def read_spectra_file(data_or_file, format=None, config_dict=None):
"""Read a FITS file of a spectrum into a SpectrumList
Parameters
----------
data_or_file : HDUList, Path or file object
The FITS data to load
format : str, optional
The format of the FITS file, by default None
config_dict : dict, optional
Used to specify the format of the FITS file, if the format string doesn't work, by default None
Returns
-------
specutils.SpectrumList
Data from the FITS file in a SpectrumList object
"""
if data_or_file is None:
return None
if format:
return SpectrumList.read(data_or_file, format=format)
elif config_dict:
return SpectrumList.read(data_or_file, **config_dict)
else:
# Try to resolve ambiguous loaders
formats = ssv.ssvloaders.whatformat(data_or_file)
if len(formats) > 1:
for i in range(len(formats) - 1):
ssv.ssvloaders.unregister(formats[i])
spectra = SpectrumList.read(data_or_file, format=formats[-1])
ssv.ssvloaders.restore_registered_loaders()
return spectra
def test_jwst_reader_fail(tmpdir, x1d_single, srctype):
"""Check that the reader fails when SRCTYPE is not set or is UNKNOWN"""
tmpfile = str(tmpdir.join('jwst.fits'))
hdulist = x1d_single
# Add a spectrum with bad SRCTYPE (mutate the fixture)
hdulist.append(create_spectrum_hdu(100, srctype, ver=2))
hdulist.writeto(tmpfile)
with pytest.raises(RuntimeError, match="^Keyword"):
SpectrumList.read(tmpfile, format='JWST x1d multi')
def marz_loader(fname):
try:
spectra = SpectrumList.read(fname,
format=SINGLE_SPLIT_LABEL,
**MARZ_CONFIG_NEXT)
except:
# fallback (to not having support for "fallback_header"!)
spectra = SpectrumList.read(fname,
format=SINGLE_SPLIT_LABEL,
**MARZ_CONFIG)
return spectra
def test_gama_gama(self, shared_datadir):
spectra = SpectrumList.read(
shared_datadir / GAMA_GAMA_TEST_FILENAME,
format=loaders.MULTILINE_SINGLE_LABEL,
**GAMA_GAMA_CONFIG
)
assert len(spectra) == 3
assert spectra[0].flux.unit == u.Unit("10^-17 erg/s/cm^2/A")
assert spectra[0].spectral_axis.unit == u.Angstrom
assert spectra[1].flux.unit == u.count
assert spectra[1].spectral_axis.unit == u.Angstrom
assert spectra[2].flux.unit == u.count
assert spectra[2].spectral_axis.unit == u.Angstrom
assert isinstance(spectra[0].uncertainty, StdDevUncertainty)
assert isinstance(spectra[1].uncertainty, StdDevUncertainty)
assert spectra[2].uncertainty is None
assert spectra[0].meta.get("label") is not None
assert spectra[0].meta.get("header") is not None
assert spectra[1].meta.get("label") is not None
assert spectra[1].meta.get("header") is not None
assert spectra[2].meta.get("label") is not None
assert spectra[2].meta.get("header") is not None
def test_ozdes_guess(self, shared_datadir):
spectra = SpectrumList.read(shared_datadir / OZDES_TEST_FILENAME)
# The test file has the combined obs, and 4 other sets
assert len(spectra) == 5
assert spectra[0].flux.unit == u.count / u.Angstrom
assert spectra[0].spectral_axis.unit == u.Angstrom
assert isinstance(spectra[0].uncertainty, VarianceUncertainty)
assert spectra[0].meta.get("label") is None
assert spectra[0].meta.get("header") is not None
assert spectra[1].flux.unit == u.count / u.Angstrom
assert spectra[1].spectral_axis.unit == u.Angstrom
assert isinstance(spectra[1].uncertainty, VarianceUncertainty)
assert spectra[1].meta.get("label") is not None
assert spectra[1].meta.get("header") is not None
assert spectra[2].flux.unit == u.count / u.Angstrom
assert spectra[2].spectral_axis.unit == u.Angstrom
assert isinstance(spectra[2].uncertainty, VarianceUncertainty)
assert spectra[2].meta.get("label") is not None
assert spectra[2].meta.get("header") is not None
