Mercurial > ift6266

annotate utils/seriestables/test_series.py @ 642:8b1a0b9fecff

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made publication list shorter.
author Frederic Bastien <nouiz@nouiz.org>
date Mon, 21 Mar 2011 11:29:09 -0400
parents bfe20d63f88c
children
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 import tempfile
220
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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2
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acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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3 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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4 import numpy.random
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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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5
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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6 from jobman import DD
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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7
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8 import tables
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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9
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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10 from series import *
218
4c137f16b013 Modifications pour stocker des timestamps/cpuclock avec chaque rangée créée, selon suggestion de Yoshua ce matin
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11 import series
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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12
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13 #################################################
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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14 # Utils
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acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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15
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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16 def compare_floats(f1,f2):
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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17 if f1-f2 < 1e-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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18 return True
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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19 return False
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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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.
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21 def compare_lists(it1, it2, floats=False):
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 len(it1) != len(it2):
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 return False
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 for el1, el2 in zip(it1, it2):
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 if 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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27 if not compare_floats(el1,el2):
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28 return False
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 elif el1 != el2:
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30 return False
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 True
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
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34 #################################################
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35 # Basic Series class tests
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36
e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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37 def test_Series_types():
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38 pass
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e172ef73cdc5 Ajouté un paquet de type/value checks à SeriesTables, et finalisé les docstrings. Ajouté 3-4 tests. Légers refactorings ici et là sans conséquences externes.
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40 #################################################
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41 # ErrorSeries tests
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42
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acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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43 def test_ErrorSeries_common_case(h5f=None):
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 if not h5f:
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45 h5f_path = tempfile.NamedTemporaryFile().name
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46 h5f = tables.openFile(h5f_path, "w")
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acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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47
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48 validation_error = series.ErrorSeries(error_name="validation_error", table_name="validation_error",
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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49 hdf5_file=h5f, index_names=('epoch','minibatch'),
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 title="Validation error indexed by epoch and minibatch")
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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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.
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52 # (1,1), (1,2) etc. are (epoch, minibatch) 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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53 validation_error.append((1,1), 32.0)
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54 validation_error.append((1,2), 30.0)
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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55 validation_error.append((2,1), 28.0)
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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56 validation_error.append((2,2), 26.0)
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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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 h5f.close()
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59
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60 h5f = tables.openFile(h5f_path, "r")
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61
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 table = h5f.getNode('/', 'validation_error')
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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 assert compare_lists(table.cols.epoch[:], [1,1,2,2])
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 assert compare_lists(table.cols.minibatch[:], [1,2,1,2])
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66 assert compare_lists(table.cols.validation_error[:], [32.0, 30.0, 28.0, 26.0])
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67
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68 def test_ErrorSeries_no_index(h5f=None):
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69 if not h5f:
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70 h5f_path = tempfile.NamedTemporaryFile().name
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71 h5f = tables.openFile(h5f_path, "w")
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72
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73 validation_error = series.ErrorSeries(error_name="validation_error",
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74 table_name="validation_error",
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75 hdf5_file=h5f,
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76 # empty tuple
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77 index_names=tuple(),
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78 title="Validation error with no index")
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79
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80 # (1,1), (1,2) etc. are (epoch, minibatch) index
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81 validation_error.append(tuple(), 32.0)
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82 validation_error.append(tuple(), 30.0)
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83 validation_error.append(tuple(), 28.0)
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84 validation_error.append(tuple(), 26.0)
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85
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86 h5f.close()
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87
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88 h5f = tables.openFile(h5f_path, "r")
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89
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90 table = h5f.getNode('/', 'validation_error')
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91
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92 assert compare_lists(table.cols.validation_error[:], [32.0, 30.0, 28.0, 26.0])
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93 assert not ("epoch" in dir(table.cols))
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94
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95 def test_ErrorSeries_notimestamp(h5f=None):
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96 if not h5f:
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97 h5f_path = tempfile.NamedTemporaryFile().name
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98 h5f = tables.openFile(h5f_path, "w")
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99
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100 validation_error = series.ErrorSeries(error_name="validation_error", table_name="validation_error",
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101 hdf5_file=h5f, index_names=('epoch','minibatch'),
