Mercurial > pylearn
view dataset.py @ 34:1b152f46ad0c
consolidated code
author | bergstrj@iro.umontreal.ca |
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date | Thu, 17 Apr 2008 12:49:48 -0400 |
parents | 46c5c90019c2 |
children | 438440ba0627 |
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from lookup_list import LookupList Example = LookupList import copy 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. All of these iterators are expected to provide, in addition to the usual 'next()' method, a 'next_index()' method which returns a non-negative integer pointing to the position of the next example that will be returned by 'next()' (or of the first example in the next minibatch returned). This is important because these iterators can wrap around the dataset in order to do multiple passes through it, in possibly unregular ways if the minibatch size is not a divisor of the dataset length. 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. Note: A dataset can recognize a potentially infinite number of field names (i.e. the field values can be computed on-demand, when particular field names are used in one of the iterators). Datasets of finite length should be sub-classes of FiniteLengthDataSet. Datasets whose elements can be indexed and whose sub-datasets (with a subset of examples) can be extracted should be sub-classes of SliceableDataSet. Datasets with a finite number of fields should be sub-classes of FiniteWidthDataSet. """ def __init__(self): pass class Iterator(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 def next_index(self): return self.ll.next_index() 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 order defined by the elements of the Example returned by this iterator), but the derived class is free to accept any type of identifier, and add extra functionality to the iterator. """ return DataSet.Iterator(self.minibatches(None, minibatch_size = 1)) 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. """ return DataSet.Iterator(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 three forms of syntax: for i in dataset.minibatches(None,**kwargs): ... for i in dataset.minibatches([f1, f2, f3],**kwargs): ... for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ... Using the first two syntaxes, "i" will be an indexable object, such as a list, tuple, or Example instance. In both cases, i[k] is a list-like container of a batch of current examples. In the second case, i[0] is 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 first syntax, all the fields will be returned in "i". Beware that some datasets may not support this syntax, if the number of fields is infinite (i.e. field values may be computed "on demand"). Using the third 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 hasFields(self,*fieldnames): """ Return true if the given field name (or field names, if multiple arguments are given) is recognized by the DataSet (i.e. can be used as a field name in one of the iterators). """ raise AbstractFunction() def merge_fields(self,*specifications): """ 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 merge_field_values(self,*field_value_pairs): """ Return the value that corresponds to merging the values of several fields, given as arguments (field_name, field_value) pairs with self.hasField(field_name). This may be used by implementations of merge_fields. Raise a ValueError if the operation is not possible. """ fieldnames,fieldvalues = zip(*field_value_pairs) raise ValueError("Unable to merge values of these fields:"+repr(fieldnames)) def examples2minibatch(self,examples): """ Combine a list of Examples into a minibatch. A minibatch is an Example whose fields are iterable over the examples of the minibatch. """ raise AbstractFunction() def rename(self,rename_dict): """ Changes a dataset into one that renames fields, using a dictionnary that maps old field names to new field names. The only fields visible by the returned dataset are those whose names are keys of the rename_dict. """ self_class = self.__class__ class SelfRenamingDataSet(RenamingDataSet,self_class): pass self.__class__ = SelfRenamingDataSet # set the rename_dict and src fields SelfRenamingDataSet.__init__(self,self,rename_dict) return self def apply_function(self,function, input_fields, output_fields, copy_inputs=True, accept_minibatches=True, cache=True): """ Changes a dataset into one 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). """ self_class = self.__class__ class SelfApplyFunctionDataSet(ApplyFunctionDataSet,self_class): pass self.__class__ = SelfApplyFunctionDataSet # set the required additional fields ApplyFunctionDataSet.__init__(self,self,function, input_fields, output_fields, copy_inputs, accept_minibatches, cache) return self class FiniteLengthDataSet(DataSet): """ Virtual interface for datasets that have a finite length (number of examples), and thus recognize a len(dataset) call. """ def __init__(self): DataSet.