def read_data_fits(input, hdu=None, **kwargs):
"""
Read an array and header from an FITS file.
Parameters
----------
input : str or compatible `astropy.io.fits` HDU object
If a string, the filename to read the table from. The
following `astropy.io.fits` HDU objects can be used as input:
- :class:`~astropy.io.fits.hdu.table.PrimaryHDU`
- :class:`~astropy.io.fits.hdu.table.ImageHDU`
- :class:`~astropy.io.fits.hdu.hdulist.HDUList`
hdu : int or str, optional
The HDU to read the table from.
"""
if isinstance(input, fits.HDUList):
# Parse all array objects
arrays = OrderedDict()
for ihdu, hdu_item in enumerate(input):
if isinstance(hdu_item, (fits.PrimaryHDU, fits.ImageHDU)):
arrays[ihdu] = hdu_item
if len(arrays) > 1:
if hdu is None:
hdu = first(arrays)
warnings.warn("hdu= was not specified but multiple arrays"
" are present, reading in first available"
" array (hdu={0})".format(hdu))
# hdu might not be an integer, so we first need to convert it
# to the correct HDU index
hdu = input.index_of(hdu)
if hdu in arrays:
array_hdu = arrays[hdu]
else:
raise ValueError("No array found in hdu={0}".format(hdu))
elif len(arrays) == 1:
array_hdu = arrays[first(arrays)]
else:
raise ValueError("No table found")
elif isinstance(input, (fits.PrimaryHDU, fits.ImageHDU)):
array_hdu = input
else:
hdulist = fits_open(input, **kwargs)
try:
return read_data_fits(hdulist, hdu=hdu)
finally:
hdulist.close()
return array_hdu.data, array_hdu.header
def read_data_fits(input, hdu=None, **kwargs):
"""
Read an array and header from an FITS file.
Parameters
----------
input : str or compatible `astropy.io.fits` HDU object
If a string, the filename to read the table from. The
following `astropy.io.fits` HDU objects can be used as input:
- :class:`~astropy.io.fits.hdu.table.PrimaryHDU`
- :class:`~astropy.io.fits.hdu.table.ImageHDU`
- :class:`~astropy.io.fits.hdu.hdulist.HDUList`
hdu : int or str, optional
The HDU to read the table from.
"""
if isinstance(input, fits.HDUList):
# Parse all array objects
arrays = OrderedDict()
for ihdu, hdu_item in enumerate(input):
if isinstance(hdu_item, (fits.PrimaryHDU, fits.ImageHDU)):
arrays[ihdu] = hdu_item
if len(arrays) > 1:
if hdu is None:
hdu = first(arrays)
warnings.warn("hdu= was not specified but multiple arrays"
" are present, reading in first available"
" array (hdu={0})".format(hdu))
# hdu might not be an integer, so we first need to convert it
# to the correct HDU index
hdu = input.index_of(hdu)
if hdu in arrays:
array_hdu = arrays[hdu]
else:
raise ValueError("No array found in hdu={0}".format(hdu))
elif len(arrays) == 1:
array_hdu = arrays[first(arrays)]
else:
raise ValueError("No table found")
elif isinstance(input, (fits.PrimaryHDU, fits.ImageHDU)):
array_hdu = input
else:
hdulist = fits_open(input, **kwargs)
try:
return read_data_fits(hdulist, hdu=hdu)
finally:
hdulist.close()
return array_hdu.data, array_hdu.header
def read_data_fits(input, hdu=None, mode='denywrite', **kwargs):
"""
Read an array and header from an FITS file.
Parameters
----------
input : str or compatible `astropy.io.fits` HDU object
If a string, the filename to read the table from. The
following `astropy.io.fits` HDU objects can be used as input:
- :class:`~astropy.io.fits.hdu.table.PrimaryHDU`
- :class:`~astropy.io.fits.hdu.table.ImageHDU`
- :class:`~astropy.io.fits.hdu.hdulist.HDUList`
hdu : int or str, optional
The HDU to read the table from.
mode : str
One of the FITS file reading modes; see `~astropy.io.fits.open`.
``denywrite`` is used by default since this prevents the system from
checking that the entire cube will fit into swap, which can prevent the
file from being opened at all.
