def fits2fits(infile, outfile, verbose=False, fix_idr=False):
"""
Returns: error string, or None on success.
"""
if fix_idr:
from astrometry.util.fix_sdss_idr import fix_sdss_idr
# Read input file.
fitsin = pyfits.open(infile)
# Print out info about input file.
if verbose:
fitsin.info()
for i, hdu in enumerate(fitsin):
if fix_idr:
hdu = fitsin[i] = fix_sdss_idr(hdu)
# verify() fails when a keywords contains invalid characters,
# so go through the primary header and fix them by converting invalid
# characters to '_'
hdr = hdu.header
logging.info('Header has %i cards' % len(hdr))
# allowed characters (FITS standard section 5.1.2.1)
pat = re.compile(r'[^A-Z0-9_\-]')
for k in hdr.keys():
# new keyword:
knew = pat.sub('_', k)
if k != knew:
logging.debug('Replacing illegal keyword %s by %s' % (k, knew))
# add the new header card
# it seems pyfits is not clever enough to notice this...
if len(knew) > 8:
knew = 'HIERARCH ' + knew
hdr.update(knew, cards[k].value, cards[k].comment, after=k)
# remove the old one.
del hdr[k]
# Fix input header
hdu.verify('fix')
# UGH! Work around stupid pyfits handling of scaled data...
# (it fails to round-trip scaled data correctly!)
bzero = hdr.get('BZERO', None)
bscale = hdr.get('BSCALE', None)
if (bzero is not None and bscale is not None
and (bzero != 0. or bscale != 1.)):
logging.debug('Scaling to bzero=%g, bscale=%g' % (bzero, bscale))
hdu.scale('int16', '', bscale, bzero)
# Describe output file we're about to write...
if verbose:
print 'Outputting:'
fitsin.info()
try:
pyfits_writeto(fitsin, outfile, output_verify='warn')
except pyfits.VerifyError, ve:
return ('Verification of output file failed: your FITS file is probably too broken to automatically fix.' +
' Error message is:' + str(ve))
def removelines(infile, outfile, xcol='X', ycol='Y', cut=None, **kwargs):
if cut is None:
cut = 100
p = pyfits.open(infile)
xy = p[1].data
hdr = p[1].header
if xy is None:
print 'removelines.py: Input file contains no sources.'
pyfits_writeto(p, outfile)
return 0
x = xy.field(xcol)
y = xy.field(ycol)
if len(x) == 0:
print 'removelines.py: Your FITS file contains 0 sources (rows)'
pyfits_writeto(p, outfile)
return 0
ix = hist_remove_lines(x, 1, 0.5, logcut=-cut)
iy = hist_remove_lines(y, 1, 0.5, logcut=-cut)
I = ix * iy
xc = x[I]
yc = y[I]
print 'removelines.py: Removed %i sources' % (len(x) - len(xc))
p[1].header.add_history('This xylist was filtered by the "removelines.py" program')
p[1].header.add_history('to remove horizontal and vertical lines of sources')
p[1].header.update('REMLINEN', len(x) - len(xc), 'Number of sources removed by "removelines.py"')
p[1].data = p[1].data[I]
pyfits_writeto(p, outfile)
return 0