annotate dataset.py @ 52:e3ac93e27e16

Automated merge with ssh://p-omega1@lgcm.iro.umontreal.ca/tlearn
author Frederic Bastien <bastienf@iro.umontreal.ca>
date Tue, 29 Apr 2008 14:40:44 -0400
parents ea7d8bc38b34 b6730f9a336d
children 1729ad44f175
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
45
a5c70dc42972 Test functions for dataset.py
bengioy@grenat.iro.umontreal.ca
parents: 44
diff changeset
7 import numpy
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
8
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
9 class AbstractFunction (Exception): """Derived class must override this function"""
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
10 class NotImplementedYet (NotImplementedError): """Work in progress, this should eventually be implemented"""
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
11
1
2cd82666b9a7 Added statscollector and started writing dataset and learner.
bengioy@esprit.iro.umontreal.ca
parents: 0
diff changeset
12 class DataSet(object):
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
13 """A virtual base class for datasets.
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
14
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
15 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
16 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
17 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
18 python object, which depends on the particular dataset.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
19
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
20 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
21 should return sys.maxint).
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
22
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
23 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
24 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
25 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
26 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
27 feasible or not recommanded on streams).
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
28
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
29 To iterate over examples, there are several possibilities:
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
30 * for example in dataset([field1, field2,field3, ...]):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
31 * for val1,val2,val3 in dataset([field1, field2,field3]):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
32 * for minibatch in dataset.minibatches([field1, field2, ...],minibatch_size=N):
50
ea7d8bc38b34 fix comment
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 46
diff changeset
33 * for mini1,mini2,mini3 in dataset.minibatches([field1, field2, field3], minibatch_size=N):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
34 * for example in dataset:
46
c5b07e87b0cb comments modif made by Yoshua
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 45
diff changeset
35 print example['x']
c5b07e87b0cb comments modif made by Yoshua
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 45
diff changeset
36 * for x,y,z in dataset:
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
37 Each of these is documented below. All of these iterators are expected
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
38 to provide, in addition to the usual 'next()' method, a 'next_index()' method
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
39 which returns a non-negative integer pointing to the position of the next
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
40 example that will be returned by 'next()' (or of the first example in the
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
41 next minibatch returned). This is important because these iterators
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
42 can wrap around the dataset in order to do multiple passes through it,
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
43 in possibly unregular ways if the minibatch size is not a divisor of the
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
44 dataset length.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
45
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
46 To iterate over fields, one can do
46
c5b07e87b0cb comments modif made by Yoshua
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 45
diff changeset
47 * for field in dataset.fields():
c5b07e87b0cb comments modif made by Yoshua
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 45
diff changeset
48 for field_value in field: # iterate over the values associated to that field for all the dataset examples
50
ea7d8bc38b34 fix comment
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 46
diff changeset
49 * for field in dataset(field1,field2,...).fields() to select a subset of fields
ea7d8bc38b34 fix comment
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 46
diff changeset
50 * 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
51 and each of these fields is iterable over the examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
52 * for field_examples in dataset.fields():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
53 for example_value in field_examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
54 ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
55 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
56 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
57 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
58 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
59 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
60 be turned back into a DataSet with its examples() method:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
61 dataset2 = dataset1.fields().examples()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
62 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
63
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
64 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
65
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
66 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
67 (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
68 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
69 What about non-numeric values? None.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
70
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
71 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
72 of examples) can be extracted. These operations are not supported
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
73 by default in the case of streams.
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 * dataset[:n] returns a dataset with the n first examples.
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
76
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
77 * dataset[i1:i2:s] returns a dataset with the examples i1,i1+s,...i2-s.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
78
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
79 * dataset[i] returns an Example.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
80
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
81 * dataset[[i1,i2,...in]] returns a dataset with examples i1,i2,...in.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
82
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
83 * dataset['key'] returns a property associated with the given 'key' string.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
84 If 'key' is a fieldname, then the VStacked field values (iterable over
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
85 field values) for that field is returned. Other keys may be supported
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
86 by different dataset subclasses. The following key names are should be supported:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
87 - 'description': a textual description or name for the dataset
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
88 - '<fieldname>.type': a type name or value for a given <fieldname>
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
89
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
90 Datasets can be concatenated either vertically (increasing the length) or
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
91 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
92 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
93 and numpy.vstack):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
94
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
95 * 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
96
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
97 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
98 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
99
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
100 * dataset1 & dataset2 & dataset3 == dataset.vstack([dataset1,dataset2,dataset3])
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
101
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
102 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
103 (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
104 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
105
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
106 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
107 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
108 a DataSetFields fields1 and fields2, and fields1 | fields2 concatenates their
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
109 examples.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
110
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
111 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
112 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
113 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
114 when key is a string (or more specifically, neither an integer, a slice, nor a list).
