Source code for sunpy.io.fits

"""
This module provides a FITS file reader.

Notes
-----

1. FITS files allow comments to be attached to every value in the header.
   This is implemented in this module as a KEYCOMMENTS dictionary in the
   sunpy header. To add a comment to the file on write, add a comment to this
   dictionary with the same name as a key in the header (upcased).

2. Due to the way `~astropy.io.fits` works with images, the header dictionary may
   differ depending on whether is accessed before or after the fits[0].data
   is requested. If the header is read before the data then the original
   header will be returned. If the header is read after the data has been
   accessed then the data will have been scaled and a modified header
   reflecting these changes will be returned: BITPIX may differ and
   BSCALE and B_ZERO may be dropped in the modified version.

3. The verify('silentfix+warn') call attempts to handle violations of the FITS
   standard. For example, ``nan`` values will be converted to "nan" strings.
   Attempting to cast a `astropy.io.fits.Header` to a dictionary while it contains
   invalid header tags will result in an error so verifying it early on
   makes the header easier to work with later.
"""
import os
import re
import sys
import warnings
import traceback
import collections

from astropy.io import fits

from sunpy.io.header import FileHeader
from sunpy.util.exceptions import SunpyUserWarning

__all__ = ['header_to_fits', 'read', 'get_header', 'write', 'extract_waveunit']

HDPair = collections.namedtuple('HDPair', ['data', 'header'])


