l
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
811
125
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 123
diff changeset
812 assert self.hasFields(*fieldnames)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
813 # find out which underlying datasets are necessary to service the required fields
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
814 # and construct corresponding minibatch iterators
140
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
815 if fieldnames and fieldnames!=self.fieldNames():
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
816 datasets=set([])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
817 fields_in_dataset=dict([(dataset,[]) for dataset in datasets])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
818 for fieldname in fieldnames:
136
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 125
diff changeset
819 dataset=self.datasets[self.fieldname2dataset[fieldname]]
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
820 datasets.add(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
821 fields_in_dataset[dataset].append(fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
822 datasets=list(datasets)
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
823 iterators=[dataset.minibatches(fields_in_dataset[dataset],minibatch_size,n_batches,offset)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
824 for dataset in datasets]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
825 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
826 datasets=self.datasets
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
827 iterators=[dataset.minibatches(None,minibatch_size,n_batches,offset) for dataset in datasets]
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
828 return HStackedIterator(self,iterators)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
829
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
830
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
831 def valuesVStack(self,fieldname,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
832 return self.datasets[self.fieldname2dataset[fieldname]].valuesVStack(fieldname,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
833
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
834 def valuesHStack(self,fieldnames,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
835 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
836 We will use the sub-dataset associated with the first fieldname in the fieldnames list
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
837 to do the work, hoping that it can cope with the other values (i.e. won't care
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
838 about the incompatible fieldnames). Hence this heuristic will always work if
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
839 all the fieldnames are of the same sub-dataset.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
840 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
841 return self.datasets[self.fieldname2dataset[fieldnames[0]]].valuesHStack(fieldnames,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
842
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
843 class VStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
844 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
845 A L{DataSet} that wraps several datasets and shows a view that includes all their examples,
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
846 in the order provided. This clearly assumes that they all have the same field names
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
847 and all (except possibly the last one) are of finite length.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
848
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
849 @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
850 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
851 def __init__(self,datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
852 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
853 self.length=0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
854 self.index2dataset={}
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
855 assert len(datasets)>0
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
856 fieldnames = datasets[-1].fieldNames()
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
857 self.datasets_start_row=[]
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
858 # We use this map from row index to dataset index for constant-time random access of examples,
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
859 # to avoid having to search for the appropriate dataset each time and slice is asked for.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
860 for dataset,k in enumerate(datasets[0:-1]):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
861 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
862 L=len(dataset)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
863 for i in xrange(L):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
864 self.index2dataset[self.length+i]=k
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
865 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
866 self.length+=L
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
867 assert dataset.fieldNames()==fieldnames
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
868 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
869 self.length+=len(datasets[-1])
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
870 # If length is very large, we should use a more memory-efficient mechanism
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
871 # that does not store all indices
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
872 if self.length>1000000:
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
873 # 1 million entries would require about 60 meg for the index2dataset map
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
874 # TODO
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
875 print "A more efficient mechanism for index2dataset should be implemented"
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
876
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
877 def __len__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
878 return self.length
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
879
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
880 def fieldNames(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
881 return self.datasets[0].fieldNames()
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
882
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
883 def hasFields(self,*fieldnames):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
884 return self.datasets[0].hasFields(*fieldnames)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
885
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
886 def locate_row(self,row):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
887 """Return (dataset_index, row_within_dataset) for global row number"""
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
888 dataset_index = self.index2dataset[row]
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
889 row_within_dataset = self.datasets_start_row[dataset_index]
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
890 return dataset_index, row_within_dataset
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
891
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
892 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
893
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
894 class VStackedIterator(object):
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
895 def __init__(self,vsds):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
896 self.vsds=vsds
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
897 self.next_row=offset