"""
beam_table = None
if isinstance(input, fits.HDUList):
# Parse all array objects
arrays = OrderedDict()
for ihdu, hdu_item in enumerate(input):
if isinstance(hdu_item, (fits.PrimaryHDU, fits.ImageHDU)):
arrays[ihdu] = hdu_item
elif isinstance(hdu_item, fits.BinTableHDU):
if 'BPA' in hdu_item.data.names:
beam_table = hdu_item.data
if len(arrays) > 1:
if hdu is None:
hdu = first(arrays)
warnings.warn("hdu= was not specified but multiple arrays"
" are present, reading in first available"
" array (hdu={0})".format(hdu))
# hdu might not be an integer, so we first need to convert it
# to the correct HDU index
hdu = input.index_of(hdu)
if hdu in arrays:
array_hdu = arrays[hdu]
else:
raise ValueError("No array found in hdu={0}".format(hdu))
elif len(arrays) == 1:
array_hdu = arrays[first(arrays)]
else:
raise ValueError("No arrays found")
elif isinstance(input, (fits.PrimaryHDU, fits.ImageHDU)):
array_hdu = input
else:
hdulist = fits_open(input, mode=mode, **kwargs)
try:
return read_data_fits(hdulist, hdu=hdu)
finally:
hdulist.close()
return array_hdu.data, array_hdu.header, beam_table
def read_data_fits(input, hdu=None, mode='denywrite', **kwargs):
"""
Read an array and header from an FITS file.
Parameters
----------
input : str or compatible `astropy.io.fits` HDU object
If a string, the filename to read the table from. The
following `astropy.io.fits` HDU objects can be used as input:
- :class:`~astropy.io.fits.hdu.table.PrimaryHDU`
- :class:`~astropy.io.fits.hdu.table.ImageHDU`
- :class:`~astropy.io.fits.hdu.hdulist.HDUList`
hdu : int or str, optional
The HDU to read the table from.
mode : str
One of the FITS file reading modes; see `~astropy.io.fits.open`.
``denywrite`` is used by default since this prevents the system from
checking that the entire cube will fit into swap, which can prevent the
file from being opened at all.
"""
beam_table = None
if isinstance(input, fits.HDUList):
# Parse all array objects
arrays = OrderedDict()
for ihdu, hdu_item in enumerate(input):
if isinstance(hdu_item, (fits.PrimaryHDU, fits.ImageHDU)):
arrays[ihdu] = hdu_item
elif isinstance(hdu_item, fits.BinTableHDU):
if 'BPA' in hdu_item.data.names:
beam_table = hdu_item.data
if len(arrays) > 1:
if hdu is None:
hdu = first(arrays)
warnings.warn(
"hdu= was not specified but multiple arrays"
" are present, reading in first available"
" array (hdu={0})".format(hdu), FITSWarning)
# hdu might not be an integer, so we first need to convert it
# to the correct HDU index
hdu = input.index_of(hdu)
if hdu in arrays:
array_hdu = arrays[hdu]
else:
raise ValueError("No array found in hdu={0}".format(hdu))
elif len(arrays) == 1:
array_hdu = arrays[first(arrays)]
else:
raise ValueError("No arrays found")
elif isinstance(input, (fits.PrimaryHDU, fits.ImageHDU)):
array_hdu = input
else:
hdulist = fits_open(input, mode=mode, **kwargs)
try:
return read_data_fits(hdulist, hdu=hdu)
finally:
hdulist.close()
return array_hdu.data, array_hdu.header, beam_table
def read_table_fits(input, hdu=None):
"""
Read a Table object from an FITS file
Parameters
----------
input : str or file-like object or compatible `astropy.io.fits` HDU object
If a string, the filename to read the table from. If a file object, or
a compatible HDU object, the object to extract the table from. The
following `astropy.io.fits` HDU objects can be used as input:
- :class:`~astropy.io.fits.hdu.table.TableHDU`
- :class:`~astropy.io.fits.hdu.table.BinTableHDU`
- :class:`~astropy.io.fits.hdu.table.GroupsHDU`
- :class:`~astropy.io.fits.hdu.hdulist.HDUList`
hdu : int or str, optional
The HDU to read the table from.
