Mercurial > ift6266
view utils/seriestables/series.py @ 613:5e481b224117
fix the reading of PNIST dataset following Dumi compression of the data.
author | Frederic Bastien <nouiz@nouiz.org> |
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date | Thu, 06 Jan 2011 13:57:05 -0500 |
parents | 0515a8901c6a |
children |
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import tables import numpy import time ############################################################################## # Utility functions to create IsDescription objects (pytables data types) ''' The way these "IsDescription constructor" work is simple: write the code as if it were in a file, then exec()ute it, leaving us with a local-scoped LocalDescription which may be used to call createTable. It's a small hack, but it's necessary as the names of the columns are retrieved based on the variable name, which we can't programmatically set otherwise. ''' def _get_description_timestamp_cpuclock_columns(store_timestamp, store_cpuclock, pos=0): toexec = "" if store_timestamp: toexec += "\ttimestamp = tables.Time32Col(pos="+str(pos)+")\n" pos += 1 if store_cpuclock: toexec += "\tcpuclock = tables.Float64Col(pos="+str(pos)+")\n" pos += 1 return toexec, pos def _get_description_n_ints(int_names, int_width=64, pos=0): """ Begins construction of a class inheriting from IsDescription to construct an HDF5 table with index columns named with int_names. See Series().__init__ to see how those are used. """ int_constructor = "tables.Int64Col" if int_width == 32: int_constructor = "tables.Int32Col" elif not int_width in (32, 64): raise "int_width must be left unspecified, or should equal 32 or 64" toexec = "" for n in int_names: toexec += "\t" + n + " = " + int_constructor + "(pos=" + str(pos) + ")\n" pos += 1 return toexec, pos def _get_description_with_n_ints_n_floats(int_names, float_names, int_width=64, float_width=32, store_timestamp=True, store_cpuclock=True): """ Constructs a class to be used when constructing a table with PyTables. This is useful to construct a series with an index with multiple levels. E.g. if you want to index your "validation error" with "epoch" first, then "minibatch_index" second, you'd use two "int_names". Parameters ---------- int_names : tuple of str Names of the int (e.g. index) columns float_names : tuple of str Names of the float (e.g. error) columns int_width : {'32', '64'} Type of ints. float_width : {'32', '64'} Type of floats. store_timestamp : bool See __init__ of Series store_cpuclock : bool See __init__ of Series Returns ------- A class object, to pass to createTable() """ toexec = "class LocalDescription(tables.IsDescription):\n" toexec_, pos = _get_description_timestamp_cpuclock_columns(store_timestamp, store_cpuclock) toexec += toexec_ toexec_, pos = _get_description_n_ints(int_names, int_width=int_width, pos=pos) toexec += toexec_ float_constructor = "tables.Float32Col" if float_width == 64: float_constructor = "tables.Float64Col" elif not float_width in (32, 64): raise "float_width must be left unspecified, or should equal 32 or 64" for n in float_names: toexec += "\t" + n + " = " + float_constructor + "(pos=" + str(pos) + ")\n" pos += 1 exec(toexec) return LocalDescription ############################################################################## # Series classes # Shortcut to allow passing a single int as index, instead of a tuple def _index_to_tuple(index): if type(index) == tuple: return index if type(index) == list: index = tuple(index) return index try: if index % 1 > 0.001 and index % 1 < 0.999: raise idx = long(index) return (idx,) except: raise TypeError("index must be a tuple of integers, or at least a single integer") class Series(): """ Base Series class, with minimal arguments and type checks. Yet cannot be used by itself (it's append() method raises an error) """ def __init__(self, table_name, hdf5_file, index_names=('epoch',), title="", hdf5_group='/', store_timestamp=True, store_cpuclock=True): """Basic arguments each Series must get. Parameters ---------- table_name : str Name of the table to create under group "hd5_group" (other parameter). No spaces, ie. follow variable naming restrictions. hdf5_file : open HDF5 file File opened with openFile() in PyTables (ie. return value of openFile). index_names : tuple of str Columns to use as index for elements in the series, other example would be ('epoch', 'minibatch'). This would then allow you to call