# Licensed under a 3-clause BSD style license - see PYFITS.rst
"""
Convenience functions
=====================
The functions in this module provide shortcuts for some of the most basic
operations on FITS files, such as reading and updating the header. They are
included directly in the 'astropy.io.fits' namespace so that they can be used
like::
astropy.io.fits.getheader(...)
These functions are primarily for convenience when working with FITS files in
the command-line interpreter. If performing several operations on the same
file, such as in a script, it is better to *not* use these functions, as each
one must open and re-parse the file. In such cases it is better to use
:func:`astropy.io.fits.open` and work directly with the
:class:`astropy.io.fits.HDUList` object and underlying HDU objects.
Several of the convenience functions, such as `getheader` and `getdata` support
special arguments for selecting which extension HDU to use when working with a
multi-extension FITS file. There are a few supported argument formats for
selecting the extension. See the documentation for `getdata` for an
explanation of all the different formats.
.. warning::
All arguments to convenience functions other than the filename that are
*not* for selecting the extension HDU should be passed in as keyword
arguments. This is to avoid ambiguity and conflicts with the
extension arguments. For example, to set NAXIS=1 on the Primary HDU:
Wrong::
astropy.io.fits.setval('myimage.fits', 'NAXIS', 1)
The above example will try to set the NAXIS value on the first extension
HDU to blank. That is, the argument '1' is assumed to specify an extension
HDU.
Right::
astropy.io.fits.setval('myimage.fits', 'NAXIS', value=1)
This will set the NAXIS keyword to 1 on the primary HDU (the default). To
specify the first extension HDU use::
astropy.io.fits.setval('myimage.fits', 'NAXIS', value=1, ext=1)
This complexity arises out of the attempt to simultaneously support
multiple argument formats that were used in past versions of PyFITS.
Unfortunately, it is not possible to support all formats without
introducing some ambiguity. A future Astropy release may standardize
around a single format and officially deprecate the other formats.
"""
import os
import numpy as np
from .file import FILE_MODES, _File
from .hdu.base import _BaseHDU, _ValidHDU
from .hdu.hdulist import fitsopen
from .hdu.image import PrimaryHDU, ImageHDU
from .hdu.table import BinTableHDU
from .header import Header
from .util import fileobj_closed, fileobj_name, fileobj_mode, _is_int
from ...extern.six import string_types
from ...utils import deprecated
__all__ = ['getheader', 'getdata', 'getval', 'setval', 'delval', 'writeto',
'append', 'update', 'info', 'tdump', 'tcreate', 'tabledump',
'tableload']
[docs]def getdata(filename, *args, **kwargs):
"""
Get the data from an extension of a FITS file (and optionally the
header).
Parameters
----------
filename : file path, file object, or file like object
File to get data from. If opened, mode must be one of the
following rb, rb+, or ab+.
ext
The rest of the arguments are for extension specification.
They are flexible and are best illustrated by examples.
No extra arguments implies the primary header::
getdata('in.fits')
By extension number::
getdata('in.fits', 0) # the primary header
getdata('in.fits', 2) # the second extension
getdata('in.fits', ext=2) # the second extension
By name, i.e., ``EXTNAME`` value (if unique)::
getdata('in.fits', 'sci')
getdata('in.fits', extname='sci') # equivalent
Note ``EXTNAME`` values are not case sensitive
By combination of ``EXTNAME`` and EXTVER`` as separate
arguments or as a tuple::
getdata('in.fits', 'sci', 2) # EXTNAME='SCI' & EXTVER=2
getdata('in.fits', extname='sci', extver=2) # equivalent
getdata('in.fits', ('sci', 2)) # equivalent
Ambiguous or conflicting specifications will raise an exception::
getdata('in.fits', ext=('sci',1), extname='err', extver=2)
header : bool, optional
If `True`, return the data and the header of the specified HDU as a
tuple.
lower, upper : bool, optional
If ``lower`` or ``upper`` are `True`, the field names in the
returned data object will be converted to lower or upper case,
respectively.
view : ndarray, optional
When given, the data will be returned wrapped in the given ndarray
subclass by calling::
data.view(view)
kwargs
Any additional keyword arguments to be passed to
`astropy.io.fits.open`.
Returns
-------
array : array, record array or groups data object
Type depends on the type of the extension being referenced.
If the optional keyword ``header`` is set to `True`, this
function will return a (``data``, ``header``) tuple.
