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annotate utils/seriestables/series.py @ 266:1e4e60ddadb1

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Merge. Ah, et dans le dernier commit, j'avais oublié de mentionner que j'ai ajouté du code pour gérer l'isolation de différents clones pour rouler des expériences et modifier le code en même temps.
author fsavard
date Fri, 19 Mar 2010 10:56:16 -0400
parents 0515a8901c6a
children
rev   line source
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e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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1 import tables
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2
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3 import numpy
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4 import time
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5
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6 ##############################################################################
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7 # Utility functions to create IsDescription objects (pytables data types)
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8
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acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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9 '''
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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10 The way these "IsDescription constructor" work is simple: write the
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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11 code as if it were in a file, then exec()ute it, leaving us with
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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12 a local-scoped LocalDescription which may be used to call createTable.
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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13
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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14 It's a small hack, but it's necessary as the names of the columns
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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15 are retrieved based on the variable name, which we can't programmatically set
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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16 otherwise.
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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17 '''
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18
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19 def _get_description_timestamp_cpuclock_columns(store_timestamp, store_cpuclock, pos=0):
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20 toexec = ""
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0515a8901c6a Corrigé un bug avec store_timestamp/cpuclock, et tests pour éviter ce cas
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21
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22 if store_timestamp:
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23 toexec += "\ttimestamp = tables.Time32Col(pos="+str(pos)+")\n"
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24 pos += 1
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25
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26 if store_cpuclock:
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27 toexec += "\tcpuclock = tables.Float64Col(pos="+str(pos)+")\n"
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28 pos += 1
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29
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30 return toexec, pos
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31
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32 def _get_description_n_ints(int_names, int_width=64, pos=0):
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dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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33 """
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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34 Begins construction of a class inheriting from IsDescription
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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35 to construct an HDF5 table with index columns named with int_names.
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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36
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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37 See Series().__init__ to see how those are used.
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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38 """
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e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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39 int_constructor = "tables.Int64Col"
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acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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40 if int_width == 32:
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e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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41 int_constructor = "tables.Int32Col"
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42 elif not int_width in (32, 64):
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43 raise "int_width must be left unspecified, or should equal 32 or 64"
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44
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45 toexec = ""
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46
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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47 for n in int_names:
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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48 toexec += "\t" + n + " = " + int_constructor + "(pos=" + str(pos) + ")\n"
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49 pos += 1
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50
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51 return toexec, pos
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52
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53 def _get_description_with_n_ints_n_floats(int_names, float_names,
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54 int_width=64, float_width=32,
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55 store_timestamp=True, store_cpuclock=True):
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acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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56 """
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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57 Constructs a class to be used when constructing a table with PyTables.
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58
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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59 This is useful to construct a series with an index with multiple levels.
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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60 E.g. if you want to index your "validation error" with "epoch" first, then
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61 "minibatch_index" second, you'd use two "int_names".
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62
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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63 Parameters
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64 ----------
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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65 int_names : tuple of str
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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66 Names of the int (e.g. index) columns
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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67 float_names : tuple of str
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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68 Names of the float (e.g. error) columns
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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69 int_width : {'32', '64'}
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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70 Type of ints.
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71 float_width : {'32', '64'}
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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72 Type of floats.
