def test_read_from_fileobj(self, tmpdir):
filename = str(tmpdir.join('test_read_from_fileobj.fits'))
hdu = BinTableHDU(self.data)
hdu.writeto(filename, overwrite=True)
with open(filename, 'rb') as f:
t = Table.read(f)
assert equal_data(t, self.data)
def test_read_from_fileobj(self, tmpdir):
filename = str(tmpdir.join('test_read_from_fileobj.fits'))
hdu = BinTableHDU(self.data)
hdu.writeto(filename, overwrite=True)
with open(filename, 'rb') as f:
t = Table.read(f)
assert equal_data(t, self.data)
def main():
usage = "usage: %(prog)s [archive file]"
description = "Build the extended archive from the master archive YAML file."
parser = argparse.ArgumentParser(usage=usage, description=description)
parser.add_argument('--outname', default=None, required=True)
parser.add_argument('--vernum', default=0, required=True)
parser.add_argument('masterfile',
help='Extended archive master YAML file.')
args = parser.parse_args()
npar_max = 5
sources = yaml.load(open(args.masterfile))
cols = [
Column(name='Source_Name', format='18A'),
Column(name='RAJ2000', format='E', unit='deg', disp='F8.4'),
Column(name='DEJ2000', format='E', unit='deg', disp='F8.4'),
Column(name='GLON', format='E', unit='deg', disp='F8.4'),
Column(name='GLAT', format='E', unit='deg', disp='F8.4'),
Column(name='Photon_Flux', format='E', unit='ph cm-2 s-1',
disp='E8.2'),
Column(name='Energy_Flux',
format='E',
unit='erg cm-2 s-1',
disp='E8.2'),
Column(name='Model_Form', format='12A'),
Column(name='Model_SemiMajor', format='E', unit='deg', disp='E7.3'),
Column(name='Model_SemiMinor', format='E', unit='deg', disp='E7.3'),
Column(name='Model_PosAng', format='E', unit='deg', disp='E6.1'),
Column(name='Spatial_Function', format='15A'),
Column(name='Spatial_Filename', format='50A'),
Column(name='Spectral_Function', format='12A'),
Column(name='Spectral_Filename', format='40A'),
Column(name='Name_1FGL', format='18A'),
Column(name='Name_2FGL', format='18A'),
Column(name='Name_3FGL', format='18A'),
Column(name='Spectral_Param_Name', format='45A9'),
Column(name='Spectral_Param_Value',
format='E',
dim=str(npar_max),
disp='E9.4'),
Column(name='Spectral_Param_Error',
format='E',
dim=str(npar_max),
disp='E9.4'),
Column(name='Spectral_Param_Scale', format='E', dim=str(npar_max)),
]
for c in cols:
c.array = build_column_array(c.name, sources, npar_max)
record = FITS_rec.from_columns(cols)
record.sort(order="RAJ2000")
outdir = args.outname + "_v" + args.vernum
mkdir(outdir)
fitsname = "LAT_extended_sources_v" + args.vernum + ".fits"
output = BinTableHDU(record)
output.writeto(os.path.join(outdir, fitsname), overwrite=True)
xmldir = os.path.join(outdir, 'XML')
mkdir(xmldir)
for k, v in sources.items():
xmlpath = os.path.join(xmldir,
v['Source_Name'].replace(' ', '') + '.xml')
to_xml(xmlpath, v['Source_Name'], v)
def write_table_fits(input, output, overwrite=False):
"""
Write a Table object to a FITS file
Parameters
----------
input : Table
The table to write out.
output : str
The filename to write the table to.
overwrite : bool
Whether to overwrite any existing file without warning.
"""
# Check if output file already exists
if isinstance(output, basestring) and os.path.exists(output):
if overwrite:
os.remove(output)
else:
raise IOError("File exists: {0}".format(output))
# Create a new HDU object
if input.masked:
table_hdu = BinTableHDU(np.array(input.filled()))
for col in table_hdu.columns:
# The astype is necessary because if the string column is less
# than one character, the fill value will be N/A by default which
# is too long, and so no values will get masked.
fill_value = input[col.name].get_fill_value()
col.null = fill_value.astype(input[col.name].dtype)
else:
table_hdu = BinTableHDU(np.array(input))
# Set units for output HDU
for col in table_hdu.columns:
if input[col.name].units is not None:
col.unit = input[col.name].units.to_string(format='fits')
for key, value in input.meta.items():
if is_column_keyword(key.upper()) or key.upper() in REMOVE_KEYWORDS:
log.warn("Meta-data keyword {0} will be ignored since it "
"conflicts with a FITS reserved keyword".format(key))
if isinstance(value, list):
for item in value:
try:
table_hdu.header.append((key, item))
except ValueError:
log.warn("Attribute `{0}` of type {1} cannot be written "
"to FITS files - skipping".format(key,
type(value)))
else:
try:
table_hdu.header[key] = value
except ValueError:
log.warn("Attribute `{0}` of type {1} cannot be written to "
"FITS files - skipping".format(key, type(value)))
# Write out file
table_hdu.writeto(output)
def write_table_fits(input, output, overwrite=False):
"""
Write a Table object to a FITS file
Parameters
----------
input : Table
The table to write out.
output : str
The filename to write the table to.
overwrite : bool
Whether to overwrite any existing file without warning.
"""
# Check if output file already exists
if isinstance(output, six.string_types) and os.path.exists(output):
if overwrite:
os.remove(output)
else:
raise IOError("File exists: {0}".format(output))
# Create a new HDU object
if input.masked:
table_hdu = BinTableHDU(np.array(input.filled()))
for col in table_hdu.columns:
# The astype is necessary because if the string column is less
# than one character, the fill value will be N/A by default which
# is too long, and so no values will get masked.
fill_value = input[col.name].get_fill_value()
col.null = fill_value.astype(input[col.name].dtype)
else:
table_hdu = BinTableHDU(np.array(input))
# Set units for output HDU
for col in table_hdu.columns:
if input[col.name].units is not None:
col.unit = input[col.name].units.to_string(format='fits')
for key, value in input.meta.items():
if is_column_keyword(key.upper()) or key.upper() in REMOVE_KEYWORDS:
log.warn("Meta-data keyword {0} will be ignored since it "
"conflicts with a FITS reserved keyword".format(key))
if isinstance(value, list):
for item in value:
try:
table_hdu.header.append((key, item))
except ValueError:
log.warn("Attribute `{0}` of type {1} cannot be written "
"to FITS files - skipping".format(
key, type(value)))
else:
try:
table_hdu.header[key] = value
except ValueError:
log.warn("Attribute `{0}` of type {1} cannot be written to "
"FITS files - skipping".format(key, type(value)))
# Write out file
table_hdu.writeto(output)