Source code for

# This is open-source software licensed under a BSD license.
# Please see the file LICENSE.txt for details.
Module wrapper for loading ASDF files.

.. note:: The API for this module is currently unstable
          and may change in a future release.

import numpy as np

    import asdf  # noqa
    from asdf.fits_embed import AsdfInFits
    have_asdf = True
except ImportError:
    have_asdf = False

from ginga import AstroImage
from ginga.util import iohelper, wcsmod
from import io_base
# need this specific WCS for ASDF loads
from ginga.util.wcsmod import wcs_astropy_ape14   # noqa

__all__ = ['have_asdf', 'load_file', 'load_asdf', 'load_from_asdf',

[docs]def load_from_asdf(asdf_obj, data_key='data', wcs_key='wcs', header_key='meta'): """ Load from an ASDF object. This method is primarily used internally to extract the correct parts of an ASDF file to reconstruct an image with WCS and metadata. Parameters ---------- asdf_obj : obj ASDF or ASDF-in-FITS object. data_key, wcs_key, header_key : str Key values to specify where to find data, WCS, and header in ASDF. Returns ------- data : ndarray or `None` Image data, if found. wcs : obj or `None` GWCS object or models, if found. ahdr : dict Header containing metadata. """ asdf_keys = asdf_obj.keys() if wcs_key in asdf_keys: wcs = asdf_obj[wcs_key] elif wcs_key in asdf_obj[header_key]: wcs = asdf_obj[header_key][wcs_key] else: wcs = None if header_key in asdf_keys: ahdr = asdf_obj[header_key] else: ahdr = {} # TODO: What about non-image ASDF data, such as table? if data_key in asdf_keys: data = np.asarray(asdf_obj[data_key]) # TODO: This hack is so earlier test files would still # load, but we need to make customization easier so # we can remove this hack. elif 'sci' in asdf_keys: data = np.asarray(asdf_obj['sci']) else: data = None return data, wcs, ahdr
[docs]def load_asdf(asdf_obj, idx=None, logger=None): """ Load data from an open ASDF object. Parameters ---------- asdf_obj : obj ASDF or ASDF-in-FITS object. idx : None Currently unused. Reserved for future use to identify specific data set of an ASDF object containing the data of interest. logger : python logging object Currently unused. Reserved for future use in logging Returns ------- data : ndarray or `None` Image data, if found. wcs : obj or `None` GWCS object or models, if found. ahdr : dict Header containing metadata. """ # TODO: support other types, like AstroTable, if ASDF can contain them data_obj = AstroImage.AstroImage(logger=logger) # TODO: idx may contain info about what part of the file to load # e.g. should we pass as 'data_key' parameter? data, wcs, ahdr = load_from_asdf(asdf_obj) data_obj.setup_data(data, naxispath=None) wcsinfo = wcsmod.get_wcs_class('astropy_ape14') data_obj.wcs = wcsinfo.wrapper_class(logger=logger) data_obj.wcs.wcs = wcs if wcs is not None: data_obj.wcs.coordsys = return data_obj
[docs]def load_file(filepath, idx=None, logger=None, **kwargs): """ Load an object from an ASDF file. See :func:`ginga.util.loader` for more info. """ # see ginga.util.loader module opener = ASDFFileHandler(logger) data_obj = opener.load_file(filepath, idx=idx, **kwargs) return data_obj
[docs]class ASDFFileHandler(io_base.BaseIOHandler): """For loading ASDF data files. """ name = 'asdf' mimetypes = ['image/asdf']
[docs] @classmethod def check_availability(cls): if not have_asdf: raise ValueError("Install 'asdf' to use this opener")
def __init__(self, logger): super(ASDFFileHandler, self).__init__(logger) self._path = None
[docs] def load_asdf(self, asdf_f, idx=None, **kwargs): data_obj = load_asdf(asdf_f, idx=idx, logger=self.logger) # set important metadata # TODO: is it possible to set the name without a filename? data_obj.set(idx=idx) = self return data_obj
[docs] def load_asdf_hdu_in_fits(self, fits_f, hdu, **kwargs): """*** This is a special method that should only be called from WITHIN to open up ASDF-embedded-in-FITS *** """ # Handle ASDF embedded in FITS (see load_hdu() in # TODO: Populate EXTNAME, EXTVER, NAXISn in ASDF meta # from HDU? # TODO: How to read from all the different ASDF layouts? # TODO: Cache the ASDF object? # TODO: hdu is ignored for now, but presumably this loader might # eventually want to check it with as asdf_f: data_obj = self.load_asdf(asdf_f, logger=self.logger, **kwargs) # metadata will be hopefully be set back in io_fits return data_obj
[docs] def load_file(self, filepath, idx=None, **kwargs): with as asdf_f: data_obj = load_asdf(asdf_f, idx=idx, logger=self.logger) # set important metadata name = iohelper.name_image_from_path(filepath, idx=None) data_obj.set(path=filepath, name=name, idx=idx, image_loader=load_file) = self return data_obj
[docs] def open_file(self, filepath, **kwargs): # TODO: this should open the ASDF file and make a full inventory # of what is available to load self._path = filepath return self
[docs] def close(self): # TODO: this should close the ASDF file self._path = None
def __len__(self): return 1 def __enter__(self): return self def __exit__(self, exc_type, exc_val, exc_tb): self.close() return False
[docs] def load_idx(self, idx, **kwargs): if self._path is None: raise ValueError("Please call open_file() first!") return self.load_file(self._path, idx=idx, **kwargs)
[docs] def load_idx_cont(self, idx_spec, loader_cont_fn, **kwargs): data_obj = self.load_idx(None, **kwargs) # call continuation function loader_cont_fn(data_obj)