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
115
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
116 A DataSet sub-class should always redefine the following methods:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
117 * __len__ if it is not a stream
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
118 * fieldNames
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
119 * minibatches_nowrap (called by DataSet.minibatches())
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
120 * valuesHStack
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
121 * valuesVStack
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
122 For efficiency of implementation, a sub-class might also want to redefine
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
123 * hasFields
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
124 * __getitem__ may not be feasible with some streams
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
125 * __iter__
2
3fddb1c8f955 Rewrote DataSet interface and created FiniteDataSet interface.
bengioy@bengiomac.local
parents: 1
diff changeset
126 """
1
2cd82666b9a7 Added statscollector and started writing dataset and learner.
bengioy@esprit.iro.umontreal.ca
parents: 0
diff changeset
127
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
128 def __init__(self,description=None,field_types=None):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
129 if description is None:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
130 # by default return "<DataSetType>(<SuperClass1>,<SuperClass2>,...)"
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
131 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
132 self.description=description
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
133 self.field_types=field_types
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
134
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
135 class MinibatchToSingleExampleIterator(object):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
136 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
137 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
138 single-example values in the result. Therefore the result of
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
139 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
140 (whereas the result of iterating over minibatches gives in each
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
141 Example field an iterable object over the individual examples in
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
142 the minibatch).
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
143 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
144 def __init__(self, minibatch_iterator):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
145 self.minibatch_iterator = minibatch_iterator
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
146 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
147 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
148 return self
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
149 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
150 size1_minibatch = self.minibatch_iterator.next()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
151 if not self.minibatch:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
152 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
153 else:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
154 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
155 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
156
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
157 def next_index(self):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
158 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
159
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
160 def __iter__(self):
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
161 """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
162
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
163 Using this syntax, "i" will be an Example instance (or equivalent) with
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
164 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
165 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
166 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
167 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
168 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
169
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
170 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
171 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
172 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
173
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
174
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
175 class MinibatchWrapAroundIterator(object):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
176 """
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
177 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
178 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
179 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
180 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
181 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
182 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
183 """
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
184 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
185 self.dataset=dataset
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
186 self.fieldnames=fieldnames
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
187 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
188 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
189 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
190 self.next_row=offset
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
191 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
192 assert offset+minibatch_size<=self.L
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
193 ds_nbatches = (self.L-offset)/minibatch_size
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
194 if n_batches is not None:
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
195 ds_nbatches = max(n_batches,ds_nbatches)
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
196 if fieldnames:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
197 assert dataset.hasFields(*fieldnames)
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
198 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
199 fieldnames=dataset.fieldNames()
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
200 self.iterator = dataset.minibatches_nowrap(fieldnames,minibatch_size,ds_nbatches,offset)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
201
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
202 def __iter__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
203 return self
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
204
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
205 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
206 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
207
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
208 def next(self):
43
e92244f30116 Corrected iterator logic errors
bengioy@grenat.iro.umontreal.ca
parents: 42
diff changeset
209 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
210 raise StopIteration
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
211 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
212 if upper <=self.L:
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
213 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
214 else:
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
215 if not self.n_batches:
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
216 raise StopIteration
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
217 # we must concatenate (vstack) the bottom and top parts of our minibatch
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
218 # first get the beginning of our minibatch (top of dataset)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
219 first_part = self.dataset.minibatches_nowrap(fieldnames,self.L-self.next_row,1,self.next_row).next()
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
220 second_part = self.dataset.minibatches_nowrap(fieldnames,upper-self.L,1,0).next()
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
221 minibatch = Example(self.fieldnames,
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
222 [self.dataset.valuesVStack(name,[first_part[name],second_part[name]])
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
223 for name in self.fieldnames])
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
224 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
225 self.n_batches_done+=1
43
e92244f30116 Corrected iterator logic errors
bengioy@grenat.iro.umontreal.ca
parents: 42
diff changeset
226 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
227 self.next_row -= self.L
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
228 return minibatch
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
229
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
230
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
231 minibatches_fieldnames = None
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
232 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
233 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
234 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
235 fieldnames = minibatches_fieldnames,
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
236 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
237 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
238 offset = 0):
6
d5738b79089a Removed MinibatchIterator and instead made minibatch_size a field of all DataSets,
bengioy@bengiomac.local
parents: 5
diff changeset
239 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
240 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
241
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
242 for i in dataset.minibatches(None,**kwargs): ...
