pylearn: dataset.py annotate

annotate dataset.py @ 324:ce79bf5fa463

- the cut and paste between file and dir conditions is always a bad thing - i made one function (hg_version) to basically call and parse hg - i made a function to include the cases of what might be returned by imp.find_modules (_input_id) - the check for a .hg folder was insufficient. Lots of things could go wrong. Instead I use the return code from the Popen process. The return code catches this and any other problem that hg runs into. - its easier to offer more rcs support in future (cvs,svn,git)

author	James Bergstra <bergstrj@iro.umontreal.ca>
date	Thu, 12 Jun 2008 20:54:49 -0400
parents	ad8be93b3c55
children	09140ba68e17 9ce791fb2cbf

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
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	2 from lookup_list import LookupList as Example
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	3 from misc import unique_elements_list_intersection
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	4 from string import join
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	5 from sys import maxint
171 895b4b60f5e8 bugfix. Otherwise the example was writed over and not a new one was returned Frederic Bastien <bastienf@iro.umontreal.ca> parents: 167 diff changeset	6 import numpy, copy
11 be128b9127c8 Debugged (to the extent of my tests) the new version of dataset bengioy@esprit.iro.umontreal.ca parents: 9 diff changeset	7
166 ee11ed427ba8 Created exceptions.py Joseph Turian <turian@gmail.com> parents: 163 diff changeset	8 from exceptions import *
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	9
110 8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression bengioy@bengiomac.local parents: 105 diff changeset	10 class AttributesHolder(object):
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression bengioy@bengiomac.local parents: 105 diff changeset	11 def __init__(self): pass
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression bengioy@bengiomac.local parents: 105 diff changeset	12
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression bengioy@bengiomac.local parents: 105 diff changeset	13 def attributeNames(self):
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression bengioy@bengiomac.local parents: 105 diff changeset	14 raise AbstractFunction()
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression bengioy@bengiomac.local parents: 105 diff changeset	15
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression bengioy@bengiomac.local parents: 105 diff changeset	16 def setAttributes(self,attribute_names,attribute_values,make_copies=False):
134 3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 132 diff changeset	17 """
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 132 diff changeset	18 Allow the attribute_values to not be a list (but a single value) if the attribute_names is of length 1.
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 132 diff changeset	19 """
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 132 diff changeset	20 if len(attribute_names)==1 and not (isinstance(attribute_values,list) or isinstance(attribute_values,tuple) ):
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 132 diff changeset	21 attribute_values = [attribute_values]
110 8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression bengioy@bengiomac.local parents: 105 diff changeset	22 if make_copies:
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression bengioy@bengiomac.local parents: 105 diff changeset	23 for name,value in zip(attribute_names,attribute_values):
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression bengioy@bengiomac.local parents: 105 diff changeset	24 self.__setattr__(name,copy.deepcopy(value))
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression bengioy@bengiomac.local parents: 105 diff changeset	25 else:
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression bengioy@bengiomac.local parents: 105 diff changeset	26 for name,value in zip(attribute_names,attribute_values):
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression bengioy@bengiomac.local parents: 105 diff changeset	27 self.__setattr__(name,value)
193 cb6b945acf5a Complete redesign of learner... Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 188 diff changeset	28
cb6b945acf5a Complete redesign of learner... Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 188 diff changeset	29 def getAttributes(self,attribute_names=None, return_copy=False):
cb6b945acf5a Complete redesign of learner... Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 188 diff changeset	30 """
cb6b945acf5a Complete redesign of learner... Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 188 diff changeset	31 Return all (if attribute_names=None, in the order of attributeNames()) or a specified subset of attributes.
cb6b945acf5a Complete redesign of learner... Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 188 diff changeset	32 """
cb6b945acf5a Complete redesign of learner... Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 188 diff changeset	33 if attribute_names is None:
cb6b945acf5a Complete redesign of learner... Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 188 diff changeset	34 attribute_names = self.attributeNames()
cb6b945acf5a Complete redesign of learner... Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 188 diff changeset	35 if return_copy:
cb6b945acf5a Complete redesign of learner... Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 188 diff changeset	36 return [copy.copy(self.__getattribute__(name)) for name in attribute_names]
cb6b945acf5a Complete redesign of learner... Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 188 diff changeset	37 else:
cb6b945acf5a Complete redesign of learner... Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 188 diff changeset	38 return [self.__getattribute__(name) for name in attribute_names]
110 8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression bengioy@bengiomac.local parents: 105 diff changeset	39
8fa1ef2411a0 Worked on OneShotTLearner and implementation of LinearRegression bengioy@bengiomac.local parents: 105 diff changeset	40 class DataSet(AttributesHolder):
16 813723310d75 commenting bergstrj@iro.umontreal.ca parents: 15 11 diff changeset	41 """A virtual base class for datasets.
813723310d75 commenting bergstrj@iro.umontreal.ca parents: 15 11 diff changeset	42
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	43 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	44 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	45 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	46 python object, which depends on the particular dataset.
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	47
241 ddb88a8e9fd2 If I understand properly, the length of an unbounded stream is sys.maxint delallea@opale.iro.umontreal.ca parents: 231 diff changeset	48 We call a DataSet a 'stream' when its length is unbounded (in which case its __len__ method
48 b6730f9a336d Fixing MinibatchDataSet getitem bengioy@grenat.iro.umontreal.ca parents: 46 diff changeset	49 should return sys.maxint).
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	50
16 813723310d75 commenting bergstrj@iro.umontreal.ca parents: 15 11 diff changeset	51 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	52 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	53 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	54 feeds on-line learning (however, as noted below, some operations are not
241 ddb88a8e9fd2 If I understand properly, the length of an unbounded stream is sys.maxint delallea@opale.iro.umontreal.ca parents: 231 diff changeset	55 feasible or not recommended on streams).
16 813723310d75 commenting bergstrj@iro.umontreal.ca parents: 15 11 diff changeset	56
813723310d75 commenting bergstrj@iro.umontreal.ca parents: 15 11 diff changeset	57 To iterate over examples, there are several possibilities:
90 a289b8bed64c corrected comment Frederic Bastien <bastienf@iro.umontreal.ca> parents: 88 diff changeset	58 - for example in dataset:
a289b8bed64c corrected comment Frederic Bastien <bastienf@iro.umontreal.ca> parents: 88 diff changeset	59 - for val1,val2,... in dataset:
a289b8bed64c corrected comment Frederic Bastien <bastienf@iro.umontreal.ca> parents: 88 diff changeset	60 - for example in dataset(field1, field2,field3, ...):
a289b8bed64c corrected comment Frederic Bastien <bastienf@iro.umontreal.ca> parents: 88 diff changeset	61 - for val1,val2,val3 in dataset(field1, field2,field3):
72 2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	62 - for minibatch in dataset.minibatches([field1, field2, ...],minibatch_size=N):
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	63 - for mini1,mini2,mini3 in dataset.minibatches([field1, field2, field3], minibatch_size=N):
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	64 Each of these is documented below. All of these iterators are expected
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	65 to provide, in addition to the usual 'next()' method, a 'next_index()' method
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	66 which returns a non-negative integer pointing to the position of the next
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	67 example that will be returned by 'next()' (or of the first example in the
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	68 next minibatch returned). This is important because these iterators
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	69 can wrap around the dataset in order to do multiple passes through it,
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	70 in possibly unregular ways if the minibatch size is not a divisor of the
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	71 dataset length.
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	72
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	73 To iterate over fields, one can do
72 2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	74 - for field in dataset.fields():
46 c5b07e87b0cb comments modif made by Yoshua Frederic Bastien <bastienf@iro.umontreal.ca> parents: 45 diff changeset	75 for field_value in field: # iterate over the values associated to that field for all the dataset examples
72 2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	76 - for field in dataset(field1,field2,...).fields() to select a subset of fields
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	77 - 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	78 and each of these fields is iterable over the examples:
72 2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	79 - for field_examples in dataset.fields():
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	80 for example_value in field_examples:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	81 ...
241 ddb88a8e9fd2 If I understand properly, the length of an unbounded stream is sys.maxint delallea@opale.iro.umontreal.ca parents: 231 diff changeset	82 but when the dataset is a stream (unbounded length), it is not recommended to do
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	83 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	84 an unsynchronized ways. Hence the fields() method is illegal for streams, by default.
132 f6505ec32dc3 Updated documentation slightly Joseph Turian <turian@gmail.com> parents: 128 diff changeset	85 The result of fields() is a L{DataSetFields} object, which iterates over fields,
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	86 and whose elements are iterable over examples. A DataSetFields object can
72 2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	87 be turned back into a DataSet with its examples() method::
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	88 dataset2 = dataset1.fields().examples()
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	89 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	90
16 813723310d75 commenting bergstrj@iro.umontreal.ca parents: 15 11 diff changeset	91 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	92
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	93 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	94 (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	95 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	96 What about non-numeric values? None.
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	97
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	98 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	99 of examples) can be extracted. These operations are not supported
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	100 by default in the case of streams.
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	101
317 14081904d8f3 doc updated regarding __getitem__ returning LookupList and .subset returning a DataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 316 diff changeset	102 - dataset[:n] returns an Example with the n first examples.
16 813723310d75 commenting bergstrj@iro.umontreal.ca parents: 15 11 diff changeset	103
317 14081904d8f3 doc updated regarding __getitem__ returning LookupList and .subset returning a DataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 316 diff changeset	104 - dataset[i1:i2:s] returns an Example with the examples i1,i1+s,...i2-s.
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	105
72 2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	106 - dataset[i] returns an Example.
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	107
317 14081904d8f3 doc updated regarding __getitem__ returning LookupList and .subset returning a DataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 316 diff changeset	108 - dataset[[i1,i2,...in]] returns a. Example with examples i1,i2,...in.
14081904d8f3 doc updated regarding __getitem__ returning LookupList and .subset returning a DataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 316 diff changeset	109
14081904d8f3 doc updated regarding __getitem__ returning LookupList and .subset returning a DataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 316 diff changeset	110 A similar command gives you a DataSet instead of Examples :
14081904d8f3 doc updated regarding __getitem__ returning LookupList and .subset returning a DataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 316 diff changeset	111
14081904d8f3 doc updated regarding __getitem__ returning LookupList and .subset returning a DataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 316 diff changeset	112 - dataset.subset[:n] returns a DataSet with the n first examples.
14081904d8f3 doc updated regarding __getitem__ returning LookupList and .subset returning a DataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 316 diff changeset	113
14081904d8f3 doc updated regarding __getitem__ returning LookupList and .subset returning a DataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 316 diff changeset	114 - dataset.subset[i1:i2:s] returns a DataSet with the examples i1,i1+s,...i2-s.
14081904d8f3 doc updated regarding __getitem__ returning LookupList and .subset returning a DataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 316 diff changeset	115
14081904d8f3 doc updated regarding __getitem__ returning LookupList and .subset returning a DataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 316 diff changeset	116 - dataset.subset[i] returns a DataSet.
