# 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 HDU to use when working with a multi-extension FITS file. There are a few supported argument formats for selecting the HDU. 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 HDU should be passed in as keyword arguments. This is to avoid ambiguity and conflicts with the HDU 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 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 operator import os import warnings import numpy as np from .diff import FITSDiff, HDUDiff from .file import FILE_MODES, _File from .hdu.base import _BaseHDU, _ValidHDU from .hdu.hdulist import fitsopen, HDUList 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, _is_dask_array) from astropy.utils.exceptions import AstropyUserWarning __all__ = ['getheader', 'getdata', 'getval', 'setval', 'delval', 'writeto', 'append', 'update', 'info', 'tabledump', 'tableload', 'table_to_hdu', 'printdiff'] def getheader(filename, *args, **kwargs): """ Get the header from an HDU of a FITS file. Parameters ---------- filename : path-like or file-like 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 HDU 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) try: hdu = hdulist[extidx] header = hdu.header finally: hdulist.close(closed=closed) return header def getdata(filename, *args, header=None, lower=None, upper=None, view=None, **kwargs): """ Get the data from an HDU of a FITS file (and optionally the header). Parameters ---------- filename : path-like or file-like 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 HDU specification. They are flexible and are best illustrated by examples. No extra arguments implies the primary HDU:: getdata('in.fits') .. note:: Exclusive to ``getdata``: if ``ext`` is not specified and primary header contains no data, ``getdata`` attempts to retrieve data from first extension HDU. By HDU number:: getdata('in.fits', 0) # the primary HDU getdata('in.fits', 2) # the second extension HDU getdata('in.fits', ext=2) # the second extension HDU 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 : ndarray or `~numpy.recarray` or `~astropy.io.fits.Group` 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. Raises ------ IndexError If no data is found in searched HDUs. """ mode, closed = _get_file_mode(filename) ext = kwargs.get('ext') extname = kwargs.get('extname') extver = kwargs.get('extver') ext_given = not (len(args) == 0 and ext is None and extname is None and extver is None) hdulist, extidx = _getext(filename, mode, *args, **kwargs) try: hdu = hdulist[extidx] data = hdu.data if data is None: if ext_given: raise IndexError(f"No data in HDU #{extidx}.") # fallback to the first extension HDU if len(hdulist) == 1: raise IndexError( "No data in Primary HDU and no extension HDU found." ) hdu = hdulist[1] data = hdu.data if data is None: raise IndexError( "No data in either Primary or first extension HDUs." ) if header: hdr = hdu.header finally: hdulist.close(closed=closed) # Change case of names if requested trans = None if lower: trans = operator.methodcaller('lower') elif upper: trans = operator.methodcaller('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 : path-like or file-like 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 HDU 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, value=None, comment=None, before=None, after=None, savecomment=False, **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 : path-like or file-like 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 HDU 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 closed = fileobj_closed(filename) hdulist, extidx = _getext(filename, 'update', *args, **kwargs) try: if keyword in hdulist[extidx].header and savecomment: comment = None hdulist[extidx].header.set(keyword, value, comment, before, after) finally: hdulist.close(closed=closed) def delval(filename, keyword, *args, **kwargs): """ Delete all instances of keyword from a header in a FITS file. Parameters ---------- filename : path-like or file-like 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 HDU 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 closed = fileobj_closed(filename) hdulist, extidx = _getext(filename, 'update', *args, **kwargs) try: del hdulist[extidx].header[keyword] finally: hdulist.close(closed=closed) def writeto(filename, data, header=None, output_verify='exception', overwrite=False, checksum=False): """ Create a new FITS file using the supplied data/header. Parameters ---------- filename : path-like or file-like File to write to. If opened, must be opened in a writable binary mode such as 'wb' or 'ab+'. data : array or `~numpy.recarray` or `~astropy.io.fits.Group` 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:`astropy:verify` for more info. overwrite : bool, optional If ``True``, overwrite the output file if it exists. Raises an ``OSError`` if ``False`` and the output file exists. 