# Licensed under a 3-clause BSD style license - see LICENSE.rst """This module implements the base CCDData class.""" from __future__ import (absolute_import, division, print_function, unicode_literals) import numpy as np from .compat import NDDataArray from .nduncertainty import StdDevUncertainty, NDUncertainty from ..io import fits, registry from .. import units as u from .. import log from ..wcs import WCS from ..utils.decorators import sharedmethod __all__ = ['CCDData', 'fits_ccddata_reader', 'fits_ccddata_writer'] # Global value which can turn on/off the unit requirements when creating a # CCDData. Should be used with care because several functions actually break # if the unit is None! _config_ccd_requires_unit = True def _arithmetic(op): """Decorator factory which temporarly disables the need for a unit when creating a new CCDData instance. The final result must have a unit. Parameters ---------- op : function The function to apply. Supported are: - ``np.add`` - ``np.subtract`` - ``np.multiply`` - ``np.true_divide`` Notes ----- Should only be used on CCDData ``add``, ``subtract``, ``divide`` or ``multiply`` because only these methods from NDArithmeticMixin are overwritten. """ def decorator(func): def inner(self, operand, operand2=None, **kwargs): global _config_ccd_requires_unit _config_ccd_requires_unit = False result = self._prepare_then_do_arithmetic(op, operand, operand2, **kwargs) # Wrap it again as CCDData so it checks the final unit. _config_ccd_requires_unit = True return result.__class__(result) inner.__doc__ = ("See `astropy.nddata.NDArithmeticMixin.{}`." "".format(func.__name__)) return sharedmethod(inner) return decorator class CCDData(NDDataArray): """A class describing basic CCD data. The CCDData class is based on the NDData object and includes a data array, uncertainty frame, mask frame, flag frame, meta data, units, and WCS information for a single CCD image. Parameters ----------- data : `~astropy.nddata.CCDData`-like or `numpy.ndarray`-like The actual data contained in this `~astropy.nddata.CCDData` object. Note that the data will always be saved by *reference*, so you should make a copy of the ``data`` before passing it in if that's the desired behavior. uncertainty : `~astropy.nddata.StdDevUncertainty`, `numpy.ndarray` or \ None, optional Uncertainties on the data. Default is ``None``. mask : `numpy.ndarray` or None, optional Mask for the data, given as a boolean Numpy array with a shape matching that of the data. The values must be `False` where the data is *valid* and `True` when it is not (like Numpy masked arrays). If ``data`` is a numpy masked array, providing ``mask`` here will causes the mask from the masked array to be ignored. Default is ``None``. flags : `numpy.ndarray` or `~astropy.nddata.FlagCollection` or None, \ optional Flags giving information about each pixel. These can be specified either as a Numpy array of any type with a shape matching that of the data, or as a `~astropy.nddata.FlagCollection` instance which has a shape matching that of the data. Default is ``None``. wcs : `~astropy.wcs.WCS` or None, optional WCS-object containing the world coordinate system for the data. Default is ``None``. meta : dict-like object or None, optional Metadata for this object. "Metadata" here means all information that is included with this object but not part of any other attribute of this particular object, e.g. creation date, unique identifier, simulation parameters, exposure time, telescope name, etc. unit : `~astropy.units.Unit` or str, optional The units of the data. Default is ``None``. .. warning:: If the unit is ``None`` or not otherwise specified it will raise a ``ValueError`` Raises ------ ValueError If the ``uncertainty`` or ``mask`` inputs cannot be broadcast (e.g., match shape) onto ``data``. Methods ------- read(\\*args, \\**kwargs) ``Classmethod`` to create an CCDData instance based on a ``FITS`` file. This method uses :func:`fits_ccddata_reader` with the provided parameters. write(\\*args, \\**kwargs) Writes the contents of the CCDData instance into a new ``FITS`` file. This method uses :func:`fits_ccddata_writer` with the provided parameters. Notes ----- `~astropy.nddata.CCDData` objects can be easily converted to a regular Numpy array using `numpy.asarray`. For example:: >>> from astropy.nddata import CCDData >>> import numpy as np >>> x = CCDData([1,2,3], unit='adu') >>> np.asarray(x) array([1, 2, 3]) This is useful, for example, when plotting a 2D image using matplotlib. >>> from astropy.nddata import CCDData >>> from matplotlib import pyplot as plt # doctest: +SKIP >>> x = CCDData([[1,2,3], [4,5,6]], unit='adu') >>> plt.imshow(x) # doctest: +SKIP """ def __init__(self, *args, **kwd): if 'meta' not in kwd: kwd['meta'] = kwd.pop('header', None) if 'header' in kwd: raise ValueError("can't have both header and meta.") super(CCDData, self).