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annotate utils/tables_series/series.py @ 208:acb942530923

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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.
author fsavard
date Fri, 05 Mar 2010 18:07:20 -0500
parents
children dc0d77c8a878
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.
fsavard
parents:
diff changeset
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.
fsavard
parents:
diff changeset
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.
fsavard
parents:
diff changeset
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.
fsavard
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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.
fsavard
parents:
diff changeset
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.
fsavard
parents:
diff changeset
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.
fsavard
parents:
diff changeset
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.
fsavard
parents:
diff changeset
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.
fsavard
parents:
diff changeset
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.
fsavard
parents:
diff changeset
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.
fsavard
parents:
diff changeset
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.
fsavard
parents:
diff changeset
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.
fsavard
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diff changeset
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.
fsavard
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diff changeset
14 def get_beginning_description_n_ints(int_names, int_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.
fsavard
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diff changeset
15 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.
fsavard
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diff changeset
16 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.
fsavard
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diff changeset
17 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.
fsavard
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diff changeset
18
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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19 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.
fsavard
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20
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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21 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.
fsavard
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22
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
parents:
diff changeset
23 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.
fsavard
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diff changeset
24 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.
fsavard
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25
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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26 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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27
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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diff changeset
28 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.
fsavard
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29 """
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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diff changeset
30 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.
fsavard
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diff changeset
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.
fsavard
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diff changeset
32 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.
fsavard
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diff changeset
33 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.
fsavard
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diff changeset
34 "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.
fsavard
parents:
diff changeset
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.
fsavard
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diff changeset
36 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.
fsavard
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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.
fsavard
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38 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.
fsavard
parents:
diff changeset
39 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.
fsavard
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40 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.
fsavard
parents:
diff changeset
41 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.
fsavard
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diff changeset
42 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.
fsavard
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diff changeset
43 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.
fsavard
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diff changeset
44 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
parents:
diff changeset
45 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.
fsavard
parents:
diff changeset
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.
fsavard
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47 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.
fsavard
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48 -------
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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diff changeset
49 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.
fsavard
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50 """
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
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
parents:
diff changeset
52 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.
fsavard
parents:
diff changeset
53
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
parents:
diff changeset
54 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.
fsavard
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diff changeset
55 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.
fsavard
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diff changeset
56 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.
fsavard
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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 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.
fsavard
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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.
fsavard
parents:
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60 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.
fsavard
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61 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.
fsavard
parents:
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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 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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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 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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diff changeset
66
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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67 class Series():
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 def __init__(self, table_name, hdf5_file, index_names=('epoch',), title=None, hdf5_group='/'):
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 """This is used as metadata in the HDF5 file to identify the series"""
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 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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71 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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72 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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73 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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74
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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75 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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76 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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77
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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78 class ErrorSeries(Series):
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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79 def __init__(self, error_name, table_name, hdf5_file, index_names=('epoch',), title=None, hdf5_group='/'):
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 Series.__init__(self, table_name, hdf5_file, index_names, 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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81
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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82 self.error_name = error_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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83
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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84 table_description = self._get_table_description()
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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85
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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86 self._table = hdf5_file.createTable(hdf5_group, self.table_name, table_description, 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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87
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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88 def _get_table_description(self):
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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89 return get_description_with_n_ints_n_floats(self.index_names, (self.error_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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90
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 def append(self, index, error):
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 if len(index) != len(self.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 raise ValueError("index provided does not have the right length (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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94 + str(len(self.index_names)) + " got " + str(len(index)))
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
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96 newrow = self._table.row
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97
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98 for col_name, value in zip(self.index_names, index):
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99 newrow[col_name] = value
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100 newrow[self.error_name] = error
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101
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102 newrow.append()
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103
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104 self.hdf5_file.flush()
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105
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106 # Does not inherit from Series because it does not itself need to
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107 # access the hdf5_file and does not need a series_name (provided
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108 # by the base_series.)
