Mercurial > pylearn
view dataset.py @ 20:266c68cb6136
Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
author | bengioy@bengiomac.local |
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date | Mon, 07 Apr 2008 09:48:39 -0400 |
parents | 57f4015e2e09 |
children | b6b36f65664f |
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from lookup_list import LookupList Example = LookupList class AbstractFunction (Exception): """Derived class must override this function""" class DataSet(object): """A virtual base class for datasets. A DataSet is a generator of iterators; these iterators can run through the examples in a variety of ways. A DataSet need not necessarily have a finite or known length, so this class can be used to interface to a 'stream' which feeds on-line learning. To iterate over examples, there are several possibilities: - for example in dataset.zip([field1, field2,field3, ...]) - for val1,val2,val3 in dataset.zip([field1, field2,field3]) - for minibatch in dataset.minibatches([field1, field2, ...],minibatch_size=N) - for example in dataset Each of these is documented below. Note: For a dataset of fixed and known length, which can implement item random-access efficiently (e.g. indexing and slicing), and which can profit from the FiniteDataSetIterator, consider using base class FiniteDataSet. Note: Fields are not mutually exclusive, i.e. two fields can overlap in their actual content. Note: The content of a field can be of any type. """ def __init__(self): pass def __iter__(self): """Supports the syntax "for i in dataset: ..." Using this syntax, "i" will be an Example instance (or equivalent) with all the fields of DataSet self. Every field of "i" will give access to a field of a single example. Fields should be accessible via i["fielname"] or i[3] (in the fieldNames() order), but the derived class is free to accept any type of identifier, and add extra functionality to the iterator. """ return self.zip(*self.fieldNames()) def zip(self, *fieldnames): """ Supports two forms of syntax: for i in dataset.zip([f1, f2, f3]): ... for i1, i2, i3 in dataset.zip([f1, f2, f3]): ... Using the first syntax, "i" will be an indexable object, such as a list, tuple, or Example instance, such that on every iteration, i[0] is the f1 field of the current example, i[1] is the f2 field, and so on. Using the second syntax, i1, i2, i3 will contain the the contents of the f1, f2, and f3 fields of a single example on each loop iteration. The derived class may accept fieldname arguments of any type. """ class Iter(LookupList): def __init__(self, ll): LookupList.__init__(self, ll.keys(), ll.values()) self.ll = ll def __iter__(self): #makes for loop work return self def next(self): self.ll.next() self._values = [v[0] for v in self.ll._values] return self return Iter(self.minibatches(fieldnames, minibatch_size = 1)) minibatches_fieldnames = None minibatches_minibatch_size = 1 minibatches_n_batches = None def minibatches(self, fieldnames = minibatches_fieldnames, minibatch_size = minibatches_minibatch_size, n_batches = minibatches_n_batches): """ Supports two forms of syntax: for i in dataset.minibatches([f1, f2, f3],**kwargs): ... for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ... Using the first syntax, "i" will be an indexable object, such as a list, tuple, or Example instance, such that on every iteration, i[0] is a list-like container of the f1 field of a batch current examples, i[1] is a list-like container of the f2 field, etc. Using the second syntax, i1, i2, i3 will be list-like containers of the f1, f2, and f3 fields of a batch of examples on each loop iteration. PARAMETERS - fieldnames (list of any type, default None): The loop variables i1, i2, i3 (in the example above) should contain the f1, f2, and f3 fields of the current batch of examples. If None, the derived class can choose a default, e.g. all fields. - minibatch_size (integer, default 1) On every iteration, the variables i1, i2, i3 will have exactly minibatch_size elements. e.g. len(i1) == minibatch_size - n_batches (integer, default None) The iterator will loop exactly this many times, and then stop. If None, the derived class can choose a default. If (-1), then the returned iterator should support looping