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102 title="Validation error indexed by epoch and minibatch",
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103 store_timestamp=False)
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104
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105 # (1,1), (1,2) etc. are (epoch, minibatch) index
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106 validation_error.append((1,1), 32.0)
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107
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108 h5f.close()
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109
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110 h5f = tables.openFile(h5f_path, "r")
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111
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112 table = h5f.getNode('/', 'validation_error')
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113
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114 assert compare_lists(table.cols.epoch[:], [1])
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115 assert not ("timestamp" in dir(table.cols))
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116 assert "cpuclock" in dir(table.cols)
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117
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118 def test_ErrorSeries_nocpuclock(h5f=None):
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119 if not h5f:
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120 h5f_path = tempfile.NamedTemporaryFile().name
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121 h5f = tables.openFile(h5f_path, "w")
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122
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123 validation_error = series.ErrorSeries(error_name="validation_error", table_name="validation_error",
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124 hdf5_file=h5f, index_names=('epoch','minibatch'),
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125 title="Validation error indexed by epoch and minibatch",
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126 store_cpuclock=False)
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127
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128 # (1,1), (1,2) etc. are (epoch, minibatch) index
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129 validation_error.append((1,1), 32.0)
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130
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131 h5f.close()
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132
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133 h5f = tables.openFile(h5f_path, "r")
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134
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135 table = h5f.getNode('/', 'validation_error')
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136
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137 assert compare_lists(table.cols.epoch[:], [1])
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138 assert not ("cpuclock" in dir(table.cols))
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139 assert "timestamp" in dir(table.cols)
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140
208
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141 def test_AccumulatorSeriesWrapper_common_case(h5f=None):
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142 if not h5f:
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143 h5f_path = tempfile.NamedTemporaryFile().name
220
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144 h5f = tables.openFile(h5f_path, "w")
208
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145
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146 validation_error = ErrorSeries(error_name="accumulated_validation_error",
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147 table_name="accumulated_validation_error",
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148 hdf5_file=h5f,
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149 index_names=('epoch','minibatch'),
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150 title="Validation error, summed every 3 minibatches, indexed by epoch and minibatch")
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151
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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152 accumulator = AccumulatorSeriesWrapper(base_series=validation_error,
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153 reduce_every=3, reduce_function=numpy.sum)
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154
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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155 # (1,1), (1,2) etc. are (epoch, minibatch) 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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156 accumulator.append((1,1), 32.0)
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157 accumulator.append((1,2), 30.0)
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158 accumulator.append((2,1), 28.0)
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159 accumulator.append((2,2), 26.0)
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160 accumulator.append((3,1), 24.0)
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161 accumulator.append((3,2), 22.0)
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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162
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163 h5f.close()
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164
220
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165 h5f = tables.openFile(h5f_path, "r")
208
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166
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167 table = h5f.getNode('/', 'accumulated_validation_error')
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168
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169 assert compare_lists(table.cols.epoch[:], [2,3])
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170 assert compare_lists(table.cols.minibatch[:], [1,2])
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171 assert compare_lists(table.cols.accumulated_validation_error[:], [90.0,72.0], floats=True)
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172
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173 def test_BasicStatisticsSeries_common_case(h5f=None):
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174 if not h5f:
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175 h5f_path = tempfile.NamedTemporaryFile().name
220
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176 h5f = tables.openFile(h5f_path, "w")
208
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177
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178 stats_series = BasicStatisticsSeries(table_name="b_vector_statistics",
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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179 hdf5_file=h5f, index_names=('epoch','minibatch'),
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180 title="Basic statistics for b vector indexed by epoch and minibatch")
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181
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182 # (1,1), (1,2) etc. are (epoch, minibatch) index
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183 stats_series.append((1,1), [0.15, 0.20, 0.30])
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184 stats_series.append((1,2), [-0.18, 0.30, 0.58])
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185 stats_series.append((2,1), [0.18, -0.38, -0.68])
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186 stats_series.append((2,2), [0.15, 0.02, 1.9])
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187
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188 h5f.close()
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189
220
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190 h5f = tables.openFile(h5f_path, "r")
208
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191
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192 table = h5f.getNode('/', 'b_vector_statistics')
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193
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194 assert compare_lists(table.cols.epoch[:], [1,1,2,2])
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195 assert compare_lists(table.cols.minibatch[:], [1,2,1,2])
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196 assert compare_lists(table.cols.mean[:], [0.21666667, 0.23333333, -0.29333332, 0.69], floats=True)
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197 assert compare_lists(table.cols.min[:], [0.15000001, -0.18000001, -0.68000001, 0.02], floats=True)
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198 assert compare_lists(table.cols.max[:], [0.30, 0.58, 0.18, 1.9], floats=True)
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199 assert compare_lists(table.cols.std[:], [0.06236095, 0.31382939, 0.35640177, 0.85724366], floats=True)
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200
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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201 def test_SharedParamsStatisticsWrapper_commoncase(h5f=None):
208
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202 import numpy.random
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203
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204 if not h5f:
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205 h5f_path = tempfile.NamedTemporaryFile().name
220
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206 h5f = tables.openFile(h5f_path, "w")
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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207
210
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
208 stats = SharedParamsStatisticsWrapper(new_group_name="params", base_group="/",
208
acb942530923 Completely rewrote my series module, now based on HDF5 and PyTables (in a separate directory called 'tables_series' for retrocompatibility of running code). Minor (inconsequential) changes to stacked_dae.