14081904d8f3 doc updated regarding __getitem__ returning LookupList and .subset returning a DataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 316 diff changeset	117
14081904d8f3 doc updated regarding __getitem__ returning LookupList and .subset returning a DataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 316 diff changeset	118 - dataset.subset[[i1,i2,...in]] returns a DataSet with examples i1,i2,...in.
14081904d8f3 doc updated regarding __getitem__ returning LookupList and .subset returning a DataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 316 diff changeset	119
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	120
72 2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	121 - dataset.<property> returns the value of a property associated with
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	122 the name <property>. The following properties should be supported:
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	123 - 'description': a textual description or name for the dataset
57 1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	124 - 'fieldtypes': a list of types (one per field)
78 3499918faa9d In the middle of designing TLearner bengioy@bengiomac.local parents: 77 diff changeset	125 A DataSet may have other attributes that it makes visible to other objects. These are
3499918faa9d In the middle of designing TLearner bengioy@bengiomac.local parents: 77 diff changeset	126 used to store information that is not example-wise but global to the dataset.
3499918faa9d In the middle of designing TLearner bengioy@bengiomac.local parents: 77 diff changeset	127 The list of names of these attributes is given by the attribute_names() method.
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	128
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	129 Datasets can be concatenated either vertically (increasing the length) or
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	130 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	131 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	132 and numpy.vstack):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	133
72 2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	134 - dataset1 \| dataset2 \| dataset3 == dataset.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	135
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	136 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	137 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	138
72 2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	139 - dataset1 & dataset2 & dataset3 == dataset.vstack([dataset1,dataset2,dataset3])
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	140
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	141 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	142 (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	143 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	144
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	145 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	146 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	147 a DataSetFields fields1 and fields2, and fields1 \| fields2 concatenates their
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	148 examples.
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	149
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	150 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	151 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	152 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	153 when key is a string (or more specifically, neither an integer, a slice, nor a list).
78 3499918faa9d In the middle of designing TLearner bengioy@bengiomac.local parents: 77 diff changeset	154
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	155 A DataSet sub-class should always redefine the following methods:
72 2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	156 - __len__ if it is not a stream
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	157 - fieldNames
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	158 - minibatches_nowrap (called by DataSet.minibatches())
269 fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	159 For efficiency of implementation, a sub-class might also want to redefine
72 2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	160 - valuesHStack
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	161 - valuesVStack
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	162 - hasFields
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	163 - __getitem__ may not be feasible with some streams
2b6656b2ef52 Changed docs slightly Joseph Turian <turian@iro.umontreal.ca> parents: 66 diff changeset	164 - __iter__
78 3499918faa9d In the middle of designing TLearner bengioy@bengiomac.local parents: 77 diff changeset	165 A sub-class should also append attributes to self._attribute_names
3499918faa9d In the middle of designing TLearner bengioy@bengiomac.local parents: 77 diff changeset	166 (the default value returned by attributeNames()).
3499918faa9d In the middle of designing TLearner bengioy@bengiomac.local parents: 77 diff changeset	167 By convention, attributes not in attributeNames() should have a name
3499918faa9d In the middle of designing TLearner bengioy@bengiomac.local parents: 77 diff changeset	168 starting with an underscore.
3499918faa9d In the middle of designing TLearner bengioy@bengiomac.local parents: 77 diff changeset	169 @todo enforce/test that convention!
2 3fddb1c8f955 Rewrote DataSet interface and created FiniteDataSet interface. bengioy@bengiomac.local parents: 1 diff changeset	170 """
1 2cd82666b9a7 Added statscollector and started writing dataset and learner. bengioy@esprit.iro.umontreal.ca parents: 0 diff changeset	171
83 c0f211213a58 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 82 diff changeset	172 numpy_vstack = lambda fieldname,values: numpy.vstack(values)
c0f211213a58 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 82 diff changeset	173 numpy_hstack = lambda fieldnames,values: numpy.hstack(values)
77 1e2bb5bad636 toying with different ways to implement learners bengioy@bengiomac.local parents: 74 diff changeset	174
292 174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	175 def __init__(self, description=None, fieldnames=None, fieldtypes=None):
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	176 """
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	177 @type fieldnames: list of strings
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	178 @type fieldtypes: list of python types, same length as fieldnames
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	179 @type description: string
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	180 @param description: description/name for this dataset
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	181 """
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	182 def default_desc():
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	183 return type(self).__name__ \
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	184 + " ( " + join([x.__name__ for x in type(self).__bases__]) + " )"
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	185
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	186 #self.fieldnames = fieldnames
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	187
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	188 self.fieldtypes = fieldtypes if fieldtypes is not None \
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	189 else [None]*1 #len(fieldnames)
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	190
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	191 self.description = default_desc() if description is None \
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	192 else description
78 3499918faa9d In the middle of designing TLearner bengioy@bengiomac.local parents: 77 diff changeset	193 self._attribute_names = ["description"]
292 174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	194
321 f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	195
292 174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	196 attributeNames = property(lambda self: copy.copy(self._attribute_names))
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	197
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	198 def __contains__(self, fieldname):
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	199 return (fieldname in self.fieldNames()) \
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	200 or (fieldname in self.attributeNames())
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	201
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	202 def __iter__(self):
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	203 """Supports the syntax "for i in dataset: ..."
78 3499918faa9d In the middle of designing TLearner bengioy@bengiomac.local parents: 77 diff changeset	204
292 174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	205 Using this syntax, "i" will be an Example instance (or equivalent) with
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	206 all the fields of DataSet self. Every field of "i" will give access to
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	207 a field of a single example. Fields should be accessible via
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	208 i["fielname"] or i[3] (in the order defined by the elements of the
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	209 Example returned by this iterator), but the derived class is free
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	210 to accept any type of identifier, and add extra functionality to the iterator.
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	211
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	212 The default implementation calls the minibatches iterator and extracts the first example of each field.
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	213 """
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	214 return DataSet.MinibatchToSingleExampleIterator(self.minibatches(None, minibatch_size = 1))
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	215
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	216 def __len__(self):
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	217 """
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	218 len(dataset) returns the number of examples in the dataset.
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	219 By default, a DataSet is a 'stream', i.e. it has an unbounded length (sys.maxint).
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	220 Sub-classes which implement finite-length datasets should redefine this method.
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	221 Some methods only make sense for finite-length datasets.
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	222 """
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	223 return None
174374d59405 merge James Bergstra <bergstrj@iro.umontreal.ca> parents: 290 diff changeset	224
78 3499918faa9d In the middle of designing TLearner bengioy@bengiomac.local parents: 77 diff changeset	225
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	226 class MinibatchToSingleExampleIterator(object):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	227 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	228 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	229 single-example values in the result. Therefore the result of
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	230 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	231 (whereas the result of iterating over minibatches gives in each
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	232 Example field an iterable object over the individual examples in
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	233 the minibatch).
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	234 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	235 def __init__(self, minibatch_iterator):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	236 self.minibatch_iterator = minibatch_iterator
44 5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	237 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	238 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	239 return self
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet, bengioy@esprit.iro.umontreal.ca parents: 20 diff changeset	240 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	241 size1_minibatch = self.minibatch_iterator.next()
44 5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	242 if not self.minibatch:
5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	243 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	244 else:
5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	245 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	246 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	247
23 526e192b0699 Working on ApplyFunctionDataSet, added constraint that bengioy@esprit.iro.umontreal.ca parents: 22 diff changeset	248 def next_index(self):
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	249 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	250
37 73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	251 class MinibatchWrapAroundIterator(object):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	252 """
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	253 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	254 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	255 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	256 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	257 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	258 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	259 """
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	260 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	261 self.dataset=dataset
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	262 self.fieldnames=fieldnames
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	263 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	264 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	265 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	266 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	267 self.L=len(dataset)
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	268 self.offset=offset % self.L
98 7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 95 diff changeset	269 ds_nbatches = (self.L-self.next_row)/self.minibatch_size
37 73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	270 if n_batches is not None:
98 7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 95 diff changeset	271 ds_nbatches = min(n_batches,ds_nbatches)
38 d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	272 if fieldnames:
d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	273 assert dataset.hasFields(*fieldnames)
d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	274 else:
98 7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 95 diff changeset	275 self.fieldnames=dataset.fieldNames()
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	276 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size, ds_nbatches,self.next_row)
37 73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	277
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	278 def __iter__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	279 return self
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	280
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	281 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	282 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	283
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	284 def next(self):
43 e92244f30116 Corrected iterator logic errors bengioy@grenat.iro.umontreal.ca parents: 42 diff changeset	285 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	286 raise StopIteration
101 a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 99 diff changeset	287 elif not self.n_batches and self.next_row ==self.L:
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 99 diff changeset	288 raise StopIteration
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	289 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	290 if upper <=self.L:
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	291 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	292 else:
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	293 if not self.n_batches:
101 a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 99 diff changeset	294 upper=min(upper, self.L)
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 99 diff changeset	295 # if their is not a fixed number of batch, we continue to the end of the dataset.
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 99 diff changeset	296 # this can create a minibatch that is smaller then the minibatch_size
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 99 diff changeset	297 assert (self.L-self.next_row)<=self.minibatch_size
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 99 diff changeset	298 minibatch = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next()
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 99 diff changeset	299 else:
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 99 diff changeset	300 # we must concatenate (vstack) the bottom and top parts of our minibatch
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 99 diff changeset	301 # first get the beginning of our minibatch (top of dataset)
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 99 diff changeset	302 first_part = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next()
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 99 diff changeset	303 second_part = self.dataset.minibatches_nowrap(self.fieldnames,upper-self.L,1,0).next()
a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 99 diff changeset	304 minibatch = Example(self.fieldnames,
268 3f1cd8897fda reverting dataset James Bergstra <bergstrj@iro.umontreal.ca> parents: 266 diff changeset	305 [self.dataset.valuesVStack(name,[first_part[name],second_part[name]])
101 a1740a99b81f by default, in a minibatch without any fixed number of batchs, we need to finish at the end of the dataset. Now we return a minibatch at the end event if this minibacht size != the gived minibatch_size. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 99 diff changeset	306 for name in self.fieldnames])
37 73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	307 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	308 self.n_batches_done+=1
43 e92244f30116 Corrected iterator logic errors bengioy@grenat.iro.umontreal.ca parents: 42 diff changeset	309 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	310 self.next_row -= self.L
98 7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 95 diff changeset	311 ds_nbatches = (self.L-self.next_row)/self.minibatch_size
7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 95 diff changeset	312 if self.n_batches is not None:
7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 95 diff changeset	313 ds_nbatches = min(self.n_batches,ds_nbatches)
7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 95 diff changeset	314 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size,
7186e4f502d1 bugfix in DataSet.minibatch to correctly wrap in all corner case. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 95 diff changeset	315 ds_nbatches,self.next_row)
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	316 return DataSetFields(MinibatchDataSet(minibatch,self.dataset.valuesVStack,
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	317 self.dataset.valuesHStack),
74 b4159cbdc06b Fixed errors raised by test_dataset Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 73 diff changeset	318 minibatch.keys())
37 73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	319
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	320
17 759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests bergstrj@iro.umontreal.ca parents: 16 12 diff changeset	321 minibatches_fieldnames = None
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests bergstrj@iro.umontreal.ca parents: 16 12 diff changeset	322 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	323 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	324 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	325 fieldnames = minibatches_fieldnames,
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	326 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	327 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	328 offset = 0):
6 d5738b79089a Removed MinibatchIterator and instead made minibatch_size a field of all DataSets, bengioy@bengiomac.local parents: 5 diff changeset	329 """
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	330 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	331
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet, bengioy@esprit.iro.umontreal.ca parents: 20 diff changeset	332 for i in dataset.minibatches(None,**kwargs): ...
