# 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 copy
import numbers
import numpy as np
from astropy.nddata import NDData
from astropy.nddata.nduncertainty import StdDevUncertainty, NDUncertainty
from astropy.io import fits, registry
from astropy import units as u
from astropy import log
from .utils.collections import CaseInsensitiveOrderedDict
__all__ = ['CCDData']
[docs]class CCDData(NDData):
"""A class describing basic CCD data
The CCDData class is based on the NDData object and includes a data array,
uncertainty frame, mask frame, meta data, units, and WCS information for a
single CCD image.
Parameters
-----------
data : `~numpy.ndarray` or :class:`~astropy.nddata.NDData`
The actual data contained in this `~astropy.nddata.NDData` object.
Note that this will always be copies by *reference* , so you should
make copy the `data` before passing it in if that's the desired
behavior.
uncertainty : `~astropy.nddata.StdDevUncertainty` or `~numpy.ndarray`, optional
Uncertainties on the data.
mask : `~numpy.ndarray`, 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.
flags : `~numpy.ndarray` or `~astropy.nddata.FlagCollection`, 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.
wcs : undefined, optional
WCS-object containing the world coordinate system for the data.
.. warning::
This is not yet defind because the discussion of how best to
represent this class's WCS system generically is still under
consideration. For now just leave it as None
meta : `dict`-like object, 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` instance or str, optional
The units of the data.
Raises
------
ValueError
If the `uncertainty` or `.mask` inputs cannot be broadcast (e.g., match
shape) onto `data`.
Notes
-----
`NDData` objects can be easily converted to a regular Numpy array
using `numpy.asarray`
For example::
>>> from astropy.nddata import NDData
>>> import numpy as np
>>> x = NDData([1,2,3])
>>> np.asarray(x)
array([1, 2, 3])
If the `~astropy.nddata.NDData` object has a `mask`, `numpy.asarray` will
return a Numpy masked array.
This is useful, for example, when plotting a 2D image using
matplotlib::
>>> from astropy.nddata import NDData
>>> from matplotlib import pyplot as plt
>>> x = NDData([[1,2,3], [4,5,6]])
>>> plt.imshow(x)
"""
def __init__(self, *args, **kwd):
super(CCDData, self).__init__(*args, **kwd)
if self.unit is None:
raise ValueError("Unit for CCDData must be specified")
@property
def header(self):
return self._meta
@header.setter
def header(self, value):
self.meta = value
@property
def meta(self):
return self._meta
@meta.setter
def meta(self, value):
if value is None:
self._meta = CaseInsensitiveOrderedDict()
else:
h = CaseInsensitiveOrderedDict()
try:
for k, v in value.items():
h[k] = v
except (ValueError, AttributeError):
raise TypeError('NDData meta attribute must be dict-like')
self._meta = h
@property
def uncertainty(self):
return self._uncertainty
@uncertainty.setter
def uncertainty(self, value):
if value is not None:
if isinstance(value, NDUncertainty):
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
[docs] def to_hdu(self):
"""Creates an HDUList object from a CCDData object.
Raises
-------
ValueError
Multi-Exenstion FITS files are not supported
Returns
-------
hdulist : astropy.io.fits.HDUList object
"""
from .core import _short_names
header = fits.Header()
for k, v in self.header.items():
if k in _short_names:
# This keyword was (hopefully) added by autologging but the
# combination of it and its value FITS-compliant in two ways.
# Shorten, sort of...
short_name = _short_names[k]
header[k] = (short_name, "Shortened name for ccdproc command")
header[short_name] = v
else:
header[k] = v
hdu = fits.PrimaryHDU(self.data, header)
hdulist = fits.HDUList([hdu])
return hdulist
[docs] def copy(self):
"""
Return a copy of the CCDData object.
"""
return copy.deepcopy(self)
def _ccddata_arithmetic(self, other, operation, scale_uncertainty=False):
"""
Perform the common parts of arithmetic operations on CCDData objects
This should only be called when `other` is a Quantity or a number
"""
# THE "1 *" IS NECESSARY to get the right result, at least in
# astropy-0.4dev. Using the np.multiply, etc, methods with a Unit
# and a Quantity is currently broken, but it works with two Quantity
# arguments.
if isinstance(other, u.Quantity):
other_value = other.value
elif isinstance(other, numbers.Number):
other_value = other
else:
raise TypeError("Cannot do arithmetic with type '{0}' "
"and 'CCDData'".format(type(other)))
result_unit = operation(1 * self.unit, other).unit
result_data = operation(self.data, other_value)
if self.uncertainty:
result_uncertainty = self.uncertainty.array
if scale_uncertainty:
result_uncertainty = operation(result_uncertainty, other_value)
result_uncertainty = StdDevUncertainty(result_uncertainty)
else:
result_uncertainty = None
result = CCDData(data=result_data, unit=result_unit,
uncertainty=result_uncertainty,
meta=self.meta)
return result
[docs] def multiply(self, other):
if isinstance(other, CCDData):
return super(CCDData, self).multiply(other)
return self._ccddata_arithmetic(other, np.multiply,
scale_uncertainty=True)
[docs] def divide(self, other):
if isinstance(other, CCDData):
return super(CCDData, self).divide(other)
return self._ccddata_arithmetic(other, np.divide,
scale_uncertainty=True)
[docs] def add(self, other):
if isinstance(other, CCDData):
return super(CCDData, self).add(other)
return self._ccddata_arithmetic(other, np.add,
scale_uncertainty=False)
[docs] def subtract(self, other):
if isinstance(other, CCDData):
return super(CCDData, self).subtract(other)
return self._ccddata_arithmetic(other, np.subtract,
scale_uncertainty=False)
def fits_ccddata_reader(filename, hdu=0, unit=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.
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.
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 to perform '
'ccdproc operations.'),
'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]))
hdus = fits.open(filename, **kwd)
hdr = hdus[hdu].header
try:
fits_unit_string = hdr['bunit']
except KeyError:
fits_unit_string = None
if unit is not None and fits_unit_string:
log.info("Using the unit {0} passed to the FITS reader instead of "
"the unit {1} in the FITS file.", unit, fits_unit_string)
use_unit = unit or fits_unit_string
ccd_data = CCDData(hdus[hdu].data, meta=hdus[hdu].header, unit=use_unit)
hdus.close()
return ccd_data
def fits_ccddata_writer(ccd_data, filename, **kwd):
"""
Write CCDData object to FITS file.
Parameters
----------
filename : str
Name of file
kwd :
All additional keywords are passed to :py:mod:`astropy.io.fits`
"""
hdu = ccd_data.to_hdu()
hdu.writeto(filename, **kwd)
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)