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Add SAMI loaders for testing updated DC loaders
This adds an initial version of the future SAMI loaders, in order to test the changes to the lower level DC loaders.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,185 @@ | ||
| from astropy.nddata import VarianceUncertainty | ||
| from astropy.table import QTable | ||
| from specutils import SpectrumList | ||
| from specutils.io.default_loaders.dc_common import ( | ||
| FITS_FILE_EXTS, add_single_spectra_to_map, | ||
| ) | ||
| from specutils.io.parsing_utils import read_fileobj_or_hdulist | ||
| from specutils.io.registers import data_loader | ||
|
|
||
| # There appears to be nothing which says "this is a SAMI 1D spectra", so guess | ||
| # it based on the headers that should be there | ||
| SAMI_1D_SPECTRA_HEADER_KEYWORDS = [ | ||
| "BUNIT", "CATADEC", "CATARA", "CDELT1", "CRPIX1", "CRVAL1", "CTYPE1", | ||
| "CUNIT1", "DROPFACT", "ELLIP", "GRATID", "IFUPROBE", "KPC_SIZE", "NAME", | ||
| "N_SPAX", "POS_ANG", "PSFALPHA", "PSFBETA", "PSFFWHM", "RADESYS", "RADIUS", | ||
| "RO_GAIN", "RO_NOISE", "STDNAME", "WCSAXES", "Z_TONRY", | ||
| ] | ||
|
|
||
|
|
||
| def identify_sami_cube(origin, *args, **kwargs): | ||
| """ | ||
| Identify if the current file is a SAMI cube file | ||
| """ | ||
| # TODO check this | ||
| with read_fileobj_or_hdulist(*args, **kwargs) as hdulist: | ||
| header = hdulist[0].header | ||
| data = hdulist[0].data | ||
| if "SAMI" in header.get("INSTRUME", "") and len(data.shape) == 3: | ||
| return True | ||
| return False | ||
|
|
||
|
|
||
| def identify_sami_1d_spec(origin, *args, **kwargs): | ||
| """ | ||
| Identify if the current file is a SAMI 1d spectra file of some kind | ||
| """ | ||
| # TODO check this | ||
| with read_fileobj_or_hdulist(*args, **kwargs) as hdulist: | ||
| header = hdulist[0].header | ||
| for key in SAMI_1D_SPECTRA_HEADER_KEYWORDS: | ||
| if key not in header: | ||
| return False | ||
| return True | ||
|
|
||
|
|
||
| @data_loader( | ||
| label="SAMI-cube", extensions=FITS_FILE_EXTS, dtype=SpectrumList, | ||
| identifier=identify_sami_cube, priority=10, | ||
| ) | ||
| def sami_cube_loader(filename): | ||
| spectra_map = { | ||
| "sky": [], | ||
| "combined": [], | ||
| "unreduced": [], | ||
| "reduced": [], | ||
| } | ||
| primary_header = None | ||
|
|
||
| with read_fileobj_or_hdulist(filename) as hdulist: | ||
| for i, hdu in enumerate(hdulist): | ||
| if i == 0: | ||
| # This is the primary extension, and the one with the | ||
| # science data. The header is fairly complete. | ||
| primary_header = hdu.header | ||
| spec = add_single_spectra_to_map( | ||
| spectra_map, | ||
| header=primary_header, | ||
| data=hdu.data, | ||
| index=None, | ||
| all_standard_units=True, | ||
| all_keywords=True, | ||
| valid_wcs=True, | ||
| ) | ||
|
|
||
| elif "VARIANCE" == hdu.header.get("EXTNAME"): | ||
| # This is the variance extension, and is missing wcs and | ||
| # units. | ||
| uncertainty = VarianceUncertainty( | ||
| hdu.data, unit=spec.flux.unit ** 2 | ||
| ) | ||
| spec.uncertainty = uncertainty | ||
|
|
||
| elif "WEIGHT" == hdu.header.get("EXTNAME"): | ||
| # This is the weight extension, and is missing wcs. The | ||
| # units are effectively "normalised" (from 0-1 it seems). | ||
| spec.meta["sami_cube_weight_map"] = hdu.data | ||