16 813723310d75 commenting bergstrj@iro.umontreal.ca parents: 15 11 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 for i in dataset.minibatches([f1, f2, f3],**kwargs): ...
16 813723310d75 commenting bergstrj@iro.umontreal.ca parents: 15 11 diff changeset	335
17 759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests bergstrj@iro.umontreal.ca parents: 16 12 diff changeset	336 for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ...
16 813723310d75 commenting bergstrj@iro.umontreal.ca parents: 15 11 diff changeset	337
22 b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet, bengioy@esprit.iro.umontreal.ca parents: 20 diff changeset	338 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	339 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	340 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	341 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	342 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	343
22 b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet, bengioy@esprit.iro.umontreal.ca parents: 20 diff changeset	344 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	345 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	346 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	347
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	348 The minibatches iterator is expected to return upon each call to next()
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	349 a DataSetFields object, which is a Example (indexed by the field names) whose
80 40476a7746e8 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 66 diff changeset	350 elements are iterable and indexable over the minibatch examples, and which keeps a pointer to
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	351 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	352 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	353 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	354
17 759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests bergstrj@iro.umontreal.ca parents: 16 12 diff changeset	355 PARAMETERS
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests bergstrj@iro.umontreal.ca parents: 16 12 diff changeset	356 - 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	357 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	358 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	359 derived class can choose a default, e.g. all fields.
16 813723310d75 commenting bergstrj@iro.umontreal.ca parents: 15 11 diff changeset	360
17 759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests bergstrj@iro.umontreal.ca parents: 16 12 diff changeset	361 - 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	362 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	363 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	364
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests bergstrj@iro.umontreal.ca parents: 16 12 diff changeset	365 - 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	366 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	367 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	368 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	369
37 73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	370 - 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	371 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	372
17 759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests bergstrj@iro.umontreal.ca parents: 16 12 diff changeset	373 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	374 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	375
11 be128b9127c8 Debugged (to the extent of my tests) the new version of dataset bengioy@esprit.iro.umontreal.ca parents: 9 diff changeset	376 """
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	377 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	378
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	379 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	380 """
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	381 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	382 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	383 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	384 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	385 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	386 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	387 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	388 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	389 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	390 """
17 759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests bergstrj@iro.umontreal.ca parents: 16 12 diff changeset	391 raise AbstractFunction()
22 b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet, bengioy@esprit.iro.umontreal.ca parents: 20 diff changeset	392
48 b6730f9a336d Fixing MinibatchDataSet getitem bengioy@grenat.iro.umontreal.ca parents: 46 diff changeset	393 def is_unbounded(self):
b6730f9a336d Fixing MinibatchDataSet getitem bengioy@grenat.iro.umontreal.ca parents: 46 diff changeset	394 """
b6730f9a336d Fixing MinibatchDataSet getitem bengioy@grenat.iro.umontreal.ca parents: 46 diff changeset	395 Tests whether a dataset is unbounded (e.g. a stream).
b6730f9a336d Fixing MinibatchDataSet getitem bengioy@grenat.iro.umontreal.ca parents: 46 diff changeset	396 """
123 8b520423d4ee bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 110 diff changeset	397 return len(self)==maxint
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	398
26 672fe4b23032 Fixed dataset errors so that _test_dataset.py works again. bengioy@grenat.iro.umontreal.ca parents: 23 diff changeset	399 def hasFields(self,*fieldnames):
20 266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works. bengioy@bengiomac.local parents: 19 diff changeset	400 """
22 b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet, bengioy@esprit.iro.umontreal.ca parents: 20 diff changeset	401 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	402 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	403 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	404
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	405 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	406 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	407 """
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	408 return len(unique_elements_list_intersection(fieldnames,self.fieldNames()))>0
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	409
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	410 def fieldNames(self):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	411 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	412 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	413 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	414 """
17 759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests bergstrj@iro.umontreal.ca parents: 16 12 diff changeset	415 raise AbstractFunction()
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests bergstrj@iro.umontreal.ca parents: 16 12 diff changeset	416
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	417 def __call__(self,*fieldnames):
23 526e192b0699 Working on ApplyFunctionDataSet, added constraint that bengioy@esprit.iro.umontreal.ca parents: 22 diff changeset	418 """
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	419 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	420 """
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	421 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	422 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	423
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	424 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	425 """
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	426 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	427 """
74 b4159cbdc06b Fixed errors raised by test_dataset Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 73 diff changeset	428 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	429
269 fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	430 def getitem_key(self, fieldname):
fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	431 """A not-so-well thought-out place to put code that used to be in
fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	432 getitem.
fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	433 """
fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	434 #removing as per discussion June 4. --JSB
fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	435
fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	436 i = fieldname
fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	437 # else check for a fieldname
fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	438 if self.hasFields(i):
fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	439 return self.minibatches(fieldnames=[i],minibatch_size=len(self),n_batches=1,offset=0).next()[0]
fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	440 # else we are trying to access a property of the dataset
fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	441 assert i in self.__dict__ # else it means we are trying to access a non-existing property
fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	442 return self.__dict__[i]
fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	443
2 3fddb1c8f955 Rewrote DataSet interface and created FiniteDataSet interface. bengioy@bengiomac.local parents: 1 diff changeset	444 def __getitem__(self,i):
28 541a273bc89f Removed __array__ method from dataset, whose bengioy@grenat.iro.umontreal.ca parents: 26 diff changeset	445 """
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	446 @rtype: Example
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	447 @returns: single or multiple examples
1 2cd82666b9a7 Added statscollector and started writing dataset and learner. bengioy@esprit.iro.umontreal.ca parents: 0 diff changeset	448
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	449 @type i: integer or slice or <iterable> of integers
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	450 @param i:
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	451 dataset[i] returns the (i+1)-th example of the dataset.
309 923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	452 dataset[i:j] returns a LookupList with examples i,i+1,...,j-1.
923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	453 dataset[i:j:s] returns a LookupList with examples i,i+2,i+4...,j-2.
923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	454 dataset[[i1,i2,..,in]] returns a LookupList with examples i1,i2,...,in.
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	455
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	456 @note:
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	457 Some stream datasets may be unable to implement random access, i.e.
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	458 arbitrary slicing/indexing because they can only iterate through
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	459 examples one or a minibatch at a time and do not actually store or keep
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	460 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	461
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets bengioy@esprit.iro.umontreal.ca parents: 39 diff changeset	462 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	463 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	464 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	465 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	466 """
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	467
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	468 if type(i) is int:
309 923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	469 assert i >= 0 # TBM: see if someone complains and want negative i
313 009ce84e9f52 behaviour is now the same as a list in pylearn, so if len(ds) = 10, ds[10] raise an IndexError, same thing for ds[[1,10]], and ds[0:14:1] returns 10 elements Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 310 diff changeset	470 if i >= len(self) :
009ce84e9f52 behaviour is now the same as a list in pylearn, so if len(ds) = 10, ds[10] raise an IndexError, same thing for ds[[1,10]], and ds[0:14:1] returns 10 elements Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 310 diff changeset	471 raise IndexError
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	472 i_batch = self.minibatches_nowrap(self.fieldNames(),
293 4bfdda107a17 still merging James Bergstra <bergstrj@iro.umontreal.ca> parents: 292 diff changeset	473 minibatch_size=1, n_batches=1, offset=i)
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	474 return DataSet.MinibatchToSingleExampleIterator(i_batch).next()
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	475
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	476 #if i is a contiguous slice
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	477 if type(i) is slice and (i.step in (None, 1)):
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	478 offset = 0 if i.start is None else i.start
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	479 upper_bound = len(self) if i.stop is None else i.stop
313 009ce84e9f52 behaviour is now the same as a list in pylearn, so if len(ds) = 10, ds[10] raise an IndexError, same thing for ds[[1,10]], and ds[0:14:1] returns 10 elements Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 310 diff changeset	480 upper_bound = min(len(self) , upper_bound)
309 923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	481 #return MinibatchDataSet(self.minibatches_nowrap(self.fieldNames(),
923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	482 # minibatch_size=upper_bound - offset,
923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	483 # n_batches=1,
923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	484 # offset=offset).next())
923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	485 # now returns a LookupList
923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	486 return self.minibatches_nowrap(self.fieldNames(),
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	487 minibatch_size=upper_bound - offset,
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	488 n_batches=1,
309 923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	489 offset=offset).next()
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	490
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	491 # if slice has a step param, convert it to list and handle it with the
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	492 # list code
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	493 if type(i) is slice:
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	494 offset = 0 if i.start is None else i.start
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	495 upper_bound = len(self) if i.stop is None else i.stop
314 105b54ac8260 bug fixed concerning the slicing, now ds[0:len(ds) + 1000 : 2] is accepted, same a python list Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 313 diff changeset	496 upper_bound = min(len(self) , upper_bound)
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	497 i = list(range(offset, upper_bound, i.step))
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	498
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	499 # handle tuples, arrays, lists
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	500 if hasattr(i, '__getitem__'):
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	501 for idx in i:
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	502 #dis-allow nested slices
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	503 if not isinstance(idx, int):
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	504 raise TypeError(idx)
313 009ce84e9f52 behaviour is now the same as a list in pylearn, so if len(ds) = 10, ds[10] raise an IndexError, same thing for ds[[1,10]], and ds[0:14:1] returns 10 elements Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 310 diff changeset	505 if idx >= len(self) :
009ce84e9f52 behaviour is now the same as a list in pylearn, so if len(ds) = 10, ds[10] raise an IndexError, same thing for ds[[1,10]], and ds[0:14:1] returns 10 elements Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 310 diff changeset	506 raise IndexError
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	507 # call back into self.__getitem__
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	508 examples = [self.minibatches_nowrap(self.fieldNames(),
293 4bfdda107a17 still merging James Bergstra <bergstrj@iro.umontreal.ca> parents: 292 diff changeset	509 minibatch_size=1, n_batches=1, offset=ii).next()
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	510 for ii in i]
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	511 # re-index the fields in each example by field instead of by example
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	512 field_values = [[] for blah in self.fieldNames()]
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	513 for e in examples:
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	514 for f,v in zip(field_values, e):
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	515 f.append(v)
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	516 #build them into a LookupList (a.ka. Example)
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	517 zz = zip(self.fieldNames(),field_values)
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	518 vst = [self.valuesVStack(fieldname,field_values) for fieldname,field_values in zz]
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	519 example = Example(self.fieldNames(), vst)
309 923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	520 #return MinibatchDataSet(example, self.valuesVStack, self.valuesHStack)
923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	521 # now returns a LookupList
923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	522 return example
923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	523
923de30457f0 get item now returns LookupLists Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 296 diff changeset	524 # what in the world is i?