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
243
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
244 for i in dataset.minibatches([f1, f2, f3],**kwargs): ...
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
245
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
246 for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ...
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
247
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
248 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
249 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
250 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
251 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
252 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
253
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
254 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
255 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
256 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
257
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
258 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
259 a DataSetFields object, which is a LookupList (indexed by the field names) whose
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
260 elements are iterable over the minibatch examples, and which keeps a pointer to
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
261 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
262 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
263 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
264
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
265 PARAMETERS
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
266 - 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
267 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
268 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
269 derived class can choose a default, e.g. all fields.
16
813723310d75 commenting
bergstrj@iro.umontreal.ca
parents: 15 11
diff changeset
270
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
271 - 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
272 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
273 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
274
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
275 - 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
276 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
277 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
278 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
279
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
280 - 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
281 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
282
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
283 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
284 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
285
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
286 """
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
287 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
288
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
289 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
290 """
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
291 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
292 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
293 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
294 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
295 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
296 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
297 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
298 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
299 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
300 """
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
301 raise AbstractFunction()
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
302
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
303 def __len__(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
304 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
305 len(dataset) returns the number of examples in the dataset.
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
306 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
307 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
308 Some methods only make sense for finite-length datasets.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
309 """
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
310 return sys.maxint
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
311
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
312 def is_unbounded(self):
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
313 """
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
314 Tests whether a dataset is unbounded (e.g. a stream).
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
315 """
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
316 return len(self)==sys.maxint
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
317
26
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
bengioy@grenat.iro.umontreal.ca
parents: 23
diff changeset
318 def hasFields(self,*fieldnames):
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
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 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
321 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
322 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
323
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
324 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
325 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
326 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
327 return len(unique_elements_list_intersection(fieldnames,self.fieldNames()))>0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
328
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
329 def fieldNames(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
330 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
331 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
332 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
333 """
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
334 raise AbstractFunction()
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
335
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
336 def __call__(self,*fieldnames):
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
337 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
338 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
339 """
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
340 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
341 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
342
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
343 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
344 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
345 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
346 """
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
347 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
348
2
3fddb1c8f955 Rewrote DataSet interface and created FiniteDataSet interface.