indefinitely. Note: A list-like container is something like a tuple, list, numpy.ndarray or any other object that supports integer indexing and slicing. """ raise AbstractFunction() def fieldNames(self): #Yoshua- # This list may not be finite; what would make sense in the use you have # in mind? # -JB #James- # You are right. I had put this to be able to iterate over the fields # but maybe an iterator mechanism (over fields rather than examples) # would be more appropriate. Fieldnames are needed in general # by the iterators over examples or minibatches, to construct # examples or minibatches with the corresponding names as attributes. # -YB """ Return an iterator (an object with an __iter__ method) that iterates over the names of the fields. As a special cases, a list or a tuple of field names can be returned. """" # Note that some datasets # may have virtual fields and support a virtually infinite number # of possible field names. In that case, fieldNames() should # either raise an error or iterate over a particular set of # names as appropriate. Another option would be to iterate # over the sub-datasets comprising a single field at a time. # I am not sure yet what is most appropriate. # -YB """ raise AbstractFunction() def rename(*new_field_specifications): #Yoshua- # Do you mean for this to be a virtual method? # Wouldn't this functionality be easier to provide via a # RenamingDataSet, such as the one I've written below? # -JB # You are right. Whichever implementation, however, we need a generic way to # 'concatenate' fields, to handle the ([old_field1, old_field2, ...], new_field) semantics. # -YB """ Return a new dataset that maps old fields (of self) to new fields (of the returned dataset). The minimal syntax that should be supported is the following: new_field_specifications = [new_field_spec1, new_field_spec2, ...] new_field_spec = ([old_field1, old_field2, ...], new_field) In general both old_field and new_field should be strings, but some datasets may also support additional indexing schemes within each field (e.g. column slice of a matrix-like field). """ raise AbstractFunction() def apply_function(function, input_fields, output_fields, copy_inputs=True, accept_minibatches=True, cache=True): """ Return a dataset that contains as fields the results of applying the given function (example-wise) to the specified input_fields. The function should return a sequence whose elements will be stored in fields whose names are given in the output_fields list. If copy_inputs is True then the resulting dataset will also contain the fields of self. If accept_minibatches, then the function may be called with minibatches as arguments (what is returned by the minibatches iterator). In any case, the computations may be delayed until the examples of the resulting dataset are requested. If cache is True, then once the output fields for some examples have been computed, then are cached (to avoid recomputation if the same examples are again requested). """ return ApplyFunctionDataSet(function, input_fields, output_fields, copy_inputs, accept_minibatches, cache) class RenamingDataSet(DataSet): """A DataSet that wraps another one, and makes it look like the field names are different Renaming is done by a dictionary that maps new names to the old ones used in self.src. """ def __init__(self, src, rename_dct): DataSet.__init__(self) self.src = src self.rename_dct = copy.copy(rename_dct) def minibatches(self, fieldnames = DataSet.minibatches_fieldnames, minibatch_size = DataSet.minibatches_minibatch_size, n_batches = DataSet.minibatches_n_batches): dct = self.rename_dct new_fieldnames = [dct.get(f, f) for f in fieldnames] return self.src.minibatches(new_fieldnames, minibatches_size, n_batches) def fieldNames(self): return [dct.get(f, f) for f in self.src.fieldNames()] class FiniteDataSet(DataSet): """ Virtual interface, a subclass of DataSet for datasets which have a finite, known length. Examples are indexed by an integer between 0 and self.length()-1, and a subdataset can be obtained by slicing. This may not be appropriate in general but only for datasets which can be thought of like ones that access rows AND fields in an efficient random access way. Users are encouraged to expect only the generic