assert spectra[3].flux.unit == u.count / u.Angstrom
assert spectra[3].spectral_axis.unit == u.Angstrom
assert isinstance(spectra[3].uncertainty, VarianceUncertainty)
assert spectra[3].meta.get("label") is not None
assert spectra[3].meta.get("header") is not None
assert spectra[4].flux.unit == u.count / u.Angstrom
assert spectra[4].spectral_axis.unit == u.Angstrom
assert isinstance(spectra[4].uncertainty, VarianceUncertainty)
assert spectra[4].meta.get("label") is not None
assert spectra[4].meta.get("header") is not None
def test_galah_guess(self, shared_datadir):
spectra = SpectrumList.read(shared_datadir / GALAH_TEST_FILENAME)
# Should be main spectra, without sky, and normalised
assert len(spectra) == 3
assert spectra[0].flux.unit == u.count
assert spectra[1].flux.unit == u.Unit('') # dimensionless
assert spectra[2].flux.unit == u.count
assert spectra[0].spectral_axis.unit == u.Angstrom
assert spectra[1].spectral_axis.unit == u.Angstrom
assert spectra[2].spectral_axis.unit == u.Angstrom
assert isinstance(spectra[0].uncertainty, StdDevUncertainty)
assert spectra[1].uncertainty is None
assert isinstance(spectra[2].uncertainty, StdDevUncertainty)
assert spectra[0].meta.get("label") is not None
assert spectra[0].meta.get("header") is not None
assert spectra[1].meta.get("label") is None
assert spectra[1].meta.get("header") is not None
assert spectra[2].meta.get("label") is not None
assert spectra[2].meta.get("header") is not None
def gama_lt_obscore_loader(fname):
spectra = SpectrumList.read(fname, format="GAMA-LT")
for spec in spectra:
spec.meta["obscore"] = {}
obscore = spec.meta["obscore"]
if spec.meta["purpose"] == "reduced":
hdr = spec.meta["header"]
t1, t2 = gama_lt_get_times(hdr)
if t1 is not None:
obscore["t_min"] = t1.to_value('mjd',subfmt='float')
if t2 is not None:
obscore["t_max"] = t2.to_value('mjd',subfmt='float')
obscore["s_ra"] = hdr["RA"]
obscore["s_dec"] = hdr["DEC"]
if "ESTSEE" in hdr:
obscore["s_seeing"] = hdr["ESTSEE"]
# obscore["obs_collection"] = "gama_dr2"
# obscore["facility_name"] = "gama_lt"
obscore["dataproduct_subtype"] = "science"
obscore["calib_level"] = 2
if "EXPTIME" in hdr:
obscore["t_exptime"] = hdr["EXPTIME"]
nspecpix = len(spec.spectral_axis)
obscore["em_xel"] = nspecpix
obscore["em_ucd"] = "em.wl"
obscore["em_unit"] = "angstrom"
obscore["s_xel1"] = nspecpix
obscore["s_xel2"] = 1
obscore["t_xel"] = 1
obscore["em_min"] = spec.spectral_axis[0].meter
obscore["em_max"] = (
spec.spectral_axis[nspecpix - 1].meter
)
obscore["o_ucd"] = "phot.count"
obscore["instrument_name"] = "FrodoSpec"
obscore["s_fov"] = 9.84 / 3600
obscore["em_calib_status"] = "calibrated"
if "GAMANAME" in hdr:
obscore["target_name"] = hdr["GAMANAME"]
if "OBJECT" in hdr:
obscore["alt_target_name"] = hdr["OBJECT"]
if "WAVRESOL" in hdr:
obscore["em_resolution"] = hdr["WAVRESOL"] * 1e-10
# if('SN' in hdr):
# obscore['em_snr'] = hdr['SN']
# alternative name: OBJECT
if "SPECID" in hdr:
obscore["obs_id"] = hdr["SPECID"]
if "Z" in hdr:
obscore["redshift"] = hdr["Z"]
return spectra
def test_guess_all(self, shared_datadir, filename):
formats = ssv.ssvloaders.whatformat(shared_datadir / filename)
spectra = SpectrumList.read(shared_datadir / filename)
print("format for {0} is {1} and number of spectra is {2}".format(
filename, formats, len(spectra)))
for spectrum in spectra:
print(spectrum)
def read_data_file(self, file_path, file_loader=None):
"""
Read spectral data from file given file path and loader.
Parameters
----------
file_path : str
Path to location of the spectrum file.
file_loader : str
Format specified for the astropy io interface.
