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‎CHANGES.rst‎

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Original file line numberDiff line numberDiff line change
@@ -4,6 +4,9 @@
44
New Features
55
^^^^^^^^^^^^
66

7+
- Added new SDSS-V ``Spectrum1D`` and ``SpectrumList`` default loaders for
8+
``astraStar`` and ``astraVisit`` model spectra datatypes. [#1203]
9+
710
Bug Fixes
811
^^^^^^^^^
912

@@ -156,15 +159,23 @@ Bug Fixes
156159
- Fixed ``Spectrum1D.with_flux_unit()`` not converting uncertainty along
157160
with flux unit. [#1181]
158161

162+
- Fixed ``mwmVisit`` SDSS-V ``Spectrum1D`` and ``SpectrumList`` default loader
163+
being unable to load files containing only BOSS instrument spectra. [#1185]
164+
165+
- Fixed automatic format detection for SDSS-V ``SpectrumList`` default loaders. [#1185]
166+
159167
- Fixed extracting a spectral region when one of spectrum/region is in wavelength
160168
and the other is in frequency units. [#1187]
161169

170+
162171
Other Changes and Additions
163172
^^^^^^^^^^^^^^^^^^^^^^^^^^^
164173

165174
- Replaced ``LevMarLSQFitter`` with ``TRFLSQFitter`` as the former is no longer
166175
recommended by ``astropy``. [#1180]
167176

177+
- "Multi" loaders have been removed from SDSS-V ``SpectrumList`` default loaders. [#1185]
178+
168179
1.17.0 (2024-10-04)
169180
-------------------
170181

‎specutils/io/default_loaders/sdss_v.py‎

Lines changed: 195 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,5 @@
11
"""Register reader functions for various spectral formats."""
2+
23
import warnings
34
from typing import Optional
45

@@ -87,7 +88,22 @@ def mwm_identify(origin, *args, **kwargs):
8788
with read_fileobj_or_hdulist(*args, **kwargs) as hdulist:
8889
return (("V_ASTRA" in hdulist[0].header.keys()) and len(hdulist) > 0
8990
and ("SDSS_ID" in hdulist[0].header.keys())
90-
and (isinstance(hdulist[i], BinTableHDU) for i in range(1, 5)))
91+
and (isinstance(hdulist[i], BinTableHDU) for i in range(1, 5))
92+
and all("model_flux" not in hdulist[i].columns.names
93+
for i in range(1, 5)))
94+
95+
96+
def astra_identify(origin, *args, **kwargs):
97+
"""
98+
Check whether given input is FITS and has SDSS-V astra model spectra
99+
BINTABLE in all 4 extensions. This is used for Astropy I/O Registry.
100+
"""
101+
with read_fileobj_or_hdulist(*args, **kwargs) as hdulist:
102+
return (("V_ASTRA" in hdulist[0].header.keys()) and len(hdulist) > 0
103+
and ("SDSS_ID" in hdulist[0].header.keys())
104+
and (isinstance(hdulist[i], BinTableHDU) for i in range(1, 5))
105+
and all("model_flux" in hdulist[i].columns.names
106+
for i in range(1, 5)))
91107

92108

93109
def _wcs_log_linear(naxis, cdelt, crval):
@@ -343,7 +359,7 @@ def load_sdss_spec_1D(file_obj, *args, hdu: Optional[int] = None, **kwargs):
343359
"""
344360
if hdu is None:
345361
# TODO: how should we handle this -- multiple things in file, but the user cannot choose.
346-
warnings.warn('HDU not specified. Loading coadd spectrum (HDU1)',
362+
warnings.warn("HDU not specified. Loading coadd spectrum (HDU1)",
347363
AstropyUserWarning)
348364
hdu = 1 # defaulting to coadd
349365
# raise ValueError("HDU not specified! Please specify a HDU to load.")
@@ -471,7 +487,6 @@ def load_sdss_mwm_1d(file_obj,
471487
if (np.array(datasums) == 0).all():
472488
raise ValueError("Specified file is empty.")
473489