[docs]def read(filepath, hdus=None, memmap=None, **kwargs): """ Read a fits file. Parameters ---------- filepath : `str` The fits file to be read. hdu: `int` or iterable The HDU indexes to read from the file. Returns ------- pairs : `list` A list of (data, header) tuples Notes ----- This routine reads all the HDU's in a fits file and returns a list of the data and a FileHeader instance for each one. Also all comments in the original file are concatenated into a single "comment" key in the returned FileHeader. """ with fits.open(filepath, ignore_blank=True, memmap=memmap) as hdulist: if hdus is not None: if isinstance(hdus, int): hdulist = hdulist[hdus] elif isinstance(hdus, collections.Iterable): hdulist = [hdulist[i] for i in hdus] hdulist.verify('silentfix+warn') headers = get_header(hdulist) pairs = [] for i, (hdu, header) in enumerate(zip(hdulist, headers)): try: pairs.append(HDPair(hdu.data, header)) except (KeyError, ValueError) as e: message = "Error when reading HDU {}. Skipping.\n".format(i) for line in traceback.format_tb(sys.exc_info()[2]): message += line message += '\n' message += repr(e) warnings.warn(message, SunpyUserWarning) return pairs
[docs]def get_header(afile): """ Read a fits file and return just the headers for all HDU's. In each header, the key WAVEUNIT denotes the wavelength unit which is used to describe the value of the key "WAVELNTH". Parameters ---------- afile : `str` or `astropy.io.fits.HDUList` The file to be read, or HDUList to process. Returns ------- headers : `list` A list of `sunpy.io.helper.FileHeader` headers. """ if isinstance(afile, fits.HDUList): hdulist = afile close = False else: hdulist = fits.open(afile, ignore_blank=True) hdulist.verify('silentfix') close = True try: headers = [] for hdu in hdulist: try: comment = "".join(hdu.header['COMMENT']).strip() except KeyError: comment = "" try: history = "".join(hdu.header['HISTORY']).strip() except KeyError: history = "" header = FileHeader(hdu.header) header['COMMENT'] = comment header['HISTORY'] = history # Strip out KEYCOMMENTS to a dict, the hard way keydict = {} for card in hdu.header.cards: if card.comment != '': keydict.update({card.keyword: card.comment}) header['KEYCOMMENTS'] = keydict header['WAVEUNIT'] = extract_waveunit(header) headers.append(header) finally: if close: hdulist.close() return headers
[docs]def write(fname, data, header, hdu_type=None, **kwargs): """ Take a data header pair and write a FITS file. Parameters ---------- fname : `str` File name, with extension. data : `numpy.ndarray` n-dimensional data array. header : `dict` A header dictionary. hdu_type: `None` or `~astropy.io.fits.CompImageHDU` `None` will return a normal FITS files. `~astropy.io.fits.CompImageHDU` will rice compress the FITS file. """ # Copy header so the one in memory is left alone while changing it for # write. header = header.copy() fits_header = header_to_fits(header) if isinstance(fname, str): fname = os.path.expanduser(fname) fitskwargs = {'output_verify': 'fix'} fitskwargs.update(kwargs) if not hdu_type: hdu_type = fits.PrimaryHDU hdu = hdu_type(data=data, header=fits_header) if not isinstance(hdu, fits.PrimaryHDU): hdul = fits.HDUList([fits.PrimaryHDU(), hdu]) else: hdul = fits.HDUList([hdu]) hdul.writeto(fname, **fitskwargs)
[docs]def header_to_fits(header): """ Convert a header dict to a `~astropy.fits.Header`. """ # The comments need to be added to the header separately from the normal # kwargs. Find and deal with them: fits_header = fits.Header() # Check Header key_comments = header.pop('KEYCOMMENTS', False) for k, v in header.items(): if isinstance(v, fits.header._HeaderCommentaryCards): if k.upper() == 'COMMENT': comments = str(v).split('\n') for com in comments: fits_header.add_comment(com) elif k.upper() == 'HISTORY': hists = str(v).split('\n') for hist in hists: fits_header.add_history(hist) elif k != '': fits_header.append(fits.Card(k, str(v).split('\n'))) else: fits_header.append(fits.Card(k, v)) if isinstance(key_comments, dict): for k, v in key_comments.items(): # Check that the Card for the comment exists before trying to write to it. if k in fits_header: fits_header.comments[k] = v elif key_comments: raise TypeError("KEYCOMMENTS must be a dictionary") return fits_header
[docs]def extract_waveunit(header): """ Attempt to read the wavelength unit from a given FITS header. Parameters ---------- header : `sunpy.io.header.FileHeader` One `~sunpy.io.header.FileHeader` instance which was created by reading a FITS file. For example, `sunpy.io.fits.get_header` returns a list of such instances. Returns ------- waveunit : `str` The wavelength unit that could be found or ``None`` otherwise. Examples -------- The goal of this function is to return a string that can be used in conjunction with the astropy.units module so that the return value can be directly passed to `astropy.units.Unit`. >>> import astropy.units >>> header = {'WAVEUNIT': 'Angstrom', 'KEYCOMMENTS': {}} >>> waveunit = extract_waveunit(header) >>> if waveunit is not None: ... unit = astropy.units.Unit(waveunit) """ # algorithm: try the following procedures in the following order and return # as soon as a waveunit could be detected # 1. read header('WAVEUNIT'). If None, go to step 2. # 1.1 -9 -> 'nm' # 1.2 -10 -> 'angstrom' # 1.3 0 -> go to step 2 # 1.4 if neither of the above, return the value itself in lowercase # 2. parse waveunit_comment # 2.1 'in meters' -> 'm' # 3. parse wavelnth_comment # 3.1 "[$UNIT] ..." -> $UNIT # 3.2 "Observed wavelength ($UNIT)" -> $UNIT def parse_waveunit_comment(waveunit_comment): if waveunit_comment == 'in meters': return 'm' waveunit_comment = header['KEYCOMMENTS'].get('WAVEUNIT') wavelnth_comment = header['KEYCOMMENTS'].get('WAVELNTH') waveunit = header.get('WAVEUNIT') if waveunit is not None: metre_submultiples = { 0: parse_waveunit_comment(waveunit_comment), -1: 'dm', -2: 'cm', -3: 'mm', -6: 'um', -9: 'nm', -10: 'angstrom', -12: 'pm', -15: 'fm', -18: 'am', -21: 'zm', -24: 'ym'} waveunit = metre_submultiples.get(waveunit, str(waveunit).lower()) elif waveunit_comment is not None: waveunit = parse_waveunit_comment(waveunit_comment) elif wavelnth_comment is not None: # supported formats (where $UNIT is the unit like "nm" or "Angstrom"): # "Observed wavelength ($UNIT)" # "[$UNIT] ..." parentheses_pattern = r'Observed wavelength \((\w+?)\)$' brackets_pattern = r'^\[(\w+?)\]' for pattern in [parentheses_pattern, brackets_pattern]: m = re.search(pattern, wavelnth_comment) if m is not None: waveunit = m.group(1) break if waveunit == '': return None # To fix problems associated with HMI FITS. return waveunit