Returns
-------
: :class:`~specutils.SpectrumList`
A `~specutils.SpectrumList` instance containing the spectra loaded from the file
"""
# In the case that the user has selected auto load, loop through every
# available loader and choose the one that 1) the registry identifier
# function allows, and 2) is the highest priority.
try:
if file_loader:
if file_loader not in self._get_matching_formats(file_path):
msg = 'Given file can not be processed as specified file format ({})'
raise IOError(msg.format(file_loader))
speclist = SpectrumList.read(file_path, format=file_loader)
except IORegistryError as e:
# In this case, assume that the registry has found several
# loaders that fit the same identifier, choose the highest
# priority one.
speclist = self._try_priority_file_loaders(file_path)
return speclist
def read_data_file(self, file_path, file_loader=None):
"""
Read spectral data from file given file path and loader.
Parameters
----------
file_path : str
Path to location of the spectrum file.
file_loader : str
Format specified for the astropy io interface.
Returns
-------
: :class:`~specutils.SpectrumList`
A `~specutils.SpectrumList` instance containing the spectra loaded from the file
"""
# In the case that the user has selected auto load, loop through every
# available loader and choose the one that 1) the registry identifier
# function allows, and 2) is the highest priority.
try:
if file_loader:
if file_loader not in self._get_matching_formats(file_path):
msg = 'Given file can not be processed as specified file format ({})'
raise IOError(msg.format(file_loader))
speclist = SpectrumList.read(file_path, format=file_loader)
except IORegistryError as e:
# In this case, assume that the registry has found several
# loaders that fit the same identifier, choose the highest
# priority one.
speclist = self._try_priority_file_loaders(file_path)
return speclist
def test_ozdes_prefer_combined(self, shared_datadir):
spectra = SpectrumList.read(shared_datadir / OZDES_TEST_FILENAME,
format=loaders.SINGLE_SPLIT_LABEL,
**OZDES_CONFIG)
tables = specutils_spectra_to_table_spectra(spectra,
prefer_combined=True)
len(tables) == 1
def gama_mgc_obscore_loader(fname):
spectra = SpectrumList.read(fname, format="GAMA-MGC")
for spec in spectra:
spec.meta["obscore"] = {}
obscore = spec.meta["obscore"]
if spec.meta["purpose"] == "reduced":
hdr = spec.meta["header"]
t1, t2 = get_times(
hdr, date_kw="DATE-OBS", start_kw="UT", duration_kw="EXPTIME"
)
if t1 is not None:
obscore["t_min"] = t1.to_value('mjd',subfmt='float')
if t2 is not None:
obscore["t_max"] = t2.to_value('mjd',subfmt='float')
obscore["s_ra"] = hdr["RA"]
obscore["s_dec"] = hdr["DEC"]
obscore["s_fov"] = 2.1 / 3600
if "SEEING" in hdr:
obscore["s_seeing"] = hdr["SEEING"]
# obscore["obs_collection"] = "gama_dr2"
# obscore["facility_name"] = "mgc"
obscore["dataproduct_subtype"] = "science"
obscore["calib_level"] = 2
if "EXPTIME" in hdr:
obscore["t_exptime"] = hdr["EXPTIME"]
nspecpix = len(spec.spectral_axis)
obscore["em_xel"] = nspecpix
obscore["em_ucd"] = "em.wl"
obscore["em_unit"] = "angstrom"
obscore["s_xel1"] = nspecpix
obscore["s_xel2"] = 1
obscore["t_xel"] = 1
obscore["em_min"] = spec.spectral_axis[0].meter
obscore["em_max"] = (
spec.spectral_axis[nspecpix - 1].meter
)
obscore["o_ucd"] = "phot.count"
obscore["instrument_name"] = "2dF"
obscore["em_calib_status"] = "calibrated"
if "GAMANAME" in hdr:
obscore["target_name"] = hdr["GAMANAME"]
if "OBJECT" in hdr:
obscore["alt_target_name"] = hdr["OBJECT"]
if "SN" in hdr:
obscore["em_snr"] = hdr["SN"]
# alternative name: OBJECT
if "SPECID" in hdr:
