def read_ms(infile, verbosity=1):
""" Convert MS to a HDF file
:param infile: Measurement Set path
:return: HDU version of Measurement Set
"""
pp = PrintLog(verbosity=verbosity)
ms = pt.table(infile)
# Create a HDU List for storing HDUs
hdul = IdiHdulist(verbosity=verbosity)
# Add each column to the main HDU
hdu_main = table2hdu(ms, "MAIN", verbosity=verbosity, close_after=False)
hdul["MAIN"] = hdu_main
# Now look for other keyword tables
for key, val in ms.getkeywords().items():
pp.debug(val)
if type(val) in (unicode, str):
if val.startswith("Table: "):
tblpath = val.strip().split("Table: ")[1]
pp.h2("Opening %s" % key)
t = pt.table(tblpath)
t_hdu = table2hdu(t, key, verbosity=verbosity)
hdul[key] = t_hdu
else:
hdul["MAIN"].header.vals[key] = val
ms.close()
return hdul
def table2hdu(table, hd, verbosity=1, close_after=True):
""" Convert MS table to a Header-Data unit
:param table: name of table (MS path)
:param hdu: header data unit, either a string or a HDU
:return: HDU version of MS table
"""
pp = PrintLog(verbosity=verbosity)
if isinstance(hd, str):
pp.h3("Creating %s HDU" % hd)
hd = IdiTableHdu(name=hd)
colnames = table.colnames()
keywords = table.getkeywords()
for colname in colnames:
try:
pp.debug("Reading col %s" % colname)
hd.add_column(table.getcol(colname), name=colname)
except RuntimeError:
# This can be raised when no data is in the column
pp.warn("Could not add %s" % colname)
for key, val in keywords.items():
hd.header.vals[key] = val
if close_after:
table.close()
return hd
def read_ms(infile, verbosity=1):
""" Convert MS to a HDF file
:param infile: Measurement Set path
:return: HDU version of Measurement Set
"""
pp = PrintLog(verbosity=verbosity)
ms = pt.table(infile)
# Create a HDU List for storing HDUs
hdul = IdiHdulist(verbosity=verbosity)
# Add each column to the main HDU
hdu_main = table2hdu(ms, "MAIN", verbosity=verbosity, close_after=False)
hdul["MAIN"] = hdu_main
# Now look for other keyword tables
for key, val in ms.getkeywords().items():
pp.debug(val)
if type(val) in (unicode, str):
if val.startswith("Table: "):
tblpath = val.strip().split("Table: ")[1]
pp.h2("Opening %s" % key)
t = pt.table(tblpath)
t_hdu = table2hdu(t, key, verbosity=verbosity)
hdul[key] = t_hdu
else:
hdul["MAIN"].header.vals[key] = val
ms.close()
return hdul
def table2hdu(table, hd, verbosity=1, close_after=True):
""" Convert MS table to a Header-Data unit
:param table: name of table (MS path)
:param hdu: header data unit, either a string or a HDU
:return: HDU version of MS table
"""
pp = PrintLog(verbosity=verbosity)
if isinstance(hd, str):
pp.h3("Creating %s HDU" % hd)
hd = IdiTableHdu(name=hd)
colnames = table.colnames()
keywords = table.getkeywords()
for colname in colnames:
try:
pp.debug("Reading col %s" % colname)
hd.add_column(table.getcol(colname), name=colname)
except RuntimeError:
# This can be raised when no data is in the column
pp.warn("Could not add %s" % colname)
for key, val in keywords.items():
hd.header.vals[key] = val
if close_after:
table.close()
return hd
def create_dataset(hgroup, name, data, **kwargs):
""" Create dataset from data, will attempt to compress
:param hgroup: h5py group in which to add dataset
:param name: name of dataset
:param data: data to write
"""
verbosity = 0
if 'verbosity' in kwargs:
verbosity = kwargs.pop('verbosity')
pp = PrintLog(verbosity)
np_types = [
np.uint8,
np.uint16,
np.uint32,
np.uint64,
np.int8,
np.int16,
np.int32,
np.int64,
np.float16,
np.float32,
np.float64,
np.complex64,
np.complex128,
np.void]
np_types = set(np_types)
#print name, str(data.dtype)
#print data.dtype.type, data.dtype.type in np_types
if data.dtype.type in np_types:
pp.debug("Creating compressed %s" % name)
dset = create_compressed(hgroup, name, data, **kwargs)
else:
try:
pp.debug("Creating non-compressed %s" % name)
dset = hgroup.create_dataset(name, data=data)
except TypeError:
#print name, data.dtype
raise
return dset
def create_dataset(hgroup, name, data, **kwargs):
""" Create dataset from data, will attempt to compress
:param hgroup: h5py group in which to add dataset
:param name: name of dataset
:param data: data to write
"""
verbosity = 0
if 'verbosity' in kwargs:
verbosity = kwargs.pop('verbosity')
pp = PrintLog(verbosity)
np_types = [
np.uint8, np.uint16, np.uint32, np.uint64, np.int8, np.int16, np.int32,
np.int64, np.float16, np.float32, np.float64, np.complex64,
np.complex128, np.void
]
np_types = set(np_types)
#print name, str(data.dtype)
#print data.dtype.type, data.dtype.type in np_types
if data.dtype.type in np_types:
pp.debug("Creating compressed %s" % name)
dset = create_compressed(hgroup, name, data, **kwargs)
else:
try:
pp.debug("Creating non-compressed %s" % name)
dset = hgroup.create_dataset(name, data=data)
except TypeError:
#print name, data.dtype
raise
return dset
