annotate utils/seriestables/series.py @ 213:a96fa4de06d2

Renommé mon module de séries
author fsavard
date Wed, 10 Mar 2010 16:52:22 -0500
parents utils/tables_series/series.py@dc0d77c8a878
children 4c137f16b013
rev   line source
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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1 from tables import *
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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2 import numpy
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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3
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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4 '''
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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5 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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6 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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7 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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8
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 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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10 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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11 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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12 '''
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 def get_beginning_description_n_ints(int_names, int_width=64):
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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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15 """
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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16 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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17 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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18
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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19 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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20 """
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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21 int_constructor = "Int64Col"
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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22 if int_width == 32:
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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23 int_constructor = "Int32Col"
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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24
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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25 toexec = "class LocalDescription(IsDescription):\n"
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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26
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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27 pos = 0
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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28
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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29 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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30 toexec += "\t" + n + " = " + int_constructor + "(pos=" + str(pos) + ")\n"
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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31
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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32 return toexec
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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33
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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34 def get_description_with_n_ints_n_floats(int_names, float_names, int_width=64, float_width=32):
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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35 """
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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36 Constructs a class to be used when constructing a table with PyTables.
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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37
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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38 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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39 E.g. if you want to index your "validation error" with "epoch" first, then
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 "minibatch_index" second, you'd use two "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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41
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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42 Parameters
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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43 ----------
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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44 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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45 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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46 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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47 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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48 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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49 Type of ints.
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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50 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.
fsavard
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51 Type of floats.
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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52
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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53 Returns
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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54 -------
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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55 A class object, to pass to 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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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
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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58 toexec = get_beginning_description_n_ints(int_names, int_width=int_width)
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
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 float_constructor = "Float32Col"
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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61 if float_width == 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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62 float_constructor = "Float64Col"
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
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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64 pos = len(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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65
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 for n in float_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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67 toexec += "\t" + n + " = " + float_constructor + "(pos=" + str(pos) + ")\n"
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
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 exec(toexec)
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
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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71 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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72
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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73 class Series():
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a96fa4de06d2 Renommé mon module de séries
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74 def __init__(self, table_name, hdf5_file, index_names=('epoch',), title="", hdf5_group='/'):
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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75 """Basic arguments each Series must get.
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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76
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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77 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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78 ----------
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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79 table_name : 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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80 Name of the table to create under group "hd5_group" (other parameter). No spaces, ie. follow variable naming restrictions.
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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81 hdf5_file : open HDF5 file
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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82 File opened with openFile() in PyTables (ie. return value of openFile).
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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83 index_names : tuple of 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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84 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.
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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85 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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86 Title to attach to this table as metadata. Can contain spaces and be longer then the table_name.
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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87 hdf5_group : 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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88 Path of the group (kind of a file) in the HDF5 file under which to create the table.
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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89 """
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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90 self.table_name = table_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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91 self.hdf5_file = hdf5_file
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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92 self.index_names = index_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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93 self.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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94
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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95 def append(self, index, element):
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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96 raise NotImplementedError
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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97
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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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98 # To put in a series dictionary instead of a real series, to do nothing
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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99 # when we don't want a given series to be saved.
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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100 class DummySeries():
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101 def append(self, index, element):
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102 pass
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103
208
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104 class ErrorSeries(Series):
213
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105 def __init__(self, error_name, table_name, hdf5_file, index_names=('epoch',), title="", hdf5_group='/'):
208
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106 Series.__init__(self, table_name, hdf5_file, index_names, title)
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107
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108 self.error_name = error_name
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109
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110 table_description = self._get_table_description()
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111
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112 self._table = hdf5_file.createTable(hdf5_group, self.table_name, table_description, title=title)
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113
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114 def _get_table_description(self):
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115 return get_description_with_n_ints_n_floats(self.index_names, (self.error_name,))
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116
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117 def append(self, index, error):
210
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118 """
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119 Parameters
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120 ----------
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121 index : tuple of int
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122 Following index_names passed to __init__, e.g. (12, 15) if index_names were ('epoch', 'minibatch_size')
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123 error : float
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124 Next error in the series.
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125 """
208
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126 if len(index) != len(self.index_names):
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127 raise ValueError("index provided does not have the right length (expected " \
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128 + str(len(self.index_names)) + " got " + str(len(index)))
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129
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130 newrow = self._table.row
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131
210
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132 # Columns for index in table are based on index_names
208
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133 for col_name, value in zip(self.index_names, index):
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134 newrow[col_name] = value
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135 newrow[self.error_name] = error
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136
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137 newrow.append()
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138
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139 self.hdf5_file.flush()
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140
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141 # Does not inherit from Series because it does not itself need to
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142 # access the hdf5_file and does not need a series_name (provided
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143 # by the base_series.)
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144 class AccumulatorSeriesWrapper():
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145 """
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146
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147 """
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148 def __init__(self, base_series, reduce_every, reduce_function=numpy.mean):
210
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149 """
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150 Parameters
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151 ----------
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152 base_series : Series
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153 This object must have an append(index, value) function.
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154 reduce_every : int
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155 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.
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156 reduce_function : function
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157 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.
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158 """
208
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159 self.base_series = base_series
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160 self.reduce_function = reduce_function
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161 self.reduce_every = reduce_every
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162
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163 self._buffer = []
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164
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165
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166 def append(self, index, element):
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167 """
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168 Parameters
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169 ----------
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170 index : tuple of int
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171 The index used is the one of the last element reduced. E.g. if
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172 you accumulate over the first 1000 minibatches, the index
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173 passed to the base_series.append() function will be 1000.