append(index, element) with index made of two ints, one for epoch index, one for minibatch index in epoch. title : str Title to attach to this table as metadata. Can contain spaces and be longer then the table_name. hdf5_group : str Path of the group (kind of a file) in the HDF5 file under which to create the table. store_timestamp : bool Whether to create a column for timestamps and store them with each record. store_cpuclock : bool Whether to create a column for cpu clock and store it with each record. """ ######################################### # checks if type(table_name) != str: raise TypeError("table_name must be a string") if table_name == "": raise ValueError("table_name must not be empty") if not isinstance(hdf5_file, tables.file.File): raise TypeError("hdf5_file must be an open HDF5 file (use tables.openFile)") #if not ('w' in hdf5_file.mode or 'a' in hdf5_file.mode): # raise ValueError("hdf5_file must be opened in write or append mode") if type(index_names) != tuple: raise TypeError("index_names must be a tuple of strings." + \ "If you have only one element in the tuple, don't forget " +\ "to add a comma, e.g. ('epoch',).") for name in index_names: if type(name) != str: raise TypeError("index_names must only contain strings, but also"+\ "contains a "+str(type(name))+".") if type(title) != str: raise TypeError("title must be a string, even if empty") if type(hdf5_group) != str: raise TypeError("hdf5_group must be a string") if type(store_timestamp) != bool: raise TypeError("store_timestamp must be a bool") if type(store_cpuclock) != bool: raise TypeError("store_timestamp must be a bool") ######################################### self.table_name = table_name self.hdf5_file = hdf5_file self.index_names = index_names self.title = title self.hdf5_group = hdf5_group self.store_timestamp = store_timestamp self.store_cpuclock = store_cpuclock def append(self, index, element): raise NotImplementedError def _timestamp_cpuclock(self, newrow): if self.store_timestamp: newrow["timestamp"] = time.time() if self.store_cpuclock: newrow["cpuclock"] = time.clock() class DummySeries(): """ To put in a series dictionary instead of a real series, to do nothing when we don't want a given series to be saved. E.g. if we'd normally have a "training_error" series in a dictionary of series, the training loop would have something like this somewhere: series["training_error"].append((15,), 20.0) but if we don't want to save the training errors this time, we simply do series["training_error"] = DummySeries() """ def append(self, index, element): pass class ErrorSeries(Series): """ Most basic Series: saves a single float (called an Error as this is the most common use case I foresee) along with an index (epoch, for example) and timestamp/cpu.clock for each of these floats. """ def __init__(self, error_name, table_name, hdf5_file, index_names=('epoch',), title="", hdf5_group='/', store_timestamp=True, store_cpuclock=True): """ For most parameters, see Series.__init__ Parameters ---------- error_name : str In the HDF5 table, column name for the error float itself. """ # most type/value checks are performed in Series.__init__ Series.__init__(self, table_name, hdf5_file, index_names, title, store_timestamp=store_timestamp, store_cpuclock=store_cpuclock) if type(error_name) != str: raise TypeError("error_name must be a string") if error_name == "": raise ValueError("error_name must not be empty") self.error_name = error_name self._create_table() def _create_table(self): table_description = _get_description_with_n_ints_n_floats( \ self.index_names, (self.error_name,), store_timestamp=self.store_timestamp, store_cpuclock=self.store_cpuclock) self._table = self.hdf5_file.createTable(self.hdf5_group, self.table_name, table_description, title=self.title) def append(self, index, error): """ Parameters ---------- index : tuple of int Following index_names passed to __init__, e.g. (12, 15) if index_names were ('epoch', 'minibatch_size'). A single int (not tuple) is acceptable if index_names has a single element. An array will be casted to a tuple, as a convenience. error : float Next error in the series. """ index = _index_to_tuple(index) if len(index) != len(self.index_names): raise ValueError("index provided does not have the right length (expected " \ + str(len(self.index_names)) + " got " + str(len(index))) # other checks are implicit when calling newrow[..] =, # which should throw an error