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73 store_timestamp : bool
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74 See __init__ of Series
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75 store_cpuclock : bool
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76 See __init__ of Series
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77
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78 Returns
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79 -------
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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80 A class object, to pass to createTable()
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81 """
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82
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83 toexec = "class LocalDescription(tables.IsDescription):\n"
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84
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85 toexec_, pos = _get_description_timestamp_cpuclock_columns(store_timestamp, store_cpuclock)
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86 toexec += toexec_
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87
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88 toexec_, pos = _get_description_n_ints(int_names, int_width=int_width, pos=pos)
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89 toexec += toexec_
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90
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91 float_constructor = "tables.Float32Col"
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92 if float_width == 64:
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93 float_constructor = "tables.Float64Col"
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94 elif not float_width in (32, 64):
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95 raise "float_width must be left unspecified, or should equal 32 or 64"
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96
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97 for n in float_names:
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98 toexec += "\t" + n + " = " + float_constructor + "(pos=" + str(pos) + ")\n"
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99 pos += 1
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100
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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101 exec(toexec)
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102
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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103 return LocalDescription
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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104
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105 ##############################################################################
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106 # Series classes
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107
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108 # Shortcut to allow passing a single int as index, instead of a tuple
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109 def _index_to_tuple(index):
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110 if type(index) == tuple:
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111 return index
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112
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113 if type(index) == list:
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114 index = tuple(index)
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115 return index
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116
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117 try:
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118 if index % 1 > 0.001 and index % 1 < 0.999:
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119 raise
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120 idx = long(index)
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121 return (idx,)
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122 except:
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123 raise TypeError("index must be a tuple of integers, or at least a single integer")
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124
208
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125 class Series():
220
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126 """
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127 Base Series class, with minimal arguments and type checks.
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128
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129 Yet cannot be used by itself (it's append() method raises an error)
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130 """
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131
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132 def __init__(self, table_name, hdf5_file, index_names=('epoch',),
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133 title="", hdf5_group='/',
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134 store_timestamp=True, store_cpuclock=True):
210
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135 """Basic arguments each Series must get.
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136
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137 Parameters
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138 ----------
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139 table_name : str
220
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140 Name of the table to create under group "hd5_group" (other
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141 parameter). No spaces, ie. follow variable naming restrictions.
210
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142 hdf5_file : open HDF5 file
220
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143 File opened with openFile() in PyTables (ie. return value of
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144 openFile).
210
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145 index_names : tuple of str
220
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146 Columns to use as index for elements in the series, other
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147 example would be ('epoch', 'minibatch'). This would then allow
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148 you to call append(index, element) with index made of two ints,
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149 one for epoch index, one for minibatch index in epoch.
210
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150 title : str
220
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151 Title to attach to this table as metadata. Can contain spaces
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152 and be longer then the table_name.
210
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153 hdf5_group : str
220
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154 Path of the group (kind of a file) in the HDF5 file under which
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155 to create the table.
218
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156 store_timestamp : bool
220
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157 Whether to create a column for timestamps and store them with
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158 each record.
218
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159 store_cpuclock : bool
220
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160 Whether to create a column for cpu clock and store it with
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161 each record.
210
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162 """
220
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163
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164 #########################################
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165 # checks
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166
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167 if type(table_name) != str:
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168 raise TypeError("table_name must be a string")
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169 if table_name == "":
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170 raise ValueError("table_name must not be empty")
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171
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172 if not isinstance(hdf5_file, tables.file.File):
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173 raise TypeError("hdf5_file must be an open HDF5 file (use tables.openFile)")
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174 #if not ('w' in hdf5_file.mode or 'a' in hdf5_file.mode):
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175 # raise ValueError("hdf5_file must be opened in write or append mode")
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176
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177 if type(index_names) != tuple:
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178 raise TypeError("index_names must be a tuple of strings." + \
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179 "If you have only one element in the tuple, don't forget " +\
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180 "to add a comma, e.g. ('epoch',).")
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181 for name in index_names:
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182 if type(name) != str:
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183 raise TypeError("index_names must only contain strings, but also"+\
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184 "contains a "+str(type(name))+".")
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185
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186 if type(title) != str:
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187 raise TypeError("title must be a string, even if empty")
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188
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189 if type(hdf5_group) != str:
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190 raise TypeError("hdf5_group must be a string")
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191
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192 if type(store_timestamp) != bool:
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193 raise TypeError("store_timestamp must be a bool")
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194
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195 if type(store_cpuclock) != bool:
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196 raise TypeError("store_timestamp must be a bool")
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197
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198 #########################################
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199
208
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200 self.table_name = table_name
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201 self.hdf5_file = hdf5_file
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202 self.index_names = index_names
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203 self.title = title
220
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204 self.hdf5_group = hdf5_group
208
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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205
218
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206 self.store_timestamp = store_timestamp
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207 self.store_cpuclock = store_cpuclock
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208
208
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209 def append(self, index, element):
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210 raise NotImplementedError
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211
218
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212 def _timestamp_cpuclock(self, newrow):
224
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213 if self.store_timestamp:
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214 newrow["timestamp"] = time.time()
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215
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216 if self.store_cpuclock:
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217 newrow["cpuclock"] = time.clock()
218
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218
210
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219 class DummySeries():
220
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220 """
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221 To put in a series dictionary instead of a real series, to do nothing
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222 when we don't want a given series to be saved.
