def test_read_write_gwf(self):
table = self.create(100, ['time', 'blah', 'frequency'])
columns = table.dtype.names
tempdir = tempfile.mkdtemp()
try:
fp = tempfile.mktemp(suffix='.gwf', dir=tempdir)
# check write
table.write(fp, 'test_read_write_gwf')
# check read gives back same table
t2 = self.TABLE.read(fp, 'test_read_write_gwf', columns=columns)
utils.assert_table_equal(table, t2, meta=False, almost_equal=True)
# check selections works
t3 = self.TABLE.read(fp, 'test_read_write_gwf',
columns=columns, selection='frequency>500')
utils.assert_table_equal(
filter_table(t2, 'frequency>500'), t3)
except ImportError as e:
pytest.skip(str(e))
finally:
if os.path.isdir(tempdir):
shutil.rmtree(tempdir)
def test_fetch_hacr(self):
table = self.create(100, names=HACR_COLUMNS)
try:
from pymysql import connect
except ImportError:
mockee = 'gwpy.table.io.hacr.connect'
else:
mockee = 'pymysql.connect'
with mock.patch(mockee) as mock_connect:
mock_connect.return_value = mock_hacr_connection(table, 123, 456)
# test simple query returns the full table
t2 = self.TABLE.fetch('hacr', 'X1:TEST-CHANNEL', 123, 456)
utils.assert_table_equal(table, t2)
# test column selection works
t2 = self.TABLE.fetch('hacr',
'X1:TEST-CHANNEL',
123,
456,
columns=['gps_start', 'snr'])
utils.assert_table_equal(table['gps_start', 'snr'], t2)
# test column selection works
t2 = self.TABLE.fetch('hacr',
'X1:TEST-CHANNEL',
123,
456,
columns=['gps_start', 'snr'],
selection='freq_central>500')
utils.assert_table_equal(
filter_table(table, 'freq_central>500')['gps_start', 'snr'],
t2)
def test_read_write_gwf(self):
table = self.create(100, ['time', 'blah', 'frequency'])
columns = table.dtype.names
tempdir = tempfile.mkdtemp()
try:
fp = tempfile.mktemp(suffix='.gwf', dir=tempdir)
# check write
table.write(fp, 'test_read_write_gwf')
# check read gives back same table
t2 = self.TABLE.read(fp, 'test_read_write_gwf', columns=columns)
utils.assert_table_equal(table, t2, meta=False, almost_equal=True)
# check selections works
t3 = self.TABLE.read(fp,
'test_read_write_gwf',
columns=columns,
selection='frequency>500')
utils.assert_table_equal(filter_table(t2, 'frequency>500'), t3)
except ImportError as e:
pytest.skip(str(e))
finally:
if os.path.isdir(tempdir):
shutil.rmtree(tempdir)
def test_fetch_hacr(self):
table = self.create(100, names=HACR_COLUMNS)
try:
from pymysql import connect
except ImportError:
mockee = 'gwpy.table.io.hacr.connect'
else:
mockee = 'pymysql.connect'
with mock.patch(mockee) as mock_connect:
mock_connect.return_value = mock_hacr_connection(
table, 123, 456)
# test simple query returns the full table
t2 = self.TABLE.fetch('hacr', 'X1:TEST-CHANNEL', 123, 456)
utils.assert_table_equal(table, t2)
# test column selection works
t2 = self.TABLE.fetch('hacr', 'X1:TEST-CHANNEL', 123, 456,
columns=['gps_start', 'snr'])
utils.assert_table_equal(table['gps_start', 'snr'], t2)
# test column selection works
t2 = self.TABLE.fetch('hacr', 'X1:TEST-CHANNEL', 123, 456,
columns=['gps_start', 'snr'],
selection='freq_central>500')
utils.assert_table_equal(
filter_table(table, 'freq_central>500')['gps_start', 'snr'],
t2)
def test_read_write_root(self, table):
tempdir = tempfile.mkdtemp()
try:
fp = tempfile.mktemp(suffix='.root', dir=tempdir)
# check write
table.write(fp)
def _read(*args, **kwargs):
return type(table).read(fp, *args, **kwargs)
# check read gives back same table
utils.assert_table_equal(table, _read())
# check that reading table from file with multiple trees without
# specifying fails
table.write(fp, treename='test')
with pytest.raises(ValueError) as exc:
_read()
assert str(exc.value).startswith('Multiple trees found')
# test selections work
t2 = _read(treename='test', selection='frequency > 500')
utils.assert_table_equal(
t2, filter_table(table, 'frequency > 500'))
finally:
if os.path.isdir(tempdir):
shutil.rmtree(tempdir)
def fetchall():
if cursor._query.get_real_name() == 'job':
return [(1, start, stop)]
if cursor._query.get_real_name() == 'mhacr':
columns = list(map(
str, list(cursor._query.get_sublists())[0].get_identifiers()))
selections = list(map(
str, list(cursor._query.get_sublists())[2].get_sublists()))
return filter_table(table, selections[3:])[columns]
def fetchall():
if cursor._query.get_real_name() == 'job':
return [(1, start, stop)]
if cursor._query.get_real_name() == 'mhacr':
columns = list(map(
str, list(cursor._query.get_sublists())[0].get_identifiers()))
selections = list(map(
str, list(cursor._query.get_sublists())[2].get_sublists()))
return filter_table(table, selections[3:])[columns]
def test_read_pycbc_live(self):
import h5py
table = self.create(
100, names=['a', 'b', 'c', 'chisq', 'd', 'e', 'f',
'mass1', 'mass2', 'snr'])
table.meta['ifo'] = 'X1'