__init__(*args, **kwd) # Check if a unit is set. This can be temporarly disabled by the # _CCDDataUnit contextmanager. if _config_ccd_requires_unit and self.unit is None: raise ValueError("a unit for CCDData must be specified.") @property def data(self): return self._data @data.setter def data(self, value): self._data = value @property def wcs(self): return self._wcs @wcs.setter def wcs(self, value): self._wcs = value @property def unit(self): return self._unit @unit.setter def unit(self, value): self._unit = u.Unit(value) @property def header(self): return self._meta @header.setter def header(self, value): self.meta = value @property def uncertainty(self): return self._uncertainty @uncertainty.setter def uncertainty(self, value): if value is not None: if isinstance(value, NDUncertainty): if getattr(value, '_parent_nddata', None) is not None: value = value.__class__(value, copy=False) self._uncertainty = value elif isinstance(value, np.ndarray): if value.shape != self.shape: raise ValueError("uncertainty must have same shape as " "data.") self._uncertainty = StdDevUncertainty(value) log.info("array provided for uncertainty; assuming it is a " "StdDevUncertainty.") else: raise TypeError("uncertainty must be an instance of a " "NDUncertainty object or a numpy array.") self._uncertainty.parent_nddata = self else: self._uncertainty = value def to_hdu(self, hdu_mask='MASK', hdu_uncertainty='UNCERT', hdu_flags=None, wcs_relax=True): """Creates an HDUList object from a CCDData object. Parameters ---------- hdu_mask, hdu_uncertainty, hdu_flags : str or None, optional If it is a string append this attribute to the HDUList as `~astropy.io.fits.ImageHDU` with the string as extension name. Flags are not supported at this time. If ``None`` this attribute is not appended. Default is ``'MASK'`` for mask, ``'UNCERT'`` for uncertainty and ``None`` for flags. wcs_relax : bool Value of the ``relax`` parameter to use in converting the WCS to a FITS header using `~astropy.wcs.WCS.to_header`. The common ``CTYPE`` ``RA---TAN-SIP`` and ``DEC--TAN-SIP`` requires ``relax=True`` for the ``-SIP`` part of the ``CTYPE`` to be preserved. Raises ------- ValueError - If ``self.mask`` is set but not a `numpy.ndarray`. - If ``self.uncertainty`` is set but not a `~astropy.nddata.StdDevUncertainty`. - If ``self.uncertainty`` is set but has another unit then ``self.data``. NotImplementedError Saving flags is not supported. Returns ------- hdulist : `~astropy.io.fits.HDUList` """ if isinstance(self.header, fits.Header): # Copy here so that we can modify the HDU header by adding WCS # information without changing the header of the CCDData object. header = self.header.copy() else: # Because _insert_in_metadata_fits_safe is written as a method # we need to create a dummy CCDData instance to hold the FITS # header we are constructing. This probably indicates that # _insert_in_metadata_fits_safe should be rewritten in a more # sensible way... dummy_ccd = CCDData([1], meta=fits.Header(), unit="adu") for k, v in self.header.items(): dummy_ccd._insert_in_metadata_fits_safe(k, v) header = dummy_ccd.header if self.unit is not u.dimensionless_unscaled: header['bunit'] = self.unit.to_string() if self.wcs: # Simply extending the FITS header with the WCS can lead to # duplicates of the WCS keywords; iterating over the WCS # header should be safer. # # Turns out if I had read the io.fits.Header.extend docs more # carefully, I would have realized that the keywords exist to # avoid duplicates and preserve, as much as possible, the # structure of the commentary cards. # # Note that until astropy/astropy#3967 is closed, the extend # will fail if there are comment cards in the WCS header but # not header. wcs_header = self.wcs.to_header(relax=wcs_relax) header.extend(wcs_header, useblanks=False, update=True) hdus = [fits.PrimaryHDU(self.data, header)] if hdu_mask and self.mask is not None: # Always assuming that the mask is a np.ndarray (check that it has # a 'shape'). if not hasattr(self.mask, 'shape'): raise ValueError('only a numpy.ndarray mask can be saved.') # Convert boolean mask to uint since io.fits cannot handle bool. hduMask = fits.ImageHDU(self.mask.astype(np.uint8), name=hdu_mask) hdus.append(hduMask) if hdu_uncertainty and self.uncertainty is not None: # We need to save some kind of information which uncertainty was # used so that loading the HDUList can infer the uncertainty type. # No idea how this can be done so only allow StdDevUncertainty. if self.uncertainty.