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209 arrays_names=('b1','b2','b3'), hdf5_file=h5f,
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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210 index_names=('epoch','minibatch'))
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211
210
dc0d77c8a878 Commented table_series code, changed ParamsStatisticsArray to take shared params instead, create DummySeries to use when we don't want to save a named series
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diff changeset
212 b1 = DD({'value':numpy.random.rand(5)})
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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213 b2 = DD({'value':numpy.random.rand(5)})
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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214 b3 = DD({'value':numpy.random.rand(5)})
208
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215 stats.append((1,1), [b1,b2,b3])
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216
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217 h5f.close()
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218
220
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219 h5f = tables.openFile(h5f_path, "r")
208
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220
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221 b1_table = h5f.getNode('/params', 'b1')
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222 b3_table = h5f.getNode('/params', 'b3')
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223
210
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224 assert b1_table.cols.mean[0] - numpy.mean(b1.value) < 1e-3
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225 assert b3_table.cols.mean[0] - numpy.mean(b3.value) < 1e-3
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226 assert b1_table.cols.min[0] - numpy.min(b1.value) < 1e-3
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227 assert b3_table.cols.min[0] - numpy.min(b3.value) < 1e-3
208
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228
224
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229 def test_SharedParamsStatisticsWrapper_notimestamp(h5f=None):
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230 import numpy.random
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231
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232 if not h5f:
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233 h5f_path = tempfile.NamedTemporaryFile().name
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234 h5f = tables.openFile(h5f_path, "w")
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235
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236 stats = SharedParamsStatisticsWrapper(new_group_name="params", base_group="/",
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237 arrays_names=('b1','b2','b3'), hdf5_file=h5f,
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238 index_names=('epoch','minibatch'),
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239 store_timestamp=False)
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240
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241 b1 = DD({'value':numpy.random.rand(5)})
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242 b2 = DD({'value':numpy.random.rand(5)})
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243 b3 = DD({'value':numpy.random.rand(5)})
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244 stats.append((1,1), [b1,b2,b3])
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245
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246 h5f.close()
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247
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248 h5f = tables.openFile(h5f_path, "r")
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249
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250 b1_table = h5f.getNode('/params', 'b1')
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251 b3_table = h5f.getNode('/params', 'b3')
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252
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253 assert b1_table.cols.mean[0] - numpy.mean(b1.value) < 1e-3
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254 assert b3_table.cols.mean[0] - numpy.mean(b3.value) < 1e-3
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255 assert b1_table.cols.min[0] - numpy.min(b1.value) < 1e-3
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256 assert b3_table.cols.min[0] - numpy.min(b3.value) < 1e-3
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257
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258 assert not ('timestamp' in dir(b1_table.cols))
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259
208
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260 def test_get_desc():
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261 h5f_path = tempfile.NamedTemporaryFile().name
220
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262 h5f = tables.openFile(h5f_path, "w")
208
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263
218
4c137f16b013 Modifications pour stocker des timestamps/cpuclock avec chaque rangée créée, selon suggestion de Yoshua ce matin
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264 desc = series._get_description_with_n_ints_n_floats(("col1","col2"), ("col3","col4"))
208
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265
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266 mytable = h5f.createTable('/', 'mytable', desc)
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267
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268 # just make sure the columns are there... otherwise this will throw an exception
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269 mytable.cols.col1
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270 mytable.cols.col2
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271 mytable.cols.col3
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272 mytable.cols.col4
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273
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274 try:
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275 # this should fail... LocalDescription must be local to get_desc_etc
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276 test = LocalDescription
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277 assert False
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278 except:
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279 assert True
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280
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281 assert True
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282
220
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283 def test_index_to_tuple_floaterror():
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284 try:
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285 series._index_to_tuple(5.1)
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286 assert False
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287 except TypeError:
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288 assert True
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289
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290 def test_index_to_tuple_arrayok():
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291 tpl = series._index_to_tuple([1,2,3])
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292 assert type(tpl) == tuple and tpl[1] == 2 and tpl[2] == 3
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293
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294 def test_index_to_tuple_intbecomestuple():
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295 tpl = series._index_to_tuple(32)
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296
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297 assert type(tpl) == tuple and tpl == (32,)
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298
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299 def test_index_to_tuple_longbecomestuple():
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300 tpl = series._index_to_tuple(928374928374928L)
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301
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302 assert type(tpl) == tuple and tpl == (928374928374928L,)
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303
208
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304 if __name__ == '__main__':
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305 import tempfile
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306 test_get_desc()
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307 test_ErrorSeries_common_case()
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308 test_BasicStatisticsSeries_common_case()
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309 test_AccumulatorSeriesWrapper_common_case()
210
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310 test_SharedParamsStatisticsWrapper_commoncase()
208
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311