269 fdce496c3b56 deprecating __getitem__[fieldname] syntax James Bergstra <bergstrj@iro.umontreal.ca> parents: 268 diff changeset	525 raise TypeError(i, type(i))
22 b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet, bengioy@esprit.iro.umontreal.ca parents: 20 diff changeset	526
310 ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	527
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	528 """
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	529 Enables the call dataset.subset[a:b:c] that will return a DataSet
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	530 around the examples returned by __getitem__(slice(a,b,c))
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	531
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	532 @SEE DataSet.__getsubset(self)
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	533 """
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	534 subset = property(lambda s : s.__getsubset(),doc="returns a subset as a DataSet")
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	535
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	536
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	537 def __getsubset(self) :
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	538 """
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	539 Enables the call data.subset[a:b:c], returns a DataSet.
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	540 Default implementation is a simple wrap around __getitem__() using MinibatchDataSet.
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	541
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	542 @RETURN DataSet
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	543 @SEE DataSet.subset = property(lambda s : s.__getsubset())
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	544 """
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	545 _self = self
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	546 class GetSliceReturnsDataSet(object) :
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	547 def __getitem__(self,slice) :
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	548 return MinibatchDataSet(_self.__getitem__(slice))
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	549 return GetSliceReturnsDataSet()
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	550
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	551
ebccfd05ccd5 dataset.subset implemented Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 309 diff changeset	552
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	553 def valuesHStack(self,fieldnames,fieldvalues):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	554 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	555 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	556 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	557 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	558 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	559 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	560 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	561 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	562 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	563 pointing to the original values for other data types.
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	564 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	565 all_numpy=True
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	566 for value in fieldvalues:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	567 if not type(value) is numpy.ndarray:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	568 all_numpy=False
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	569 if all_numpy:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	570 return numpy.hstack(fieldvalues)
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	571 # 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	572 return fieldvalues
26 672fe4b23032 Fixed dataset errors so that _test_dataset.py works again. bengioy@grenat.iro.umontreal.ca parents: 23 diff changeset	573
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	574 def valuesVStack(self,fieldname,values):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	575 """
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	576 @param fieldname: the name of the field from which the values were taken
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	577 @type fieldname: any type
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	578
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	579 @param values: bits near the beginning or end of the dataset
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	580 @type values: list of minibatches (returned by minibatch_nowrap)
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	581
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	582 @return: the concatenation (stacking) of the values
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	583 @rtype: something suitable as a minibatch field
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	584 """
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	585 rval = []
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	586 for v in values:
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	587 rval.extend(v)
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	588 return rval
17 759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests bergstrj@iro.umontreal.ca parents: 16 12 diff changeset	589
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	590 def __or__(self,other):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	591 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	592 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	593 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	594 """
135 0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 134 diff changeset	595 return HStackedDataSet([self,other])
3 378b68d5c4ad Added first (untested) version of ArrayDataSet bengioy@bengiomac.local parents: 2 diff changeset	596
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	597 def __and__(self,other):
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	598 """
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	599 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	600 (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	601 works if they all have the same fields.
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	602 """
135 0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 134 diff changeset	603 return VStackedDataSet([self,other])
23 526e192b0699 Working on ApplyFunctionDataSet, added constraint that bengioy@esprit.iro.umontreal.ca parents: 22 diff changeset	604
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	605 def hstack(datasets):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	606 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	607 hstack(dataset1,dataset2,...) returns dataset1 \| datataset2 \| ...
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	608 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	609 of the individual datasets.
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	610 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	611 assert len(datasets)>0
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	612 if len(datasets)==1:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	613 return datasets[0]
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	614 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	615
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	616 def vstack(datasets):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	617 """
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	618 vstack(dataset1,dataset2,...) returns dataset1 & datataset2 & ...
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	619 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	620 over those of dataset2, etc.
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	621 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	622 assert len(datasets)>0
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	623 if len(datasets)==1:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	624 return datasets[0]
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	625 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	626
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	627 class FieldsSubsetDataSet(DataSet):
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	628 """
167 4803cb76e26b Updated documentation Joseph Turian <turian@gmail.com> parents: 166 diff changeset	629 A sub-class of L{DataSet} that selects a subset of the fields.
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	630 """
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	631 def __init__(self,src,fieldnames):
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	632 self.src=src
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	633 self.fieldnames=fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	634 assert src.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	635 self.valuesHStack = src.valuesHStack
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	636 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	637
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	638 def __len__(self): return len(self.src)
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	639
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	640 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	641 return self.fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	642
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	643 def __iter__(self):
44 5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	644 class FieldsSubsetIterator(object):
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	645 def __init__(self,ds):
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	646 self.ds=ds
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	647 self.src_iter=ds.src.__iter__()
44 5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	648 self.example=None
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	649 def __iter__(self): return self
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	650 def next(self):
44 5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	651 complete_example = self.src_iter.next()
5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	652 if self.example:
5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	653 self.example._values=[complete_example[field]
5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	654 for field in self.ds.fieldnames]
5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	655 else:
5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	656 self.example=Example(self.ds.fieldnames,
5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	657 [complete_example[field] for field in self.ds.fieldnames])
5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	658 return self.example
5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	659 return FieldsSubsetIterator(self)
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	660
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	661 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	662 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	663 return self.src.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset)
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	664 def dontuse__getitem__(self,i):
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	665 return FieldsSubsetDataSet(self.src[i],self.fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	666
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	667
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	668 class DataSetFields(Example):
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	669 """
167 4803cb76e26b Updated documentation Joseph Turian <turian@gmail.com> parents: 166 diff changeset	670 Although a L{DataSet} iterates over examples (like rows of a matrix), an associated
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	671 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	672 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	673
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	674 To iterate over fields, one can do
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	675 * for fields in dataset.fields()
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	676 * 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	677 * 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	678 and each of these fields is iterable over the examples:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	679 * for field_examples in dataset.fields():
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	680 for example_value in field_examples:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	681 ...
241 ddb88a8e9fd2 If I understand properly, the length of an unbounded stream is sys.maxint delallea@opale.iro.umontreal.ca parents: 231 diff changeset	682 but when the dataset is a stream (unbounded length), it is not recommended to do
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	683 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	684 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	685 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	686 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	687 be turned back into a DataSet with its examples() method:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	688 dataset2 = dataset1.fields().examples()
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	689 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	690
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets bengioy@esprit.iro.umontreal.ca parents: 39 diff changeset	691 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	692 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	693 the examples.
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	694 """
74 b4159cbdc06b Fixed errors raised by test_dataset Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 73 diff changeset	695 def __init__(self,dataset,fieldnames):
65 d48eba49a2f4 fixed the infinite loop Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 64 diff changeset	696 original_dataset=dataset
40 88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets bengioy@esprit.iro.umontreal.ca parents: 39 diff changeset	697 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	698 fieldnames=dataset.fieldNames()
274 ed70580f2324 bugfix in FieldSubsetDataSet Frederic Bastien <bastienf@iro.umontreal.ca> parents: 273 diff changeset	699 elif not list(fieldnames)==list(dataset.fieldNames()):
ed70580f2324 bugfix in FieldSubsetDataSet Frederic Bastien <bastienf@iro.umontreal.ca> parents: 273 diff changeset	700 #we must cast to list, othersize('x','y')!=['x','y']
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	701 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	702 assert dataset.hasFields(*fieldnames)
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	703 self.dataset=dataset
66 dde1fb1b63ba fixed test and removed print Frederic Bastien <bastienf@iro.umontreal.ca> parents: 65 diff changeset	704
64 863da25a60f1 trying to fix infinite loop Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 62 diff changeset	705 if isinstance(dataset,MinibatchDataSet):
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	706 Example.__init__(self,fieldnames,list(dataset._fields))
65 d48eba49a2f4 fixed the infinite loop Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 64 diff changeset	707 elif isinstance(original_dataset,MinibatchDataSet):
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	708 Example.__init__(self,fieldnames,
65 d48eba49a2f4 fixed the infinite loop Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 64 diff changeset	709 [original_dataset._fields[field]
d48eba49a2f4 fixed the infinite loop Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 64 diff changeset	710 for field in fieldnames])
64 863da25a60f1 trying to fix infinite loop Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 62 diff changeset	711 else:
863da25a60f1 trying to fix infinite loop Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 62 diff changeset	712 minibatch_iterator = dataset.minibatches(fieldnames,
863da25a60f1 trying to fix infinite loop Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 62 diff changeset	713 minibatch_size=len(dataset),
863da25a60f1 trying to fix infinite loop Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 62 diff changeset	714 n_batches=1)
863da25a60f1 trying to fix infinite loop Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 62 diff changeset	715 minibatch=minibatch_iterator.next()
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	716 Example.__init__(self,fieldnames,minibatch)
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	717
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	718 def examples(self):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	719 return self.dataset
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	720
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	721 def __or__(self,other):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	722 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	723 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	724 of the list of examples of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	725 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	726 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	727
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	728 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	729 """
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	730 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	731 of the fields of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	732 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	733 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	734
37 73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	735
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	736 class MinibatchDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	737 """
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	738 Turn a L{Example} of same-length (iterable) fields into an example-iterable dataset.