dataset interface in general. A FiniteDataSet is mainly useful when one has to obtain a subset of examples (e.g. for splitting a dataset into training and test sets). """ class FiniteDataSetIterator(object): """ If the fieldnames list is empty, it means that we want to see ALL the fields. """ def __init__(self,dataset,minibatch_size=1,fieldnames=[]): self.dataset=dataset self.minibatch_size=minibatch_size assert minibatch_size>=1 and minibatch_size<=len(dataset) self.current = -self.minibatch_size self.fieldnames = fieldnames if len(dataset) % minibatch_size: raise NotImplementedError() def __iter__(self): return self def next(self): self.current+=self.minibatch_size if self.current>=len(self.dataset): self.current=-self.minibatch_size raise StopIteration if self.minibatch_size==1: complete_example=self.dataset[self.current] else: complete_example=self.dataset[self.current:self.current+self.minibatch_size] if self.fieldnames: return Example(self.fieldnames,list(complete_example)) else: return complete_example def __init__(self): pass def minibatches(self, fieldnames = DataSet.minibatches_fieldnames, minibatch_size = DataSet.minibatches_minibatch_size, n_batches = DataSet.minibatches_n_batches): """ If the fieldnames list is empty, it means that we want to see ALL the fields. If the n_batches is empty, we want to see all the examples possible for the give minibatch_size. """ # substitute the defaults: if fieldnames is None: fieldnames = self.fieldNames() if n_batches is None: n_batches = len(self) / minibatch_size return DataSet.Iterator(self, fieldnames, minibatch_size, n_batches) def __getattr__(self,fieldname): """Return an that can iterate over the values of the field in this dataset.""" return self(fieldname) def __call__(self,*fieldnames): """Return a sub-dataset containing only the given fieldnames as fields. The return value's default iterator will iterate only over the given fields. """ raise AbstractFunction() def __len__(self): """len(dataset) returns the number of examples in the dataset.""" raise AbstractFunction() def __getitem__(self,i): """dataset[i] returns the (i+1)-th example of the dataset.""" raise AbstractFunction() def __getslice__(self,*slice_args): """dataset[i:j] returns the subdataset with examples i,i+1,...,j-1.""" raise AbstractFunction() # we may want ArrayDataSet defined in another python file import numpy def as_array_dataset(dataset): # Generally datasets can be efficient by making data fields overlap, but # this function doesn't know which fields overlap. So, it should check if # dataset supports an as_array_dataset member function, and return that if # possible. if hasattr(dataset, 'as_array_dataset'): return dataset.as_array_dataset() raise NotImplementedError() # Make ONE big minibatch with all the examples, to separate the fields. n_examples = len(dataset) batch = dataset.minibatches( minibatch_size = len(dataset)).next() # Each field of the underlying dataset must be convertible to a numpy array of the same type # currently just double, but should use the smallest compatible dtype n_fields = len(batch) fieldnames = batch.fields.keys() total_width = 0 type = None fields = LookupList() for i in xrange(n_fields): field = array(batch[i]) assert field.shape[0]==n_examples width = field.shape[1] start=total_width total_width += width fields[fieldnames[i]]=slice(start,total_width,1) # many complicated things remain to be done: # - find common dtype # - decide what to do with extra dimensions if not the same in all fields # - try to see if we can avoid the copy? class ArrayDataSet(FiniteDataSet): """ An ArrayDataSet behaves like a numpy array but adds the notion of named fields from DataSet (and the ability to view the values of multiple fields as an 'Example'). It is a fixed-length and fixed-width dataset in which each element is a fixed dimension numpy array or a number, hence the whole dataset corresponds to a numpy array. Fields must correspond to a slice of array columns. If the dataset has fields, each 'example' is just a one-row ArrayDataSet, otherwise it is a numpy array. Any dataset can also be converted to a numpy array (losing the notion of fields by the numpy.array(dataset) call. """ class Iterator(LookupList): """An iterator over a finite dataset that implements wrap-around""" def __init__(self, dataset, fieldnames, minibatch_size, next_max): LookupList.