"""
mode, closed = _get_file_mode(filename)
header = kwargs.pop('header', None)
lower = kwargs.pop('lower', None)
upper = kwargs.pop('upper', None)
view = kwargs.pop('view', None)
hdulist, extidx = _getext(filename, mode, *args, **kwargs)
hdu = hdulist[extidx]
data = hdu.data
if data is None and extidx == 0:
try:
hdu = hdulist[1]
data = hdu.data
except IndexError:
raise IndexError('No data in this HDU.')
if data is None:
raise IndexError('No data in this HDU.')
if header:
hdr = hdu.header
hdulist.close(closed=closed)
# Change case of names if requested
trans = None
if lower:
trans = lambda s: s.lower()
elif upper:
trans = lambda s: s.upper()
if trans:
if data.dtype.names is None:
# this data does not have fields
return
if data.dtype.descr[0][0] == '':
# this data does not have fields
return
data.dtype.names = [trans(n) for n in data.dtype.names]
# allow different views into the underlying ndarray. Keep the original
# view just in case there is a problem
if isinstance(view, type) and issubclass(view, np.ndarray):
data = data.view(view)
if header:
return data, hdr
else:
return data
[docs]def getval(filename, keyword, *args, **kwargs):
"""
Get a keyword's value from a header in a FITS file.
Parameters
----------
filename : file path, file object, or file like object
Name of the FITS file, or file object (if opened, mode must be
one of the following rb, rb+, or ab+).
keyword : str
Keyword name
ext, extname, extver
The rest of the arguments are for extension specification.
See `getdata` for explanations/examples.
kwargs
Any additional keyword arguments to be passed to
`astropy.io.fits.open`.
*Note:* This function automatically specifies ``do_not_scale_image_data
= True`` when opening the file so that values can be retrieved from the
unmodified header.
Returns
-------
keyword value : str, int, or float
"""
if 'do_not_scale_image_data' not in kwargs:
kwargs['do_not_scale_image_data'] = True
hdr = getheader(filename, *args, **kwargs)
return hdr[keyword]
[docs]def setval(filename, keyword, *args, **kwargs):
"""
Set a keyword's value from a header in a FITS file.
If the keyword already exists, it's value/comment will be updated.
If it does not exist, a new card will be created and it will be
placed before or after the specified location. If no ``before`` or
``after`` is specified, it will be appended at the end.
When updating more than one keyword in a file, this convenience
function is a much less efficient approach compared with opening
the file for update, modifying the header, and closing the file.
Parameters
----------
filename : file path, file object, or file like object
Name of the FITS file, or file object If opened, mode must be update
(rb+). An opened file object or `~gzip.GzipFile` object will be closed
upon return.
keyword : str
Keyword name
value : str, int, float, optional
Keyword value (default: `None`, meaning don't modify)
comment : str, optional
Keyword comment, (default: `None`, meaning don't modify)
before : str, int, optional
Name of the keyword, or index of the card before which the new card
will be placed. The argument ``before`` takes precedence over
``after`` if both are specified (default: `None`).
after : str, int, optional
Name of the keyword, or index of the card after which the new card will
be placed. (default: `None`).
savecomment : bool, optional
When `True`, preserve the current comment for an existing keyword. The
argument ``savecomment`` takes precedence over ``comment`` if both
specified. If ``comment`` is not specified then the current comment
will automatically be preserved (default: `False`).
ext, extname, extver
The rest of the arguments are for extension specification.
See `getdata` for explanations/examples.
kwargs
Any additional keyword arguments to be passed to
`astropy.io.fits.open`.
*Note:* This function automatically specifies ``do_not_scale_image_data
= True`` when opening the file so that values can be retrieved from the
unmodified header.
"""
if 'do_not_scale_image_data' not in kwargs:
kwargs['do_not_scale_image_data'] = True
value = kwargs.pop('value', None)
comment = kwargs.pop('comment', None)
before = kwargs.pop('before', None)
after = kwargs.pop('after', None)
savecomment = kwargs.pop('savecomment', False)
hdulist, extidx = _getext(filename, 'update', *args, **kwargs)
if keyword in hdulist[extidx].header and savecomment:
comment = None
hdulist[extidx].header.set(keyword, value, comment, before, after)
hdulist.close()
[docs]def delval(filename, keyword, *args, **kwargs):
"""
Delete all instances of keyword from a header in a FITS file.
Parameters
----------
filename : file path, file object, or file like object
Name of the FITS file, or file object If opened, mode must be update
(rb+). An opened file object or `~gzip.GzipFile` object will be closed
upon return.
keyword : str, int
Keyword name or index
ext, extname, extver
The rest of the arguments are for extension specification.