bengioy@bengiomac.local
parents: 1
diff changeset
349 def __getitem__(self,i):
28
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
350 """
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
351 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
352 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
353 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
354 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
355 dataset['key'] returns a property associated with the given 'key' string.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
356 If 'key' is a fieldname, then the VStacked field values (iterable over
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
357 field values) for that field is returned. Other keys may be supported
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
358 by different dataset subclasses. The following key names are encouraged:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
359 - 'description': a textual description or name for the dataset
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
360 - '<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
361
39
c682c6e9bf93 Minor edits
bengioy@esprit.iro.umontreal.ca
parents: 38
diff changeset
362 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
363 arbitrary slicing/indexing
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
364 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
365 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
366
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
367 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
368 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
369 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
370 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
371 """
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
372 # 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
373 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
374 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
375 self.minibatches(minibatch_size=1,n_batches=1,offset=i)).next()
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
376 rows=None
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
377 # 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
378 if type(i) is slice:
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
379 if not i.start: i.start=0
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
380 if not i.step: i.step=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
381 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
382 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
383 rows = range(i.start,i.stop,i.step)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
384 # or a list of indices
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
385 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
386 rows = i
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
387 if rows is not None:
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
388 examples = [self[row] for row in rows]
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
389 fields_values = zip(*examples)
45
a5c70dc42972 Test functions for dataset.py
bengioy@grenat.iro.umontreal.ca
parents: 44
diff changeset
390 return MinibatchDataSet(
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
391 Example(self.fieldNames(),[ self.valuesVStack(fieldname,field_values)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
392 for fieldname,field_values
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
393 in zip(self.fieldNames(),fields_values)]))
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
394 # else check for a fieldname
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
395 if self.hasFields(i):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
396 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
397 # else we are trying to access a property of the dataset
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
398 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
399 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
400
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
401 def valuesHStack(self,fieldnames,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
402 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
403 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
404 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
405 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
406 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
407 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
408 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
409 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
410 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
411 pointing to the original values for other data types.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
412 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
413 all_numpy=True
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
414 for value in fieldvalues:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
415 if not type(value) is numpy.ndarray:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
416 all_numpy=False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
417 if all_numpy:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
418 return numpy.hstack(fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
419 # 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
420 return fieldvalues
26
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
bengioy@grenat.iro.umontreal.ca
parents: 23
diff changeset
421
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
bengioy@grenat.iro.umontreal.ca
parents: 23
diff changeset
422
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
423 def valuesVStack(self,fieldname,values):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
424 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
425 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
426 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
427 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
428 result should be numpy.vstack(values).
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
429 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
430 pointing to the original values for other data types.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
431 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
432 all_numpy=True
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
433 for value in values:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
434 if not type(value) is numpy.ndarray:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
435 all_numpy=False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
436 if all_numpy:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
437 return numpy.vstack(values)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
438 # 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
439 return values
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
440
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
441 def __or__(self,other):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
442 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
443 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
444 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
445 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
446 return HStackedDataSet(self,other)
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
447
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
448 def __and__(self,other):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
449 """
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
450 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
451 (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
452 works if they all have the same fields.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
453 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
454 return VStackedDataSet(self,other)
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
455
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
456 def hstack(datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
457 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
458 hstack(dataset1,dataset2,...) returns dataset1 | datataset2 | ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
459 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
460 of the individual datasets.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
461 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
462 assert len(datasets)>0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
463 if len(datasets)==1:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
464 return datasets[0]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
465 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
466
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
467 def vstack(datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
468 """
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
469 vstack(dataset1,dataset2,...) returns dataset1 & datataset2 & ...
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
470 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
471 over those of dataset2, etc.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
472 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
473 assert len(datasets)>0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
474 if len(datasets)==1:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
475 return datasets[0]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
476 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
477
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
478 class FieldsSubsetDataSet(DataSet):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
479 """
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
480 A sub-class of DataSet that selects a subset of the fields.
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
481 """
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
482 def __init__(self,src,fieldnames):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
483 self.src=src
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
484 self.fieldnames=fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
485 assert src.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
486 self.valuesHStack = src.valuesHStack
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
487 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
488
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
489 def __len__(self): return len(self.src)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
490
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
491 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
492 return self.fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
493
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
494 def __iter__(self):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
495 class FieldsSubsetIterator(object):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
496 def __init__(self,ds):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
497 self.ds=ds
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
498 self.src_iter=ds.src.__iter__()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
499 self.example=None
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
500 def __iter__(self): return self
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
501 def next(self):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
502 complete_example = self.src_iter.next()
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
503 if self.example:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
504 self.example._values=[complete_example[field]
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
505 for field in self.ds.fieldnames]
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
506 else:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
507 self.example=Example(self.ds.fieldnames,
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
508 [complete_example[field] for field in self.ds.fieldnames])
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
509 return self.example
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
510 return FieldsSubsetIterator(self)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
511
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
512 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