__init__(self, fieldnames, [0] * len(fieldnames)) self.dataset=dataset self.minibatch_size=minibatch_size self.next_count = 0 self.next_max = next_max self.current = -self.minibatch_size assert minibatch_size > 0 if minibatch_size >= len(dataset): raise NotImplementedError() def __iter__(self): #makes for loop work return self @staticmethod def matcat(a, b): a0, a1 = a.shape b0, b1 = b.shape assert a1 == b1 assert a.dtype is b.dtype rval = numpy.empty( (a0 + b0, a1), dtype=a.dtype) rval[:a0,:] = a rval[a0:,:] = b return rval def next(self): #check for end-of-loop self.next_count += 1 if self.next_count == self.next_max: raise StopIteration #determine the first and last elements of the slice we'll return rows = self.dataset.data.shape[0] self.current += self.minibatch_size if self.current >= rows: self.current -= rows upper = self.current + self.minibatch_size data = self.dataset.data if upper <= rows: #this is the easy case, we only need once slice dataview = data[self.current:upper] else: # the minibatch wraps around the end of the dataset dataview = data[self.current:] upper -= rows assert upper > 0 dataview = self.matcat(dataview, data[:upper]) self._values = [dataview[:, self.dataset.fields[f]]\ for f in self._names] return self def __init__(self, data, fields=None): """ There are two ways to construct an ArrayDataSet: (1) from an existing dataset (which may result in a copy of the data in a numpy array), or (2) from a numpy.array (the data argument), along with an optional description of the fields (a LookupList of column slices indexed by field names). """ self.data=data self.fields=fields rows, cols = data.shape if fields: for fieldname,fieldslice in fields.items(): # make sure fieldslice.start and fieldslice.step are defined start=fieldslice.start step=fieldslice.step if not start: start=0 if not step: step=1 if not fieldslice.start or not fieldslice.step: fields[fieldname] = fieldslice = slice(start,fieldslice.stop,step) # and coherent with the data array assert fieldslice.start >= 0 and fieldslice.stop <= cols def minibatches(self, fieldnames = DataSet.minibatches_fieldnames, minibatch_size = DataSet.minibatches_minibatch_size, n_batches = DataSet.minibatches_n_batches): """ If the fieldnames list is empty, it means that we want to see ALL the fields. If the n_batches is empty, we want to see all the examples possible for the give minibatch_size. """ # substitute the defaults: if fieldnames is None: fieldnames = self.fieldNames() if n_batches is None: n_batches = len(self) / minibatch_size return ArrayDataSet.Iterator(self, fieldnames, minibatch_size, n_batches) def __getattr__(self,fieldname): """ Return a numpy array with the content associated with the given field name. If this is a one-example dataset, then a row, i.e., numpy array (of one less dimension than the dataset itself) is returned. """ if len(self.data)==1: return self.data[0,self.fields[fieldname]] return self.data[:,self.fields[fieldname]] def __call__(self,*fieldnames): """Return a sub-dataset containing only the given fieldnames as fields.""" min_col=self.data.shape[1] max_col=0 for field_slice in self.fields.values(): min_col=min(min_col,field_slice.start) max_col=max(max_col,field_slice.stop) new_fields=LookupList() for fieldname,fieldslice in self.fields.items(): new_fields[fieldname]=slice(fieldslice.start-min_col,fieldslice.stop-min_col,fieldslice.step) return ArrayDataSet(self.data[:,min_col:max_col],fields=new_fields) def fieldNames(self): """Return the list of field names that are supported by getattr and getFields.""" return self.fields.keys() def __len__(self): """len(dataset) returns the number of examples in the dataset.""" return len(self.data) def __getitem__(self,i): """ dataset[i] returns the (i+1)-th Example of the dataset. If there are no fields the result is just a numpy array (for the i-th row of the dataset data matrix). """ if self.fields: fieldnames,fieldslices=zip(*self.fields.items()) return Example(self.fields.keys(),[self.data[i,fieldslice] for fieldslice in self.fields.values()]) else: return self.data[i] def __getslice__(self,*args): """dataset[i:j] returns the subdataset with examples i,i+1,...,j-1.""" return ArrayDataSet(self.data.