__init__(self) def __len__(self): """len(dataset) returns the number of examples in the dataset.""" raise AbstractFunction() def __call__(self,fieldname_or_fieldnames): """ Extract one or more fields. This may be an expensive operation when the dataset is large. It is not the recommanded way to access individual values (use the iterators instead). If the argument is a string fieldname, then the result is a sequence (iterable object) of values for that field, for the whole dataset. If the argument is a list of field names, then the result is a 'batch', i.e., an Example with keys corresponding to the given field names and values being iterable objects over the individual example values. """ if type(fieldname_or_fieldnames) is string: minibatch = self.minibatches([fieldname_or_fieldnames],len(self)).next() return minibatch[fieldname_or_fieldnames] return self.minibatches(fieldname_or_fieldnames,len(self)).next() class SliceableDataSet(DataSet): """ Virtual interface, a subclass of DataSet for datasets which are sliceable and whose individual elements can be accessed, generally respecting the python semantics for [spec], where spec is either a non-negative integer (for selecting one example), a python slice(start,stop,step) for selecting a regular sub-dataset comprising examples start,start+step,start+2*step,...,n (with n<stop), or a sequence (e.g. a list) of integers [i1,i2,...,in] for selecting an arbitrary subset of examples. This is useful for obtaining sub-datasets, e.g. for splitting a dataset into training and test sets. """ def __init__(self): DataSet.__init__(self) def minibatches(self, fieldnames = DataSet.minibatches_fieldnames, minibatch_size = DataSet.minibatches_minibatch_size, n_batches = DataSet.minibatches_n_batches): """ If the n_batches is empty, we want to see all the examples possible for the given minibatch_size (possibly missing a few at the end of the dataset). """ # substitute the defaults: if n_batches is None: n_batches = len(self) / minibatch_size return DataSet.Iterator(self, fieldnames, minibatch_size, n_batches) def __getitem__(self,i): """ dataset[i] returns the (i+1)-th example of the dataset. dataset[i:j] returns the subdataset with examples i,i+1,...,j-1. dataset[i:j:s] returns the subdataset with examples i,i+2,i+4...,j-2. dataset[[i1,i2,..,in]] returns the subdataset with examples i1,i2,...,in. """ raise AbstractFunction() def __getslice__(self,*slice_args): """ dataset[i:j] returns the subdataset with examples i,i+1,...,j-1. dataset[i:j:s] returns the subdataset with examples i,i+2,i+4...,j-2. """ raise AbstractFunction() class FiniteWidthDataSet(DataSet): """ Virtual interface for datasets that have a finite width (number of fields), and thus return a list of fieldNames. """ def __init__(self): DataSet.__init__(self) def hasFields(self,*fields): has_fields=True fieldnames = self.fieldNames() for name in fields: if name not in fieldnames: has_fields=False return has_fields def fieldNames(self): """Return the list of field names that are supported by the iterators, and for which hasFields(fieldname) would return True.""" raise AbstractFunction() class RenamingDataSet(FiniteWidthDataSet): """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 fieldNames(self): return self.rename_dct.keys() 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) # 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(FiniteLengthDataSet,FiniteWidthDataSet,SliceableDataSet): """ 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 or to a list of column numbers. 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): if fieldnames is None: fieldnames = dataset.fieldNames() 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_index(self): n_rows = self.dataset.data.shape[0] next_i = self.current+self.minibatch_size if next_i >= n_rows: next_i -= n_rows return next_i 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 minibatch slice we'll return n_rows = self.dataset.data.shape[0] self.current = self.next_index() upper = self.current + self.minibatch_size data = self.dataset.data if upper <= n_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 -= n_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 (or column lists) indexed by field names). """ self.data=data self.fields=fields rows, cols = data.shape if fields: for fieldname,fieldslice in fields.items(): assert type(fieldslice) is int or isinstance(fieldslice,slice) or hasattr(fieldslice,"__iter__") if hasattr(fieldslice,"__iter__"): # is a sequence for i in fieldslice: assert type(i) is int elif isinstance(fieldslice,slice): # 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 None, it means that we want to see ALL the fields. If the n_batches is None, we want to see all the examples possible for the given minibatch_size (possibly missing some near the end). """ # substitute the defaults: if n_batches is None: n_batches = len(self) / minibatch_size return ArrayDataSet.Iterator(self, fieldnames, minibatch_size, n_batches) def fieldNames(self): """Return the list of field names that are supported by getattr and hasField.""" 