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	739 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	740 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	741 def __init__(self,fields_lookuplist,values_vstack=DataSet().valuesVStack,
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	742 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	743 """
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	744 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	745 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	746 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	747 """
211 bd728c83faff in __get__, problem if the i.stop was None, i being the slice, added one line replacing None by the len(self) Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 203 diff changeset	748
61 a8b70a9117ad bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 60 diff changeset	749 self._fields=fields_lookuplist
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	750 assert len(fields_lookuplist)>0
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	751 self.length=len(fields_lookuplist[0])
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	752 for field in fields_lookuplist[1:]:
223 517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	753 if self.length != len(field) :
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	754 print 'self.length = ',self.length
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	755 print 'len(field) = ', len(field)
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	756 print 'self._fields.keys() = ', self._fields.keys()
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	757 print 'field=',field
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	758 print 'fields_lookuplist=', fields_lookuplist
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	759 assert self.length==len(field)
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	760 self.valuesVStack=values_vstack
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	761 self.valuesHStack=values_hstack
3 378b68d5c4ad Added first (untested) version of ArrayDataSet bengioy@bengiomac.local parents: 2 diff changeset	762
378b68d5c4ad Added first (untested) version of ArrayDataSet bengioy@bengiomac.local parents: 2 diff changeset	763 def __len__(self):
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	764 return self.length
28 541a273bc89f Removed __array__ method from dataset, whose bengioy@grenat.iro.umontreal.ca parents: 26 diff changeset	765
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	766 def dontuse__getitem__(self,i):
80 40476a7746e8 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 66 diff changeset	767 if type(i) in (slice,list):
48 b6730f9a336d Fixing MinibatchDataSet getitem bengioy@grenat.iro.umontreal.ca parents: 46 diff changeset	768 return DataSetFields(MinibatchDataSet(
80 40476a7746e8 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 66 diff changeset	769 Example(self._fields.keys(),[field[i] for field in self._fields])),self.fieldNames())
40476a7746e8 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 66 diff changeset	770 if type(i) is int:
85 7b1f3ad3d60b bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 83 diff changeset	771 return Example(self._fields.keys(),[field[i] for field in self._fields])
48 b6730f9a336d Fixing MinibatchDataSet getitem bengioy@grenat.iro.umontreal.ca parents: 46 diff changeset	772 if self.hasFields(i):
61 a8b70a9117ad bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 60 diff changeset	773 return self._fields[i]
55 66619ce44497 Efficient implementation of getitem for ArrayDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 48 diff changeset	774 assert i in self.__dict__ # else it means we are trying to access a non-existing property
48 b6730f9a336d Fixing MinibatchDataSet getitem bengioy@grenat.iro.umontreal.ca parents: 46 diff changeset	775 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	776
29 46c5c90019c2 Changed apply_function so that it propagates methods of the source. bengioy@grenat.iro.umontreal.ca parents: 28 diff changeset	777 def fieldNames(self):
61 a8b70a9117ad bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 60 diff changeset	778 return self._fields.keys()
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	779
37 73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	780 def hasFields(self,*fieldnames):
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	781 for fieldname in fieldnames:
61 a8b70a9117ad bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 60 diff changeset	782 if fieldname not in self._fields.keys():
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	783 return False
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	784 return True
20 266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works. bengioy@bengiomac.local parents: 19 diff changeset	785
37 73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	786 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
223 517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	787 #@TODO bug somewhere here, fieldnames doesnt seem to be well handled
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	788 class Iterator(object):
223 517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	789 def __init__(self,ds,fieldnames):
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	790 # tbm: added two next lines to handle fieldnames
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	791 if fieldnames is None: fieldnames = ds._fields.keys()
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	792 self.fieldnames = fieldnames
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	793
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	794 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	795 self.next_example=offset
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	796 assert minibatch_size >= 0
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	797 if offset+minibatch_size > ds.length:
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	798 raise NotImplementedError()
20 266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works. bengioy@bengiomac.local parents: 19 diff changeset	799 def __iter__(self):
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works. bengioy@bengiomac.local parents: 19 diff changeset	800 return self
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works. bengioy@bengiomac.local parents: 19 diff changeset	801 def next(self):
61 a8b70a9117ad bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 60 diff changeset	802 upper = self.next_example+minibatch_size
37 73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	803 assert upper<=self.ds.length
223 517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	804 #minibatch = Example(self.ds._fields.keys(),
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	805 # [field[self.next_example:upper]
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	806 # for field in self.ds._fields])
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	807 # tbm: modif to use fieldnames
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	808 values = []
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	809 for f in self.fieldnames :
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	810 #print 'we have field',f,'in fieldnames'
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	811 values.append( self.ds._fields[f][self.next_example:upper] )
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	812 minibatch = Example(self.fieldnames,values)
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	813 #print minibatch
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	814 self.next_example+=minibatch_size
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	815 return minibatch
20 266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works. bengioy@bengiomac.local parents: 19 diff changeset	816
223 517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	817 # tbm: added fieldnames to handle subset of fieldnames
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 218 diff changeset	818 return Iterator(self,fieldnames)
20 266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works. bengioy@bengiomac.local parents: 19 diff changeset	819
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	820 class HStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	821 """
167 4803cb76e26b Updated documentation Joseph Turian <turian@gmail.com> parents: 166 diff changeset	822 A L{DataSet} that wraps several datasets and shows a view that includes all their fields,
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	823 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	824
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	825 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	826 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	827 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	828
167 4803cb76e26b Updated documentation Joseph Turian <turian@gmail.com> parents: 166 diff changeset	829 @todo: automatically detect a chain of stacked datasets due to A \| B \| C \| D ...
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	830 """
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	831 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	832 DataSet.__init__(self,description,field_types)
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	833 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	834 self.accept_nonunique_names=accept_nonunique_names
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	835 self.fieldname2dataset={}
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	836
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	837 def rename_field(fieldname,dataset,i):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	838 if hasattr(dataset,"__name__"):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	839 return dataset.__name__ + "." + fieldname
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	840 return fieldname+"."+str(i)
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	841
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	842 # 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	843 self.length=None
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	844 names_to_change=[]
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	845 for i in xrange(len(datasets)):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	846 dataset = datasets[i]
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	847 length=len(dataset)
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	848 if self.length:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	849 assert self.length==length
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	850 else:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	851 self.length=length
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	852 for fieldname in dataset.fieldNames():
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	853 if fieldname in self.fieldname2dataset: # name conflict!
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	854 if accept_nonunique_names:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	855 fieldname=rename_field(fieldname,dataset,i)
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	856 names2change.append((fieldname,i))
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	857 else:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	858 raise ValueError("Incompatible datasets: non-unique field name = "+fieldname)
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	859 self.fieldname2dataset[fieldname]=i
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	860 for fieldname,i in names_to_change:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	861 del self.fieldname2dataset[fieldname]
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	862 self.fieldname2dataset[rename_field(fieldname,self.datasets[i],i)]=i
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	863
37 73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	864 def hasFields(self,*fieldnames):
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	865 for fieldname in fieldnames:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	866 if not fieldname in self.fieldname2dataset:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	867 return False
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	868 return True
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	869
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	870 def fieldNames(self):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	871 return self.fieldname2dataset.keys()
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	872
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	873 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	874
44 5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	875 class HStackedIterator(object):
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	876 def __init__(self,hsds,iterators):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	877 self.hsds=hsds
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	878 self.iterators=iterators
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	879 def __iter__(self):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	880 return self
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	881 def next(self):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	882 # concatenate all the fields of the minibatches
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	883 l=Example()
140 488ad6398b12 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 136 diff changeset	884 for iter in self.iterators:
488ad6398b12 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 136 diff changeset	885 l.append_lookuplist(iter.next())
488ad6398b12 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 136 diff changeset	886 return l
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	887
125 7d8b3d6dd4e9 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 123 diff changeset	888 assert self.hasFields(*fieldnames)
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	889 # 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	890 # and construct corresponding minibatch iterators
140 488ad6398b12 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 136 diff changeset	891 if fieldnames and fieldnames!=self.fieldNames():
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	892 datasets=set([])
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	893 fields_in_dataset=dict([(dataset,[]) for dataset in datasets])
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	894 for fieldname in fieldnames:
136 fa752c55aa09 typo Frederic Bastien <bastienf@iro.umontreal.ca> parents: 125 diff changeset	895 dataset=self.datasets[self.fieldname2dataset[fieldname]]
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	896 datasets.add(dataset)
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	897 fields_in_dataset[dataset].append(fieldname)
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	898 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	899 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	900 for dataset in datasets]
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	901 else:
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	902 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	903 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	904 return HStackedIterator(self,iterators)
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	905
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	906
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	907 def untested_valuesVStack(self,fieldname,fieldvalues):
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	908 return self.datasets[self.fieldname2dataset[fieldname]].valuesVStack(fieldname,fieldvalues)
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	909
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	910 def untested_valuesHStack(self,fieldnames,fieldvalues):
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	911 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	912 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	913 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	914 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	915 all the fieldnames are of the same sub-dataset.
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	916 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	917 return self.datasets[self.fieldname2dataset[fieldnames[0]]].valuesHStack(fieldnames,fieldvalues)
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	918
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	919 class VStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	920 """
167 4803cb76e26b Updated documentation Joseph Turian <turian@gmail.com> parents: 166 diff changeset	921 A L{DataSet} that wraps several datasets and shows a view that includes all their examples,
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	922 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	923 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	924
167 4803cb76e26b Updated documentation Joseph Turian <turian@gmail.com> parents: 166 diff changeset	925 @todo: automatically detect a chain of stacked datasets due to A + B + C + D ...
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	926 """
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	927 def __init__(self,datasets):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	928 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	929 self.length=0
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	930 self.index2dataset={}
37 73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	931 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	932 fieldnames = datasets[-1].fieldNames()
38 d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	933 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	934 # 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	935 # 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	936 for dataset,k in enumerate(datasets[0:-1]):
48 b6730f9a336d Fixing MinibatchDataSet getitem bengioy@grenat.iro.umontreal.ca parents: 46 diff changeset	937 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	938 L=len(dataset)
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	939 for i in xrange(L):
438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	940 self.index2dataset[self.length+i]=k
38 d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	941 self.datasets_start_row.append(self.length)
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	942 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	943 assert dataset.fieldNames()==fieldnames
38 d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	944 self.datasets_start_row.append(self.length)
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	945 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	946 # 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	947 # 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	948 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	949 # 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	950 # TODO
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	951 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	952
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	953 def __len__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	954 return self.length
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	955
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	956 def fieldNames(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	957 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	958
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	959 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	960 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	961
38 d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	962 def locate_row(self,row):
d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	963 """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	964 dataset_index = self.index2dataset[row]
d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	965 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	966 return dataset_index, row_within_dataset
d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	967
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	968 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	969
5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	970 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	971 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	972 self.vsds=vsds
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	973 self.next_row=offset
38 d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	974 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	975 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	976 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	977
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	978 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	979 L=len(dataset)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	980 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	981 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	982 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	983 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	984 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	985 n_left_in_mb=minibatch_size-L
38 d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	986 ds_nbatches=1
d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	987 else:
d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	988 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	989 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	990 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	991
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	992 def move_to_next_dataset(self):
38 d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	993 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	994 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	995 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	996 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	997 else:
d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	998 self.next_dataset_index +=1
d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	999 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	1000 self.next_dataset_index = 0
d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	1001 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	1002 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	1003
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	1004 def __iter__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	1005 return self
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	1006
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	1007 def next(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	1008 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	1009 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	1010 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	1011 extra_mb = []
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	1012 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	1013 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	1014 extra_mb.append(self.next_iterator.next())
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1015 mb = Example(fieldnames,
40 88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets bengioy@esprit.iro.umontreal.ca parents: 39 diff changeset	1016 [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	1017 [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	1018 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	1019
37 73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet bengioy@esprit.iro.umontreal.ca parents: 36 diff changeset	1020 self.next_row+=minibatch_size
38 d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	1021 self.next_dataset_row+=minibatch_size
d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	1022 if self.next_row+minibatch_size>len(dataset):
d637ad8f7352 Finished first untested version of VStackedDataset bengioy@esprit.iro.umontreal.ca parents: 37 diff changeset	1023 self.move_to_next_dataset()
44 5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	1024 return examples
5a85fda9b19b Fixed some more iterator bugs bengioy@grenat.iro.umontreal.ca parents: 43 diff changeset	1025 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	1026
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1027 class ArrayFieldsDataSet(DataSet):
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1028 """
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1029 Virtual super-class of datasets whose field values are numpy array,
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1030 thus defining valuesHStack and valuesVStack for sub-classes.