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223
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224 E.g. if we'd normally have a "training_error" series in a dictionary
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225 of series, the training loop would have something like this somewhere:
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226
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227 series["training_error"].append((15,), 20.0)
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228
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229 but if we don't want to save the training errors this time, we simply
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230 do
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231
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232 series["training_error"] = DummySeries()
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233 """
210
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234 def append(self, index, element):
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235 pass
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236
208
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237 class ErrorSeries(Series):
220
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238 """
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239 Most basic Series: saves a single float (called an Error as this is
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240 the most common use case I foresee) along with an index (epoch, for
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241 example) and timestamp/cpu.clock for each of these floats.
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242 """
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243
218
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244 def __init__(self, error_name, table_name,
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245 hdf5_file, index_names=('epoch',),
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246 title="", hdf5_group='/',
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247 store_timestamp=True, store_cpuclock=True):
220
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248 """
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249 For most parameters, see Series.__init__
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250
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251 Parameters
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252 ----------
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253 error_name : str
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254 In the HDF5 table, column name for the error float itself.
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255 """
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256
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257 # most type/value checks are performed in Series.__init__
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258 Series.__init__(self, table_name, hdf5_file, index_names, title,
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259 store_timestamp=store_timestamp,
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260 store_cpuclock=store_cpuclock)
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261
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262 if type(error_name) != str:
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263 raise TypeError("error_name must be a string")
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264 if error_name == "":
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265 raise ValueError("error_name must not be empty")
208
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266
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267 self.error_name = error_name
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268
220
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269 self._create_table()
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270
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271 def _create_table(self):
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272 table_description = _get_description_with_n_ints_n_floats( \
224
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273 self.index_names, (self.error_name,),
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274 store_timestamp=self.store_timestamp,
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275 store_cpuclock=self.store_cpuclock)
208
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276
220
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277 self._table = self.hdf5_file.createTable(self.hdf5_group,
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278 self.table_name,
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279 table_description,
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280 title=self.title)
208
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281
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282
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283 def append(self, index, error):
210
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284 """
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285 Parameters
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286 ----------
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287 index : tuple of int
220
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288 Following index_names passed to __init__, e.g. (12, 15) if
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289 index_names were ('epoch', 'minibatch_size').
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290 A single int (not tuple) is acceptable if index_names has a single
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291 element.
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292 An array will be casted to a tuple, as a convenience.
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293
210
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294 error : float
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295 Next error in the series.
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296 """
220
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297 index = _index_to_tuple(index)
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298
208
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299 if len(index) != len(self.index_names):
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300 raise ValueError("index provided does not have the right length (expected " \
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301 + str(len(self.index_names)) + " got " + str(len(index)))
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302
220
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303 # other checks are implicit when calling newrow[..] =,
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304 # which should throw an error if not of the right type
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305
208
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306 newrow = self._table.row
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307
210
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308 # Columns for index in table are based on index_names
208
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309 for col_name, value in zip(self.index_names, index):
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310 newrow[col_name] = value
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311 newrow[self.error_name] = error
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312
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313 # adds timestamp and cpuclock to newrow if necessary
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314 self._timestamp_cpuclock(newrow)
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315
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316 newrow.append()
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317
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318 self.hdf5_file.flush()
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319
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320 # Does not inherit from Series because it does not itself need to
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321 # access the hdf5_file and does not need a series_name (provided
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322 # by the base_series.)
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323 class AccumulatorSeriesWrapper():
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324 '''
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325 Wraps a Series by accumulating objects passed its Accumulator.append()
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326 method and "reducing" (e.g. calling numpy.mean(list)) once in a while,
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327 every "reduce_every" calls in fact.