__class__.__name__ != 'StdDevUncertainty': raise ValueError('only StdDevUncertainty can be saved.') # Assuming uncertainty is an StdDevUncertainty save just the array # this might be problematic if the Uncertainty has a unit differing # from the data so abort for different units. This is important for # astropy > 1.2 if (hasattr(self.uncertainty, 'unit') and self.uncertainty.unit is not None and self.uncertainty.unit != self.unit): raise ValueError('saving uncertainties with a unit differing' 'from the data unit is not supported.') hduUncert = fits.ImageHDU(self.uncertainty.array, name=hdu_uncertainty) hdus.append(hduUncert) if hdu_flags and self.flags: raise NotImplementedError('adding the flags to a HDU is not ' 'supported at this time.') hdulist = fits.HDUList(hdus) return hdulist def copy(self): """ Return a copy of the CCDData object. """ return self.__class__(self, copy=True) add = _arithmetic(np.add)(NDDataArray.add) subtract = _arithmetic(np.subtract)(NDDataArray.subtract) multiply = _arithmetic(np.multiply)(NDDataArray.multiply) divide = _arithmetic(np.true_divide)(NDDataArray.divide) def _insert_in_metadata_fits_safe(self, key, value): """ Insert key/value pair into metadata in a way that FITS can serialize. Parameters ---------- key : str Key to be inserted in dictionary. value : str or None Value to be inserted. Notes ----- This addresses a shortcoming of the FITS standard. There are length restrictions on both the ``key`` (8 characters) and ``value`` (72 characters) in the FITS standard. There is a convention for handling long keywords and a convention for handling long values, but the two conventions cannot be used at the same time. This addresses that case by checking the length of the ``key`` and ``value`` and, if necessary, shortening the key. """ if len(key) > 8 and len(value) > 72: short_name = key[:8] self.meta['HIERARCH {0}'.format(key.upper())] = ( short_name, "Shortened name for {}".format(key)) self.meta[short_name] = value else: self.meta[key] = value # This needs to be importable by the tests... _KEEP_THESE_KEYWORDS_IN_HEADER = [ 'JD-OBS', 'MJD-OBS', 'DATE-OBS' ] def _generate_wcs_and_update_header(hdr): """ Generate a WCS object from a header and remove the WCS-specific keywords from the header. Parameters ---------- hdr : astropy.io.fits.header or other dict-like Returns ------- new_header, wcs """ # Try constructing a WCS object. try: wcs = WCS(hdr) except Exception as exc: # Normally WCS only raises Warnings and doesn't fail but in rare # cases (malformed header) it could fail... log.info('An exception happened while extracting WCS informations from ' 'the Header.\n{}: {}'.format(type(exc).__name__, str(exc))) return hdr, None # Test for success by checking to see if the wcs ctype has a non-empty # value, return None for wcs if ctype is empty. if not wcs.wcs.ctype[0]: return (hdr, None) new_hdr = hdr.copy() # If the keywords below are in the header they are also added to WCS. # It seems like they should *not* be removed from the header, though. wcs_header = wcs.to_header(relax=True) for k in wcs_header: if k not in _KEEP_THESE_KEYWORDS_IN_HEADER: new_hdr.remove(k, ignore_missing=True) return (new_hdr, wcs) def fits_ccddata_reader(filename, hdu=0, unit=None, hdu_uncertainty='UNCERT', hdu_mask='MASK', hdu_flags=None, **kwd): """ Generate a CCDData object from a FITS file. Parameters ---------- filename : str Name of fits file. hdu : int, optional FITS extension from which CCDData should be initialized. If zero and and no data in the primary extension, it will search for the first extension with data. The header will be added to the primary header. Default is ``0``. unit : `~astropy.units.Unit`, optional Units of the image data. If this argument is provided and there is a unit for the image in the FITS header (the keyword ``BUNIT`` is used as the unit, if present), this argument is used for the unit. Default is ``None``. hdu_uncertainty : str or None, optional FITS extension from which the uncertainty should be initialized. If the extension does not exist the uncertainty of the CCDData is ``None``. Default is ``'UNCERT'``. hdu_mask : str or None, optional FITS extension from which the mask should be initialized. If the extension does not exist the mask of the CCDData is ``None``. Default is ``'MASK'``. hdu_flags : str or None, optional Currently not implemented. Default is ``None``. kwd : Any additional keyword parameters are passed through to the FITS reader in :mod:`astropy.io.fits`; see Notes for additional discussion. Notes ----- FITS files that contained scaled data (e.g. unsigned integer images) will be scaled and the keywords used to manage scaled data in :mod:`astropy.io.fits` are disabled. """ unsupport_open_keywords = { 'do_not_scale_image_data': 'Image data must be scaled.', 'scale_back': 'Scale information is not preserved.' } for key, msg in unsupport_open_keywords.items(): if key in kwd: prefix = 'unsupported keyword: {0}.'.format(key) raise TypeError(' '.join([prefix, msg])) with fits.open(filename, **kwd) as hdus: hdr = hdus[hdu].header if hdu_uncertainty is not None and hdu_uncertainty in hdus: uncertainty = StdDevUncertainty(hdus[hdu_uncertainty].data) else: uncertainty = None if hdu_mask is not None and hdu_mask in hdus: # Mask is saved as uint but we want it to be boolean. mask = hdus[hdu_mask].data.astype(np.bool_) else: mask = None if hdu_flags is not None and hdu_flags in hdus: raise NotImplementedError('loading flags is currently not ' 'supported.') # search for the first instance with data if # the primary header is empty. if hdu == 0 and hdus[hdu].data is None: for i in range(len(hdus)): if (hdus.info(hdu)[i][3] == 'ImageHDU' and hdus.fileinfo(i)['datSpan'] > 0): hdu = i comb_hdr = hdus[hdu].header.copy() # Add header values from the primary header that aren't # present in the extension header. comb_hdr.extend(hdr, unique=True) hdr = comb_hdr log.info("first HDU with data is extension " "{0}.".format(hdu)) break if 'bunit' in hdr: fits_unit_string = hdr['bunit'] # patch to handle FITS files using ADU for the unit instead of the # standard version of 'adu' if fits_unit_string.strip().lower() == 'adu': fits_unit_string = fits_unit_string.lower() else: fits_unit_string = None if fits_unit_string: if unit is None: # Convert the BUNIT header keyword to a unit and if that's not # possible raise a meaningful error message. try: fits_unit_string = u.Unit(fits_unit_string) except ValueError: raise ValueError( 'The Header value for the key BUNIT ({}) cannot be ' 'interpreted as valid unit. To successfully read the ' 'file as CCDData you can pass in a valid `unit` ' 'argument explicitly or change the header of the FITS ' 'file before reading it.' .format(fits_unit_string)) else: log.info("using the unit {0} passed to the FITS reader instead " "of the unit {1} in the FITS file." .format(unit, fits_unit_string)) use_unit = unit or fits_unit_string hdr, wcs = _generate_wcs_and_update_header(hdr) ccd_data = CCDData(hdus[hdu].data, meta=hdr, unit=use_unit, mask=mask, uncertainty=uncertainty, wcs=wcs) return ccd_data def fits_ccddata_writer(ccd_data, filename, hdu_mask='MASK', hdu_uncertainty='UNCERT', hdu_flags=None, **kwd): """ Write CCDData object to FITS file. Parameters ---------- filename : str Name of file. hdu_mask, hdu_uncertainty, hdu_flags : str or None, optional If it is a string append this attribute to the HDUList as `~astropy.io.fits.ImageHDU` with the string as extension name. Flags are not supported at this time. If ``None`` this attribute is not appended. Default is ``'MASK'`` for mask, ``'UNCERT'`` for uncertainty and ``None`` for flags. kwd : All additional keywords are passed to :py:mod:`astropy.io.fits` Raises ------- ValueError - If ``self.mask`` is set but not a `numpy.ndarray`. - If ``self.uncertainty`` is set but not a `~astropy.nddata.StdDevUncertainty`. - If ``self.uncertainty`` is set but has another unit then ``self.data``. NotImplementedError Saving flags is not supported. """ hdu = ccd_data.to_hdu(hdu_mask=hdu_mask, hdu_uncertainty=hdu_uncertainty, hdu_flags=hdu_flags) hdu.writeto(filename, **kwd) with registry.delay_doc_updates(CCDData): registry.register_reader('fits', CCDData, fits_ccddata_reader) registry.register_writer('fits', CCDData, fits_ccddata_writer) registry.register_identifier('fits', CCDData, fits.connect.is_fits) try: CCDData.read.__doc__ = fits_ccddata_reader.__doc__ except AttributeError: CCDData.read.__func__.__doc__ = fits_ccddata_reader.__doc__ try: CCDData.write.__doc__ = fits_ccddata_writer.__doc__ except AttributeError: CCDData.write.__func__.__doc__ = fits_ccddata_writer.__doc__