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1031 """
268 3f1cd8897fda reverting dataset James Bergstra <bergstrj@iro.umontreal.ca> parents: 266 diff changeset	1032 def __init__(self,description=None,field_types=None):
3f1cd8897fda reverting dataset James Bergstra <bergstrj@iro.umontreal.ca> parents: 266 diff changeset	1033 DataSet.__init__(self,description,field_types)
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1034 def untested_valuesHStack(self,fieldnames,fieldvalues):
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1035 """Concatenate field values horizontally, e.g. two vectors
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1036 become a longer vector, two matrices become a wider matrix, etc."""
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1037 return numpy.hstack(fieldvalues)
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1038 def untested_valuesVStack(self,fieldname,values):
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1039 """Concatenate field values vertically, e.g. two vectors
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1040 become a two-row matrix, two matrices become a longer matrix, etc."""
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1041 return numpy.vstack(values)
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1042
316 5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1043
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1044
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1045 class NArraysDataSet(ArrayFieldsDataSet) :
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1046 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1047 An NArraysDataSet stores fields that are numpy tensor, whose first axis
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1048 iterates over examples. It's a generalization of ArrayDataSet.
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1049 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1050 #@TODO not completely implemented yet
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1051 def __init__(self, data_arrays, fieldnames, **kwargs) :
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1052 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1053 Construct an NArraysDataSet from a list of numpy tensor (data_arrays) and a list
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1054 of fieldnames. The number of arrays must be the same as the number of
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1055 fieldnames. Each set of numpy tensor must have the same first dimension (first
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1056 axis) corresponding to the number of examples.
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1057
321 f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1058 Every tensor is treated as a numpy array (using numpy.asarray)
316 5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1059 """
318 e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1060 ArrayFieldsDataSet.__init__(self,**kwargs)
316 5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1061 assert len(data_arrays) == len(fieldnames)
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1062 assert len(fieldnames) > 0
322 ad8be93b3c55 small bugs fixed with NArrayDataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 321 diff changeset	1063 ndarrays = [numpy.asarray(a) for a in data_arrays]
321 f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1064 lens = [a.shape[0] for a in ndarrays]
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1065 num_examples = lens[0] #they must all be equal anyway
316 5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1066 self._fieldnames = fieldnames
322 ad8be93b3c55 small bugs fixed with NArrayDataSet Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 321 diff changeset	1067 for k in ndarrays :
321 f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1068 assert k.shape[0] == num_examples
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1069 self._datas = ndarrays
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1070 # create dict
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1071 self.map_field_idx = dict()
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1072 for k in range(len(fieldnames)):
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1073 self.map_field_idx[fieldnames[k]] = k
316 5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1074
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1075
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1076 def __len__(self) :
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1077 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1078 Length of the dataset is based on the first array = data_arrays[0], using its shape
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1079 """
318 e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1080 return self._datas[0].shape[0]
316 5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1081
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1082 def fieldNames(self) :
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1083 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1084 Returns the fieldnames as set in self.__init__
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1085 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1086 return self._fieldnames
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1087
321 f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1088 def field_pos(self,fieldname) :
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1089 """
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1090 Returns the index of a given fieldname. Fieldname must exists! see fieldNames().
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1091 """
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1092 return self.map_field_idx[fieldname]
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1093
318 e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1094 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1095 cursor = Example(fieldnames,[0]*len(fieldnames))
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1096 fieldnames = self.fieldNames() if fieldnames is None else fieldnames
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1097 for n in xrange(n_batches):
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1098 if offset == len(self):
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1099 break
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1100 for f in range(len(cursor._names)) :
321 f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1101 idx = self.field_pos(cursor._names[f])
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 320 diff changeset	1102 sub_data = self._datas[idx][offset : offset+minibatch_size]
318 e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1103 cursor._values[f] = sub_data
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1104 offset += len(sub_data) #can be less than minibatch_size at end
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1105 yield cursor
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1106
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1107 #return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset)
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1108
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff... Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 317 diff changeset	1109
316 5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1110
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1111
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1112 class ArrayDataSet(ArrayFieldsDataSet):
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1113 """
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1114 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	1115 whose first axis iterates over examples, second axis determines fields.
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1116 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	1117 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	1118 """
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1119
188 f01ac276c6fb added __contains__ to Dataset, added parent constructor call to ArrayDataSet James Bergstra <bergstrj@iro.umontreal.ca> parents: 171 diff changeset	1120 def __init__(self, data_array, fields_columns, **kwargs):
55 66619ce44497 Efficient implementation of getitem for ArrayDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 48 diff changeset	1121 """
66619ce44497 Efficient implementation of getitem for ArrayDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 48 diff changeset	1122 Construct an ArrayDataSet from the underlying numpy array (data) and
66619ce44497 Efficient implementation of getitem for ArrayDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 48 diff changeset	1123 a map (fields_columns) from fieldnames to field columns. The columns of a field are specified
66619ce44497 Efficient implementation of getitem for ArrayDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 48 diff changeset	1124 using the standard arguments for indexing/slicing: integer for a column index,
66619ce44497 Efficient implementation of getitem for ArrayDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 48 diff changeset	1125 slice for an interval of columns (with possible stride), or iterable of column indices.
66619ce44497 Efficient implementation of getitem for ArrayDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 48 diff changeset	1126 """
188 f01ac276c6fb added __contains__ to Dataset, added parent constructor call to ArrayDataSet James Bergstra <bergstrj@iro.umontreal.ca> parents: 171 diff changeset	1127 ArrayFieldsDataSet.__init__(self, **kwargs)
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1128 self.data=data_array
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	1129 self.fields_columns=fields_columns
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1130
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1131 # check consistency and complete slices definitions
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	1132 for fieldname, fieldcolumns in self.fields_columns.items():
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1133 if type(fieldcolumns) is int:
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1134 assert fieldcolumns>=0 and fieldcolumns<data_array.shape[1]
268 3f1cd8897fda reverting dataset James Bergstra <bergstrj@iro.umontreal.ca> parents: 266 diff changeset	1135 if 1:
227 17c5d080964b reinstating changeset 216 clobbered accidentally by 218 James Bergstra <bergstrj@iro.umontreal.ca> parents: 223 diff changeset	1136 #I changed this because it didn't make sense to me,
17c5d080964b reinstating changeset 216 clobbered accidentally by 218 James Bergstra <bergstrj@iro.umontreal.ca> parents: 223 diff changeset	1137 # and it made it more difficult to write my learner.
17c5d080964b reinstating changeset 216 clobbered accidentally by 218 James Bergstra <bergstrj@iro.umontreal.ca> parents: 223 diff changeset	1138 # If it breaks stuff, let's talk about it.
17c5d080964b reinstating changeset 216 clobbered accidentally by 218 James Bergstra <bergstrj@iro.umontreal.ca> parents: 223 diff changeset	1139 # - James 22/05/2008
17c5d080964b reinstating changeset 216 clobbered accidentally by 218 James Bergstra <bergstrj@iro.umontreal.ca> parents: 223 diff changeset	1140 self.fields_columns[fieldname]=[fieldcolumns]
17c5d080964b reinstating changeset 216 clobbered accidentally by 218 James Bergstra <bergstrj@iro.umontreal.ca> parents: 223 diff changeset	1141 else:
17c5d080964b reinstating changeset 216 clobbered accidentally by 218 James Bergstra <bergstrj@iro.umontreal.ca> parents: 223 diff changeset	1142 self.fields_columns[fieldname]=fieldcolumns
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1143 elif type(fieldcolumns) is slice:
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1144 start,step=None,None
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1145 if not fieldcolumns.start:
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1146 start=0
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1147 if not fieldcolumns.step:
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1148 step=1
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1149 if start or step:
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	1150 self.fields_columns[fieldname]=slice(start,fieldcolumns.stop,step)
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1151 elif hasattr(fieldcolumns,"__iter__"): # something like a list
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1152 for i in fieldcolumns:
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1153 assert i>=0 and i<data_array.shape[1]
283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1154
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	1155 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	1156 return self.fields_columns.keys()
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1157
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	1158 def __len__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	1159 return len(self.data)
41 283e95c15b47 Added ArrayDataSet bengioy@grenat.iro.umontreal.ca parents: 40 diff changeset	1160
316 5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1161 def __getitem__(self,key):
55 66619ce44497 Efficient implementation of getitem for ArrayDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 48 diff changeset	1162 """More efficient implementation than the default __getitem__"""
66619ce44497 Efficient implementation of getitem for ArrayDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 48 diff changeset	1163 fieldnames=self.fields_columns.keys()
243 c8f19a9eb10f Optimisation in ArrayDataSet::__getitem__ Frederic Bastien <bastienf@iro.umontreal.ca> parents: 242 diff changeset	1164 values=self.fields_columns.values()
80 40476a7746e8 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 66 diff changeset	1165 if type(key) is int:
55 66619ce44497 Efficient implementation of getitem for ArrayDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 48 diff changeset	1166 return Example(fieldnames,
243 c8f19a9eb10f Optimisation in ArrayDataSet::__getitem__ Frederic Bastien <bastienf@iro.umontreal.ca> parents: 242 diff changeset	1167 [self.data[key,col] for col in values])
80 40476a7746e8 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 66 diff changeset	1168 if type(key) is slice:
316 5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1169 return Example(fieldnames,[self.data[key,col] for col in values])
80 40476a7746e8 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 66 diff changeset	1170 if type(key) is list:
40476a7746e8 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 66 diff changeset	1171 for i in range(len(key)):
40476a7746e8 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 66 diff changeset	1172 if self.hasFields(key[i]):
40476a7746e8 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 66 diff changeset	1173 key[i]=self.fields_columns[key[i]]
316 5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1174 return Example(fieldnames,
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1175 #we must separate differently for list as numpy
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1176 # doesn't support self.data[[i1,...],[i2,...]]