See `getdata` for explanations/examples.
kwargs
Any additional keyword arguments to be passed to
`astropy.io.fits.open`.
*Note:* This function automatically specifies ``do_not_scale_image_data
= True`` when opening the file so that values can be retrieved from the
unmodified header.
"""
if 'do_not_scale_image_data' not in kwargs:
kwargs['do_not_scale_image_data'] = True
hdulist, extidx = _getext(filename, 'update', *args, **kwargs)
del hdulist[extidx].header[keyword]
hdulist.close()
[docs]def writeto(filename, data, header=None, output_verify='exception',
clobber=False, checksum=False):
"""
Create a new FITS file using the supplied data/header.
Parameters
----------
filename : file path, file object, or file like object
File to write to. If opened, must be opened in a writeable binary
mode such as 'wb' or 'ab+'.
data : array, record array, or groups data object
data to write to the new file
header : `Header` object, optional
the header associated with ``data``. If `None`, a header
of the appropriate type is created for the supplied data. This
argument is optional.
output_verify : str
Output verification option. Must be one of ``"fix"``, ``"silentfix"``,
``"ignore"``, ``"warn"``, or ``"exception"``. May also be any
combination of ``"fix"`` or ``"silentfix"`` with ``"+ignore"``,
``+warn``, or ``+exception" (e.g. ``"fix+warn"``). See :ref:`verify`
for more info.
clobber : bool, optional
If `True`, and if filename already exists, it will overwrite
the file. Default is `False`.
checksum : bool, optional
If `True`, adds both ``DATASUM`` and ``CHECKSUM`` cards to the
headers of all HDU's written to the file.
"""
hdu = _makehdu(data, header)
if hdu.is_image and not isinstance(hdu, PrimaryHDU):
hdu = PrimaryHDU(data, header=header)
hdu.writeto(filename, clobber=clobber, output_verify=output_verify,
checksum=checksum)
[docs]def append(filename, data, header=None, checksum=False, verify=True, **kwargs):
"""
Append the header/data to FITS file if filename exists, create if not.
If only ``data`` is supplied, a minimal header is created.
Parameters
----------
filename : file path, file object, or file like object
File to write to. If opened, must be opened for update (rb+) unless it
is a new file, then it must be opened for append (ab+). A file or
`~gzip.GzipFile` object opened for update will be closed after return.
data : array, table, or group data object
the new data used for appending
header : `Header` object, optional
The header associated with ``data``. If `None`, an appropriate header
will be created for the data object supplied.
checksum : bool, optional
When `True` adds both ``DATASUM`` and ``CHECKSUM`` cards to the header
of the HDU when written to the file.
verify : bool, optional
When `True`, the existing FITS file will be read in to verify it for
correctness before appending. When `False`, content is simply appended
to the end of the file. Setting ``verify`` to `False` can be much
faster.
kwargs
Any additional keyword arguments to be passed to
`astropy.io.fits.open`.
"""
name, closed, noexist_or_empty = _stat_filename_or_fileobj(filename)
if noexist_or_empty:
#
# The input file or file like object either doesn't exits or is
# empty. Use the writeto convenience function to write the
# output to the empty object.
#
writeto(filename, data, header, checksum=checksum, **kwargs)
else:
hdu = _makehdu(data, header)
if isinstance(hdu, PrimaryHDU):
hdu = ImageHDU(data, header)
if verify or not closed:
f = fitsopen(filename, mode='append')
f.append(hdu)
# Set a flag in the HDU so that only this HDU gets a checksum when
# writing the file.
hdu._output_checksum = checksum
f.close(closed=closed)
else:
f = _File(filename, mode='append')
hdu._output_checksum = checksum
hdu._writeto(f)
f.close()
[docs]def update(filename, data, *args, **kwargs):
"""
Update the specified extension with the input data/header.
Parameters
----------
filename : file path, file object, or file like object
File to update. If opened, mode must be update (rb+). An opened file
object or `~gzip.GzipFile` object will be closed upon return.
data : array, table, or group data object
the new data used for updating
header : `Header` object, optional
The header associated with ``data``. If `None`, an appropriate header
will be created for the data object supplied.
ext, extname, extver
The rest of the arguments are flexible: the 3rd argument can be the
header associated with the data. If the 3rd argument is not a
`Header`, it (and other positional arguments) are assumed to be the
extension specification(s). Header and extension specs can also be
keyword arguments. For example::
update(file, dat, hdr, 'sci') # update the 'sci' extension
update(file, dat, 3) # update the 3rd extension
update(file, dat, hdr, 3) # update the 3rd extension
update(file, dat, 'sci', 2) # update the 2nd SCI extension
update(file, dat, 3, header=hdr) # update the 3rd extension
update(file, dat, header=hdr, ext=5) # update the 5th extension
kwargs
Any additional keyword arguments to be passed to
`astropy.io.fits.open`.
