def test_tohdf5():
# set up a new hdf5 table to work with
h5file = openFile("test2.h5", mode="w", title="Test file")
h5file.createGroup('/', 'testgroup', 'Test Group')
class FooBar(IsDescription):
foo = Int32Col(pos=0)
bar = StringCol(6, pos=2)
h5file.createTable('/testgroup', 'testtable', FooBar, 'Test Table')
h5file.flush()
h5file.close()
# load some data via tohdf5
table1 = (('foo', 'bar'),
(1, 'asdfgh'),
(2, 'qwerty'),
(3, 'zxcvbn'))
tohdf5(table1, 'test2.h5', '/testgroup', 'testtable')
ieq(table1, fromhdf5('test2.h5', '/testgroup', 'testtable'))
tohdf5(table1, 'test2.h5', '/testgroup/testtable')
ieq(table1, fromhdf5('test2.h5', '/testgroup/testtable'))
h5file = openFile("test2.h5", mode="a")
tohdf5(table1, h5file, '/testgroup/testtable')
ieq(table1, fromhdf5(h5file, '/testgroup/testtable'))
h5table = h5file.getNode('/testgroup/testtable')
tohdf5(table1, h5table)
ieq(table1, fromhdf5(h5table))
# clean up
h5file.close()
def test_fromhdf5():
# set up a new hdf5 table to work with
h5file = openFile("test1.h5", mode="w", title="Test file")
h5file.createGroup('/', 'testgroup', 'Test Group')
class FooBar(IsDescription):
foo = Int32Col(pos=0)
bar = StringCol(6, pos=2)
h5table = h5file.createTable('/testgroup', 'testtable', FooBar, 'Test Table')
# load some data into the table
table1 = (('foo', 'bar'),
(1, 'asdfgh'),
(2, 'qwerty'),
(3, 'zxcvbn'))
for row in table1[1:]:
for i, f in enumerate(table1[0]):
h5table.row[f] = row[i]
h5table.row.append()
h5file.flush()
h5file.close()
# verify we can get the data back out
table2a = fromhdf5('test1.h5', '/testgroup', 'testtable')
ieq(table1, table2a)
ieq(table1, table2a)
# verify we can get the data back out
table2b = fromhdf5('test1.h5', '/testgroup/testtable')
ieq(table1, table2b)
ieq(table1, table2b)
# verify using an existing tables.File object
h5file = openFile('test1.h5')
table3 = fromhdf5(h5file, '/testgroup/testtable')
ieq(table1, table3)
# verify using an existing tables.Table object
h5tbl = h5file.getNode('/testgroup/testtable')
table4 = fromhdf5(h5tbl)
ieq(table1, table4)
# verify using a condition to filter data
table5 = fromhdf5(h5tbl, condition="(foo < 3)")
ieq(table1[:3], table5)
# clean up
h5file.close()
def test_tohdf5_create():
class FooBar(IsDescription):
foo = Int32Col(pos=0)
bar = StringCol(6, pos=2)
table1 = (('foo', 'bar'),
(1, 'asdfgh'),
(2, 'qwerty'),
(3, 'zxcvbn'))
# test creation with defined datatype
tohdf5(table1, 'test3.h5', '/testgroup', 'testtable', create=True,
description=FooBar, createparents=True)
ieq(table1, fromhdf5('test3.h5', '/testgroup', 'testtable'))
# test dynamically determined datatype
tohdf5(table1, 'test3.h5', '/testgroup', 'testtable2', create=True,
createparents=True)
ieq(table1, fromhdf5('test3.h5', '/testgroup', 'testtable2'))
def test_appendhdf5():
# set up a new hdf5 table to work with
h5file = openFile("test4.h5", mode="w", title="Test file")
h5file.createGroup('/', 'testgroup', 'Test Group')
class FooBar(IsDescription):
foo = Int32Col(pos=0)
bar = StringCol(6, pos=2)
h5file.createTable('/testgroup', 'testtable', FooBar, 'Test Table')
h5file.flush()
h5file.close()
# load some initial data via tohdf5()
table1 = (('foo', 'bar'),
(1, 'asdfgh'),
(2, 'qwerty'),
(3, 'zxcvbn'))
tohdf5(table1, 'test4.h5', '/testgroup', 'testtable')
ieq(table1, fromhdf5('test4.h5', '/testgroup', 'testtable'))
# append some more data
appendhdf5(table1, 'test4.h5', '/testgroup', 'testtable')
ieq(chain(table1, table1[1:]), fromhdf5('test4.h5', '/testgroup', 'testtable'))
table1 = (('foo', 'bar'),
(1, 'asdfgh'),
(2, 'qwerty'),
(3, 'zxcvbn'))
for row in table1[1:]:
for i, f in enumerate(table1[0]):
h5table.row[f] = row[i]
h5table.row.append()
h5file.flush()
h5file.close()
from petl import look
from petlx.hdf5 import fromhdf5
table1 = fromhdf5('test1.h5', '/testgroup', 'testtable')
look(table1)
# just specify path to table node
table1 = fromhdf5('test1.h5', '/testgroup/testtable')
# use an existing tables.File object
import tables
h5file = tables.openFile('test1.h5')
table1 = fromhdf5(h5file, '/testgroup/testtable')
# use an existing tables.Table object
h5tbl = h5file.getNode('/testgroup/testtable')
table1 = fromhdf5(h5tbl)
# use a condition to filter data
h5table = h5file.createTable('/testgroup', 'testtable', FooBar, 'Test Table')
# load some data into the table
table1 = (('foo', 'bar'), (1, 'asdfgh'), (2, 'qwerty'), (3, 'zxcvbn'))
for row in table1[1:]:
for i, f in enumerate(table1[0]):
h5table.row[f] = row[i]
h5table.row.append()
h5file.flush()
h5file.close()
from petl import look
from petlx.hdf5 import fromhdf5
table1 = fromhdf5('test1.h5', '/testgroup', 'testtable')
look(table1)
# just specify path to table node
table1 = fromhdf5('test1.h5', '/testgroup/testtable')
# use an existing tables.File object
import tables
h5file = tables.openFile('test1.h5')
table1 = fromhdf5(h5file, '/testgroup/testtable')
# use an existing tables.Table object
h5tbl = h5file.getNode('/testgroup/testtable')
table1 = fromhdf5(h5tbl)
# use a condition to filter data