--- a/utils/seriestables/series.py	Wed Mar 10 20:14:20 2010 -0500
+++ b/utils/seriestables/series.py	Thu Mar 11 10:48:54 2010 -0500
@@ -1,7 +1,11 @@
-from tables import *
+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
@@ -16,11 +20,11 @@
     toexec = ""
     
     if store_timestamp:
-        toexec += "\ttimestamp = Time32Col(pos="+str(pos)+")\n"
+        toexec += "\ttimestamp = tables.Time32Col(pos="+str(pos)+")\n"
         pos += 1
 
     if store_cpuclock:
-        toexec += "\tcpuclock = Float64Col(pos="+str(pos)+")\n"
+        toexec += "\tcpuclock = tables.Float64Col(pos="+str(pos)+")\n"
         pos += 1
 
     return toexec, pos
@@ -32,9 +36,9 @@
 
     See Series().__init__ to see how those are used.
     """
-    int_constructor = "Int64Col"
+    int_constructor = "tables.Int64Col"
     if int_width == 32:
-        int_constructor = "Int32Col"
+        int_constructor = "tables.Int32Col"
 
     toexec = ""
 
@@ -74,7 +78,7 @@
     A class object, to pass to createTable()
     """
 
-    toexec = "class LocalDescription(IsDescription):\n"
+    toexec = "class LocalDescription(tables.IsDescription):\n"
 
     toexec_, pos = _get_description_timestamp_cpuclock_columns(store_timestamp, store_cpuclock)
     toexec += toexec_
@@ -82,9 +86,9 @@
     toexec_, pos = _get_description_n_ints(int_names, int_width=int_width, pos=pos)
     toexec += toexec_
 
-    float_constructor = "Float32Col"
+    float_constructor = "tables.Float32Col"
     if float_width == 64:
-        float_constructor = "Float64Col"
+        float_constructor = "tables.Float64Col"
 
     for n in float_names:
         toexec += "\t" + n + " = " + float_constructor + "(pos=" + str(pos) + ")\n"
@@ -94,7 +98,33 @@
 
     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):
@@ -103,24 +133,71 @@
         Parameters
         ----------
         table_name : str
-            Name of the table to create under group "hd5_group" (other parameter). No spaces, ie. follow variable naming restrictions.
+            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).
+            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.
+            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.
+            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.
+            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.
+            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.
+            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
@@ -132,41 +209,91 @@
         newrow["timestamp"] = time.time()
         newrow["cpuclock"] = time.clock()
 
-# 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.
 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):
-        Series.__init__(self, table_name, hdf5_file, index_names, title, store_timestamp, store_cpuclock)
+        """
+        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
 
-        table_description = self._get_table_description()
+        self._create_table()
+
+    def _create_table(self):
+       table_description = _get_description_with_n_ints_n_floats( \
+                                  self.index_names, (self.error_name,))
 
-        self._table = hdf5_file.createTable(hdf5_group, self.table_name, table_description, title=title)
+       self._table = self.hdf5_file.createTable(self.hdf5_group,
+                            self.table_name, 
+                            table_description,
+                            title=self.title)
 
-    def _get_table_description(self):
-        return _get_description_with_n_ints_n_floats(self.index_names, (self.error_name,))
 
     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')
+            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
@@ -174,6 +301,7 @@
             newrow[col_name] = value
         newrow[self.error_name] = error
 
+        # adds timestamp and cpuclock to newrow if necessary
         self._timestamp_cpuclock(newrow)
 
         newrow.append()
@@ -184,19 +312,29 @@
 # 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.
+            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.
+            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
@@ -213,6 +351,10 @@
             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.
         """
@@ -223,14 +365,14 @@
             self.base_series.append(index, reduced)
             self._buffer = []
 
-        # This should never happen, except if lists
+        # The >= case should never happen, except if lists
         # were appended, 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.
+# My sorries to the god of pretty code.
 def _BasicStatisticsSeries_construct_table_toexec(index_names, store_timestamp, store_cpuclock):
-    toexec = "class LocalDescription(IsDescription):\n"
+    toexec = "class LocalDescription(tables.IsDescription):\n"
 
     toexec_, pos = _get_description_timestamp_cpuclock_columns(store_timestamp, store_cpuclock)
     toexec += toexec_
@@ -238,56 +380,87 @@
     toexec_, pos = _get_description_n_ints(index_names, pos=pos)
     toexec += toexec_
 
-    toexec += "\tmean = Float32Col(pos=" + str(pos) + ")\n"
-    toexec += "\tmin = Float32Col(pos=" + str(pos+1) + ")\n"
-    toexec += "\tmax = Float32Col(pos=" + str(pos+2) + ")\n"
-    toexec += "\tstd = Float32Col(pos=" + str(pos+3) + ")\n"
+    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
 
-basic_stats_functions = {'mean': lambda(x): numpy.mean(x),
+# 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):
-    """
-    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).
-    """
+    
     def __init__(self, table_name, hdf5_file, 
-                    stats_functions=basic_stats_functions, 
+                    stats_functions=_basic_stats_functions, 
                     index_names=('epoch',), title="", hdf5_group='/', 
                     store_timestamp=True, store_cpuclock=True):
-        Series.__init__(self, table_name, hdf5_file, index_names, title, store_timestamp, store_cpuclock)
+        """
+        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._construct_table()
+        self._create_table()
 