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). dataset[i:j] returns the subdataset with examples i,i+1,...,j-1. dataset[i:j:s] returns the subdataset with examples i,i+2,i+4...,j-2. dataset[[i1,i2,..,in]] returns the subdataset with examples i1,i2,...,in. """ 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. dataset[i:j:s] returns the subdataset with examples i,i+2,i+4...,j-2. """ return ArrayDataSet(self.data.__getslice__(*args), fields=self.fields) def indices_of_unique_columns_used(self): """ Return the unique indices of the columns actually used by the fields, and a boolean that signals (if True) that used columns overlap. If they do then the indices are not repeated in the result. """ columns_used = numpy.zeros((self.data.shape[1]),dtype=bool) overlapping_columns = False for field_slice in self.fields.values(): if sum(columns_used[field_slice])>0: overlapping_columns=True columns_used[field_slice]=True return [i for i,used in enumerate(columns_used) if used],overlapping_columns def slice_of_unique_columns_used(self): """ Return None if the indices_of_unique_columns_used do not form a slice. If they do, return that slice. It means that the columns used can be extracted from the data array without making a copy. If the fields overlap but their unique columns used form a slice, still return that slice. """ columns_used,overlapping_columns = self.indices_of_columns_used() mappable_to_one_slice = True if not overlapping_fields: 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 return slice(start,stop,step) class ApplyFunctionDataSet(FiniteWidthDataSet): """ 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, compute_now=False): DataSet.__init__(self) self.src=src self.function=function assert src.hasFields(input_fields) self.input_fields=input_fields self.output_fields=output_fields assert not (copy_inputs and compute_now and not hasattr(src,'fieldNames')) self.copy_inputs=copy_inputs self.accept_minibatches=accept_minibatches self.cache=cache self.compute_now=compute_now if compute_now: assert hasattr(src,'__len__') and len(src)>=0 fieldnames = output_fields if copy_inputs: fieldnames = src.fieldNames() + output_fields if accept_minibatches: # make a single minibatch with all the inputs inputs = src.minibatches(input_fields,len(src)).next() # and apply the function to it, and transpose into a list of examples (field values, actually) self.cached_examples = zip(*Example(output_fields,function(*inputs))) else: # compute a list with one tuple per example, with the function outputs self.cached_examples = [ function(input) for input in src.zip(input_fields) ] elif 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): if self.copy_inputs: return self.output_fields + self.src.fieldNames() return self.output_fields 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): if fieldnames is None: assert hasattr(dataset,"fieldNames") fieldnames = dataset.fieldNames() self.example_index=0 LookupList.__init__(self, fieldnames, [0]*len(fieldnames)) self.dataset=dataset self.src_iterator=self.src.minibatches(list(set.union(set(fieldnames),set(dataset.input_fields))), minibatch_size,n_batches) self.fieldnames_not_in_input = [] if self.copy_inputs: self.fieldnames_not_in_input = filter(lambda x: not x in dataset.input_fields, fieldnames) def __iter__(self): return self def next_index(self): return self.src_iterator.next_index() def next(self): example_index = self.src_iterator.next_index() src_examples = self.src_iterator.next() if self.dataset.copy_inputs: function_inputs = [src_examples[field_name] for field_name in self.dataset.input_fields] else: function_inputs = src_examples if self.dataset.cached_examples: cache_len=len(self.cached_examples) if example_index<cache_len+minibatch_size: outputs_list = self.cached_examples[example_index:example_index+minibatch_size] # convert the minibatch list of examples # into a list of fields each of which iterate over the minibatch outputs = zip(*outputs_list) else: outputs = self.dataset.function(*function_inputs) if self.dataset.cache: # convert the list of fields, each of which can iterate over the minibatch # into a list of examples in the minibatch (each of which is a list of field values) outputs_list = zip(*outputs) # copy the outputs_list into the cache for i in xrange(cache_len,example_index): self.cached_examples.append(None) self.cached_examples += outputs_list else: outputs = self.dataset.function(*function_inputs) return Example(self.fieldnames_not_in_input+self.dataset.output_fields, [src_examples[field_name] for field_name in self.fieldnames_not_in_input]+outputs) for fieldname in fieldnames: assert fieldname in self.output_fields or self.src.hasFields(fieldname) return Iterator(self) def supervised_learning_dataset(src_dataset,input_fields,target_fields,weight_field=None): """ Wraps an arbitrary DataSet into one for supervised learning tasks by forcing the user to define a set of fields as the 'input' field and a set of fields as the 'target' field. Optionally, a single weight_field can also be defined. """ args = ((input_fields,'input'),(output_fields,'target')) if weight_field: args+=(([weight_field],'weight')) return src_dataset.rename(*args)