"""
if isinstance(input, basestring):
input = fits_open(input)
to_close = input
else:
to_close = None
if hasattr(input, 'read'):
input = fits_open(input)
try:
# Parse all table objects
tables = OrderedDict()
if isinstance(input, HDUList):
for ihdu, hdu_item in enumerate(input):
if isinstance(hdu_item, (TableHDU, BinTableHDU, GroupsHDU)):
tables[ihdu] = hdu_item
if len(tables) > 1:
if hdu is None:
warnings.warn("hdu= was not specified but multiple tables"
" are present, reading in first available"
" table (hdu={0})".format(tables.keys()[0]))
hdu = tables.keys()[0]
# hdu might not be an integer, so we first need to convert it
# to the correct HDU index
hdu = input.index_of(hdu)
if hdu in tables:
table = tables[hdu]
else:
raise ValueError("No table found in hdu={0}".format(hdu))
elif len(tables) == 1:
table = tables[tables.keys()[0]]
else:
raise ValueError("No table found")
elif isinstance(input, (TableHDU, BinTableHDU, GroupsHDU)):
table = input
else:
raise ValueError("Input should be a string, a file-like object, "
"an HDUList, TableHDU, BinTableHDU, or "
"GroupsHDU instance")
# Check if table is masked
masked = False
for col in table.columns:
if col.null is not None:
masked = True
break
# Convert to an astropy.table.Table object
t = Table(table.data, masked=masked)
# Copy over null values if needed
if masked:
for col in table.columns:
t[col.name].set_fill_value(col.null)
t[col.name].mask[t[col.name] == col.null] = True
# Copy over units
for col in table.columns:
if col.unit is not None:
try:
t[col.name].units = u.Unit(col.unit, format='fits')
except ValueError:
t[col.name].units = u.UnrecognizedUnit(col.unit)
# TODO: deal properly with unsigned integers
for key, value, comment in table.header.cards:
if key in ['COMMENT', 'HISTORY']:
if key in t.meta:
t.meta[key].append(value)
else:
t.meta[key] = [value]
elif key in t.meta: # key is duplicate
if isinstance(t.meta[key], list):
t.meta[key].append(value)
else:
t.meta[key] = [t.meta[key], value]
elif (is_column_keyword(key.upper()) or
key.upper() in REMOVE_KEYWORDS):
pass
else:
t.meta[key] = value
# TODO: implement masking
finally:
if to_close is not None:
to_close.close()
return t
def read_table_fits(input, hdu=None):
"""
Read a Table object from an FITS file
Parameters
----------
input : str or file-like object or compatible `astropy.io.fits` HDU object
If a string, the filename to read the table from. If a file object, or
a compatible HDU object, the object to extract the table from. The
following `astropy.io.fits` HDU objects can be used as input:
- :class:`~astropy.io.fits.hdu.table.TableHDU`
- :class:`~astropy.io.fits.hdu.table.BinTableHDU`
- :class:`~astropy.io.fits.hdu.table.GroupsHDU`
- :class:`~astropy.io.fits.hdu.hdulist.HDUList`
hdu : int or str, optional
The HDU to read the table from.
"""
if isinstance(input, six.string_types):
input = fits_open(input)
to_close = input
else:
to_close = None
if hasattr(input, 'read'):
input = fits_open(input)
try:
# Parse all table objects
tables = OrderedDict()
if isinstance(input, HDUList):
for ihdu, hdu_item in enumerate(input):
if isinstance(hdu_item, (TableHDU, BinTableHDU, GroupsHDU)):
tables[ihdu] = hdu_item
if len(tables) > 1:
if hdu is None:
warnings.warn("hdu= was not specified but multiple tables"
" are present, reading in first available"
" table (hdu={0})".format(
list(tables.keys())[0]))
hdu = list(tables.keys())[0]
# hdu might not be an integer, so we first need to convert it
# to the correct HDU index
hdu = input.index_of(hdu)
if hdu in tables:
table = tables[hdu]
else:
raise ValueError("No table found in hdu={0}".format(hdu))
elif len(tables) == 1:
table = tables[list(tables.keys())[0]]
else:
raise ValueError("No table found")
elif isinstance(input, (TableHDU, BinTableHDU, GroupsHDU)):
table = input
else:
raise ValueError("Input should be a string, a file-like object, "
"an HDUList, TableHDU, BinTableHDU, or "
"GroupsHDU instance")
# Check if table is masked
masked = False
for col in table.columns:
if col.null is not None:
masked = True
break
# Convert to an astropy.table.Table object
t = Table(table.data, masked=masked)
# Copy over null values if needed
if masked:
for col in table.columns:
t[col.name].set_fill_value(col.null)
t[col.name].mask[t[col.name] == col.null] = True
# Copy over units
for col in table.columns:
if col.unit is not None:
try:
t[col.name].units = u.Unit(col.unit, format='fits')
except ValueError:
t[col.name].units = u.UnrecognizedUnit(col.unit)
# TODO: deal properly with unsigned integers
for key, value, comment in table.header.cards:
if key in ['COMMENT', 'HISTORY']:
if key in t.meta:
t.meta[key].append(value)
else:
t.meta[key] = [value]
elif key in t.meta: # key is duplicate
if isinstance(t.meta[key], list):
t.meta[key].append(value)
else:
t.meta[key] = [t.meta[key], value]
elif (is_column_keyword(key.upper())
or key.upper() in REMOVE_KEYWORDS):
pass
else:
t.meta[key] = value
# TODO: implement masking
finally:
if to_close is not None:
to_close.close()
return t