obscore["obs_id"] = hdr["SPECID"]
if "Z" in hdr:
obscore["redshift"] = hdr["Z"]
return spectra
def galah_loader(filename):
with read_fileobj_or_hdulist(filename) as hdulist:
if len(hdulist) == 5:
spectra = SpectrumList.read(
hdulist, format=SINGLE_SPLIT_LABEL, **GALAH_5EXT_CONFIG
)
spectra[0].meta["galah_hdu_format"] = 5
elif len(hdulist) == 4:
spectra = SpectrumList.read(
hdulist, format=SINGLE_SPLIT_LABEL, **GALAH_4EXT_CONFIG
)
spectra[0].meta["galah_hdu_format"] = 4
else:
raise RuntimeError(
"Unknown GALAH format, has {} extensions".format(len(hdulist))
)
return spectra
def test_without_rwss_guess(self, shared_datadir):
spectra = SpectrumList.read(shared_datadir / AAOMEGA_WITHOUT_RWSS, )
assert len(spectra) == 153
for spec in spectra:
assert spec.meta.get("label") is not None
assert spec.meta.get("header") is not None
assert spec.meta.get("purpose") is not None
assert spec.meta.get("fibre_index") is not None
def test_marz_guess_1(self, shared_datadir):
formats = loaders.whatformat(shared_datadir / "marz/quasarLinearSkyAirNoHelio.fits")
if len(formats) > 1:
loaders.unregister(formats[0])
spectra = SpectrumList.read(
shared_datadir / "marz/quasarLinearSkyAirNoHelio.fits"
)
# Should be main spectra, with sky, and normalised
assert len(spectra) == 2
def test_ozdes(self, shared_datadir):
spectra = SpectrumList.read(
shared_datadir / OZDES_TEST_FILENAME, format="OzDES obscore",
)
spec = spectra[0]
obscore = spec.meta.get("obscore")
assert obscore is not None
assert obscore.get("calib_level") == 3
assert obscore.get("t_xel") == 4
def test_not_marz_guess_1(self, shared_datadir):
formats = ssv.ssvloaders.whatformat(shared_datadir / "OBJ0032red.fits")
if len(formats) > 1:
ssv.ssvloaders.unregister(formats[0])
spectra = SpectrumList.read(shared_datadir / "OBJ0032red.fits")
# Should be main spectra, with sky, and normalised
assert len(spectra) > 0
assert spectra[0].spectral_axis.unit == u.Angstrom
assert spectra[0].meta.get("header") is not None
def test_galah(self, shared_datadir):
spectra = SpectrumList.read(
shared_datadir / GALAH_TEST_FILENAME, format="GALAH obscore",
)
spec = spectra[0]
obscore = spec.meta.get("obscore")
assert obscore is not None
assert obscore.get("calib_level") == 2
assert obscore.get("t_xel") == 1
def test_2dfgrs(self, shared_datadir):
spectra = SpectrumList.read(
shared_datadir / TWODFGRS_TEST_FILENAME, format="2dFGRS obscore",
)
spec = spectra[0]
obscore = spec.meta.get("obscore")
assert obscore is not None
assert obscore.get("calib_level") == 2
assert obscore.get("t_xel") == 1
def test_jwst_s2d_multi_reader(tmpdir, s2d_multi):
path = str(tmpdir.join("test.fits"))
model = s2d_multi
model.save(path)
speclist = SpectrumList.read(path, format="JWST s2d multi")
assert len(speclist) == 2
assert hasattr(speclist[0], "spectral_axis")
assert speclist[1].unit == u.Jy
def test_jwst_x1d_multi_reader_check_units(tmpdir, x1d_multi):
"""Test units for Spectrum1D.read for JWST x1d data"""
tmpfile = str(tmpdir.join('jwst.fits'))
x1d_multi.writeto(tmpfile)
data = SpectrumList.read(tmpfile)
assert data[0].unit == u.Jy
assert data[1].unit == u.MJy / u.sr
assert data[2].unit == u.Jy
def test_marz_guess_2(self, shared_datadir):
formats = ssv.ssvloaders.whatformat(
shared_datadir / "marz/alldata_combined_runz_x12_b02.fits")
if len(formats) > 1:
ssv.ssvloaders.unregister(formats[0])
spectra = SpectrumList.read(shared_datadir /
"marz/alldata_combined_runz_x12_b02.fits")
# Should be main spectra, with sky, and normalised
assert len(spectra) == 2
def test_2slaq_qso(self, shared_datadir):
spectra = SpectrumList.read(