fp = os.path.join(tempfile.mkdtemp(), 'X1-Live-0-0.hdf')
try:
# write table in pycbc_live format (by hand)
with h5py.File(fp, 'w') as h5f:
group = h5f.create_group('X1')
for col in table.columns:
group.create_dataset(data=table[col], name=col)
# check that we can read
t2 = self.TABLE.read(fp)
utils.assert_table_equal(table, t2)
# check keyword arguments result in same table
t2 = self.TABLE.read(fp, format='hdf5.pycbc_live')
utils.assert_table_equal(table, t2)
t2 = self.TABLE.read(fp, format='hdf5.pycbc_live', ifo='X1')
utils.assert_table_equal(table, t2)
# add another IFO, then assert that reading the table without
# specifying the IFO fails
with h5py.File(fp) as h5f:
h5f.create_group('Z1')
with pytest.raises(ValueError) as exc:
self.TABLE.read(fp)
assert str(exc.value).startswith(
'PyCBC live HDF5 file contains dataset groups')
# but check that we can still read the original
t2 = self.TABLE.read(fp, format='hdf5.pycbc_live', ifo='X1')
utils.assert_table_equal(table, t2)
# assert processed colums works
t2 = self.TABLE.read(fp, ifo='X1', columns=['mchirp', 'new_snr'])
mchirp = (table['mass1'] * table['mass2']) ** (3/5.) / (
table['mass1'] + table['mass2']) ** (1/5.)
utils.assert_array_equal(t2['mchirp'], mchirp)
# test with selection
t2 = self.TABLE.read(fp, format='hdf5.pycbc_live',
ifo='X1', selection='snr>.5')
utils.assert_table_equal(filter_table(table, 'snr>.5'), t2)
finally:
if os.path.isdir(os.path.dirname(fp)):
shutil.rmtree(os.path.dirname(fp))
def test_read_write_root(self, table):
tempdir = tempfile.mkdtemp()
try:
fp = tempfile.mktemp(suffix='.root', dir=tempdir)
# check write
table.write(fp)
def _read(*args, **kwargs):
return type(table).read(fp, *args, **kwargs)
# check read gives back same table
utils.assert_table_equal(table, _read())
# check that reading table from file with multiple trees without
# specifying fails
table.write(fp, treename='test')
with pytest.raises(ValueError) as exc:
_read()
assert str(exc.value).startswith('Multiple trees found')
# test selections work
segs = SegmentList([Segment(100, 200), Segment(400, 500)])
t2 = _read(treename='test',
selection=['200 < frequency < 500',
('time', filters.in_segmentlist, segs)])
utils.assert_table_equal(
t2, filter_table(table,
'frequency > 200',
'frequency < 500',
('time', filters.in_segmentlist, segs)),
)
finally:
if os.path.isdir(tempdir):
shutil.rmtree(tempdir)
def test_read_pycbc_live(self):
import h5py
table = self.create(100,
names=[
'a', 'b', 'c', 'chisq', 'd', 'e', 'f', 'mass1',
'mass2', 'snr'
])
loudest = (table['snr'] > 500).nonzero()[0]
psd = FrequencySeries(random.randn(1000), df=1)
fp = os.path.join(tempfile.mkdtemp(), 'X1-Live-0-0.hdf')
try:
# write table in pycbc_live format (by hand)
with h5py.File(fp, 'w') as h5f:
group = h5f.create_group('X1')
for col in table.columns:
group.create_dataset(data=table[col], name=col)
group.create_dataset('loudest', data=loudest)
group.create_dataset('psd', data=psd.value)
group['psd'].attrs['delta_f'] = psd.df.to('Hz').value
# check that we can read
t2 = self.TABLE.read(fp)
utils.assert_table_equal(table, t2)
# and check metadata was recorded correctly
assert t2.meta['ifo'] == 'X1'
# check keyword arguments result in same table
t2 = self.TABLE.read(fp, format='hdf5.pycbc_live')
utils.assert_table_equal(table, t2)
t2 = self.TABLE.read(fp, format='hdf5.pycbc_live', ifo='X1')
# assert loudest works
t2 = self.TABLE.read(fp, loudest=True)
utils.assert_table_equal(table.filter('snr > 500'), t2)
# check extended_metadata=True works (default)
t2 = self.TABLE.read(fp, extended_metadata=True)
utils.assert_table_equal(table, t2)
utils.assert_array_equal(t2.meta['loudest'], loudest)
utils.assert_quantity_sub_equal(
t2.meta['psd'],
psd,
exclude=['name', 'channel', 'unit', 'epoch'])
# check extended_metadata=False works
t2 = self.TABLE.read(fp, extended_metadata=False)
assert t2.meta == {'ifo': 'X1'}
# double-check that loudest and extended_metadata=False work
t2 = self.TABLE.read(fp, loudest=True, extended_metadata=False)
utils.assert_table_equal(table.filter('snr > 500'), t2)
assert t2.meta == {'ifo': 'X1'}
# add another IFO, then assert that reading the table without
# specifying the IFO fails
with h5py.File(fp) as h5f:
h5f.create_group('Z1')
with pytest.raises(ValueError) as exc:
self.TABLE.read(fp)
assert str(exc.value).startswith(
'PyCBC live HDF5 file contains dataset groups')
# but check that we can still read the original
t2 = self.TABLE.read(fp, format='hdf5.pycbc_live', ifo='X1')
utils.assert_table_equal(table, t2)
# assert processed colums works
t2 = self.TABLE.read(fp, ifo='X1', columns=['mchirp', 'new_snr'])
mchirp = (table['mass1'] * table['mass2'])**(3 / 5.) / (
table['mass1'] + table['mass2'])**(1 / 5.)