|
|
||
| elif "COVAR" == hdu.header.get("EXTNAME"): | ||
| # This is the spatial covariance extension. It's not clear | ||
| # as to how best to expose this, so skipping for now. | ||
| pass | ||
|
|
||
| elif "QC" == hdu.header.get("EXTNAME"): | ||
| # This is the QC extension, and is a binary table. This we | ||
| # add to the metadata. | ||
| spec.meta["sami_QC_table"] = QTable.read(hdu) | ||
|
|
||
| elif "DUST" == hdu.header.get("EXTNAME"): | ||
| # This is the dust extension, and is missing wcs and | ||
| # units. This should likely be represented as an array plus | ||
| # the metadata in the header. | ||
| spec.meta["sami_dust_vector_weights"] = hdu.data | ||
|
|
||
| elif "BIN_MASK" == hdu.header.get("EXTNAME"): | ||
| # This is the bin mask extension, where the value of each | ||
| # pixel indicates the bin to which it belongs. The bin mask | ||
| # is used to construct the binned fluxes and variances in | ||
| # the above two extensions from the default cubes. | ||
| # This is not the same as the aperture spectra mask with the | ||
| # same HDU name. | ||
| spec.meta["sami_bin_mask"] = hdu.data | ||
|
|
||
| else: | ||
| raise NotImplementedError( | ||
| "Extension is not handled: index {}; name {}".format( | ||
| i, hdu.header.get("EXTNAME") | ||
| ) | ||
| ) | ||
|
|
||
| spectra = SpectrumList( | ||
| spectra_map["combined"] + | ||
| spectra_map["reduced"] + | ||
| spectra_map["unreduced"] + | ||
| spectra_map["sky"] | ||
| ) | ||
| return spectra | ||
|
|
||
|
|
||
| @data_loader( | ||
| label="SAMI-1d-spec", extensions=FITS_FILE_EXTS, dtype=SpectrumList, | ||
| identifier=identify_sami_1d_spec, priority=10, | ||
| ) | ||
| def sami_1d_spec_loader(filename): | ||
| spectra_map = { | ||
| "sky": [], | ||
| "combined": [], | ||
| "unreduced": [], | ||
| "reduced": [], | ||
| } | ||
| primary_header = None | ||
|
|
||
| with read_fileobj_or_hdulist(filename) as hdulist: | ||
| for i, hdu in enumerate(hdulist): | ||
| if i == 0: | ||
| # This is the primary extension, and the one with the | ||
| # science data. The header is fairly complete. | ||
| primary_header = hdu.header | ||
| spec = add_single_spectra_to_map( | ||
| spectra_map, | ||
| header=primary_header, | ||
| data=hdu.data, | ||
| index=None, | ||
| all_standard_units=True, | ||
| all_keywords=True, | ||
| valid_wcs=True, | ||
| ) | ||
|
|
||
| elif "VARIANCE" == hdu.header.get("EXTNAME"): | ||
| # This is the variance extension, and is missing wcs and | ||
| # units. | ||
| uncertainty = VarianceUncertainty( | ||
| hdu.data, unit=spec.flux.unit ** 2 | ||
| ) | ||
| spec.uncertainty = uncertainty | ||
|
|
||
| elif "BIN_MASK" == hdu.header.get("EXTNAME"): | ||
| # Contains the bin mask used to construct the aperture | ||
| # spectra. A 1 indicates a spaxel was included in the | ||
| # aperture, a 0 indicates a spaxel was not included. | ||
| spec.meta["sami_aperture_spectra_mask"] = hdu.data | ||
|
|
||
| else: | ||
| raise NotImplementedError( | ||
| "Extension is not handled: index {}; name {}".format( | ||
| i, hdu.header.get("EXTNAME") | ||
| ) | ||
| ) | ||
|
|
||
| spectra = SpectrumList( | ||
| spectra_map["combined"] + | ||
| spectra_map["reduced"] + | ||
| spectra_map["unreduced"] + | ||
| spectra_map["sky"] | ||
| ) | ||
| return spectra | ||
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