shared_datadir / GAMA_2SLAQ_QSO_TEST_FILENAME,
format="GAMA-2SLAQ-QSO obscore",
)
spec = spectra[0]
obscore = spec.meta.get("obscore")
assert obscore is not None
assert obscore.get("calib_level") == 2
assert obscore.get("t_xel") == 1
def test_gama_wigglez(self, shared_datadir):
spectra = SpectrumList.read(
shared_datadir / GAMA_WIGGLEZ_TEST_FILENAME,
format="GAMA-WiggleZ obscore",
)
spec = spectra[0]
obscore = spec.meta.get("obscore")
assert obscore is not None
assert obscore.get("calib_level") == 2
assert obscore.get("t_xel") == 1
def test_6dfgs_table(self, shared_datadir):
spectra = SpectrumList.read(
shared_datadir / SIXDFGS_TABLE_TEST_FILENAME,
format="6dFGS-tabular obscore",
)
spec = spectra[0]
obscore = spec.meta.get("obscore")
assert obscore is not None
assert obscore.get("calib_level") == 2
assert obscore.get("t_xel") == 1
def test_6dfgs_combined(self, shared_datadir):
spectra = SpectrumList.read(
shared_datadir / SIXDFGS_COMBINED_TEST_FILENAME,
format="6dFGS-combined obscore",
)
spec = spectra[0]
obscore = spec.meta.get("obscore")
assert obscore is not None
assert obscore.get("calib_level") == 2
assert obscore.get("t_xel") == 4
def test_with_rwss(self, shared_datadir):
spectra = SpectrumList.read(
shared_datadir / AAOMEGA_WITH_RWSS,
format="Data Central AAOmega",
)
assert len(spectra) == 139
for spec in spectra:
assert spec.meta.get("label") is not None
assert spec.meta.get("header") is not None
assert spec.meta.get("purpose") is not None
assert spec.meta.get("fibre_index") is not None
def test_jwst_x1d_multi_reader_no_format(tmpdir, x1d_multi):
"""Test Spectrum1D.read for JWST x1d data without format arg"""
tmpfile = str(tmpdir.join('jwst.fits'))
x1d_multi.writeto(tmpfile)
data = SpectrumList.read(tmpfile)
assert type(data) is SpectrumList
assert len(data) == 3
for item in data:
assert isinstance(item, Spectrum1D)
def test_aaomega_without_rwss(self, shared_datadir):
spectra = SpectrumList.read(
shared_datadir / AAOMEGA_WITHOUT_RWSS,
format="Data Central AAOmega obscore",
)
for spec in spectra:
if spec.meta["purpose"] == "reduced":
obscore = spec.meta.get("obscore")
assert obscore is not None
assert obscore.get("calib_level") == 2
assert obscore.get("t_xel") == 1
def test_not_marz_guess_2(self, shared_datadir):
formats = ssv.ssvloaders.whatformat(
shared_datadir / "J091726.21+003424.0_a14_040423.fit")
if len(formats) > 1:
ssv.ssvloaders.unregister(formats[0])
spectra = SpectrumList.read(shared_datadir /
"J091726.21+003424.0_a14_040423.fit")
ssv.ssvloaders.restore_registered_loaders()
# Should be main spectra, with sky, and normalised
assert len(spectra) > 0
assert spectra[0].spectral_axis.unit == u.Angstrom
assert spectra[0].meta.get("header") is not None
def test_gama_wigglez_guess(self, shared_datadir):
spectra = SpectrumList.read(
shared_datadir / GAMA_WIGGLEZ_TEST_FILENAME,
)
assert len(spectra) == 1
assert spectra[0].flux.unit == u.count
assert spectra[0].spectral_axis.unit == u.Angstrom
assert isinstance(spectra[0].uncertainty, VarianceUncertainty)
assert spectra[0].meta.get("label") is not None
assert spectra[0].meta.get("header") is not None
def _try_priority_file_loaders(self, file_path):
fmts = self._get_matching_formats(file_path)
logging.warning("Loaders for '%s' matched for this data set. "
"Iterating based on priority."
"", ', '.join(fmts))
for fmt in fmts:
try:
speclist = SpectrumList.read(file_path, format=fmt)
return speclist
except IORegistryError:
logging.warning("Attempted load with '%s' failed, "
"trying next loader.", fmt)
raise IOError('Could not find appropriate loader for given file')