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, overwrite=overwrite, output_verify=output_verify, checksum=checksum) def table_to_hdu(table, character_as_bytes=False): """ Convert an `~astropy.table.Table` object to a FITS `~astropy.io.fits.BinTableHDU`. Parameters ---------- table : astropy.table.Table The table to convert. character_as_bytes : bool Whether to return bytes for string columns when accessed from the HDU. By default this is `False` and (unicode) strings are returned, but for large tables this may use up a lot of memory. Returns ------- table_hdu : `~astropy.io.fits.BinTableHDU` The FITS binary table HDU. """ # Avoid circular imports from .connect import is_column_keyword, REMOVE_KEYWORDS from .column import python_to_tdisp # Header to store Time related metadata hdr = None # Not all tables with mixin columns are supported if table.has_mixin_columns: # Import is done here, in order to avoid it at build time as erfa is not # yet available then. from astropy.table.column import BaseColumn from astropy.time import Time from astropy.units import Quantity from .fitstime import time_to_fits # Only those columns which are instances of BaseColumn, Quantity or Time can # be written unsupported_cols = table.columns.not_isinstance((BaseColumn, Quantity, Time)) if unsupported_cols: unsupported_names = [col.info.name for col in unsupported_cols] raise ValueError(f'cannot write table with mixin column(s) ' f'{unsupported_names}') time_cols = table.columns.isinstance(Time) if time_cols: table, hdr = time_to_fits(table) # Create a new HDU object tarray = table.as_array() if isinstance(tarray, np.ma.MaskedArray): # Fill masked values carefully: # float column's default mask value needs to be Nan and # string column's default mask should be an empty string. # Note: getting the fill value for the structured array is # more reliable than for individual columns for string entries. # (no 'N/A' for a single-element string, where it should be 'N'). default_fill_value = np.ma.default_fill_value(tarray.dtype) for colname, (coldtype, _) in tarray.dtype.fields.items(): if np.all(tarray.fill_value[colname] == default_fill_value[colname]): # Since multi-element columns with dtypes such as '2f8' have # a subdtype, we should look up the type of column on that. coltype = (coldtype.subdtype[0].type if coldtype.subdtype else coldtype.type) if issubclass(coltype, np.complexfloating): tarray.fill_value[colname] = complex(np.nan, np.nan) elif issubclass(coltype, np.inexact): tarray.fill_value[colname] = np.nan elif issubclass(coltype, np.character): tarray.fill_value[colname] = '' # TODO: it might be better to construct the FITS table directly from # the Table columns, rather than go via a structured array. table_hdu = BinTableHDU.from_columns(tarray.filled(), header=hdr, character_as_bytes=character_as_bytes) for col in table_hdu.columns: # Binary FITS tables support TNULL *only* for integer data columns # TODO: Determine a schema for handling non-integer masked columns # with non-default fill values in FITS (if at all possible). int_formats = ('B', 'I', 'J', 'K') if not (col.format in int_formats or col.format.p_format in int_formats): continue fill_value = tarray[col.name].fill_value col.null = fill_value.astype(int) else: table_hdu = BinTableHDU.from_columns(tarray, header=hdr, character_as_bytes=character_as_bytes) # Set units and format display for output HDU for col in table_hdu.columns: if table[col.name].info.format is not None: # check for boolean types, special format case logical = table[col.name].info.dtype == bool tdisp_format = python_to_tdisp(table[col.name].info.format, logical_dtype=logical) if tdisp_format is not None: col.disp = tdisp_format unit = table[col.name].unit if unit is not None: # Local imports to avoid importing units when it is not required, # e.g. for command-line scripts from astropy.units import Unit from astropy.units.format.fits import UnitScaleError try: col.unit = unit.to_string(format='fits') except UnitScaleError: scale = unit.scale raise UnitScaleError( f"The column '{col.name}' could not be stored in FITS " f"format because it has a scale '({str(scale)})' that " f"is not recognized by the FITS standard. Either scale " f"the data or change the units.") except ValueError: # Warn that the unit is lost, but let the details depend on # whether the column was serialized (because it was a # quantity), since then the unit can be recovered by astropy. warning = ( f"The unit '{unit.to_string()}' could not be saved in " f"native FITS format ") if any('SerializedColumn' in item and 'name: '+col.name in item for item in table.meta.get('comments', [])): warning += ( "and hence will be lost to non-astropy fits readers. " "Within astropy, the unit