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
898 self.next_dataset_index,self.next_dataset_row=self.vsds.locate_row(offset)
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
899 self.current_iterator,self.n_left_at_the_end_of_ds,self.n_left_in_mb= \
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
900 self.next_iterator(vsds.datasets[0],offset,n_batches)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
901
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
902 def next_iterator(self,dataset,starting_offset,batches_left):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
903 L=len(dataset)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
904 ds_nbatches = (L-starting_offset)/minibatch_size
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
905 if batches_left is not None:
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
906 ds_nbatches = max(batches_left,ds_nbatches)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
907 if minibatch_size>L:
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
908 ds_minibatch_size=L
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
909 n_left_in_mb=minibatch_size-L
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
910 ds_nbatches=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
911 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
912 n_left_in_mb=0
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
913 return dataset.minibatches(fieldnames,minibatch_size,ds_nbatches,starting_offset), \
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
914 L-(starting_offset+ds_nbatches*minibatch_size), n_left_in_mb
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
915
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
916 def move_to_next_dataset(self):
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
917 if self.n_left_at_the_end_of_ds>0:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
918 self.current_iterator,self.n_left_at_the_end_of_ds,self.n_left_in_mb= \
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
919 self.next_iterator(vsds.datasets[self.next_dataset_index],
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
920 self.n_left_at_the_end_of_ds,1)
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
921 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
922 self.next_dataset_index +=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
923 if self.next_dataset_index==len(self.vsds.datasets):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
924 self.next_dataset_index = 0
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
925 self.current_iterator,self.n_left_at_the_end_of_ds,self.n_left_in_mb= \
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
926 self.next_iterator(vsds.datasets[self.next_dataset_index],starting_offset,n_batches)
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
927
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
928 def __iter__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
929 return self
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
930
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
931 def next(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
932 dataset=self.vsds.datasets[self.next_dataset_index]
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
933 mb = self.next_iterator.next()
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
934 if self.n_left_in_mb:
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
935 extra_mb = []
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
936 while self.n_left_in_mb>0:
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
937 self.move_to_next_dataset()
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
938 extra_mb.append(self.next_iterator.next())
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
939 mb = Example(fieldnames,
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
940 [dataset.valuesVStack(name,
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
941 [mb[name]]+[b[name] for b in extra_mb])
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
942 for name in fieldnames])
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
943
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
944 self.next_row+=minibatch_size
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
945 self.next_dataset_row+=minibatch_size
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
946 if self.next_row+minibatch_size>len(dataset):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
947 self.move_to_next_dataset()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
948 return examples
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
949 return VStackedIterator(self)
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
950
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
951 class ArrayFieldsDataSet(DataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
952 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
953 Virtual super-class of datasets whose field values are numpy array,
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
954 thus defining valuesHStack and valuesVStack for sub-classes.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
955 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
956 def __init__(self,description=None,field_types=None):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
957 DataSet.__init__(self,description,field_types)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
958 def valuesHStack(self,fieldnames,fieldvalues):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
959 """Concatenate field values horizontally, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
960 become a longer vector, two matrices become a wider matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
961 return numpy.hstack(fieldvalues)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
962 def valuesVStack(self,fieldname,values):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
963 """Concatenate field values vertically, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
964 become a two-row matrix, two matrices become a longer matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
965 return numpy.vstack(values)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
966
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
967 class ArrayDataSet(ArrayFieldsDataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
968 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
969 An ArrayDataSet stores the fields as groups of columns in a numpy tensor,
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
970 whose first axis iterates over examples, second axis determines fields.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
971 If the underlying array is N-dimensional (has N axes), then the field
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
972 values are (N-2)-dimensional objects (i.e. ordinary numbers if N=2).
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
973 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
974
188
f01ac276c6fb added __contains__ to Dataset, added parent constructor call to ArrayDataSet
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 171
diff changeset
975 def __init__(self, data_array, fields_columns, **kwargs):
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
976 """
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
977 Construct an ArrayDataSet from the underlying numpy array (data) and
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
978 a map (fields_columns) from fieldnames to field columns. The columns of a field are specified
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
979 using the standard arguments for indexing/slicing: integer for a column index,
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
980 slice for an interval of columns (with possible stride), or iterable of column indices.