"""
# The arguments to this function are a bit trickier to deal with than others
# in this module, since the documentation has promised that the header
# argument can be an optional positional argument.
if args and isinstance(args[0], Header):
header = args[0]
args = args[1:]
else:
header = None
# The header can also be a keyword argument--if both are provided the
# keyword takes precedence
header = kwargs.pop('header', header)
new_hdu = _makehdu(data, header)
closed = fileobj_closed(filename)
hdulist, _ext = _getext(filename, 'update', *args, **kwargs)
hdulist[_ext] = new_hdu
hdulist.close(closed=closed)
[docs]def info(filename, output=None, **kwargs):
"""
Print the summary information on a FITS file.
This includes the name, type, length of header, data shape and type
for each extension.
Parameters
----------
filename : file path, file object, or file like object
FITS file to obtain info from. If opened, mode must be one of
the following: rb, rb+, or ab+ (i.e. the file must be readable).
output : file, bool, optional
A file-like object to write the output to. If ``False``, does not
output to a file and instead returns a list of tuples representing the
HDU info. Writes to ``sys.stdout`` by default.
kwargs
Any additional keyword arguments to be passed to
`astropy.io.fits.open`.
*Note:* This function sets ``ignore_missing_end=True`` by default.
"""
mode, closed = _get_file_mode(filename, default='readonly')
# Set the default value for the ignore_missing_end parameter
if not 'ignore_missing_end' in kwargs:
kwargs['ignore_missing_end'] = True
f = fitsopen(filename, mode=mode, **kwargs)
ret = f.info(output=output)
if closed:
f.close()
return ret
[docs]def tabledump(filename, datafile=None, cdfile=None, hfile=None, ext=1,
clobber=False):
"""
Dump a table HDU to a file in ASCII format. The table may be
dumped in three separate files, one containing column definitions,
one containing header parameters, and one for table data.
Parameters
----------
filename : file path, file object or file-like object
Input fits file.
datafile : file path, file object or file-like object, optional
Output data file. The default is the root name of the input
fits file appended with an underscore, followed by the
extension number (ext), followed by the extension ``.txt``.
cdfile : file path, file object or file-like object, optional
Output column definitions file. The default is `None`,
no column definitions output is produced.
hfile : file path, file object or file-like object, optional
Output header parameters file. The default is `None`,
no header parameters output is produced.
ext : int
The number of the extension containing the table HDU to be
dumped.
clobber : bool
Overwrite the output files if they exist.
Notes
-----
The primary use for the `tabledump` function is to allow editing in a
standard text editor of the table data and parameters. The
``tcreate`` function can be used to reassemble the table from the
three ASCII files.
"""
# allow file object to already be opened in any of the valid modes
# and leave the file in the same state (opened or closed) as when
# the function was called
mode, closed = _get_file_mode(filename, default='readonly')
f = fitsopen(filename, mode=mode)
# Create the default data file name if one was not provided
if not datafile:
# TODO: Really need to provide a better way to access the name of any
# files underlying an HDU
root, tail = os.path.splitext(f._HDUList__file.name)
datafile = root + '_' + repr(ext) + '.txt'
# Dump the data from the HDU to the files
f[ext].dump(datafile, cdfile, hfile, clobber)
if closed:
f.close()
if isinstance(tabledump.__doc__, string_types):
tabledump.__doc__ += BinTableHDU._tdump_file_format.replace('\n', '\n ')
@deprecated('0.1', alternative=':func:`tabledump`')
def tdump(filename, datafile=None, cdfile=None, hfile=None, ext=1,
clobber=False):
tabledump(filename, datafile, cdfile, hfile, ext, clobber)
[docs]def tableload(datafile, cdfile, hfile=None):
"""
Create a table from the input ASCII files. The input is from up
to three separate files, one containing column definitions, one
containing header parameters, and one containing column data. The
header parameters file is not required. When the header
parameters file is absent a minimal header is constructed.
Parameters
----------
datafile : file path, file object or file-like object
Input data file containing the table data in ASCII format.
cdfile : file path, file object or file-like object
Input column definition file containing the names, formats,
display formats, physical units, multidimensional array
dimensions, undefined values, scale factors, and offsets
associated with the columns in the table.
hfile : file path, file object or file-like object, optional
Input parameter definition file containing the header
parameter definitions to be associated with the table.