513 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
514 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
515 def __getitem__(self,i):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
516 return FieldsSubsetDataSet(self.src[i],self.fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
517
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
518
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
519 class DataSetFields(LookupList):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
520 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
521 Although a DataSet iterates over examples (like rows of a matrix), an associated
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
522 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
523 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
524
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
525 To iterate over fields, one can do
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
526 * for fields in dataset.fields()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
527 * 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
528 * 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
529 and each of these fields is iterable over the examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
530 * for field_examples in dataset.fields():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
531 for example_value in field_examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
532 ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
533 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
534 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
535 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
536 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
537 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
538 be turned back into a DataSet with its examples() method:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
539 dataset2 = dataset1.fields().examples()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
540 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
541
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
542 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
543 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
544 the examples.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
545 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
546 def __init__(self,dataset,*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
547 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
548 fieldnames=dataset.fieldNames()
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
549 elif fieldnames is not dataset.fieldNames():
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
550 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
551 assert dataset.hasFields(*fieldnames)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
552 self.dataset=dataset
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
553 minibatch_iterator = dataset.minibatches(fieldnames,
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
554 minibatch_size=len(dataset),
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
555 n_batches=1)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
556 minibatch=minibatch_iterator.next()
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
557 LookupList.__init__(self,fieldnames,minibatch)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
558
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
559 def examples(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
560 return self.dataset
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
561
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
562 def __or__(self,other):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
563 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
564 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
565 of the list of examples of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
566 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
567 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
568
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
569 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
570 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
571 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
572 of the fields of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
573 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
574 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
575
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
576
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
577 class MinibatchDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
578 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
579 Turn a LookupList of same-length fields into an example-iterable dataset.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
580 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
581 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
582 def __init__(self,fields_lookuplist,values_vstack=DataSet().valuesVStack,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
583 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
584 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
585 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
586 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
587 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
588 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
589 self.fields=fields_lookuplist
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
590 assert len(fields_lookuplist)>0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
591 self.length=len(fields_lookuplist[0])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
592 for field in fields_lookuplist[1:]:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
593 assert self.length==len(field)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
594 self.values_vstack=values_vstack
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
595 self.values_hstack=values_hstack
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
596
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
597 def __len__(self):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
598 return self.length
28
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
599
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
600 def __getitem__(self,i):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
601 if type(i) in (int,slice,list):
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
602 return DataSetFields(MinibatchDataSet(
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
603 Example(self.fields.keys(),[field[i] for field in self.fields])),self.fields)
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
604 if self.hasFields(i):
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
605 return self.fields[i]
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
606 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
607
29
46c5c90019c2 Changed apply_function so that it propagates methods of the source.
bengioy@grenat.iro.umontreal.ca
parents: 28
diff changeset
608 def fieldNames(self):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
609 return self.fields.keys()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
610
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
611 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
612 for fieldname in fieldnames:
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
613 if fieldname not in self.fields.keys():
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
614 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
615 return True
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
616
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
617 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
618 class Iterator(object):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
619 def __init__(self,ds):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
620 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
621 self.next_example=offset
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
622 assert minibatch_size > 0
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
623 if offset+minibatch_size > ds.length:
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
624 raise NotImplementedError()
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
625 def __iter__(self):
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
626 return self
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
627 def next(self):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
628 upper = 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
629 assert upper<=self.ds.length
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
630 minibatch = Example(self.ds.fields.keys(),
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
631 [field[next_example:upper]
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
632 for field in self.ds.fields])
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
633 self.next_example+=minibatch_size
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
634 return DataSetFields(MinibatchDataSet(minibatch),fieldnames)
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
635
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
636 return Iterator(self)
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
637
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
638 def valuesVStack(self,fieldname,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
639 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
640
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
641 def valuesHStack(self,fieldnames,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
642 return self.values_hstack(fieldnames,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
643
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
644 class HStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
645 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
646 A DataSet that wraps several datasets and shows a view that includes all their fields,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
647 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
648
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
649 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
650 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
651 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
652
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
653 TODO: automatically detect a chain of stacked datasets due to A | B | C | D ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
654 """
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
655 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
656 DataSet.__init__(self,description,field_types)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
657 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
658 self.accept_nonunique_names=accept_nonunique_names
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
659 self.fieldname2dataset={}
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
660
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
661 def rename_field(fieldname,dataset,i):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
662 if hasattr(dataset,"__name__"):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
663 return dataset.__name__ + "." + fieldname
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
664 return fieldname+"."+str(i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
665
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
666 # 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
667 self.length=None
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
668 names_to_change=[]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
669 for i in xrange(len(datasets)):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
670 dataset = datasets[i]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
671 length=len(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
672 if self.length:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
673 assert self.length==length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
674 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
675 self.length=length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
676 for fieldname in dataset.fieldNames():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
677 if fieldname in self.fieldname2dataset: # name conflict!