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
981 """
188
f01ac276c6fb added __contains__ to Dataset, added parent constructor call to ArrayDataSet
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 171
diff changeset
982 ArrayFieldsDataSet.__init__(self, **kwargs)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
983 self.data=data_array
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
984 self.fields_columns=fields_columns
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
985
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
986 # check consistency and complete slices definitions
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
987 for fieldname, fieldcolumns in self.fields_columns.items():
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
988 if type(fieldcolumns) is int:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
989 assert fieldcolumns>=0 and fieldcolumns<data_array.shape[1]
227
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
990 if 0:
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
991 #I changed this because it didn't make sense to me,
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
992 # and it made it more difficult to write my learner.
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
993 # If it breaks stuff, let's talk about it.
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
994 # - James 22/05/2008
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
995 self.fields_columns[fieldname]=[fieldcolumns]
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
996 else:
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
997 self.fields_columns[fieldname]=fieldcolumns
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
998 elif type(fieldcolumns) is slice:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
999 start,step=None,None
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1000 if not fieldcolumns.start:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1001 start=0
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1002 if not fieldcolumns.step:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1003 step=1
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1004 if start or step:
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1005 self.fields_columns[fieldname]=slice(start,fieldcolumns.stop,step)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1006 elif hasattr(fieldcolumns,"__iter__"): # something like a list
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1007 for i in fieldcolumns:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1008 assert i>=0 and i<data_array.shape[1]
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1009
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1010 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1011 return self.fields_columns.keys()
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1012
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1013 def __len__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1014 return len(self.data)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1015
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1016 def __getitem__(self,key):
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1017 """More efficient implementation than the default __getitem__"""
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1018 fieldnames=self.fields_columns.keys()
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1019 if type(key) is int:
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1020 return Example(fieldnames,
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1021 [self.data[key,self.fields_columns[f]] for f in fieldnames])
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1022 if type(key) is slice:
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1023 return MinibatchDataSet(Example(fieldnames,
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1024 [self.data[key,self.fields_columns[f]] for f in fieldnames]))
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1025 if type(key) is list:
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1026 for i in range(len(key)):
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1027 if self.hasFields(key[i]):
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1028 key[i]=self.fields_columns[key[i]]
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1029 return MinibatchDataSet(Example(fieldnames,
88
6749d18e11c8 bugfix as numpy numpy don't support self.data[[i1,...],[i2,...]] when their is more then two i1 and i2
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 85
diff changeset
1030 #we must separate differently for list as numpy
128
ee5507af2c60 minor edits
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 125
diff changeset
1031 # doesn't support self.data[[i1,...],[i2,...]]
88
6749d18e11c8 bugfix as numpy numpy don't support self.data[[i1,...],[i2,...]] when their is more then two i1 and i2
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 85
diff changeset
1032 # when their is more then two i1 and i2
6749d18e11c8 bugfix as numpy numpy don't support self.data[[i1,...],[i2,...]] when their is more then two i1 and i2
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 85
diff changeset
1033 [self.data[key,:][:,self.fields_columns[f]]
6749d18e11c8 bugfix as numpy numpy don't support self.data[[i1,...],[i2,...]] when their is more then two i1 and i2
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 85
diff changeset
1034 if isinstance(self.fields_columns[f],list) else
128
ee5507af2c60 minor edits
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 125
diff changeset
1035 self.data[key,self.fields_columns[f]] for f in fieldnames]),
ee5507af2c60 minor edits
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 125
diff changeset
1036
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1037 self.valuesVStack,self.valuesHStack)
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1038
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1039 # else check for a fieldname
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1040 if self.hasFields(key):
105
8c0a1b11b007 bugfix, we keep all the line, but only a some columns
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 101
diff changeset
1041 return self.data[:,self.fields_columns[key]]
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1042 # else we are trying to access a property of the dataset
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1043 assert key in self.__dict__ # else it means we are trying to access a non-existing property
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1044 return self.__dict__[key]
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1045
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1046 def __iter__(self):
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1047 class ArrayDataSetIterator2(object):
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1048 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset):
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1049 if fieldnames is None: fieldnames = dataset.fieldNames()
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1050 # store the resulting minibatch in a lookup-list of values
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1051 self.minibatch = LookupList(fieldnames,[0]*len(fieldnames))
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1052 self.dataset=dataset
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1053 self.minibatch_size=minibatch_size
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1054 assert offset>=0 and offset<len(dataset.data)
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1055 assert offset+minibatch_size<=len(dataset.data)
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1056 self.current=offset
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1057 def __iter__(self):
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1058 return self
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1059 def next(self):
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1060 #@todo: we suppose that we need to stop only when minibatch_size == 1.
