python-pyfits 1:2.4.0-1build1 / usr / bin / fitscheck

#!/usr/bin/python2.7
#-*-python-*-

"""fitscheck is a command line script based on pyfits 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 pyfits 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. Verify and update checksums, tolerating non-standard checksums,
updating to standard checksum:

% fitscheck --checksum either --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. Verify original nonstandard checksums only:

% fitscheck --checksum nonstandard *.fits

5. Only check and fix compliance problems,  ignoring checksums:

% fitscheck --checksum none --compliance --write *.fits

6. Verify standard interoperable checksums

% fitscheck *.fits

7. Delete checksum keywords

% fitscheck --checksum none --write *.fits
"""
import sys
import optparse
import warnings

import pyfits

warnings.filterwarnings("error",  message="Warning:\s+Checksum verification failed")
warnings.filterwarnings("error",  message="Warning:\s+Datasum verification failed")
warnings.filterwarnings("ignore", message="Overwrite existing file")

def handle_options(args):

    if not len(args):
        args = ["-h"]

    parser = optparse.OptionParser(usage="""%prog [options] <.fits files...>

.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.""")

    parser.add_option(
        "-k", "--checksum", dest="checksum_kind",
        type="choice", choices=["standard", "nonstandard", "either", "none"],
        help="Choose FITS checksum mode or none.  Defaults standard.",
        default="standard", metavar="[standard | nonstandard | either | none]")

    parser.add_option(
        "-w", "--write", dest="write_file",
        help="Write out file checksums and/or FITS compliance fixes.",
        default=False, action="store_true")

    parser.add_option(
        "-f", "--force", dest="force",
        help="Do file update even if original checksum was bad.",
        default=False, action="store_true")

    parser.add_option(
        "-c", "--compliance", dest="compliance",
        help="Do FITS compliance checking, fix if possible.",
        default=False, action="store_true")

    parser.add_option(
        "-i", "--ignore-missing", dest="ignore_missing",
        help="Ignore missing checksums.",
        default=False, action="store_true")

    parser.add_option(
        "-v", "--verbose", dest="verbose",
        help="Generate extra output.",
        default=False, action="store_true")

    global OPTIONS
    OPTIONS, fits_files = parser.parse_args(args)

    if OPTIONS.checksum_kind == "none":
        OPTIONS.checksum_kind = False

    return fits_files

EOL = "\n"   # global to know when an EOL wasn't just output.
def out(*s, **keys):
    """output a message to stdout or `file`."""
    global EOL
    EOL = keys.get("eol", "\n")
    file = keys.get("file", sys.stdout)
    file.write(" ".join([str(x) for x in s]))
    if EOL:
        file.write("\n")
    file.flush()

def verbose(*s, **keys):
    """output a message only if option -v was specified."""
    if OPTIONS.verbose:
        out(*s, **keys)

def get_checksum():
    """Map checksum command line option to function parameter."""
    if OPTIONS.checksum_kind in ["standard", "nonstandard", "either"]:
        return OPTIONS.checksum_kind
    else:
        return False

def verify_checksums(filename):
    """Prints a message if any HDU in `filename` has a bad checksum or datasum.
    """
    errors = 0
    try:
        hdulist = pyfits.open(filename, checksum=OPTIONS.checksum_kind)
    except UserWarning, w:
        remainder = ".. " + " ".join(str(w).split(" ")[1:]).strip()
        # if "Checksum" in str(w) or "Datasum" in str(w):
        out("BAD", repr(filename), remainder)
        return 1
    if not OPTIONS.ignore_missing:
        for i, hdu in enumerate(hdulist):
            if not hdu._checksum:
                out("MISSING", repr(filename), ".. Checksum not found in HDU #" + str(i))
                return 1
            if not hdu._datasum:
                out("MISSING", repr(filename), ".. Datasum not found in HDU #" + str(i))
                return 1
    if not errors:
        verbose("OK", repr(filename))
    return errors

def verify_compliance(filename):
    """Check for FITS standard compliance."""
    hdulist = pyfits.open(filename)
    try:
        hdulist.verify("exception")
    except pyfits.VerifyError, e:
        out("NONCOMPLIANT", repr(filename), "..", str(e).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.
    """
    hdulist = pyfits.open(filename)
    try:
        hdulist.writeto(filename, checksum=OPTIONS.checksum_kind, clobber=True,
            output_verify=OPTIONS.compliance and "silentfix" or "ignore")
    except pyfits.VerifyError, e:
        pass # unfixable errors already noted during verification phase
    finally:
        hdulist.close()

def process_file(fits):
    """Handle a single .fits file,  returning the count of checksum and compliance
    errors.
    """
    try:
        checksum_errors = verify_checksums(fits)
        if OPTIONS.compliance:
            compliance_errors = verify_compliance(fits)
        else:
            compliance_errors = 0
        if OPTIONS.write_file and checksum_errors == 0 or OPTIONS.force:
            update(fits)
        return checksum_errors + compliance_errors
    except Exception, e:
        out("EXCEPTION",repr(fits),"..",str(e))
        return 1

def main():
    """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(sys.argv[1:])
    for fits in fits_files:
        errors += process_file(fits)
    if errors:
        out(str(errors), "errors")
    sys.exit(errors)

if __name__ == "__main__":
    main()