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wrapper around pytables/hd5f to simplify using structured data

Project description

This module removes some of the boiler-plate code required to use the excellent pytables module to save and access structured data.

Example Usage:

>>> from simpletable import SimpleTable
>>> import tables

define a table as a subclass of simple table.

>>> RGB = tables.Enum(list('RGB'))
>>> class ATable(SimpleTable):
...     x = tables.Float32Col()
...     y = tables.Float32Col()
...     name = tables.StringCol(16)
...     color = tables.EnumCol(RGB, 'R', 'uint8')

instantiate with: args: filename, tablename

>>> tbl = ATable('test_docs.h5', 'atable1')

insert as with pytables:

>>> row = tbl.row
>>> for i in range(50):
...    row['x'], row['y'] = i, i * 10
...    row['name'] = "name_%i" % i
...    # NOTE how we have to manually translate the enum column.
...    row['color'] = RGB['G']
...    row.append()
>>> tbl.flush()

can have the enum cols automatically translated using insert

>>> data = {'x': 1000, 'y': 2000, 'color': 'G', 'name': 'flintstone'}
>>> tbl.insert(data, row)
>>> row.append()
>>> tbl.flush()

there is also insert_many() method with takes an iterable of dicts with keys matching the colunns (x, y, name) in this case.

query the data (query() alias of tables’ readWhere() note that pytables sends back the data with enum cols as they were and does nothing to translate them to their original values.

>>> tbl.query('(x > 4) & (y < 70)') #doctest: +NORMALIZE_WHITESPACE
array([(1, 'name_5', 5.0, 50.0), (1, 'name_6', 6.0, 60.0)],
       dtype=[('color', '|u1'), ('name', '|S16'), ('x', '<f4'), ('y', '<f4')])

get translated enumcols in an iterator with the .q method.

>>> r = tbl.q('x == 1000') # doctest: +NORMALIZE_WHITESPACE
>>> r # doctest: +ELLIPSIS
<generator ...>
>>> list(r)
[{'color': 'G', 'x': 1000.0, 'name': 'flintstone', 'y': 2000.0}]

or use the translate_enum method

>>> for row_with_enum in tbl.query('(x > 4) & (y < 70)'):
...     tbl.translate_enum(row_with_enum)
{'color': 'G', 'x': 5.0, 'name': 'name_5', 'y': 50.0}
{'color': 'G', 'x': 6.0, 'name': 'name_6', 'y': 60.0}

Note that using q or translate_enum will affect performance.

Project details


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