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1061 # Otherwise, MinibatchWrapAroundIterator do it.
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1062 if self.current>=self.dataset.data.shape[0]:
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1063 raise StopIteration
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1064 sub_data = self.dataset.data[self.current]
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1065 self.minibatch._values = [sub_data[self.dataset.fields_columns[f]] for f in self.minibatch._names]
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1066 self.current+=self.minibatch_size
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1067 return self.minibatch
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1068
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1069 return ArrayDataSetIterator2(self,self.fieldNames(),1,0,0)
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1070
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1071 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1072 class ArrayDataSetIterator(object):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1073 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1074 if fieldnames is None: fieldnames = dataset.fieldNames()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1075 # store the resulting minibatch in a lookup-list of values
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1076 self.minibatch = LookupList(fieldnames,[0]*len(fieldnames))
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1077 self.dataset=dataset
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1078 self.minibatch_size=minibatch_size
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1079 assert offset>=0 and offset<len(dataset.data)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1080 assert offset+minibatch_size<=len(dataset.data)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1081 self.current=offset
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1082 def __iter__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1083 return self
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1084 def next(self):
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1085 #@todo: we suppose that MinibatchWrapAroundIterator stop the iterator
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1086 sub_data = self.dataset.data[self.current:self.current+self.minibatch_size]
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1087 self.minibatch._values = [sub_data[:,self.dataset.fields_columns[f]] for f in self.minibatch._names]
43
e92244f30116 Corrected iterator logic errors
bengioy@grenat.iro.umontreal.ca
parents: 42
diff changeset
1088 self.current+=self.minibatch_size
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1089 return self.minibatch
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1090
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1091 return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset)
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1092
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1093
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1094 class CachedDataSet(DataSet):
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1095 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1096 Wrap a L{DataSet} whose values are computationally expensive to obtain
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1097 (e.g. because they involve some computation, or disk access),
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1098 so that repeated accesses to the same example are done cheaply,
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1099 by caching every example value that has been accessed at least once.
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1100
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1101 Optionally, for finite-length dataset, all the values can be computed
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1102 (and cached) upon construction of the CachedDataSet, rather at the
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1103 first access.
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1104
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1105 @todo: when cache_all_upon_construction create mini-batches that are as
77
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1106 large as possible but not so large as to fill up memory.
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1107
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1108 @todo: add disk-buffering capability, so that when the cache becomes too
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1109 big for memory, we cache things on disk, trying to keep in memory only
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1110 the record most likely to be accessed next.
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1111 """
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1112 def __init__(self,source_dataset,cache_all_upon_construction=False):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1113 self.source_dataset=source_dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1114 self.cache_all_upon_construction=cache_all_upon_construction
152
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1115 self.cached_examples = []
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1116 if cache_all_upon_construction:
77
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1117 # this potentially brings all the source examples
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1118 # into memory at once, which may be too much
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1119 # the work could possibly be done by minibatches
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1120 # that are as large as possible but no more than what memory allows.