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1177 # when their is more then two i1 and i2
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1178 [self.data[key,:][:,col]
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1179 if isinstance(col,list) else
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 314 diff changeset	1180 self.data[key,col] for col in values])
80 40476a7746e8 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 66 diff changeset	1181
55 66619ce44497 Efficient implementation of getitem for ArrayDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 48 diff changeset	1182 # else check for a fieldname
80 40476a7746e8 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 66 diff changeset	1183 if self.hasFields(key):
105 8c0a1b11b007 bugfix, we keep all the line, but only a some columns Frederic Bastien <bastienf@iro.umontreal.ca> parents: 101 diff changeset	1184 return self.data[:,self.fields_columns[key]]
55 66619ce44497 Efficient implementation of getitem for ArrayDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 48 diff changeset	1185 # else we are trying to access a property of the dataset
80 40476a7746e8 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 66 diff changeset	1186 assert key in self.__dict__ # else it means we are trying to access a non-existing property
40476a7746e8 bugfix Frederic Bastien <bastienf@iro.umontreal.ca> parents: 66 diff changeset	1187 return self.__dict__[key]
55 66619ce44497 Efficient implementation of getitem for ArrayDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 48 diff changeset	1188
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1189 def dontuse__iter__(self):
270 1cafd495098c code cleanup and small optimisation Frederic Bastien <bastienf@iro.umontreal.ca> parents: 254 diff changeset	1190 class ArrayDataSetIteratorIter(object):
1cafd495098c code cleanup and small optimisation Frederic Bastien <bastienf@iro.umontreal.ca> parents: 254 diff changeset	1191 def __init__(self,dataset,fieldnames):
228 6f55e301c687 optimisation of ArrayDataSet Frederic Bastien <bastienf@iro.umontreal.ca> parents: 203 diff changeset	1192 if fieldnames is None: fieldnames = dataset.fieldNames()
6f55e301c687 optimisation of ArrayDataSet Frederic Bastien <bastienf@iro.umontreal.ca> parents: 203 diff changeset	1193 # store the resulting minibatch in a lookup-list of values
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1194 self.minibatch = Example(fieldnames,[0]*len(fieldnames))
228 6f55e301c687 optimisation of ArrayDataSet Frederic Bastien <bastienf@iro.umontreal.ca> parents: 203 diff changeset	1195 self.dataset=dataset
270 1cafd495098c code cleanup and small optimisation Frederic Bastien <bastienf@iro.umontreal.ca> parents: 254 diff changeset	1196 self.current=0
238 ae1d85aca858 optimization in ArrayDataSet::__iter__ Frederic Bastien <bastienf@iro.umontreal.ca> parents: 235 diff changeset	1197 self.columns = [self.dataset.fields_columns[f]
ae1d85aca858 optimization in ArrayDataSet::__iter__ Frederic Bastien <bastienf@iro.umontreal.ca> parents: 235 diff changeset	1198 for f in self.minibatch._names]
270 1cafd495098c code cleanup and small optimisation Frederic Bastien <bastienf@iro.umontreal.ca> parents: 254 diff changeset	1199 self.l = self.dataset.data.shape[0]
228 6f55e301c687 optimisation of ArrayDataSet Frederic Bastien <bastienf@iro.umontreal.ca> parents: 203 diff changeset	1200 def __iter__(self):
6f55e301c687 optimisation of ArrayDataSet Frederic Bastien <bastienf@iro.umontreal.ca> parents: 203 diff changeset	1201 return self
6f55e301c687 optimisation of ArrayDataSet Frederic Bastien <bastienf@iro.umontreal.ca> parents: 203 diff changeset	1202 def next(self):
6f55e301c687 optimisation of ArrayDataSet Frederic Bastien <bastienf@iro.umontreal.ca> parents: 203 diff changeset	1203 #@todo: we suppose that we need to stop only when minibatch_size == 1.
6f55e301c687 optimisation of ArrayDataSet Frederic Bastien <bastienf@iro.umontreal.ca> parents: 203 diff changeset	1204 # Otherwise, MinibatchWrapAroundIterator do it.
270 1cafd495098c code cleanup and small optimisation Frederic Bastien <bastienf@iro.umontreal.ca> parents: 254 diff changeset	1205 if self.current>=self.l:
228 6f55e301c687 optimisation of ArrayDataSet Frederic Bastien <bastienf@iro.umontreal.ca> parents: 203 diff changeset	1206 raise StopIteration
6f55e301c687 optimisation of ArrayDataSet Frederic Bastien <bastienf@iro.umontreal.ca> parents: 203 diff changeset	1207 sub_data = self.dataset.data[self.current]
238 ae1d85aca858 optimization in ArrayDataSet::__iter__ Frederic Bastien <bastienf@iro.umontreal.ca> parents: 235 diff changeset	1208 self.minibatch._values = [sub_data[c] for c in self.columns]
ae1d85aca858 optimization in ArrayDataSet::__iter__ Frederic Bastien <bastienf@iro.umontreal.ca> parents: 235 diff changeset	1209
270 1cafd495098c code cleanup and small optimisation Frederic Bastien <bastienf@iro.umontreal.ca> parents: 254 diff changeset	1210 self.current+=1
228 6f55e301c687 optimisation of ArrayDataSet Frederic Bastien <bastienf@iro.umontreal.ca> parents: 203 diff changeset	1211 return self.minibatch
6f55e301c687 optimisation of ArrayDataSet Frederic Bastien <bastienf@iro.umontreal.ca> parents: 203 diff changeset	1212
270 1cafd495098c code cleanup and small optimisation Frederic Bastien <bastienf@iro.umontreal.ca> parents: 254 diff changeset	1213 return ArrayDataSetIteratorIter(self,self.fieldNames())
228 6f55e301c687 optimisation of ArrayDataSet Frederic Bastien <bastienf@iro.umontreal.ca> parents: 203 diff changeset	1214
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	1215 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1216 cursor = Example(fieldnames,[0]*len(fieldnames))
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1217 fieldnames = self.fieldNames() if fieldnames is None else fieldnames
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1218 for n in xrange(n_batches):
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1219 if offset == len(self):
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1220 break
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1221 sub_data = self.data[offset : offset+minibatch_size]
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1222 offset += len(sub_data) #can be less than minibatch_size at end
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1223 cursor._values = [sub_data[:,self.fields_columns[f]] for f in cursor._names]
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1224 yield cursor
42 9b68774fcc6b Testing basic functionality and removing obvious bugs bengioy@grenat.iro.umontreal.ca parents: 41 diff changeset	1225
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1226 #return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset)
57 1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	1227
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	1228
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	1229 class CachedDataSet(DataSet):
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	1230 """
167 4803cb76e26b Updated documentation Joseph Turian <turian@gmail.com> parents: 166 diff changeset	1231 Wrap a L{DataSet} whose values are computationally expensive to obtain
57 1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	1232 (e.g. because they involve some computation, or disk access),
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	1233 so that repeated accesses to the same example are done cheaply,
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	1234 by caching every example value that has been accessed at least once.
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	1235
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	1236 Optionally, for finite-length dataset, all the values can be computed
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	1237 (and cached) upon construction of the CachedDataSet, rather at the
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	1238 first access.
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1239
167 4803cb76e26b Updated documentation Joseph Turian <turian@gmail.com> parents: 166 diff changeset	1240 @todo: when cache_all_upon_construction create mini-batches that are as
77 1e2bb5bad636 toying with different ways to implement learners bengioy@bengiomac.local parents: 74 diff changeset	1241 large as possible but not so large as to fill up memory.
1e2bb5bad636 toying with different ways to implement learners bengioy@bengiomac.local parents: 74 diff changeset	1242
167 4803cb76e26b Updated documentation Joseph Turian <turian@gmail.com> parents: 166 diff changeset	1243 @todo: add disk-buffering capability, so that when the cache becomes too
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1244 big for memory, we cache things on disk, trying to keep in memory only
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1245 the record most likely to be accessed next.
57 1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	1246 """
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1247 def __init__(self,source_dataset,cache_all_upon_construction=False):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1248 self.source_dataset=source_dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1249 self.cache_all_upon_construction=cache_all_upon_construction
152 3f627e844cba Fixes in CacheDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 151 diff changeset	1250 self.cached_examples = []
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1251 if cache_all_upon_construction:
77 1e2bb5bad636 toying with different ways to implement learners bengioy@bengiomac.local parents: 74 diff changeset	1252 # this potentially brings all the source examples
1e2bb5bad636 toying with different ways to implement learners bengioy@bengiomac.local parents: 74 diff changeset	1253 # into memory at once, which may be too much
1e2bb5bad636 toying with different ways to implement learners bengioy@bengiomac.local parents: 74 diff changeset	1254 # the work could possibly be done by minibatches
1e2bb5bad636 toying with different ways to implement learners bengioy@bengiomac.local parents: 74 diff changeset	1255 # that are as large as possible but no more than what memory allows.
146 8173e196e291 Trying to make CacheDataSet work Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 144 diff changeset	1256 fields_values = source_dataset.minibatches(minibatch_size=len(source_dataset)).__iter__().next()
152 3f627e844cba Fixes in CacheDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 151 diff changeset	1257 assert all([len(self)==len(field_values) for field_values in fields_values])
3f627e844cba Fixes in CacheDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 151 diff changeset	1258 for example in fields_values.examples():
171 895b4b60f5e8 bugfix. Otherwise the example was writed over and not a new one was returned Frederic Bastien <bastienf@iro.umontreal.ca> parents: 167 diff changeset	1259 self.cached_examples.append(copy.copy(example))
57 1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	1260
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1261 self.fieldNames = source_dataset.fieldNames
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1262 self.hasFields = source_dataset.hasFields
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1263 self.valuesHStack = source_dataset.valuesHStack
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1264 self.valuesVStack = source_dataset.valuesVStack
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1265
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1266 def __len__(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1267 return len(self.source_dataset)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1268
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1269 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1270 class CacheIterator(object):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1271 def __init__(self,dataset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1272 self.dataset=dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1273 self.current=offset
254 8ec867d12428 optimication in CachedDataSet.minibatches_nowrap Frederic Bastien <bastienf@iro.umontreal.ca> parents: 253 diff changeset	1274 self.all_fields = self.dataset.fieldNames()==fieldnames
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1275 def __iter__(self): return self
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1276 def next(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1277 upper = self.current+minibatch_size
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1278 cache_len = len(self.dataset.cached_examples)
135 0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 134 diff changeset	1279 if upper>cache_len: # whole minibatch is not already in cache
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1280 # cache everything from current length to upper
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1281 for example in self.dataset.source_dataset[cache_len:upper]:
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1282 self.dataset.cached_examples.append(example)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1283 all_fields_minibatch = Example(self.dataset.fieldNames(),
152 3f627e844cba Fixes in CacheDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 151 diff changeset	1284 zip(*self.dataset.cached_examples[self.current:self.current+minibatch_size]))
163 d7d67651d67c bugfix, we should advence by the minibatch size. Frederic Bastien <bastienf@iro.umontreal.ca> parents: 159 diff changeset	1285 self.current+=minibatch_size
254 8ec867d12428 optimication in CachedDataSet.minibatches_nowrap Frederic Bastien <bastienf@iro.umontreal.ca> parents: 253 diff changeset	1286 if self.all_fields:
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1287 return all_fields_minibatch
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1288 return Example(fieldnames,[all_fields_minibatch[name] for name in fieldnames])
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1289 return CacheIterator(self)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1290
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1291 def dontuse__getitem__(self,i):
153 71107b0ac860 optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 151 diff changeset	1292 if type(i)==int and len(self.cached_examples)>i:
71107b0ac860 optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 151 diff changeset	1293 return self.cached_examples[i]
71107b0ac860 optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 151 diff changeset	1294 else:
251 7e6edee187e3 optimization of CachedDataSet__getitem__ Frederic Bastien <bastienf@iro.umontreal.ca> parents: 243 diff changeset	1295 return self.source_dataset[i]
252 856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1296
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1297 def __iter__(self):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1298 class CacheIteratorIter(object):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1299 def __init__(self,dataset):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1300 self.dataset=dataset
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1301 self.l = len(dataset)
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1302 self.current = 0
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1303 self.fieldnames = self.dataset.fieldNames()
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1304 self.example = Example(self.fieldnames,[0]*len(self.fieldnames))
252 856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1305 def __iter__(self): return self
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1306 def next(self):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1307 if self.current>=self.l:
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1308 raise StopIteration
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1309 cache_len = len(self.dataset.cached_examples)
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1310 if self.current>=cache_len: # whole minibatch is not already in cache
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1311 # cache everything from current length to upper
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1312 self.dataset.cached_examples.append(
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1313 self.dataset.source_dataset[self.current])
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1314 self.example._values = self.dataset.cached_examples[self.current]
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1315 self.current+=1
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1316 return self.example
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1317
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1318 return CacheIteratorIter(self)
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization Frederic Bastien <bastienf@iro.umontreal.ca> parents: 251 diff changeset	1319
57 1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	1320 class ApplyFunctionDataSet(DataSet):
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1321 """
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1322 A L{DataSet} that contains as fields the results of applying a
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1323 given function example-wise or minibatch-wise to all the fields of
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1324 an input dataset. The output of the function should be an iterable
296 f5d33f9c0b9c ApplyFunctionDataSet passing James Bergstra <bergstrj@iro.umontreal.ca> parents: 293 diff changeset	1325 (e.g. a list or a LookupList) over the resulting values.