If `None`, a minimal header is constructed.
Notes
-----
The primary use for the `tableload` function is to allow the input of
ASCII data that was edited in a standard text editor of the table
data and parameters. The tabledump function can be used to create the
initial ASCII files.
"""
return BinTableHDU.load(datafile, cdfile, hfile, replace=True)
if isinstance(tableload.__doc__, string_types):
tableload.__doc__ += BinTableHDU._tdump_file_format.replace('\n', '\n ')
@deprecated('0.1', alternative=':func:`tableload`')
def tcreate(datafile, cdfile, hfile=None):
return tableload(datafile, cdfile, hfile)
def _getext(filename, mode, *args, **kwargs):
"""
Open the input file, return the `HDUList` and the extension.
This supports several different styles of extension selection. See the
:func:`getdata()` documentation for the different possibilities.
"""
ext = kwargs.pop('ext', None)
extname = kwargs.pop('extname', None)
extver = kwargs.pop('extver', None)
err_msg = ('Redundant/conflicting extension arguments(s): %s' %
({'args': args, 'ext': ext, 'extname': extname,
'extver': extver},))
# This code would be much simpler if just one way of specifying an
# extension were picked. But now we need to support all possible ways for
# the time being.
if len(args) == 1:
# Must be either an extension number, an extension name, or an
# (extname, extver) tuple
if _is_int(args[0]) or (isinstance(ext, tuple) and len(ext) == 2):
if ext is not None or extname is not None or extver is not None:
raise TypeError(err_msg)
ext = args[0]
elif isinstance(args[0], string_types):
# The first arg is an extension name; it could still be valid
# to provide an extver kwarg
if ext is not None or extname is not None:
raise TypeError(err_msg)
extname = args[0]
else:
# Take whatever we have as the ext argument; we'll validate it
# below
ext = args[0]
elif len(args) == 2:
# Must be an extname and extver
if ext is not None or extname is not None or extver is not None:
raise TypeError(err_msg)
extname = args[0]
extver = args[1]
elif len(args) > 2:
raise TypeError('Too many positional arguments.')
if (ext is not None and
not (_is_int(ext) or
(isinstance(ext, tuple) and len(ext) == 2 and
isinstance(ext[0], string_types) and _is_int(ext[1])))):
raise ValueError(
'The ext keyword must be either an extension number '
'(zero-indexed) or a (extname, extver) tuple.')
if extname is not None and not isinstance(extname, string_types):
raise ValueError('The extname argument must be a string.')
if extver is not None and not _is_int(extver):
raise ValueError('The extver argument must be an integer.')
if ext is None and extname is None and extver is None:
ext = 0
elif ext is not None and (extname is not None or extver is not None):
raise TypeError(err_msg)
elif extname:
if extver:
ext = (extname, extver)
else:
ext = (extname, 1)
elif extver and extname is None:
raise TypeError('extver alone cannot specify an extension.')
hdulist = fitsopen(filename, mode=mode, **kwargs)
return hdulist, ext
def _makehdu(data, header):
if header is None:
header = Header()
hdu = _BaseHDU(data, header)
if hdu.__class__ in (_BaseHDU, _ValidHDU):
# The HDU type was unrecognized, possibly due to a
# nonexistent/incomplete header
if ((isinstance(data, np.ndarray) and data.dtype.fields is not None)
or isinstance(data, np.recarray)):
hdu = BinTableHDU(data)
elif isinstance(data, np.ndarray):
hdu = ImageHDU(data)
else:
raise KeyError('Data must be a numpy array.')
return hdu
def _stat_filename_or_fileobj(filename):
closed = fileobj_closed(filename)
name = fileobj_name(filename) or ''
try:
loc = filename.tell()
except AttributeError:
loc = 0
noexist_or_empty = ((name and
(not os.path.exists(name) or
(os.path.getsize(name) == 0)))
or (not name and loc == 0))
return name, closed, noexist_or_empty
def _get_file_mode(filename, default='readonly'):
"""
Allow file object to already be opened in any of the valid modes and
and leave the file in the same state (opened or closed) as when
the function was called.
"""
mode = default
closed = fileobj_closed(filename)
fmode = fileobj_mode(filename)
if fmode is not None:
mode = FILE_MODES.get(fmode)
if mode is None:
raise IOError(
"File mode of the input file object (%r) cannot be used to "
"read/write FITS files." % fmode)
return mode, closed