146
8173e196e291 Trying to make CacheDataSet work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 144
diff changeset
1121 fields_values = source_dataset.minibatches(minibatch_size=len(source_dataset)).__iter__().next()
152
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1122 assert all([len(self)==len(field_values) for field_values in fields_values])
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1123 for example in fields_values.examples():
171
895b4b60f5e8 bugfix. Otherwise the example was writed over and not a new one was returned
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 167
diff changeset
1124 self.cached_examples.append(copy.copy(example))
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1125
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1126 self.fieldNames = source_dataset.fieldNames
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1127 self.hasFields = source_dataset.hasFields
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1128 self.valuesHStack = source_dataset.valuesHStack
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1129 self.valuesVStack = source_dataset.valuesVStack
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1130
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1131 def __len__(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1132 return len(self.source_dataset)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1133
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1134 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1135 class CacheIterator(object):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1136 def __init__(self,dataset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1137 self.dataset=dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1138 self.current=offset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1139 def __iter__(self): return self
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1140 def next(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1141 upper = self.current+minibatch_size
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1142 cache_len = len(self.dataset.cached_examples)
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
1143 if upper>cache_len: # whole minibatch is not already in cache
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1144 # cache everything from current length to upper
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1145 for example in self.dataset.source_dataset[cache_len:upper]:
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1146 self.dataset.cached_examples.append(example)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1147 all_fields_minibatch = Example(self.dataset.fieldNames(),
152
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1148 zip(*self.dataset.cached_examples[self.current:self.current+minibatch_size]))
163
d7d67651d67c bugfix, we should advence by the minibatch size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 159
diff changeset
1149 self.current+=minibatch_size
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1150 if self.dataset.fieldNames()==fieldnames:
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1151 return all_fields_minibatch
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1152 return Example(fieldnames,[all_fields_minibatch[name] for name in fieldnames])
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1153 return CacheIterator(self)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1154
153
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1155 def __getitem__(self,i):
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1156 if type(i)==int and len(self.cached_examples)>i:
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1157 return self.cached_examples[i]
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1158 else:
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1159 return DataSet.__getitem__(self,i)
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1160
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1161 class ApplyFunctionDataSet(DataSet):
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1162 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1163 A L{DataSet} that contains as fields the results of applying a
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1164 given function example-wise or minibatch-wise to all the fields of
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1165 an input dataset. The output of the function should be an iterable
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1166 (e.g. a list or a LookupList) over the resulting values.
197
96d891448107 more explicit comment
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 196
diff changeset
1167
96d891448107 more explicit comment
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 196
diff changeset
1168 The function take as input the fields of the dataset, not the examples.
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1169
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1170 In minibatch mode, the function is expected to work on minibatches
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1171 (takes a minibatch in input and returns a minibatch in output). More
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1172 precisely, it means that each element of the input or output list
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1173 should be iterable and indexable over the individual example values
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1174 (typically these elements will be numpy arrays). All of the elements
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1175 in the input and output lists should have the same length, which is
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1176 the length of the minibatch.
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1177
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1178 The function is applied each time an example or a minibatch is accessed.
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1179 To avoid re-doing computation, wrap this dataset inside a CachedDataSet.
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1180
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1181 If the values_{h,v}stack functions are not provided, then
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1182 the input_dataset.values{H,V}Stack functions are used by default.
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1183 """
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1184 def __init__(self,input_dataset,function,output_names,minibatch_mode=True,
74
b4159cbdc06b Fixed errors raised by test_dataset
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 73
diff changeset
1185 values_hstack=None,values_vstack=None,
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1186 description=None,fieldtypes=None):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1187 """
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1188 Constructor takes an input dataset that has as many fields as the function
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1189 expects as inputs. The resulting dataset has as many fields as the function
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1190 produces as outputs, and that should correspond to the number of output names
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1191 (provided in a list).
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1192
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1193 Note that the expected semantics of the function differs in minibatch mode
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1194 (it takes minibatches of inputs and produces minibatches of outputs, as
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1195 documented in the class comment).
211
bd728c83faff in __get__, problem if the i.stop was None, i being the slice, added one line replacing None by the len(self)
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 203
diff changeset
1196
bd728c83faff in __get__, problem if the i.stop was None, i being the slice, added one line replacing None by the len(self)
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 203
diff changeset
1197 TBM: are filedtypes the old field types (from input_dataset) or the new ones
bd728c83faff in __get__, problem if the i.stop was None, i being the slice, added one line replacing None by the len(self)
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 203
diff changeset
1198 (for the new dataset created)?