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1326
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1327 The function take as input the fields of the dataset, not the examples.
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1328
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1329 In minibatch mode, the function is expected to work on minibatches
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1330 (takes a minibatch in input and returns a minibatch in output). More
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1331 precisely, it means that each element of the input or output list
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1332 should be iterable and indexable over the individual example values
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1333 (typically these elements will be numpy arrays). All of the elements
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1334 in the input and output lists should have the same length, which is
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1335 the length of the minibatch.
57 1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet Yoshua Bengio <bengioy@iro.umontreal.ca> parents: 56 diff changeset	1336
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1337 The function is applied each time an example or a minibatch is accessed.
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1338 To avoid re-doing computation, wrap this dataset inside a CachedDataSet.
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1339
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1340 If the values_{h,v}stack functions are not provided, then
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1341 the input_dataset.values{H,V}Stack functions are used by default.
296 f5d33f9c0b9c ApplyFunctionDataSet passing James Bergstra <bergstrj@iro.umontreal.ca> parents: 293 diff changeset	1342
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1343 """
296 f5d33f9c0b9c ApplyFunctionDataSet passing James Bergstra <bergstrj@iro.umontreal.ca> parents: 293 diff changeset	1344
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1345 def __init__(self,input_dataset,function,output_names,minibatch_mode=True,
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1346 values_hstack=None,values_vstack=None,
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1347 description=None,fieldtypes=None):
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1348 """
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1349 Constructor takes an input dataset that has as many fields as the function
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1350 expects as inputs. The resulting dataset has as many fields as the function
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1351 produces as outputs, and that should correspond to the number of output names
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1352 (provided in a list).
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1353
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1354 Note that the expected semantics of the function differs in minibatch mode
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1355 (it takes minibatches of inputs and produces minibatches of outputs, as
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1356 documented in the class comment).
211 bd728c83faff in __get__, problem if the i.stop was None, i being the slice, added one line replacing None by the len(self) Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> parents: 203 diff changeset	1357
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1358 TBM: are filedtypes the old field types (from input_dataset) or the new ones
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1359 (for the new dataset created)?
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1360 """
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1361 self.input_dataset=input_dataset
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1362 self.function=function
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1363 self.output_names=output_names
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1364 self.minibatch_mode=minibatch_mode
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1365 DataSet.__init__(self,description,fieldtypes)
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1366 self.valuesHStack = values_hstack if values_hstack else input_dataset.valuesHStack
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1367 self.valuesVStack = values_vstack if values_vstack else input_dataset.valuesVStack
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1368
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1369 def __len__(self):
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1370 return len(self.input_dataset)
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1371
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1372 def fieldNames(self):
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1373 return self.output_names
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1374
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1375 def minibatches_nowrap(self, fieldnames, args, *kwargs):
296 f5d33f9c0b9c ApplyFunctionDataSet passing James Bergstra <bergstrj@iro.umontreal.ca> parents: 293 diff changeset	1376 all_input_fieldNames = self.input_dataset.fieldNames()
f5d33f9c0b9c ApplyFunctionDataSet passing James Bergstra <bergstrj@iro.umontreal.ca> parents: 293 diff changeset	1377 mbnw = self.input_dataset.minibatches_nowrap
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1378
296 f5d33f9c0b9c ApplyFunctionDataSet passing James Bergstra <bergstrj@iro.umontreal.ca> parents: 293 diff changeset	1379 for input_fields in mbnw(all_input_fieldNames, args, *kwargs):
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1380 if self.minibatch_mode:
296 f5d33f9c0b9c ApplyFunctionDataSet passing James Bergstra <bergstrj@iro.umontreal.ca> parents: 293 diff changeset	1381 all_output_fields = self.function(*input_fields)
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1382 else:
296 f5d33f9c0b9c ApplyFunctionDataSet passing James Bergstra <bergstrj@iro.umontreal.ca> parents: 293 diff changeset	1383 input_examples = zip(*input_fields) #makes so that [i] means example i
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1384 output_examples = [self.function(*input_example)
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1385 for input_example in input_examples]
296 f5d33f9c0b9c ApplyFunctionDataSet passing James Bergstra <bergstrj@iro.umontreal.ca> parents: 293 diff changeset	1386 all_output_fields = zip(*output_examples)
f5d33f9c0b9c ApplyFunctionDataSet passing James Bergstra <bergstrj@iro.umontreal.ca> parents: 293 diff changeset	1387
f5d33f9c0b9c ApplyFunctionDataSet passing James Bergstra <bergstrj@iro.umontreal.ca> parents: 293 diff changeset	1388 all_outputs = Example(self.output_names, all_output_fields)
f5d33f9c0b9c ApplyFunctionDataSet passing James Bergstra <bergstrj@iro.umontreal.ca> parents: 293 diff changeset	1389 #print 'input_fields', input_fields
f5d33f9c0b9c ApplyFunctionDataSet passing James Bergstra <bergstrj@iro.umontreal.ca> parents: 293 diff changeset	1390 #print 'all_outputs', all_outputs
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1391 if fieldnames==self.output_names:
293 4bfdda107a17 still merging James Bergstra <bergstrj@iro.umontreal.ca> parents: 292 diff changeset	1392 rval = all_outputs
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1393 else:
293 4bfdda107a17 still merging James Bergstra <bergstrj@iro.umontreal.ca> parents: 292 diff changeset	1394 rval = Example(fieldnames,[all_outputs[name] for name in fieldnames])
296 f5d33f9c0b9c ApplyFunctionDataSet passing James Bergstra <bergstrj@iro.umontreal.ca> parents: 293 diff changeset	1395 #print 'rval', rval
f5d33f9c0b9c ApplyFunctionDataSet passing James Bergstra <bergstrj@iro.umontreal.ca> parents: 293 diff changeset	1396 #print '--------'
293 4bfdda107a17 still merging James Bergstra <bergstrj@iro.umontreal.ca> parents: 292 diff changeset	1397 yield rval
73 69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet bengioy@bengiomac.local parents: 72 diff changeset	1398
290 9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1399 def untested__iter__(self): # only implemented for increased efficiency
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1400 class ApplyFunctionSingleExampleIterator(object):
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1401 def __init__(self,output_dataset):
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1402 self.current=0
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1403 self.output_dataset=output_dataset
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1404 self.input_iterator=output_dataset.input_dataset.__iter__()
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1405 def __iter__(self): return self
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1406 def next(self):
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1407 if self.output_dataset.minibatch_mode:
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1408 function_inputs = [[input] for input in self.input_iterator.next()]
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1409 outputs = self.output_dataset.function(*function_inputs)
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1410 assert all([hasattr(output,'__iter__') for output in outputs])
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1411 function_outputs = [output[0] for output in outputs]
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1412 else:
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1413 function_inputs = self.input_iterator.next()
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1414 function_outputs = self.output_dataset.function(*function_inputs)
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1415 return Example(self.output_dataset.output_names,function_outputs)
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1416 return ApplyFunctionSingleExampleIterator(self)
9b533cc7874a trying to get default implemenations to work James Bergstra <bergstrj@iro.umontreal.ca> parents: 274 diff changeset	1417
23 526e192b0699 Working on ApplyFunctionDataSet, added constraint that bengioy@esprit.iro.umontreal.ca parents: 22 diff changeset	1418 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	1419 """
167 4803cb76e26b Updated documentation Joseph Turian <turian@gmail.com> parents: 166 diff changeset	1420 Wraps an arbitrary L{DataSet} into one for supervised learning tasks
4803cb76e26b Updated documentation Joseph Turian <turian@gmail.com> parents: 166 diff changeset	1421 by forcing the user to define a set of fields as the 'input' field
4803cb76e26b Updated documentation Joseph Turian <turian@gmail.com> parents: 166 diff changeset	1422 and a set of fields as the 'target' field. Optionally, a single
4803cb76e26b Updated documentation Joseph Turian <turian@gmail.com> parents: 166 diff changeset	1423 weight_field can also be defined.
23 526e192b0699 Working on ApplyFunctionDataSet, added constraint that bengioy@esprit.iro.umontreal.ca parents: 22 diff changeset	1424 """
526e192b0699 Working on ApplyFunctionDataSet, added constraint that bengioy@esprit.iro.umontreal.ca parents: 22 diff changeset	1425 args = ((input_fields,'input'),(output_fields,'target'))
526e192b0699 Working on ApplyFunctionDataSet, added constraint that bengioy@esprit.iro.umontreal.ca parents: 22 diff changeset	1426 if weight_field: args+=(([weight_field],'weight'))
36 438440ba0627 Rewriting dataset.py completely bengioy@zircon.iro.umontreal.ca parents: 29 diff changeset	1427 return src_dataset.merge_fields(*args)
23 526e192b0699 Working on ApplyFunctionDataSet, added constraint that bengioy@esprit.iro.umontreal.ca parents: 22 diff changeset	1428
526e192b0699 Working on ApplyFunctionDataSet, added constraint that bengioy@esprit.iro.umontreal.ca parents: 22 diff changeset	1429
526e192b0699 Working on ApplyFunctionDataSet, added constraint that bengioy@esprit.iro.umontreal.ca parents: 22 diff changeset	1430
526e192b0699 Working on ApplyFunctionDataSet, added constraint that bengioy@esprit.iro.umontreal.ca parents: 22 diff changeset	1431

Mercurial > pylearn

annotate dataset.py @ 324:ce79bf5fa463