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# Source code for astropy.io.fits.convenience

    # 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']

    def getheader(filename, *args, **kwargs):
        """
        Get the header from an extension of a FITS file.

        Parameters
        ----------
        filename : file path, file object, or file like object
            File to get header from.  If an opened file object, its mode
            must be one of the following rb, rb+, or ab+).

        ext, extname, extver
            The rest of the arguments are for extension specification.  See the
            `getdata` documentation for explanations/examples.

        kwargs
            Any additional keyword arguments to be passed to
            `astropy.io.fits.open`.

        Returns
        -------
        header : `Header` object
        """

        mode, closed = _get_file_mode(filename)
        hdulist, extidx = _getext(filename, mode, *args, **kwargs)
        hdu = hdulist[extidx]
        header = hdu.header
        hdulist.close(closed=closed)
        return header

    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

    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]

    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()

    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()

    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)

    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()

    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)

    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

    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)

    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