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328 '''
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329
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330 def __init__(self, base_series, reduce_every, reduce_function=numpy.mean):
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331 """
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332 Parameters
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333 ----------
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334 base_series : Series
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335 This object must have an append(index, value) function.
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336
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337 reduce_every : int
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338 Apply the reduction function (e.g. mean()) every time we get this
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339 number of elements. E.g. if this is 100, then every 100 numbers
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340 passed to append(), we'll take the mean and call append(this_mean)
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341 on the BaseSeries.
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342
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343 reduce_function : function
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344 Must take as input an array of "elements", as passed to (this
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345 accumulator's) append(). Basic case would be to take an array of
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346 floats and sum them into one float, for example.
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347 """
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348 self.base_series = base_series
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349 self.reduce_function = reduce_function
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350 self.reduce_every = reduce_every
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351
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352 self._buffer = []
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353
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354
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355 def append(self, index, element):
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356 """
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357 Parameters
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358 ----------
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359 index : tuple of int
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360 The index used is the one of the last element reduced. E.g. if
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361 you accumulate over the first 1000 minibatches, the index
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362 passed to the base_series.append() function will be 1000.
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363 A single int (not tuple) is acceptable if index_names has a single
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364 element.
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365 An array will be casted to a tuple, as a convenience.
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366
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367 element : float
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368 Element that will be accumulated.
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369 """
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370 self._buffer.append(element)
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371
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372 if len(self._buffer) == self.reduce_every:
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373 reduced = self.reduce_function(self._buffer)
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374 self.base_series.append(index, reduced)
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375 self._buffer = []
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376
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377 # The >= case should never happen, except if lists
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378 # were appended by accessing _buffer externally (when it's
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379 # intended to be private), which should be a red flag.
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380 assert len(self._buffer) < self.reduce_every
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381
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382 # Outside of class to fix an issue with exec in Python 2.6.
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383 # My sorries to the god of pretty code.
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384 def _BasicStatisticsSeries_construct_table_toexec(index_names, store_timestamp, store_cpuclock):
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385 toexec = "class LocalDescription(tables.IsDescription):\n"
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386
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387 toexec_, pos = _get_description_timestamp_cpuclock_columns(store_timestamp, store_cpuclock)
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388 toexec += toexec_
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389
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390 toexec_, pos = _get_description_n_ints(index_names, pos=pos)
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391 toexec += toexec_
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392
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393 toexec += "\tmean = tables.Float32Col(pos=" + str(pos) + ")\n"
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394 toexec += "\tmin = tables.Float32Col(pos=" + str(pos+1) + ")\n"
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395 toexec += "\tmax = tables.Float32Col(pos=" + str(pos+2) + ")\n"
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396 toexec += "\tstd = tables.Float32Col(pos=" + str(pos+3) + ")\n"
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397
208
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398 # This creates "LocalDescription", which we may then use
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399 exec(toexec)
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400
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401 return LocalDescription
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402
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403 # Defaults functions for BasicStatsSeries. These can be replaced.
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404 _basic_stats_functions = {'mean': lambda(x): numpy.mean(x),
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405 'min': lambda(x): numpy.min(x),
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406 'max': lambda(x): numpy.max(x),
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407 'std': lambda(x): numpy.std(x)}
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408
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409 class BasicStatisticsSeries(Series):
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410
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411 def __init__(self, table_name, hdf5_file,
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412 stats_functions=_basic_stats_functions,
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413 index_names=('epoch',), title="", hdf5_group='/',
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414 store_timestamp=True, store_cpuclock=True):
220
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415 """
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416 For most parameters, see Series.__init__
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417
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418 Parameters
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419 ----------
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420 series_name : str
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421 Not optional here. Will be prepended with "Basic statistics for "
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422
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423 stats_functions : dict, optional
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424 Dictionary with a function for each key "mean", "min", "max",
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425 "std". The function must take whatever is passed to append(...)
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426 and return a single number (float).