__getslice__(*args), fields=self.fields) def __array__(self): """Return a view of this dataset which is an numpy.ndarray (i.e. losing the identity and name of fields within the dataset). Numpy uses this special function name to retrieve an ndarray view for function such as numpy.sum, numpy.dot, numpy.asarray, etc. If this dataset has no fields, then we simply return self.data, otherwise things are complicated. - why do we want this behaviour when there are fields? (JB) - for convenience and completeness (but maybe it would make more sense to implement this through a 'field-merging' dataset). (YB) """ if not self.fields: return self.data # else, select subsets of columns mapped by the fields columns_used = numpy.zeros((self.data.shape[1]),dtype=bool) for field_slice in self.fields.values(): for c in xrange(field_slice.start,field_slice.stop,field_slice.step): columns_used[c]=True # try to figure out if we can map all the slices into one slice: mappable_to_one_slice = True start=0 while start<len(columns_used) and not columns_used[start]: start+=1 stop=len(columns_used) while stop>0 and not columns_used[stop-1]: stop-=1 step=0 i=start while i<stop: j=i+1 while j<stop and not columns_used[j]: j+=1 if step: if step!=j-i: mappable_to_one_slice = False break else: step = j-i i=j if mappable_to_one_slice: return self.data[:,slice(start,stop,step)] # else make contiguous copy n_columns = sum(columns_used) result = zeros((len(self.data),n_columns)+self.data.shape[2:],self.data.dtype) print result.shape c=0 for field_slice in self.fields.values(): slice_width=field_slice.stop-field_slice.start/field_slice.step # copy the field here result[:,slice(c,slice_width)]=self.data[:,field_slice] c+=slice_width return result class ApplyFunctionDataset(DataSet): """ A dataset that contains as fields the results of applying a given function (example-wise) to specified input_fields of a source dataset. The function should return a sequence whose elements will be stored in fields whose names are given in the output_fields list. If copy_inputs is True then the resulting dataset will also contain the fields of the source. dataset. If accept_minibatches, then the function expects minibatches as arguments (what is returned by the minibatches iterator). In any case, the computations may be delayed until the examples of self are requested. If cache is True, then once the output fields for some examples have been computed, then are cached (to avoid recomputation if the same examples are again requested). """ def __init__(src,function, input_fields, output_fields, copy_inputs=True, accept_minibatches=True, cache=True): DataSet.__init__(self) self.src=src self.function=function self.input_fields=input_fields self.output_fields=output_fields self.copy_inputs=copy_inputs self.accept_minibatches=accept_minibatches src_fieldnames = src.fieldNames() if copy_inputs: for src_field in src_fieldnames: assert src_field not in output_fields self.fieldnames=src_fieldnames+output_fields else: self.fieldnames=output_fields for input_field in input_fields: assert input_field in src_fieldnames self.cache=cache if cache: # maybe a fixed-size array kind of structure would be more efficient than a list # in the case where src is FiniteDataSet. -YB self.cached_examples = [] def fieldNames(self): return self.fieldnames def minibatches(self, fieldnames = DataSet.minibatches_fieldnames, minibatch_size = DataSet.minibatches_minibatch_size, n_batches = DataSet.minibatches_n_batches): class Iterator(LookupList): def __init__(self,dataset): LookupList.__init__(self, fieldnames, [0]*len(fieldnames)) self.dataset=dataset if dataset.copy_inputs: src_fields=dataset.fieldNames() else: src_fields=dataset.input_fields self.src_iterator=self.src.minibatches(src_fields,minibatch_size,n_batches) def __iter__(self): return self def next(self): src_examples = self.src_iterator.next() if self.dataset.copy_inputs: function_inputs = src_examples else: function_inputs = [src_examples[field_name] for field_name in self.dataset.input_fields]) return self.dataset.function(*function_inputs) for fieldname in fieldnames: assert fieldname in self.input_fields return Iterator(self)