# Licensed under a 3-clause BSD style license - see LICENSE.rst """ ``fitscheck`` is a command line script based on astropy.io.fits for verifying and updating the CHECKSUM and DATASUM keywords of .fits files. ``fitscheck`` can also detect and often fix other FITS standards violations. ``fitscheck`` facilitates re-writing the non-standard checksums originally generated by astropy.io.fits with standard checksums which will interoperate with CFITSIO. ``fitscheck`` will refuse to write new checksums if the checksum keywords are missing or their values are bad. Use ``--force`` to write new checksums regardless of whether or not they currently exist or pass. Use ``--ignore-missing`` to tolerate missing checksum keywords without comment. Example uses of fitscheck: 1. Add checksums:: $ fitscheck --write *.fits 2. Write new checksums, even if existing checksums are bad or missing:: $ fitscheck --write --force *.fits 3. Verify standard checksums and FITS compliance without changing the files:: $ fitscheck --compliance *.fits 4. Only check and fix compliance problems, ignoring checksums:: $ fitscheck --checksum none --compliance --write *.fits 5. Verify standard interoperable checksums:: $ fitscheck *.fits 6. Delete checksum keywords:: $ fitscheck --checksum remove --write *.fits """ import sys import logging import argparse import warnings from astropy.io import fits from astropy import __version__ log = logging.getLogger('fitscheck') DESCRIPTION = """ e.g. fitscheck example.fits Verifies and optionally re-writes the CHECKSUM and DATASUM keywords for a .fits file. Optionally detects and fixes FITS standard compliance problems. This script is part of the Astropy package. See https://docs.astropy.org/en/latest/io/fits/usage/scripts.html#module-astropy.io.fits.scripts.fitscheck for further documentation. """.strip() def handle_options(args): if not len(args): args = ['-h'] parser = argparse.ArgumentParser( description=DESCRIPTION, formatter_class=argparse.RawDescriptionHelpFormatter) parser.add_argument( '--version', action='version', version=f'%(prog)s {__version__}') parser.add_argument( 'fits_files', metavar='file', nargs='+', help='.fits files to process.') parser.add_argument( '-k', '--checksum', dest='checksum_kind', choices=['standard', 'remove', 'none'], help='Choose FITS checksum mode or none. Defaults standard.', default='standard') parser.add_argument( '-w', '--write', dest='write_file', help='Write out file checksums and/or FITS compliance fixes.', default=False, action='store_true') parser.add_argument( '-f', '--force', dest='force', help='Do file update even if original checksum was bad.', default=False, action='store_true') parser.add_argument( '-c', '--compliance', dest='compliance', help='Do FITS compliance checking; fix if possible.', default=False, action='store_true') parser.add_argument( '-i', '--ignore-missing', dest='ignore_missing', help='Ignore missing checksums.', default=False, action='store_true') parser.add_argument( '-v', '--verbose', dest='verbose', help='Generate extra output.', default=False, action='store_true') global OPTIONS OPTIONS = parser.parse_args(args) if OPTIONS.checksum_kind == 'none': OPTIONS.checksum_kind = False elif OPTIONS.checksum_kind == 'standard': OPTIONS.checksum_kind = True elif OPTIONS.checksum_kind == 'remove': OPTIONS.write_file = True OPTIONS.force = True return OPTIONS.fits_files def setup_logging(): log.handlers.clear() if OPTIONS.verbose: log.setLevel(logging.INFO) else: log.setLevel(logging.WARNING) handler = logging.StreamHandler() handler.setFormatter(logging.Formatter('%(message)s')) log.addHandler(handler) def verify_checksums(filename): """ Prints a message if any HDU in `filename` has a bad checksum or datasum. """ with warnings.catch_warnings(record=True) as wlist: warnings.simplefilter('always') with fits.open(filename, checksum=OPTIONS.checksum_kind) as hdulist: for i, hdu in enumerate(hdulist): # looping on HDUs is needed to read them and verify the # checksums if not OPTIONS.ignore_missing: if not hdu._checksum: log.warning('MISSING {!r} .. Checksum not found ' 'in HDU #{}'.format(filename, i)) return 1 if not hdu._datasum: log.warning('MISSING {!r} .. Datasum not found ' 'in HDU #{}'.format(filename, i)) return 1 for w in wlist: if str(w.message).startswith(('Checksum verification failed', 'Datasum verification failed')): log.warning('BAD %r %s', filename, str(w.message)) return 1 log.info(f'OK {filename!r}') return 0 def verify_compliance(filename): """Check for FITS standard compliance.""" with fits.open(filename) as hdulist: try: hdulist.verify('exception') except fits.VerifyError as exc: log.warning('NONCOMPLIANT %r .. %s', filename, str(exc).replace('\n', ' ')) return 1 return 0 def update(filename): """ Sets the ``CHECKSUM`` and ``DATASUM`` keywords for each HDU of `filename`. Also updates fixes standards violations if possible and requested. """ output_verify = 'silentfix' if OPTIONS.compliance else 'ignore' # For unit tests we reset temporarily the warning filters. Indeed, before # updating the checksums, fits.open will verify the existing checksums and # raise warnings, which are later catched and converted to log.warning... # which is an issue when testing, using the "error" action to convert # warnings to exceptions. with warnings.catch_warnings(): warnings.resetwarnings() with fits.open(filename, do_not_scale_image_data=True, checksum=OPTIONS.checksum_kind, mode='update') as hdulist: hdulist.flush(output_verify=output_verify) def process_file(filename): """ Handle a single .fits file, returning the count of checksum and compliance errors. """ try: checksum_errors = verify_checksums(filename) if OPTIONS.compliance: compliance_errors = verify_compliance(filename) else: compliance_errors = 0 if OPTIONS.write_file and checksum_errors == 0 or OPTIONS.force: update(filename) return checksum_errors + compliance_errors except Exception as e: log.error(f'EXCEPTION {filename!r} .. {e}') return 1 def main(args=None): """ Processes command line parameters into options and files, then checks or update FITS DATASUM and CHECKSUM keywords for the specified files. """ errors = 0 fits_files = handle_options(args or sys.argv[1:]) setup_logging() for filename in fits_files: errors += process_file(filename) if errors: log.warning(f'{errors} errors') return int(bool(errors))