can roundtrip using QTable, " "though one has to enable the unit before reading.") else: warning += ( "and cannot be recovered in reading. It can roundtrip " "within astropy by using QTable both to write and read " "back, though one has to enable the unit before reading.") warnings.warn(warning, AstropyUserWarning) else: # Try creating a Unit to issue a warning if the unit is not # FITS compliant Unit(col.unit, format='fits', parse_strict='warn') # Column-specific override keywords for coordinate columns coord_meta = table.meta.pop('__coordinate_columns__', {}) for col_name, col_info in coord_meta.items(): col = table_hdu.columns[col_name] # Set the column coordinate attributes from data saved earlier. # Note: have to set these, even if we have no data. for attr in 'coord_type', 'coord_unit': setattr(col, attr, col_info.get(attr, None)) trpos = col_info.get('time_ref_pos', None) if trpos is not None: setattr(col, 'time_ref_pos', trpos) for key, value in table.meta.items(): if is_column_keyword(key.upper()) or key.upper() in REMOVE_KEYWORDS: warnings.warn( f"Meta-data keyword {key} will be ignored since it conflicts " f"with a FITS reserved keyword", AstropyUserWarning) continue # Convert to FITS format if key == 'comments': key = 'comment' if isinstance(value, list): for item in value: try: table_hdu.header.append((key, item)) except ValueError: warnings.warn( f"Attribute `{key}` of type {type(value)} cannot be " f"added to FITS Header - skipping", AstropyUserWarning) else: try: table_hdu.header[key] = value except ValueError: warnings.warn( f"Attribute `{key}` of type {type(value)} cannot be " f"added to FITS Header - skipping", AstropyUserWarning) return table_hdu 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 : path-like or file-like 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, :class:`~astropy.table.Table`, or `~astropy.io.fits.Group` 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 Additional arguments are passed to: - `~astropy.io.fits.writeto` if the file does not exist or is empty. In this case ``output_verify`` is the only possible argument. - `~astropy.io.fits.open` if ``verify`` is True or if ``filename`` is a file object. - Otherwise no additional arguments can be used. """ 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', **kwargs) try: 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 finally: f.close(closed=closed) else: f = _File(filename, mode='append') try: hdu._output_checksum = checksum hdu._writeto(f) finally: f.close() def update(filename, data, *args, **kwargs): """ Update the specified HDU with the input data/header. Parameters ---------- filename : path-like or file-like 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, `~astropy.table.Table`, or `~astropy.io.fits.Group` 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 HDU specification(s). Header and HDU 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 HDU update(file, dat, hdr, 3) # update the 3rd extension HDU update(file, dat, 'sci', 2) # update the 2nd extension HDU named 'sci' update(file, dat, 3, header=hdr) # update the 3rd extension HDU update(file, dat, header=hdr, ext=5) # update the 5th extension HDU **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) try: hdulist[_ext] = new_hdu finally: 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 HDU. Parameters ---------- filename : path-like or file-like 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 'ignore_missing_end' not in kwargs: kwargs['ignore_missing_end'] = True f = fitsopen(filename, mode=mode, **kwargs) try: ret = f.info(output=output) finally: if closed: f.close() return ret def printdiff(inputa, inputb, *args, **kwargs): """ Compare two parts of a FITS file, including entire FITS files, FITS `HDUList` objects and FITS ``HDU`` objects. Parameters ---------- inputa : str, `HDUList` object, or ``HDU`` object The filename of a FITS file, `HDUList`, or ``HDU`` object to compare to ``inputb``. inputb : str, `HDUList` object, or ``HDU`` object The filename of a FITS file, `HDUList`, or ``HDU`` object to compare to ``inputa``. ext, extname, extver Additional positional arguments are for HDU specification if your inputs are string filenames (will not work if ``inputa`` and ``inputb`` are ``HDU`` objects or `HDUList` objects). They are flexible and are best illustrated by examples. In addition to using these arguments positionally you can directly call the keyword parameters ``ext``, ``extname``. By HDU number:: printdiff('inA.fits', 'inB.fits', 0) # the primary HDU printdiff('inA.fits', 'inB.fits', 2) # the second extension HDU printdiff('inA.fits', 'inB.fits', ext=2) # the second extension HDU By name, i.e., ``EXTNAME`` value (if unique). ``EXTNAME`` values are not case sensitive: printdiff('inA.fits', 'inB.fits', 'sci') printdiff('inA.fits', 