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427 """
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428
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429 # Most type/value checks performed in Series.__init__
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430 Series.__init__(self, table_name, hdf5_file, index_names, title,
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431 store_timestamp=store_timestamp,
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432 store_cpuclock=store_cpuclock)
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433
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434 if type(hdf5_group) != str:
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435 raise TypeError("hdf5_group must be a string")
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436
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437 if type(stats_functions) != dict:
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438 # just a basic check. We'll suppose caller knows what he's doing.
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439 raise TypeError("stats_functions must be a dict")
208
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440
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441 self.hdf5_group = hdf5_group
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442
210
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443 self.stats_functions = stats_functions
208
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444
220
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445 self._create_table()
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446
220
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447 def _create_table(self):
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448 table_description = \
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449 _BasicStatisticsSeries_construct_table_toexec( \
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450 self.index_names,
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451 self.store_timestamp, self.store_cpuclock)
208
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452
220
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453 self._table = self.hdf5_file.createTable(self.hdf5_group,
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454 self.table_name, table_description)
208
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455
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456 def append(self, index, array):
210
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457 """
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458 Parameters
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459 ----------
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460 index : tuple of int
220
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461 Following index_names passed to __init__, e.g. (12, 15)
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462 if index_names were ('epoch', 'minibatch_size')
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463 A single int (not tuple) is acceptable if index_names has a single
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464 element.
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465 An array will be casted to a tuple, as a convenience.
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466
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467 array
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468 Is of whatever type the stats_functions passed to
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469 __init__ can take. Default is anything numpy.mean(),
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470 min(), max(), std() can take.
210
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471 """
220
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472 index = _index_to_tuple(index)
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473
208
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474 if len(index) != len(self.index_names):
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475 raise ValueError("index provided does not have the right length (expected " \
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476 + str(len(self.index_names)) + " got " + str(len(index)))
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477
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478 newrow = self._table.row
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479
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480 for col_name, value in zip(self.index_names, index):
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481 newrow[col_name] = value
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482
210
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483 newrow["mean"] = self.stats_functions['mean'](array)
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484 newrow["min"] = self.stats_functions['min'](array)
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485 newrow["max"] = self.stats_functions['max'](array)
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486 newrow["std"] = self.stats_functions['std'](array)
208
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487
218
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488 self._timestamp_cpuclock(newrow)
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489
208
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490 newrow.append()
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491
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492 self.hdf5_file.flush()
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493
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494 class SeriesArrayWrapper():
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495 """
220
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496 Simply redistributes any number of elements to sub-series to respective
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497 append()s.
210
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498
220
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499 To use if you have many elements to append in similar series, e.g. if you
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500 have an array containing [train_error, valid_error, test_error], and 3
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501 corresponding series, this allows you to simply pass this array of 3
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502 values to append() instead of passing each element to each individual
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503 series in turn.
208
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504 """
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505
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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506 def __init__(self, base_series_list):
220
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507 """
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508 Parameters
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509 ----------
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510 base_series_list : array or tuple of Series
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511 You must have previously created and configured each of those
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512 series, then put them in an array. This array must follow the
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513 same order as the array passed as ``elements`` parameter of
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diff changeset
514 append().
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515 """
208
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516 self.base_series_list = base_series_list
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517
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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518 def append(self, index, elements):
220
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519 """
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520 Parameters
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521 ----------
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522 index : tuple of int
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523 See for example ErrorSeries.append()
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diff changeset
524
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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525 elements : array or tuple
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526 Array or tuple of elements that will be passed down to
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527 the base_series passed to __init__, in the same order.
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528 """
208
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
529 if len(elements) != len(self.base_series_list):
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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530 raise ValueError("not enough or too much elements provided (expected " \
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
531 + str(len(self.base_series_list)) + " got " + str(len(elements)))
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
532
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
533 for series, el in zip(self.base_series_list, elements):
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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534 series.append(index, el)
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
535
210
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536 class SharedParamsStatisticsWrapper(SeriesArrayWrapper):
220
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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537 '''
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
538 Save mean, min/max, std of shared parameters place in an array.
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diff changeset
539
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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540 Here "shared" means "theano.shared", which means elements of the
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
541 array will have a .value to use for numpy.mean(), etc.