if not of the right type newrow = self._table.row # Columns for index in table are based on index_names for col_name, value in zip(self.index_names, index): newrow[col_name] = value newrow[self.error_name] = error # adds timestamp and cpuclock to newrow if necessary self._timestamp_cpuclock(newrow) newrow.append() self.hdf5_file.flush() # Does not inherit from Series because it does not itself need to # access the hdf5_file and does not need a series_name (provided # by the base_series.) class AccumulatorSeriesWrapper(): ''' Wraps a Series by accumulating objects passed its Accumulator.append() method and "reducing" (e.g. calling numpy.mean(list)) once in a while, every "reduce_every" calls in fact. ''' def __init__(self, base_series, reduce_every, reduce_function=numpy.mean): """ Parameters ---------- base_series : Series This object must have an append(index, value) function. reduce_every : int Apply the reduction function (e.g. mean()) every time we get this number of elements. E.g. if this is 100, then every 100 numbers passed to append(), we'll take the mean and call append(this_mean) on the BaseSeries. reduce_function : function Must take as input an array of "elements", as passed to (this accumulator's) append(). Basic case would be to take an array of floats and sum them into one float, for example. """ self.base_series = base_series self.reduce_function = reduce_function self.reduce_every = reduce_every self._buffer = [] def append(self, index, element): """ Parameters ---------- index : tuple of int The index used is the one of the last element reduced. E.g. if you accumulate over the first 1000 minibatches, the index passed to the base_series.append() function will be 1000. A single int (not tuple) is acceptable if index_names has a single element. An array will be casted to a tuple, as a convenience. element : float Element that will be accumulated. """ self._buffer.append(element) if len(self._buffer) == self.reduce_every: reduced = self.reduce_function(self._buffer) self.base_series.append(index, reduced) self._buffer = [] # The >= case should never happen, except if lists # were appended by accessing _buffer externally (when it's # intended to be private), which should be a red flag. assert len(self._buffer) < self.reduce_every # Outside of class to fix an issue with exec in Python 2.6. # My sorries to the god of pretty code. def _BasicStatisticsSeries_construct_table_toexec(index_names, store_timestamp, store_cpuclock): toexec = "class LocalDescription(tables.IsDescription):\n" toexec_, pos = _get_description_timestamp_cpuclock_columns(store_timestamp, store_cpuclock) toexec += toexec_ toexec_, pos = _get_description_n_ints(index_names, pos=pos) toexec += toexec_ toexec += "\tmean = tables.Float32Col(pos=" + str(pos) + ")\n" toexec += "\tmin = tables.Float32Col(pos=" + str(pos+1) + ")\n" toexec += "\tmax = tables.Float32Col(pos=" + str(pos+2) + ")\n" toexec += "\tstd = tables.Float32Col(pos=" + str(pos+3) + ")\n" # This creates "LocalDescription", which we may then use exec(toexec) return LocalDescription # Defaults functions for BasicStatsSeries. These can be replaced. _basic_stats_functions = {'mean': lambda(x): numpy.mean(x), 'min': lambda(x): numpy.min(x), 'max': lambda(x): numpy.max(x), 'std': lambda(x): numpy.std(x)} class BasicStatisticsSeries(Series): def __init__(self, table_name, hdf5_file, stats_functions=_basic_stats_functions, index_names=('epoch',), title="", hdf5_group='/', store_timestamp=True, store_cpuclock=True): """ For most parameters, see Series.__init__ Parameters ---------- series_name : str Not optional here. Will be prepended with "Basic statistics for " stats_functions : dict, optional Dictionary with a function for each key "mean", "min", "max", "std". The function must take whatever is passed to append(...) and return a single number (float). """ # Most type/value checks performed in Series.__init__ Series.