Source code for drizzlepac.resetbits

#!/usr/bin/env python

"""
resetbits - A module to set the value of specified array pixels to zero

This module allows a user to reset the pixel values of any integer array,
such as the DQ array from an HST image, to zero.

:Authors: Warren Hack

:License: :doc:`LICENSE`

PARAMETERS
----------
filename : str
    full filename with path
bits : str
    sum or list of integers corresponding to all the bits to be reset

Optional Parameters
-------------------
extver : int, optional
    List of version numbers of the arrays to be corrected
    (default: None, will reset all matching arrays)
extname : str, optional
    EXTNAME of the arrays in the FITS files to be reset
    (default: 'dq')

NOTES
-----
This module performs a simple bitwise-and on all the pixels in the specified
array and the integer value provided as input using the operation (array & ~bits).

Usage
-----
It can be called not only from within Python, but also from the host-level
operating system command line using the syntax::

    resetbits filename bits [extver [extname]]


EXAMPLES
--------
1. The following command will reset the 4096 bits in all
   the DQ arrays of the file 'input_flt.fits'::

        resetbits input_flt.fits 4096

   or from the Python command line::

        >>> import resetbits
        >>> resetbits.reset_dq_bits("input_file_flt.fits", 4096)

2. To reset the 2,32,64 and 4096 (sum of 4194) bits in the
   second DQ array, specified as 'dq,2', in the file 'input_flt.fits'::

        resetbits input_flt.fits 4194 2

   or from the Python command line::

        >>> import resetbits
        >>> resetbits.reset_dq_bits("input_file_flt.fits", 2+32+64+4096, extver=2)

"""
import os
import numpy as np
from astropy.nddata import interpret_bit_flags

from stsci.tools import stpyfits as fits
from stsci.tools import parseinput, logutil

from . import util

__taskname__ = "drizzlepac.resetbits"

# This is specifically NOT intended to match the package-wide version information.
__version__ = '1.0.1'
__version_date__ = '23-March-2017'


log = logutil.create_logger(__name__, level=logutil.logging.NOTSET)


[docs]def reset_dq_bits(input,bits,extver=None,extname='dq'): """ This function resets bits in the integer array(s) of a FITS file. Parameters ---------- filename : str full filename with path bits : str sum or list of integers corresponding to all the bits to be reset extver : int, optional List of version numbers of the DQ arrays to be corrected [Default Value: None, will do all] extname : str, optional EXTNAME of the DQ arrays in the FITS file [Default Value: 'dq'] Notes ----- The default value of None for the 'extver' parameter specifies that all extensions with EXTNAME matching 'dq' (as specified by the 'extname' parameter) will have their bits reset. Examples -------- 1. The following command will reset the 4096 bits in all the DQ arrays of the file input_file_flt.fits:: reset_dq_bits("input_file_flt.fits", 4096) 2. To reset the 2,32,64 and 4096 bits in the second DQ array, specified as 'dq,2', in the file input_file_flt.fits:: reset_dq_bits("input_file_flt.fits", "2,32,64,4096", extver=2) """ # Interpret bits value bits = interpret_bit_flags(bits) flist, fcol = parseinput.parseinput(input) for filename in flist: # open input file in write mode to allow updating the DQ array in-place p = fits.open(filename, mode='update', memmap=False) # Identify the DQ array to be updated # If no extver is specified, build a list of all DQ arrays in the file if extver is None: extver = [] for hdu in p: # find only those extensions which match the input extname # using case-insensitive name comparisons for 'extname' if 'extver' in hdu.header and \ hdu.header['extname'].lower() == extname.lower(): extver.append(int(hdu.header['extver'])) else: # Otherwise, insure that input extver values are a list if not isinstance(extver, list): extver = [extver] # for each DQ array identified in the file... for extn in extver: dqarr = p[extname,extn].data dqdtype = dqarr.dtype # reset the desired bits p[extname,extn].data = (dqarr & ~bits).astype(dqdtype) # preserve original dtype log.info('Reset bit values of %s to a value of 0 in %s[%s,%s]' % (bits, filename, extname, extn)) # close the file with the updated DQ array(s) p.close()
# #### Interfaces used by TEAL #
[docs]def run(configobj=None): """ Teal interface for running this code. """ reset_dq_bits(configobj['input'],configobj['bits'], extver=configobj['extver'],extname=configobj['extname'])
def main(): import getopt, sys try: optlist, args = getopt.getopt(sys.argv[1:], 'h') except getopt.error as e: print(str(e)) print(__doc__) print("\t", __version__) # initialize default values help = 0 # read options for opt, value in optlist: if opt == "-h": help = 1 if len(args) < 4: if len(args) < 3: args.append(None) args.append('dq') if (help): print(__doc__) print("\t", __version__+'('+__version_date__+')') else: reset_dq_bits(args[0],args[1],args[2], args[3]) if __name__ == "__main__": main()
[docs]def help(file=None): """ Print out syntax help for running astrodrizzle Parameters ---------- file : str (Default = None) If given, write out help to the filename specified by this parameter Any previously existing file with this name will be deleted before writing out the help. """ helpstr = getHelpAsString(docstring=True, show_ver = True) if file is None: print(helpstr) else: if os.path.exists(file): os.remove(file) f = open(file, mode = 'w') f.write(helpstr) f.close()
[docs]def getHelpAsString(docstring = False, show_ver = True): """ return useful help from a file in the script directory called __taskname__.help """ install_dir = os.path.dirname(__file__) taskname = util.base_taskname(__taskname__, __package__) htmlfile = os.path.join(install_dir, 'htmlhelp', taskname + '.html') helpfile = os.path.join(install_dir, taskname + '.help') if docstring or (not docstring and not os.path.exists(htmlfile)): if show_ver: helpString = os.linesep + \ ' '.join([__taskname__, 'Version', __version__, ' updated on ', __version_date__]) + 2*os.linesep else: helpString = '' if os.path.exists(helpfile): helpString += teal.getHelpFileAsString(taskname, __file__) else: if __doc__ is not None: helpString += __doc__ + os.linesep else: helpString = 'file://' + htmlfile return helpString