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
678 if accept_nonunique_names:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
679 fieldname=rename_field(fieldname,dataset,i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
680 names2change.append((fieldname,i))
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
681 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
682 raise ValueError("Incompatible datasets: non-unique field name = "+fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
683 self.fieldname2dataset[fieldname]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
684 for fieldname,i in names_to_change:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
685 del self.fieldname2dataset[fieldname]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
686 self.fieldname2dataset[rename_field(fieldname,self.datasets[i],i)]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
687
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
688 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
689 for fieldname in fieldnames:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
690 if not fieldname in self.fieldname2dataset:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
691 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
692 return True
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
693
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
694 def fieldNames(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
695 return self.fieldname2dataset.keys()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
696
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
697 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
698
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
699 class HStackedIterator(object):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
700 def __init__(self,hsds,iterators):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
701 self.hsds=hsds
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
702 self.iterators=iterators
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
703 def __iter__(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
704 return self
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
705 def next(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
706 # concatenate all the fields of the minibatches
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
707 minibatch = reduce(LookupList.__add__,[iterator.next() for iterator in self.iterators])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
708 # and return a DataSetFields whose dataset is the transpose (=examples()) of this minibatch
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
709 return DataSetFields(MinibatchDataSet(minibatch,self.hsds.valuesVStack,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
710 self.hsds.valuesHStack),
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
711 fieldnames if fieldnames else hsds.fieldNames())
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
712
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
713 assert self.hasfields(fieldnames)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
714 # 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
715 # and construct corresponding minibatch iterators
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
716 if fieldnames:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
717 datasets=set([])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
718 fields_in_dataset=dict([(dataset,[]) for dataset in datasets])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
719 for fieldname in fieldnames:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
720 dataset=self.datasets[self.fieldnames2dataset[fieldname]]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
721 datasets.add(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
722 fields_in_dataset[dataset].append(fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
723 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
724 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
725 for dataset in datasets]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
726 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
727 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
728 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
729 return HStackedIterator(self,iterators)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
730
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
731
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
732 def valuesVStack(self,fieldname,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
733 return self.datasets[self.fieldname2dataset[fieldname]].valuesVStack(fieldname,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
734
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
735 def valuesHStack(self,fieldnames,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
736 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
737 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
738 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
739 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
740 all the fieldnames are of the same sub-dataset.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
741 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
742 return self.datasets[self.fieldname2dataset[fieldnames[0]]].valuesHStack(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 VStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
745 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
746 A DataSet that wraps several datasets and shows a view that includes all their examples,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
747 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
748 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
749
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
750 TODO: automatically detect a chain of stacked datasets due to A + B + C + D ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
751 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
752 def __init__(self,datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
753 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
754 self.length=0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
755 self.index2dataset={}
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
756 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
757 fieldnames = datasets[-1].fieldNames()
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
758 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
759 # 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
760 # 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
761 for dataset,k in enumerate(datasets[0:-1]):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
762 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
763 L=len(dataset)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
764 for i in xrange(L):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
765 self.index2dataset[self.length+i]=k
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
766 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
767 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
768 assert dataset.fieldNames()==fieldnames
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
769 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
770 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
771 # 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
772 # 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
773 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
774 # 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
775 # TODO
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
776 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
777
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
778 def __len__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
779 return self.length
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
780
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
781 def fieldNames(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
782 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
783
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
784 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
785 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
786
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
787 def locate_row(self,row):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
788 """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
789 dataset_index = self.index2dataset[row]
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
790 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
791 return dataset_index, row_within_dataset
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
792
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
793 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
794
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
795 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
796 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
797 self.vsds=vsds
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
798 self.next_row=offset
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
799 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
800 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
801 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
802
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
803 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
804 L=len(dataset)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
805 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
806 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
807 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
808 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
809 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
810 n_left_in_mb=minibatch_size-L
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
811 ds_nbatches=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
812 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
813 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
814 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
815 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
816
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