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109 class AccumulatorSeriesWrapper():
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110 """
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111
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112 """
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113 def __init__(self, base_series, reduce_every, reduce_function=numpy.mean):
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114 self.base_series = base_series
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115 self.reduce_function = reduce_function
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116 self.reduce_every = reduce_every
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117
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118 self._buffer = []
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119
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120
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121 def append(self, index, element):
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122 """
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123 Parameters
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124 ----------
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125 index : tuple of int
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126 The index used is the one of the last element reduced. E.g. if
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127 you accumulate over the first 1000 minibatches, the index
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128 passed to the base_series.append() function will be 1000.
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129 """
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130 self._buffer.append(element)
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131
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132 if len(self._buffer) == self.reduce_every:
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133 reduced = self.reduce_function(self._buffer)
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134 self.base_series.append(index, reduced)
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135 self._buffer = []
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136
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137 # This should never happen, except if lists
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138 # were appended, which should be a red flag.
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139 assert len(self._buffer) < self.reduce_every
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140
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141 # Outside of class to fix an issue with exec in Python 2.6.
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142 # My sorries to the God of pretty code.
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143 def BasicStatisticsSeries_construct_table_toexec(index_names):
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144 toexec = get_beginning_description_n_ints(index_names)
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145
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146 bpos = len(index_names)
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147 toexec += "\tmean = Float32Col(pos=" + str(bpos) + ")\n"
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148 toexec += "\tmin = Float32Col(pos=" + str(bpos+1) + ")\n"
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149 toexec += "\tmax = Float32Col(pos=" + str(bpos+2) + ")\n"
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150 toexec += "\tstd = Float32Col(pos=" + str(bpos+3) + ")\n"
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151
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152 # This creates "LocalDescription", which we may then use
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153 exec(toexec)
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154
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155 return LocalDescription
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156
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157 class BasicStatisticsSeries(Series):
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158 """
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159 Parameters
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160 ----------
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161 series_name : str
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162 Not optional here. Will be prepended with "Basic statistics for "
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163 """
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164 def __init__(self, table_name, hdf5_file, index_names=('epoch',), title=None, hdf5_group='/'):
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165 Series.__init__(self, table_name, hdf5_file, index_names, title)
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166
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167 self.hdf5_group = hdf5_group
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168
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169 self.construct_table()
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170
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171 def construct_table(self):
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172 table_description = BasicStatisticsSeries_construct_table_toexec(self.index_names)
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173
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174 self._table = self.hdf5_file.createTable(self.hdf5_group, self.table_name, table_description)
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175
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176 def append(self, index, array):
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177 if len(index) != len(self.index_names):
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178 raise ValueError("index provided does not have the right length (expected " \
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179 + str(len(self.index_names)) + " got " + str(len(index)))
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180
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181 newrow = self._table.row
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182
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183 for col_name, value in zip(self.index_names, index):
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184 newrow[col_name] = value
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185
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186 newrow["mean"] = numpy.mean(array)
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187 newrow["min"] = numpy.min(array)
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188 newrow["max"] = numpy.max(array)
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189 newrow["std"] = numpy.std(array)
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190
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191 newrow.append()
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192
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193 self.hdf5_file.flush()
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194
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195 class SeriesArrayWrapper():
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196 """
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197 Simply redistributes any number of elements to sub-series to respective append()s.
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198 """
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199
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200 def __init__(self, base_series_list):
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201 self.base_series_list = base_series_list
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202
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203 def append(self, index, elements):
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204 if len(elements) != len(self.base_series_list):
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205 raise ValueError("not enough or too much elements provided (expected " \
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206 + str(len(self.base_series_list)) + " got " + str(len(elements)))
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207
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208 for series, el in zip(self.base_series_list, elements):
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209 series.append(index, el)
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210
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211 class ParamsStatisticsWrapper(SeriesArrayWrapper):
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212 def __init__(self, arrays_names, new_group_name, hdf5_file, base_group='/', index_names=('epoch',), title=""):
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213 base_series_list = []
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214
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215 new_group = hdf5_file.createGroup(base_group, new_group_name, title=title)
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216
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217 for name in arrays_names:
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218 base_series_list.append(
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219 BasicStatisticsSeries(
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220 table_name=name,
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221 hdf5_file=hdf5_file,
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222 index_names=('epoch','minibatch'),
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223 hdf5_group=new_group._v_pathname))
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224
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225 SeriesArrayWrapper.__init__(self, base_series_list)
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226
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227