def from_recarray(cls, array, columns=None):
"""Create a new table from a `numpy.recarray`
Parameters
----------
array : `numpy.recarray`
an array of data
column : `list` of `str`, optional
the columns to populate, if not given, all columns present in the
`~numpy.recarray` are mapped
Notes
-----
The columns populated in the `numpy.recarray` must all map exactly to
valid columns of the target `~glue.ligolw.table.Table`.
"""
if columns is None:
columns = list(array.dtype.names)
out = New(cls, columns=columns)
tblname = strip_table_name(out.tableName)
ilwdchar = dict((col, get_ilwdchar_class(tblname, col))
for (col, llwtype) in zip(out.columnnames, out.columntypes)
if llwtype == 'ilwd:char')
for rec in array:
row = out.RowType()
for col, llwtype in zip(out.columnnames, out.columntypes):
if llwtype == 'ilwd:char':
setattr(row, col, ilwdchar[col](rec[col]))
else:
setattr(row, col, rec[col])
out.append(row)
return out
def table_to_ligolw(table, tablename):
"""Convert a `astropy.table.Table` to a :class:`glue.ligolw.table.Table`
"""
from glue.ligolw import (lsctables, types)
from glue.ligolw.ilwd import get_ilwdchar_class
# create new LIGO_LW table
columns = table.columns.keys()
table_class = lsctables.TableByName[tablename]
llwtable = lsctables.New(table_class, columns=columns)
# map rows across
for row in table:
llwrow = llwtable.RowType()
for name in columns:
llwtype = llwtable.validcolumns[name]
if row[name] is None:
val = None
elif llwtype == 'ilwd:char':
val = get_ilwdchar_class(tablename, name)(row[name])
else:
val = types.ToPyType[llwtype](row[name])
setattr(llwrow, name, val)
llwtable.append(llwrow)
return llwtable
def from_recarray(cls, array, columns=None):
"""Create a new table from a `numpy.recarray`
Parameters
----------
array : `numpy.recarray`
an array of data
column : `list` of `str`, optional
the columns to populate, if not given, all columns present in the
`~numpy.recarray` are mapped
Notes
-----
The columns populated in the `numpy.recarray` must all map exactly to
valid columns of the target `~glue.ligolw.table.Table`.
"""
if columns is None:
columns = list(array.dtype.names)
out = New(cls, columns=columns)
tblname = strip_table_name(out.tableName)
ilwdchar = dict((col, get_ilwdchar_class(tblname, col))
for (col, llwtype) in zip(out.columnnames, out.columntypes)
if llwtype == 'ilwd:char')
for rec in array:
row = out.RowType()
for col, llwtype in zip(out.columnnames, out.columntypes):
if llwtype == 'ilwd:char':
setattr(row, col, ilwdchar[col](rec[col]))
else:
setattr(row, col, rec[col])
out.append(row)
return out
def _to_ilwd(value, tablename, colname):
from glue.ligolw.ilwd import (ilwdchar, get_ilwdchar_class)
from glue.ligolw._ilwd import ilwdchar as IlwdChar
if isinstance(value, IlwdChar) and value.column_name != colname:
raise ValueError("ilwdchar '{0!s}' doesn't match column "
"{1!r}".format(value, colname))
if isinstance(value, IlwdChar):
return value
if isinstance(value, int):
return get_ilwdchar_class(tablename, colname)(value)
return ilwdchar(value)
def _to_ilwd(value, tablename, colname):
from glue.ligolw.ilwd import (ilwdchar, get_ilwdchar_class)
from glue.ligolw._ilwd import ilwdchar as IlwdChar
if isinstance(value, IlwdChar) and value.column_name != colname:
raise ValueError("ilwdchar '{0!s}' doesn't match column "
"{1!r}".format(value, colname))
if isinstance(value, IlwdChar):
return value
if isinstance(value, int):
return get_ilwdchar_class(tablename, colname)(value)
return ilwdchar(value)
def test_read_write_ligolw_ilwdchar_compat(self):
from glue.ligolw.ilwd import get_ilwdchar_class
from glue.ligolw.lsctables import SnglBurstTable
eid_type = get_ilwdchar_class("sngl_burst", "event_id")
table = self.create(
100,
["peak", "snr", "central_freq", "event_id"],
["f8", "f4", "f4", "i8"],
)
with tempfile.NamedTemporaryFile(suffix=".xml") as tmp:
# write table with ilwdchar_compat=True
table.write(tmp,
format="ligolw",
tablename="sngl_burst",
ilwdchar_compat=True)
# read raw ligolw and check type is correct
llw = io_ligolw.read_table(tmp,
tablename="sngl_burst",
ilwdchar_compat=True)
assert type(llw.getColumnByName("event_id")[0]) is eid_type