-    def _construct_table(self):
-        table_description = _BasicStatisticsSeries_construct_table_toexec(self.index_names, self.store_timestamp, self.store_cpuclock)
+    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)
+        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')
+            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. 
+            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)))
@@ -310,15 +483,39 @@
 
 class SeriesArrayWrapper():
     """
-    Simply redistributes any number of elements to sub-series to respective append()s.
+    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.
+    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)))
@@ -327,24 +524,45 @@
             series.append(index, el)
 
 class SharedParamsStatisticsWrapper(SeriesArrayWrapper):
-    '''Save mean, min/max, std of shared parameters place in an array.
+    '''
+    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 is specifically for cases where we have _shared_ parameters,
-    as we take the .value of each array'''
+    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=""):
+    def __init__(self, arrays_names, new_group_name, hdf5_file,
+                    base_group='/', index_names=('epoch',), title=""):
         """
+        For other parameters, see Series.__init__
+
         Parameters
         ----------
-        array_names : array of str
-            Name of each array, in order of the array passed to append(). E.g. ('layer1_b', 'layer1_W', 'layer2_b', 'layer2_W')
+        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.
+            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.
+            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.
         """
+
+        # 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)

--- a/utils/seriestables/test_series.py	Wed Mar 10 20:14:20 2010 -0500
+++ b/utils/seriestables/test_series.py	Thu Mar 11 10:48:54 2010 -0500
@@ -1,14 +1,17 @@
 import tempfile
+
 import numpy
 import numpy.random
 
 from jobman import DD
 
-from tables import *
+import tables
 
 from series import *
 import series
 
+#################################################
+# Utils
 
 def compare_floats(f1,f2):
     if f1-f2 < 1e-3:
@@ -28,12 +31,21 @@
 
     return True
 
+#################################################
+# Basic Series class tests
+
+def test_Series_types():
+    pass
+
+#################################################
+# ErrorSeries tests
+
 def test_ErrorSeries_common_case(h5f=None):
     if not h5f:
         h5f_path = tempfile.NamedTemporaryFile().name
-        h5f = openFile(h5f_path, "w")
+        h5f = tables.openFile(h5f_path, "w")
 
-    validation_error = ErrorSeries(error_name="validation_error", table_name="validation_error",
+    validation_error = series.ErrorSeries(error_name="validation_error", table_name="validation_error",
                                 hdf5_file=h5f, index_names=('epoch','minibatch'),
                                 title="Validation error indexed by epoch and minibatch")
 
@@ -45,7 +57,7 @@
 
     h5f.close()
 
-    h5f = openFile(h5f_path, "r")
+    h5f = tables.openFile(h5f_path, "r")
     
     table = h5f.getNode('/', 'validation_error')
 
@@ -56,7 +68,7 @@
 def test_AccumulatorSeriesWrapper_common_case(h5f=None):
     if not h5f:
         h5f_path = tempfile.NamedTemporaryFile().name
-        h5f = openFile(h5f_path, "w")
+        h5f = tables.openFile(h5f_path, "w")
 
     validation_error = ErrorSeries(error_name="accumulated_validation_error",
                                 table_name="accumulated_validation_error",
@@ -77,7 +89,7 @@
 
     h5f.close()
 
-    h5f = openFile(h5f_path, "r")
+    h5f = tables.openFile(h5f_path, "r")
     
     table = h5f.getNode('/', 'accumulated_validation_error')
 
@@ -88,7 +100,7 @@
 def test_BasicStatisticsSeries_common_case(h5f=None):
     if not h5f:
         h5f_path = tempfile.NamedTemporaryFile().name
-        h5f = openFile(h5f_path, "w")
+        h5f = tables.openFile(h5f_path, "w")
 
     stats_series = BasicStatisticsSeries(table_name="b_vector_statistics",
                                 hdf5_file=h5f, index_names=('epoch','minibatch'),
@@ -102,7 +114,7 @@
 
     h5f.close()
 
-    h5f = openFile(h5f_path, "r")
+    h5f = tables.openFile(h5f_path, "r")
     
     table = h5f.getNode('/', 'b_vector_statistics')
 
@@ -118,7 +130,7 @@
 
     if not h5f:
         h5f_path = tempfile.NamedTemporaryFile().name
-        h5f = openFile(h5f_path, "w")
+        h5f = tables.openFile(h5f_path, "w")
 
     stats = SharedParamsStatisticsWrapper(new_group_name="params", base_group="/",
                                 arrays_names=('b1','b2','b3'), hdf5_file=h5f,
@@ -131,7 +143,7 @@
 
     h5f.close()
 
-    h5f = openFile(h5f_path, "r")
+    h5f = tables.openFile(h5f_path, "r")
 
     b1_table = h5f.getNode('/params', 'b1')
     b3_table = h5f.getNode('/params', 'b3')
@@ -143,7 +155,7 @@
 
 def test_get_desc():
     h5f_path = tempfile.NamedTemporaryFile().name
-    h5f = openFile(h5f_path, "w")
+    h5f = tables.openFile(h5f_path, "w")
 
     desc = series._get_description_with_n_ints_n_floats(("col1","col2"), ("col3","col4"))
 
@@ -164,6 +176,27 @@
 
     assert True
 
+def test_index_to_tuple_floaterror():
+    try:
+        series._index_to_tuple(5.1)
+        assert False
+    except TypeError:
+        assert True
+
+def test_index_to_tuple_arrayok():
+    tpl = series._index_to_tuple([1,2,3])
+    assert type(tpl) == tuple and tpl[1] == 2 and tpl[2] == 3
+
+def test_index_to_tuple_intbecomestuple():
+    tpl = series._index_to_tuple(32)
+
+    assert type(tpl) == tuple and tpl == (32,)
+
+def test_index_to_tuple_longbecomestuple():
+    tpl = series._index_to_tuple(928374928374928L)
+
+    assert type(tpl) == tuple and tpl == (928374928374928L,)
+
 if __name__ == '__main__':
     import tempfile
     test_get_desc()