utils.assert_array_equal(t2['mchirp'], mchirp)
# test with selection
t2 = self.TABLE.read(fp,
format='hdf5.pycbc_live',
ifo='X1',
selection='snr>.5')
utils.assert_table_equal(filter_table(table, 'snr>.5'), t2)
finally:
if os.path.isdir(os.path.dirname(fp)):
shutil.rmtree(os.path.dirname(fp))
def test_read_pycbc_live(self):
import h5py
table = self.create(
100, names=['a', 'b', 'c', 'chisq', 'd', 'e', 'f',
'mass1', 'mass2', 'snr'])
loudest = (table['snr'] > 500).nonzero()[0]
psd = FrequencySeries(random.randn(1000), df=1)
fp = os.path.join(tempfile.mkdtemp(), 'X1-Live-0-0.hdf')
try:
# write table in pycbc_live format (by hand)
with h5py.File(fp, 'w') as h5f:
group = h5f.create_group('X1')
for col in table.columns:
group.create_dataset(data=table[col], name=col)
group.create_dataset('loudest', data=loudest)
group.create_dataset('psd', data=psd.value)
group['psd'].attrs['delta_f'] = psd.df.to('Hz').value
# check that we can read
t2 = self.TABLE.read(fp)
utils.assert_table_equal(table, t2)
# and check metadata was recorded correctly
assert t2.meta['ifo'] == 'X1'
# check keyword arguments result in same table
t2 = self.TABLE.read(fp, format='hdf5.pycbc_live')
utils.assert_table_equal(table, t2)
t2 = self.TABLE.read(fp, format='hdf5.pycbc_live', ifo='X1')
# assert loudest works
t2 = self.TABLE.read(fp, loudest=True)
utils.assert_table_equal(table.filter('snr > 500'), t2)
# check extended_metadata=True works (default)
t2 = self.TABLE.read(fp, extended_metadata=True)
utils.assert_table_equal(table, t2)
utils.assert_array_equal(t2.meta['loudest'], loudest)
utils.assert_quantity_sub_equal(
t2.meta['psd'], psd,
exclude=['name', 'channel', 'unit', 'epoch'])
# check extended_metadata=False works
t2 = self.TABLE.read(fp, extended_metadata=False)
assert t2.meta == {'ifo': 'X1'}
# double-check that loudest and extended_metadata=False work
t2 = self.TABLE.read(fp, loudest=True, extended_metadata=False)
utils.assert_table_equal(table.filter('snr > 500'), t2)
assert t2.meta == {'ifo': 'X1'}
# add another IFO, then assert that reading the table without
# specifying the IFO fails
with h5py.File(fp) as h5f:
h5f.create_group('Z1')
with pytest.raises(ValueError) as exc:
self.TABLE.read(fp)
assert str(exc.value).startswith(
'PyCBC live HDF5 file contains dataset groups')
# but check that we can still read the original
t2 = self.TABLE.read(fp, format='hdf5.pycbc_live', ifo='X1')
utils.assert_table_equal(table, t2)
# assert processed colums works
t2 = self.TABLE.read(fp, ifo='X1', columns=['mchirp', 'new_snr'])
mchirp = (table['mass1'] * table['mass2']) ** (3/5.) / (
table['mass1'] + table['mass2']) ** (1/5.)
utils.assert_array_equal(t2['mchirp'], mchirp)
# test with selection
t2 = self.TABLE.read(fp, format='hdf5.pycbc_live',
ifo='X1', selection='snr>.5')
utils.assert_table_equal(filter_table(table, 'snr>.5'), t2)
finally:
if os.path.isdir(os.path.dirname(fp)):
shutil.rmtree(os.path.dirname(fp))