# reset IDs to 0
SnglBurstTable.reset_next_id()
# read without explicit use of ilwdchar_compat
t2 = self.TABLE.read(tmp, columns=table.colnames)
assert type(t2[0]["event_id"]) is eid_type
# read again with explicit use of ilwdchar_compat
SnglBurstTable.reset_next_id()
utils.assert_table_equal(
self.TABLE.read(tmp,
columns=table.colnames,
ilwdchar_compat=True),
t2,
)
# and check that ilwdchar_compat=True, use_numpy_dtypes=True works
SnglBurstTable.reset_next_id()
utils.assert_table_equal(
self.TABLE.read(tmp,
columns=table.colnames,
ilwdchar_compat=True,
use_numpy_dtypes=True),
table,
almost_equal=True,
)
def test_read_write_ligolw_ilwdchar_compat(self):
from glue.ligolw.ilwd import get_ilwdchar_class
from glue.ligolw.lsctables import SnglBurstTable
eid_type = get_ilwdchar_class("sngl_burst", "event_id")
table = self.create(
100,
["peak", "snr", "central_freq", "event_id"],
["f8", "f4", "f4", "i8"],
)
with tempfile.NamedTemporaryFile(suffix=".xml") as tmp:
# write table with ilwdchar_compat=True
table.write(tmp, format="ligolw", tablename="sngl_burst",
ilwdchar_compat=True)
# read raw ligolw and check type is correct
llw = io_ligolw.read_table(tmp, tablename="sngl_burst",
ilwdchar_compat=True)
assert type(llw.getColumnByName("event_id")[0]) is eid_type
# reset IDs to 0
SnglBurstTable.reset_next_id()
# read without explicit use of ilwdchar_compat
t2 = self.TABLE.read(tmp, columns=table.colnames)
assert type(t2[0]["event_id"]) is eid_type
# read again with explicit use of ilwdchar_compat
SnglBurstTable.reset_next_id()
utils.assert_table_equal(
self.TABLE.read(tmp, columns=table.colnames,
ilwdchar_compat=True),
t2,
)
# and check that ilwdchar_compat=True, use_numpy_dtypes=True works
SnglBurstTable.reset_next_id()
utils.assert_table_equal(
self.TABLE.read(tmp, columns=table.colnames,
ilwdchar_compat=True, use_numpy_dtypes=True),
table,
almost_equal=True,
)
for colname in list(colnamemap):
colnamemap[colname], = (
destripped
for destripped in ligo_lw_TableByName[tblname].validcolumns
if ligo_lw_Column.ColumnName(destripped) == colname)
for tblname, colnamemap in ilwdchar_tables.items():
for colname in list(colnamemap):
destripped = destrip_column[tblname][colname]
try:
tblprefix = ligo_lw_Column.ColumnName.table_name(destripped)
except ValueError:
# columns whose names don't have a prefix are in
# their own table
tblprefix = tblname
colnamemap[colname] = ilwd.get_ilwdchar_class(
tblprefix, ligo_lw_Column.ColumnName(colname))
#
# =============================================================================
#
# Main
#
# =============================================================================
#
def do_it_to(xmldoc):
"""
NOTE: this performs an in-place transcription of the contents of
the XML document tree. This should be assumed to be a destructive
operation on the contents of the tree. If you wish to hold
__date__ = git_version.date
## \addtogroup laldetchar_py_idq_idq_tables
# @{
# contains definitions for iDQ xml table classes and objects
#
# =============================================================================
#
# idq_glitch:table
#
# =============================================================================
#
IDQGlitchID = ilwd.get_ilwdchar_class(u"idq_glitch", u"event_id")
class IDQGlitchTable(table.Table):
tableName = 'idq_glitch:table'
validcolumns = {
'event_id': 'ilwd:char',
'ifo': 'lstring',
'gps': 'int_4s',
'gps_ns': 'int_4s',
'rank': 'real_4',
'fap': 'real_4',
'likelihood': 'real_4',
}
constraints = "PRIMARY KEY (event_id)"
# @{
# contains definitions for iDQ xml table classes and objects
#
# =============================================================================
#
# idq_glitch:table
#
# =============================================================================
#
IDQGlitchID = ilwd.get_ilwdchar_class(u"idq_glitch", u"event_id")
class IDQGlitchTable(table.Table):
tableName = 'idq_glitch:table'
validcolumns = {
'event_id': 'ilwd:char',
'ifo': 'lstring',
'gps': 'int_4s',
'gps_ns': 'int_4s',
'rank': 'real_4',
'fap': 'real_4',
'likelihood': 'real_4',
}
constraints = "PRIMARY KEY (event_id)"
next_id = IDQGlitchID(0)