'inB.fits', extname='sci') # equivalent By combination of ``EXTNAME`` and ``EXTVER`` as separate arguments or as a tuple:: printdiff('inA.fits', 'inB.fits', 'sci', 2) # EXTNAME='SCI' # & EXTVER=2 printdiff('inA.fits', 'inB.fits', extname='sci', extver=2) # equivalent printdiff('inA.fits', 'inB.fits', ('sci', 2)) # equivalent Ambiguous or conflicting specifications will raise an exception:: printdiff('inA.fits', 'inB.fits', ext=('sci', 1), extname='err', extver=2) **kwargs Any additional keyword arguments to be passed to `~astropy.io.fits.FITSDiff`. Notes ----- The primary use for the `printdiff` function is to allow quick print out of a FITS difference report and will write to ``sys.stdout``. To save the diff report to a file please use `~astropy.io.fits.FITSDiff` directly. """ # Pop extension keywords extension = {key: kwargs.pop(key) for key in ['ext', 'extname', 'extver'] if key in kwargs} has_extensions = args or extension if isinstance(inputa, str) and has_extensions: # Use handy _getext to interpret any ext keywords, but # will need to close a if fails modea, closeda = _get_file_mode(inputa) modeb, closedb = _get_file_mode(inputb) hdulista, extidxa = _getext(inputa, modea, *args, **extension) # Have to close a if b doesn't make it try: hdulistb, extidxb = _getext(inputb, modeb, *args, **extension) except Exception: hdulista.close(closed=closeda) raise try: hdua = hdulista[extidxa] hdub = hdulistb[extidxb] # See below print for note print(HDUDiff(hdua, hdub, **kwargs).report()) finally: hdulista.close(closed=closeda) hdulistb.close(closed=closedb) # If input is not a string, can feed HDU objects or HDUList directly, # but can't currently handle extensions elif isinstance(inputa, _ValidHDU) and has_extensions: raise ValueError("Cannot use extension keywords when providing an " "HDU object.") elif isinstance(inputa, _ValidHDU) and not has_extensions: print(HDUDiff(inputa, inputb, **kwargs).report()) elif isinstance(inputa, HDUList) and has_extensions: raise NotImplementedError("Extension specification with HDUList " "objects not implemented.") # This function is EXCLUSIVELY for printing the diff report to screen # in a one-liner call, hence the use of print instead of logging else: print(FITSDiff(inputa, inputb, **kwargs).report()) def tabledump(filename, datafile=None, cdfile=None, hfile=None, ext=1, overwrite=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 : path-like or file-like Input fits file. datafile : path-like or file-like, 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 : path-like or file-like, optional Output column definitions file. The default is `None`, no column definitions output is produced. hfile : path-like or file-like, 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. overwrite : bool, optional If ``True``, overwrite the output file if it exists. Raises an ``OSError`` if ``False`` and the output file exists. Default is ``False``. Notes ----- The primary use for the `tabledump` function is to allow editing in a standard text editor of the table data and parameters. The `tableload` 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 try: if not datafile: root, tail = os.path.splitext(f._file.name) datafile = root + '_' + repr(ext) + '.txt' # Dump the data from the HDU to the files f[ext].dump(datafile, cdfile, hfile, overwrite) finally: if closed: f.close() if isinstance(tabledump.__doc__, str): tabledump.__doc__ += BinTableHDU._tdump_file_format.replace('\n', '\n ') 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 : path-like or file-like Input data file containing the table data in ASCII format. cdfile : path-like or file-like 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 : path-like or file-like, 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__, str): tableload.__doc__ += BinTableHDU._tdump_file_format.replace('\n', '\n ') def _getext(filename, mode, *args, ext=None, extname=None, extver=None, **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. """ err_msg = ('Redundant/conflicting extension arguments(s): {}'.format( {'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], str): # 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], str) 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, str): 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._from_data(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, header=header) elif isinstance(data, np.ndarray) or _is_dask_array(data): hdu = ImageHDU(data, header=header) else: raise KeyError('Data must be a numpy array.') return hdu def _stat_filename_or_fileobj(filename): if isinstance(filename, os.PathLike): filename = os.fspath(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 OSError( "File mode of the input file object ({!r}) cannot be used to " "read/write FITS files.".format(fmode)) return mode, closed