210
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174 element : float
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175 Element that will be accumulated.
208
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176 """
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177 self._buffer.append(element)
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178
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179 if len(self._buffer) == self.reduce_every:
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180 reduced = self.reduce_function(self._buffer)
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181 self.base_series.append(index, reduced)
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182 self._buffer = []
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183
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184 # This should never happen, except if lists
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185 # were appended, which should be a red flag.
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186 assert len(self._buffer) < self.reduce_every
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187
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188 # Outside of class to fix an issue with exec in Python 2.6.
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189 # My sorries to the God of pretty code.
210
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190 def _BasicStatisticsSeries_construct_table_toexec(index_names):
208
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191 toexec = get_beginning_description_n_ints(index_names)
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192
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193 bpos = len(index_names)
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194 toexec += "\tmean = Float32Col(pos=" + str(bpos) + ")\n"
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195 toexec += "\tmin = Float32Col(pos=" + str(bpos+1) + ")\n"
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196 toexec += "\tmax = Float32Col(pos=" + str(bpos+2) + ")\n"
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197 toexec += "\tstd = Float32Col(pos=" + str(bpos+3) + ")\n"
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198
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199 # This creates "LocalDescription", which we may then use
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200 exec(toexec)
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201
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202 return LocalDescription
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203
210
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204 basic_stats_functions = {'mean': lambda(x): numpy.mean(x),
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205 'min': lambda(x): numpy.min(x),
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206 'max': lambda(x): numpy.max(x),
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207 'std': lambda(x): numpy.std(x)}
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208
208
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209 class BasicStatisticsSeries(Series):
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210 """
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211 Parameters
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212 ----------
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213 series_name : str
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214 Not optional here. Will be prepended with "Basic statistics for "
210
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215 stats_functions : dict, optional
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216 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).
208
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217 """
213
a96fa4de06d2 Renommé mon module de séries
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218 def __init__(self, table_name, hdf5_file, stats_functions=basic_stats_functions, index_names=('epoch',), title="", hdf5_group='/'):
208
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219 Series.__init__(self, table_name, hdf5_file, index_names, title)
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220
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221 self.hdf5_group = hdf5_group
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222
210
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223 self.stats_functions = stats_functions
208
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224
210
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225 self._construct_table()
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226
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227 def _construct_table(self):
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228 table_description = _BasicStatisticsSeries_construct_table_toexec(self.index_names)
208
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229
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230 self._table = self.hdf5_file.createTable(self.hdf5_group, self.table_name, table_description)
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231
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232 def append(self, index, array):
210
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233 """
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234 Parameters
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235 ----------
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236 index : tuple of int
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237 Following index_names passed to __init__, e.g. (12, 15) if index_names were ('epoch', 'minibatch_size')
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238 array
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239 Is of whatever type the stats_functions passed to __init__ can take. Default is anything numpy.mean(), min(), max(), std() can take.
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240 """
208
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241 if len(index) != len(self.index_names):
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242 raise ValueError("index provided does not have the right length (expected " \
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243 + str(len(self.index_names)) + " got " + str(len(index)))
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244
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245 newrow = self._table.row
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246
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247 for col_name, value in zip(self.index_names, index):
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248 newrow[col_name] = value
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249
210
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250 newrow["mean"] = self.stats_functions['mean'](array)
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251 newrow["min"] = self.stats_functions['min'](array)
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252 newrow["max"] = self.stats_functions['max'](array)
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253 newrow["std"] = self.stats_functions['std'](array)
208
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254
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255 newrow.append()
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256
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257 self.hdf5_file.flush()
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258
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259 class SeriesArrayWrapper():
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260 """
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261 Simply redistributes any number of elements to sub-series to respective append()s.
210
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262
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263 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.
208
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264 """
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265
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266 def __init__(self, base_series_list):
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267 self.base_series_list = base_series_list
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268
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269 def append(self, index, elements):
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270 if len(elements) != len(self.base_series_list):
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271 raise ValueError("not enough or too much elements provided (expected " \
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272 + str(len(self.base_series_list)) + " got " + str(len(elements)))
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273
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274 for series, el in zip(self.base_series_list, elements):
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275 series.append(index, el)
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276
210
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277 class SharedParamsStatisticsWrapper(SeriesArrayWrapper):
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278 '''Save mean, min/max, std of shared parameters place in an array.
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279
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280 This is specifically for cases where we have _shared_ parameters,
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281 as we take the .value of each array'''
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282
208
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283 def __init__(self, arrays_names, new_group_name, hdf5_file, base_group='/', index_names=('epoch',), title=""):
210
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284 """
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285 Parameters
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286 ----------
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287 array_names : array of str
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288 Name of each array, in order of the array passed to append(). E.g. ('layer1_b', 'layer1_W', 'layer2_b', 'layer2_W')
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289 new_group_name : str
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290 Name of a new HDF5 group which will be created under base_group to store the new series.
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291 base_group : str
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292 Path of the group under which to create the new group which will store the series.
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293 title : str
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294 Here the title is attached to the new group, not a table.
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295 """
208
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296 base_series_list = []
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297
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298 new_group = hdf5_file.createGroup(base_group, new_group_name, title=title)
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299
210
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300 stats_functions = {'mean': lambda(x): numpy.mean(x.value),
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301 'min': lambda(x): numpy.min(x.value),
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302 '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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303 'std': lambda(x): numpy.std(x.value)}
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304
208
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305 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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306 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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307 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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308 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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309 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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310 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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311 stats_functions=stats_functions,
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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312 hdf5_group=new_group._v_pathname))
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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313
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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314 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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315
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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316