474-
# TODO: how should we handle this -- multiple things in file, but the user cannot choose.
475490
if hdu is None:
476491
for i, hduext in enumerate(hdulist):
477492
if hduext.header.get("DATASUM") != "0" and len(hduext.data) > 0:
@@ -597,15 +612,190 @@ def _load_mwmVisit_or_mwmStar_hdu(hdulist: HDUList, hdu: int, **kwargs):
597612

598613
# choose between mwmVisit/Star via KeyError except
599614
try:
600-
meta['mjd'] = hdulist[hdu].data['mjd']
615+
meta["mjd"] = hdulist[hdu].data["mjd"]
601616
meta["datatype"] = "mwmVisit"
602617
except KeyError:
603618
meta["min_mjd"] = str(hdulist[hdu].data["min_mjd"][0])
604619
meta["max_mjd"] = str(hdulist[hdu].data["max_mjd"][0])
605620
meta["datatype"] = "mwmStar"
606621
finally:
607622
meta["name"] = hdulist[hdu].name
608-
meta["sdss_id"] = hdulist[hdu].data['sdss_id']
623+
meta["sdss_id"] = hdulist[hdu].data["sdss_id"]
624+
625+
# drop back a list of Spectrum1Ds to unpack
626+
return Spectrum1D(
627+
spectral_axis=spectral_axis,
628+
flux=flux,
629+
uncertainty=e_flux,
630+
mask=mask,
631+
meta=meta,
632+
)
633+
634+
635+
@data_loader(
636+
"SDSS-V astra model",
637+
identifier=astra_identify,
638+
dtype=Spectrum1D,
639+
priority=20,
640+
extensions=["fits"],
641+
)
642+
def load_astra_1d(file_obj, hdu: Optional[int] = None, **kwargs):
643+
"""
644+
Load an astra model spectrum file as a Spectrum1D.
645+
646+
Parameters
647+
----------
648+
file_obj : str, file-like, or HDUList
649+
FITS file name, file object, or HDUList.
650+
hdu : int
651+
Specified HDU to load.
652+
653+
Returns
654+
-------
655+
spectrum : Spectrum1D
656+
The spectra contained in the file from the provided HDU OR the first entry.
657+
"""
658+
with read_fileobj_or_hdulist(file_obj, memmap=False, **kwargs) as hdulist:
659+
# Check if file is empty first
660+
datasums = []
661+
for i in range(1, len(hdulist)):
662+
datasums.append(int(hdulist[i].header.get("DATASUM")))
663+
if (np.array(datasums) == 0).all():
664+
raise ValueError("Specified file is empty.")
665+
666+
if hdu is None:
667+
for i in range(1, len(hdulist)):
668+
if hdulist[i].header.get("DATASUM") != "0":
669+
hdu = i
670+
warnings.warn(
671+
"HDU not specified. Loading spectrum at (HDU{})".
672+
format(i),
673+
AstropyUserWarning,
674+
)
675+
break
676+
677+
return _load_astra_hdu(hdulist, hdu, **kwargs)
678+
679+
680+
@data_loader(
681+
"SDSS-V astra model",
682+
identifier=astra_identify,
683+
force=True,
684+
dtype=SpectrumList,
685+
priority=20,
686+
extensions=["fits"],
687+
)
688+
def load_astra_list(file_obj, **kwargs):
689+
"""
690+
Load an astra model spectrum file as a SpectrumList.
691+
692+
Parameters
693+
----------
694+
file_obj : str, file-like, or HDUList
695+
FITS file name, file object, or HDUList.
696+
697+
Returns
698+
-------
699+
spectra: SpectrumList
700+
All of the spectra contained in the file.
701+
"""
702+
spectra = SpectrumList()
703+
with read_fileobj_or_hdulist(file_obj, memmap=False, **kwargs) as hdulist:
704+
# Check if file is empty first
705+
datasums = []
706+
for hdu in range(1, len(hdulist)):
707+