210
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
542
220
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
543 This inherits from SeriesArrayWrapper, which provides the append()
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
544 method.
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
545 '''
210
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
546
220
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
547 def __init__(self, arrays_names, new_group_name, hdf5_file,
224
0515a8901c6a Corrigé un bug avec store_timestamp/cpuclock, et tests pour éviter ce cas
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diff changeset
548 base_group='/', index_names=('epoch',), title="",
0515a8901c6a Corrigé un bug avec store_timestamp/cpuclock, et tests pour éviter ce cas
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diff changeset
549 store_timestamp=True, store_cpuclock=True):
210
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
550 """
220
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
551 For other parameters, see Series.__init__
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
552
210
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
553 Parameters
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
554 ----------
220
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
555 array_names : array or tuple of str
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
556 Name of each array, in order of the array passed to append(). E.g.
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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557 ('layer1_b', 'layer1_W', 'layer2_b', 'layer2_W')
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
558
210
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
559 new_group_name : str
220
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
560 Name of a new HDF5 group which will be created under base_group to
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
561 store the new series.
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
562
210
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
563 base_group : str
220
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
564 Path of the group under which to create the new group which will
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
565 store the series.
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
566
210
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
567 title : str
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
568 Here the title is attached to the new group, not a table.
224
0515a8901c6a Corrigé un bug avec store_timestamp/cpuclock, et tests pour éviter ce cas
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diff changeset
569
0515a8901c6a Corrigé un bug avec store_timestamp/cpuclock, et tests pour éviter ce cas
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diff changeset
570 store_timestamp : bool
0515a8901c6a Corrigé un bug avec store_timestamp/cpuclock, et tests pour éviter ce cas
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diff changeset
571 Here timestamp and cpuclock are stored in *each* table
0515a8901c6a Corrigé un bug avec store_timestamp/cpuclock, et tests pour éviter ce cas
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diff changeset
572
0515a8901c6a Corrigé un bug avec store_timestamp/cpuclock, et tests pour éviter ce cas
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diff changeset
573 store_cpuclock : bool
0515a8901c6a Corrigé un bug avec store_timestamp/cpuclock, et tests pour éviter ce cas
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diff changeset
574 Here timestamp and cpuclock are stored in *each* table
210
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
575 """
220
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
576
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
577 # most other checks done when calling BasicStatisticsSeries
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
578 if type(new_group_name) != str:
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
579 raise TypeError("new_group_name must be a string")
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
580 if new_group_name == "":
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
581 raise ValueError("new_group_name must not be empty")
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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diff changeset
582
208
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
583 base_series_list = []
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
584
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
585 new_group = hdf5_file.createGroup(base_group, new_group_name, title=title)
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
586
210
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
587 stats_functions = {'mean': lambda(x): numpy.mean(x.value),
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
588 'min': lambda(x): numpy.min(x.value),
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
589 'max': lambda(x): numpy.max(x.value),
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
590 'std': lambda(x): numpy.std(x.value)}
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
savardf
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diff changeset
591
208
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
592 for name in arrays_names:
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
593 base_series_list.append(
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
594 BasicStatisticsSeries(
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
595 table_name=name,
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
596 hdf5_file=hdf5_file,
210
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
597 index_names=index_names,
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
598 stats_functions=stats_functions,
224
0515a8901c6a Corrigé un bug avec store_timestamp/cpuclock, et tests pour éviter ce cas
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diff changeset
599 hdf5_group=new_group._v_pathname,
0515a8901c6a Corrigé un bug avec store_timestamp/cpuclock, et tests pour éviter ce cas
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diff changeset
600 store_timestamp=store_timestamp,
0515a8901c6a Corrigé un bug avec store_timestamp/cpuclock, et tests pour éviter ce cas
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diff changeset
601 store_cpuclock=store_cpuclock))
208
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
602
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
603 SeriesArrayWrapper.__init__(self, base_series_list)
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
604
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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diff changeset
605