import logging
import os
import numpy as np
from astropy.io import fits
from spectral_cube import SpectralCube
from spectral_cube.io.fits import FITSReadError
from specutils import Spectrum1D
from jdaviz.core.registries import data_parser_registry
__all__ = ['parse_data']
EXT_TYPES = dict(flux=['flux', 'sci'],
uncert=['ivar', 'err', 'var', 'uncert'],
mask=['mask', 'dq'])
[docs]@data_parser_registry("cubeviz-data-parser")
def parse_data(app, file_obj, data_type=None, data_label=None):
"""
Attempts to parse a data file and auto-populate available viewers in
cubeviz.
Parameters
----------
app : `~jdaviz.app.Application`
The application-level object used to reference the viewers.
file_path : str
The path to a cube-like data file.
data_type : str, {'flux', 'mask', 'uncert'}
The data type used to explicitly differentiate parsed data.
data_label : str, optional
The label applicad to the glue data component.
"""
if data_type is not None and data_type.lower() not in ['flux', 'mask', 'uncert']:
msg = "Data type must be one of 'flux', 'mask', or 'uncertainty'."
logging.error(msg)
return msg
# If the file object is an hdulist or a string, use the generic parser for
# fits files.
# TODO: this currently only supports fits files. We will want to make this
# generic enough to work with other file types (e.g. ASDF). For now, this
# supports MaNGA and JWST data.
if isinstance(file_obj, fits.hdu.hdulist.HDUList):
_parse_hdu(app, file_obj)
elif isinstance(file_obj, str) and os.path.exists(file_obj):
file_name = os.path.basename(file_obj)
with fits.open(file_obj) as hdulist:
hdulist = fits.open(file_obj)
_parse_hdu(app, hdulist, file_name)
# If the data types are custom data objects, use explicit parsers. Note
# that this relies on the glue-astronomy machinery to turn the data object
# into something glue can understand.
elif isinstance(file_obj, SpectralCube):
_parse_spectral_cube(app, file_obj, data_type or 'flux', data_label)
elif isinstance(file_obj, Spectrum1D):
_parse_spectrum1d(app, file_obj)
def _parse_hdu(app, hdulist, file_name=None):
if hasattr(hdulist, 'file_name'):
file_name = hdulist.file_name
file_name = file_name or "Unknown HDU object"
# WCS may only exist in a single extension (in this case, just the flux
# flux extention), so first find and store then wcs information.
wcs = None
for hdu in hdulist:
if hdu.data is None:
continue
try:
sc = SpectralCube.read(hdulist, format='fits')
wcs = sc.wcs
except (ValueError, FITSReadError):
continue
# Now loop through and attempt to parse the fits extensions as spectral
# cube object. If the wcs fails to parse in any case, use the wcs
# information we scraped above.
for hdu in hdulist:
data_label = f"{file_name}[{hdu.name}]"
if hdu.data is None:
continue
# This is supposed to fail on attempting to load anything that
# isn't cube-shaped. But it's not terribly reliable
try:
sc = SpectralCube.read(hdu, format='fits')
except (ValueError, OSError):
# This will fail if the parsing of the wcs does not provide
# proper celestial axes
try:
hdu.header.update(wcs.to_header())
sc = SpectralCube.read(hdu)
except (ValueError, AttributeError) as e:
logging.warn(e)
continue
except FITSReadError as e:
logging.warn(e)
continue
app.data_collection[data_label] = sc
# If the data type is some kind of integer, assume it's the mask/dq
if hdu.data.dtype in (np.int, np.uint, np.uint32) or \
any(x in hdu.name.lower() for x in EXT_TYPES['mask']):
app.add_data_to_viewer('mask-viewer', data_label)
if 'errtype' in [x.lower() for x in hdu.header.keys()] or \
any(x in hdu.name.lower() for x in EXT_TYPES['uncert']):
app.add_data_to_viewer('uncert-viewer', data_label)
if any(x in hdu.name.lower() for x in EXT_TYPES['flux']):
app.add_data_to_viewer('flux-viewer', data_label)
app.add_data_to_viewer('spectrum-viewer', data_label)
def _parse_spectral_cube(app, file_obj, data_type='flux', data_label=None):
data_label = data_label or f"Unknown spectral cube[{data_type.upper()}]"
app.data_collection[f"{data_label}"] = file_obj
if data_type == 'flux':
app.add_data_to_viewer('flux-viewer', f"{data_label}")
app.add_data_to_viewer('spectrum-viewer', f"{data_label}")
elif data_type == 'mask':
app.add_data_to_viewer('mask-viewer', f"{data_label}")
elif data_type == 'uncert':
app.add_data_to_viewer('uncert-viewer', f"{data_label}")
# TODO: SpectralCube does not store mask information
# TODO: SpectralCube does not store data quality information
def _parse_spectrum1d(app, file_obj):
data_label = "Unknown spectrum object"
# TODO: glue-astronomy translators only look at the flux property of
# specutils Spectrum1D objects. Fix to support uncertainties and masks.
app.data_collection[f"{data_label}[FLUX]"] = file_obj
app.add_data_to_viewer('spectrum-viewer', f"{data_label}[FLUX]")