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1199 """
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1200 self.input_dataset=input_dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1201 self.function=function
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1202 self.output_names=output_names
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1203 self.minibatch_mode=minibatch_mode
134
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 132
diff changeset
1204 DataSet.__init__(self,description,fieldtypes)
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1205 self.valuesHStack = values_hstack if values_hstack else input_dataset.valuesHStack
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1206 self.valuesVStack = values_vstack if values_vstack else input_dataset.valuesVStack
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1207
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1208 def __len__(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1209 return len(self.input_dataset)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1210
134
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 132
diff changeset
1211 def fieldNames(self):
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1212 return self.output_names
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1213
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1214 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1215 class ApplyFunctionIterator(object):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1216 def __init__(self,output_dataset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1217 self.input_dataset=output_dataset.input_dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1218 self.output_dataset=output_dataset
134
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 132
diff changeset
1219 self.input_iterator=self.input_dataset.minibatches(minibatch_size=minibatch_size,
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 132
diff changeset
1220 n_batches=n_batches,offset=offset).__iter__()
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1221
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1222 def __iter__(self): return self
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1223
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1224 def next(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1225 function_inputs = self.input_iterator.next()
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1226 all_output_names = self.output_dataset.output_names
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1227 if self.output_dataset.minibatch_mode:
134
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 132
diff changeset
1228 function_outputs = self.output_dataset.function(*function_inputs)
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1229 else:
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1230 input_examples = zip(*function_inputs)
201
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 200
diff changeset
1231 output_examples = [self.output_dataset.function(*input_example)
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1232 for input_example in input_examples]
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1233 function_outputs = [self.output_dataset.valuesVStack(name,values)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1234 for name,values in zip(all_output_names,
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1235 zip(*output_examples))]
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1236 all_outputs = Example(all_output_names,function_outputs)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1237 if fieldnames==all_output_names:
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1238 return all_outputs
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1239 return Example(fieldnames,[all_outputs[name] for name in fieldnames])
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1240
211
bd728c83faff in __get__, problem if the i.stop was None, i being the slice, added one line replacing None by the len(self)
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 203
diff changeset
1241
134
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 132
diff changeset
1242 return ApplyFunctionIterator(self)
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1243
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1244 def __iter__(self): # only implemented for increased efficiency
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1245 class ApplyFunctionSingleExampleIterator(object):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1246 def __init__(self,output_dataset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1247 self.current=0
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1248 self.output_dataset=output_dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1249 self.input_iterator=output_dataset.input_dataset.__iter__()
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1250 def __iter__(self): return self
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1251 def next(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1252 if self.output_dataset.minibatch_mode:
200
ac61f1178f88 bugfix?
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 199
diff changeset
1253 function_inputs = [[input] for input in self.input_iterator.next()]
199
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 198
diff changeset
1254 outputs = self.output_dataset.function(*function_inputs)
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 198
diff changeset
1255 assert all([hasattr(output,'__iter__') for output in outputs])
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 198
diff changeset
1256 function_outputs = [output[0] for output in outputs]
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1257 else:
200
ac61f1178f88 bugfix?
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 199
diff changeset
1258 function_inputs = self.input_iterator.next()
199
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 198
diff changeset
1259 function_outputs = self.output_dataset.function(*function_inputs)
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1260 return Example(self.output_dataset.output_names,function_outputs)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1261 return ApplyFunctionSingleExampleIterator(self)
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1262
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1263
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1264 def supervised_learning_dataset(src_dataset,input_fields,target_fields,weight_field=None):
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1265 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1266 Wraps an arbitrary L{DataSet} into one for supervised learning tasks
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1267 by forcing the user to define a set of fields as the 'input' field
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1268 and a set of fields as the 'target' field. Optionally, a single
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1269 weight_field can also be defined.
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1270 """
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1271 args = ((input_fields,'input'),(output_fields,'target'))
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1272 if weight_field: args+=(([weight_field],'weight'))
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1273 return src_dataset.merge_fields(*args)
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1274
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1275
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1276
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1277