datasums.append(int(hdulist[hdu].header.get("DATASUM")))
708+
if (np.array(datasums) == 0).all():
709+
raise ValueError("Specified file is empty.")
710+
711+
# Now load file
712+
for hdu in range(1, len(hdulist)):
713+
if hdulist[hdu].header.get("DATASUM") == "0":
714+
# Skip zero data HDU's
715+
continue
716+
spectra.append(_load_astra_hdu(hdulist, hdu))
717+
return spectra
718+
719+
720+
def _load_astra_hdu(hdulist: HDUList, hdu: int, **kwargs):
721+
"""
722+
HDU loader subfunction for astra model spectrum files
723+
724+
Parameters
725+
----------
726+
hdulist: HDUList
727+
HDUList generated from imported file.
728+
hdu: int
729+
Specified HDU to load.
730+
731+
Returns
732+
-------
733+
Spectrum1D
734+
The spectrum with nD flux contained in the HDU.
735+
736+
"""
737+
if hdulist[hdu].header.get("DATASUM") == "0":
738+
raise IndexError(
739+
"Attemped to load an empty HDU specified at HDU{}".format(hdu))
740+
741+
# Fetch wavelength
742+
# encoded as WCS for visit, and 'wavelength' for star
743+
try:
744+
wavelength = np.array(hdulist[hdu].data["wavelength"])[0]
745+
except KeyError:
746+
wavelength = _wcs_log_linear(
747+
hdulist[hdu].header.get("NPIXELS"),
748+
hdulist[hdu].header.get("CDELT"),
749+
hdulist[hdu].header.get("CRVAL"),
750+
)
751+
finally:
752+
if wavelength is None:
753+
raise ValueError(
754+
"Couldn't find wavelength data in HDU{}.".format(hdu))
755+
spectral_axis = Quantity(wavelength, unit=Angstrom)
756+
757+
# Fetch flux, e_flux
758+
# NOTE:: flux info is not written
759+
flux_unit = Unit("1e-17 erg / (Angstrom cm2 s)") # NOTE: hardcoded unit
760+
flux = Quantity(hdulist[hdu].data["model_flux"] *
761+
hdulist[hdu].data["continuum"],
762+
unit=flux_unit)
763+
e_flux = InverseVariance(array=hdulist[hdu].data["ivar"])
764+
765+
# Collect bitmask
766+
mask = hdulist[hdu].data["pixel_flags"]
767+
# NOTE: specutils considers 0/False as valid values, simlar to numpy convention
768+
mask = mask != 0
769+
770+
# collapse shape if 1D spectra in 2D array, makes readout easier
771+
if flux.shape[0] == 1:
772+
flux = np.ravel(flux)
773+
e_flux = e_flux[0] # different class
774+
mask = np.ravel(mask)
775+
776+
# Create metadata
777+
meta = dict()
778+
meta["header"] = hdulist[0].header
779+
780+
# Add identifiers (obj, telescope, mjd, datatype)
781+
meta["telescope"] = hdulist[hdu].data["telescope"]
782+
meta["instrument"] = hdulist[hdu].header.get("INSTRMNT")
783+
try: # get obj if exists
784+
meta["obj"] = hdulist[hdu].data["obj"]
785+
except KeyError:
786+
pass
787+
788+
# choose between mwmVisit/Star via KeyError except
789+
try:
790+
meta["mjd"] = hdulist[hdu].data["mjd"]
791+
meta["datatype"] = "astraVisit"
792+
except KeyError:
793+
meta["min_mjd"] = str(hdulist[hdu].data["min_mjd"][0])
794+
meta["max_mjd"] = str(hdulist[hdu].data["max_mjd"][0])
795+
meta["datatype"] = "astraStar"
796+
finally:
797+
meta["name"] = hdulist[hdu].name
798+
meta["sdss_id"] = hdulist[hdu].data["sdss_id"]
609799

610800
# drop back a list of Spectrum objects to unpack
611801
return Spectrum(

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