817 def move_to_next_dataset(self):
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
818 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
819 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
820 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
821 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
822 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
823 self.next_dataset_index +=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
824 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
825 self.next_dataset_index = 0
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
826 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
827 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
828
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
829 def __iter__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
830 return self
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
831
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
832 def next(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
833 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
834 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
835 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
836 extra_mb = []
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
837 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
838 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
839 extra_mb.append(self.next_iterator.next())
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
840 examples = Example(names,
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
841 [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
842 [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
843 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
844 mb = DataSetFields(MinibatchDataSet(examples),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
845
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
846 self.next_row+=minibatch_size
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
847 self.next_dataset_row+=minibatch_size
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
848 if self.next_row+minibatch_size>len(dataset):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
849 self.move_to_next_dataset()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
850 return examples
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
851 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
852
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
853 class ArrayFieldsDataSet(DataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
854 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
855 Virtual super-class of datasets whose field values are numpy array,
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
856 thus defining valuesHStack and valuesVStack for sub-classes.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
857 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
858 def __init__(self,description=None,field_types=None):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
859 DataSet.__init__(self,description,field_types)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
860 def valuesHStack(self,fieldnames,fieldvalues):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
861 """Concatenate field values horizontally, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
862 become a longer vector, two matrices become a wider matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
863 return numpy.hstack(fieldvalues)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
864 def valuesVStack(self,fieldname,values):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
865 """Concatenate field values vertically, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
866 become a two-row matrix, two matrices become a longer matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
867 return numpy.vstack(values)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
868
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
869 class ArrayDataSet(ArrayFieldsDataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
870 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
871 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
872 whose first axis iterates over examples, second axis determines fields.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
873 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
874 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
875 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
876
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
877 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
878 Construct an ArrayDataSet from the underlying numpy array (data) and
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
879 a map (fields_columns) from fieldnames to field columns. The columns of a field are specified
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
880 using the standard arguments for indexing/slicing: integer for a column index,
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
881 slice for an interval of columns (with possible stride), or iterable of column indices.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
882 """
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
883 def __init__(self, data_array, fields_columns):
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
884 self.data=data_array
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
885 self.fields_columns=fields_columns
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
886
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
887 # check consistency and complete slices definitions
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
888 for fieldname, fieldcolumns in self.fields_columns.items():
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
889 if type(fieldcolumns) is int:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
890 assert fieldcolumns>=0 and fieldcolumns<data_array.shape[1]
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
891 elif type(fieldcolumns) is slice:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
892 start,step=None,None
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
893 if not fieldcolumns.start:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
894 start=0
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
895 if not fieldcolumns.step:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
896 step=1
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
897 if start or step:
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
898 self.fields_columns[fieldname]=slice(start,fieldcolumns.stop,step)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
899 elif hasattr(fieldcolumns,"__iter__"): # something like a list
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
900 for i in fieldcolumns:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
901 assert i>=0 and i<data_array.shape[1]
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
902
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
903 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
904 return self.fields_columns.keys()
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
905
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
906 def __len__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
907 return len(self.data)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
908
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
909 #def __getitem__(self,i):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
910 # """More efficient implementation than the default"""
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
911
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
912 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
913 class ArrayDataSetIterator(object):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
914 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
915 if fieldnames is None: fieldnames = dataset.fieldNames()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
916 # 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
917 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
918 self.dataset=dataset
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
919 self.minibatch_size=minibatch_size
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
920 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
921 assert offset+minibatch_size<=len(dataset.data)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
922 self.current=offset
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
923 def __iter__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
924 return self
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
925 def next(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
926 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
927 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
928 self.current+=self.minibatch_size
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
929 return self.minibatch
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
930
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
931 return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
932
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
933 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
934 """
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
935 Wraps an arbitrary DataSet into one for supervised learning tasks by forcing the
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
936 user to define a set of fields as the 'input' field and a set of fields
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
937 as the 'target' field. Optionally, a single weight_field can also be defined.
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
938 """
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
939 args = ((input_fields,'input'),(output_fields,'target'))
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
940 if weight_field: args+=(([weight_field],'weight'))
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
941 return src_dataset.merge_fields(*args)
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
942
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
943
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
944
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
945