__init__(self, table_name, hdf5_file, index_names, title, store_timestamp=store_timestamp, store_cpuclock=store_cpuclock) if type(hdf5_group) != str: raise TypeError("hdf5_group must be a string") if type(stats_functions) != dict: # just a basic check. We'll suppose caller knows what he's doing. raise TypeError("stats_functions must be a dict") self.hdf5_group = hdf5_group self.stats_functions = stats_functions self._create_table() def _create_table(self): table_description = \ _BasicStatisticsSeries_construct_table_toexec( \ self.index_names, self.store_timestamp, self.store_cpuclock) self._table = self.hdf5_file.createTable(self.hdf5_group, self.table_name, table_description) def append(self, index, array): """ Parameters ---------- index : tuple of int Following index_names passed to __init__, e.g. (12, 15) if index_names were ('epoch', 'minibatch_size') A single int (not tuple) is acceptable if index_names has a single element. An array will be casted to a tuple, as a convenience. array Is of whatever type the stats_functions passed to __init__ can take. Default is anything numpy.mean(), min(), max(), std() can take. """ index = _index_to_tuple(index) if len(index) != len(self.index_names): raise ValueError("index provided does not have the right length (expected " \ + str(len(self.index_names)) + " got " + str(len(index))) newrow = self._table.row for col_name, value in zip(self.index_names, index): newrow[col_name] = value newrow["mean"] = self.stats_functions['mean'](array) newrow["min"] = self.stats_functions['min'](array) newrow["max"] = self.stats_functions['max'](array) newrow["std"] = self.stats_functions['std'](array) self._timestamp_cpuclock(newrow) newrow.append() self.hdf5_file.flush() class SeriesArrayWrapper(): """ Simply redistributes any number of elements to sub-series to respective append()s. To use if you have many elements to append in similar series, e.g. if you have an array containing [train_error, valid_error, test_error], and 3 corresponding series, this allows you to simply pass this array of 3 values to append() instead of passing each element to each individual series in turn. """ def __init__(self, base_series_list): """ Parameters ---------- base_series_list : array or tuple of Series You must have previously created and configured each of those series, then put them in an array. This array must follow the same order as the array passed as ``elements`` parameter of append(). """ self.base_series_list = base_series_list def append(self, index, elements): """ Parameters ---------- index : tuple of int See for example ErrorSeries.append() elements : array or tuple Array or tuple of elements that will be passed down to the base_series passed to __init__, in the same order. """ if len(elements) != len(self.base_series_list): raise ValueError("not enough or too much elements provided (expected " \ + str(len(self.base_series_list)) + " got " + str(len(elements))) for series, el in zip(self.base_series_list, elements): series.append(index, el) class SharedParamsStatisticsWrapper(SeriesArrayWrapper): ''' Save mean, min/max, std of shared parameters place in an array. Here "shared" means "theano.shared", which means elements of the array will have a .value to use for numpy.mean(), etc. This inherits from SeriesArrayWrapper, which provides the append() method. ''' def __init__(self, arrays_names, new_group_name, hdf5_file, base_group='/', index_names=('epoch',), title="", store_timestamp=True, store_cpuclock=True): """ For other parameters, see Series.__init__ Parameters ---------- array_names : array or tuple of str Name of each array, in order of the array passed to append(). E.g. ('layer1_b', 'layer1_W', 'layer2_b', 'layer2_W') new_group_name : str Name of a new HDF5 group which will be created under base_group to store the new series. base_group : str Path of the group under which to create the new group which will store the series. title : str Here the title is attached to the new group, not a table. store_timestamp : bool Here timestamp and cpuclock are stored in *each* table store_cpuclock : bool Here timestamp and cpuclock are stored in *each* table """ # most other checks done when calling BasicStatisticsSeries if type(new_group_name) != str: raise TypeError("new_group_name must be a string") if new_group_name == "": raise ValueError("new_group_name must not be empty") base_series_list = [] new_group = hdf5_file.createGroup(base_group, new_group_name, title=title) stats_functions = {'mean': lambda(x): numpy.mean(x.value), 'min': lambda(x): numpy.min(x.value), 'max': lambda(x): numpy.max(x.value), 'std': lambda(x): numpy.std(x.value)} for name in arrays_names: base_series_list.append( BasicStatisticsSeries( table_name=name, hdf5_file=hdf5_file, index_names=index_names, stats_functions=stats_functions, hdf5_group=new_group._v_pathname, store_timestamp=store_timestamp, store_cpuclock=store_cpuclock)) SeriesArrayWrapper.__init__(self, base_series_list)