diff options
Diffstat (limited to 'lib/stwcs/wcsutil/headerlet.py')
| -rw-r--r-- | lib/stwcs/wcsutil/headerlet.py | 567 |
1 files changed, 304 insertions, 263 deletions
diff --git a/lib/stwcs/wcsutil/headerlet.py b/lib/stwcs/wcsutil/headerlet.py index 50b92f8..fd4c287 100644 --- a/lib/stwcs/wcsutil/headerlet.py +++ b/lib/stwcs/wcsutil/headerlet.py @@ -30,10 +30,14 @@ from stsci.tools import fileutil as fu from stsci.tools import parseinput #### Logging support functions -modulelogger = logging.getLogger('headerlet') - -import atexit -atexit.register(logging.shutdown) +logger = logging.getLogger(__name__) +formatter = logging.Formatter( + "%(funcName)s %(levelname)s: %(message)s") +ch = logging.StreamHandler() +ch.setFormatter(formatter) +ch.setLevel(logging.CRITICAL) +logger.addHandler(ch) +logger.setLevel(logging.DEBUG) FITS_STD_KW = ['XTENSION', 'BITPIX', 'NAXIS', 'PCOUNT', 'GCOUNT', 'EXTNAME', 'EXTVER', 'ORIGIN', @@ -43,41 +47,41 @@ DEFAULT_SUMMARY_COLS = ['HDRNAME', 'WCSNAME', 'DISTNAME', 'AUTHOR', 'DATE', 'SIPNAME', 'NPOLFILE', 'D2IMFILE', 'DESCRIP'] COLUMN_DICT = {'vals': [], 'width': []} COLUMN_FMT = '{:<{width}}' - -def set_logger(logger, level, mode='w'): - formatter = logging.Formatter( - "%(asctime)s - %(name)s - %(levelname)s - %(message)s") - log_filename = 'headerlet.log' - fh = logging.FileHandler(log_filename, mode=mode) - fh.setLevel(logging.DEBUG) - fh.setFormatter(formatter) - logger.addHandler(fh) - logger.setLevel(level) - -def init_logging(function_name, logger = None, level=100, - verbose=False, logmode='w'): + +def init_logging(funcname=None, level=100, mode='w', **kwargs): """ Initialize logging for a function Parameters ---------- - function_name: string + funcname: string Name of function which will be recorded in log - level: int - Logging level - verbose: bool - If True, will set logging to report more activity + level: int, or bool, or string + int or string : Logging level + bool: False - switch off logging + Text logging level for the message ("DEBUG", "INFO", + "WARNING", "ERROR", "CRITICAL") + mode: 'w' or 'a' + attach to logfile ('a' or start a new logfile ('w') """ - if logger is None: - logger = modulelogger - - if verbose: - set_logger(logger, verbose, mode=logmode) - else: - logger.setLevel(level) - - logger.info("Starting %s: %s" % (function_name, time.asctime())) - - + for hndl in logger.handlers: + if isinstance(hndl, logging.FileHandler): + has_file_handler = True + else: + has_file_handler = False + if level: + if not has_file_handler: + logname = 'headerlet.log' + fh = logging.FileHandler(logname, mode=mode) + fh.setFormatter(formatter) + fh.setLevel(logging.DEBUG) + logger.addHandler(fh) + logger.info("%s: Starting %s with arguments:\n\t %s" % + (time.asctime(), funcname, kwargs)) + +def release_handlers(): + for hndl in logger.handlers: + hndl.close() + #### Utility functions def is_par_blank(par): return par in ['', ' ', 'INDEF', "None", None] @@ -160,7 +164,7 @@ def get_header_kw_vals(hdr, kwname, kwval, default=0): return kwval def find_headerlet_HDUs(fobj, hdrext=None, hdrname=None, distname=None, - strict=True): + strict=True, logging=False, logmode='w'): """ Returns all HeaderletHDU extensions in a science file that matches the inputs specified by the user. If no hdrext, hdrname or distname are @@ -181,21 +185,33 @@ def find_headerlet_HDUs(fobj, hdrext=None, hdrname=None, distname=None, If False, all extension indices returned if hdrext, hdrname and distname are all None. If True and hdrext, hdrname, and distname are all None, raise an Exception requiring one to be specified. - + logging: boolean + enable logging to a file called headerlet.log + logmode: 'w' or 'a' + log file open mode + Returns ------- hdrlets: list A list of all matching HeaderletHDU extension indices (could be just one) + """ + kwargs = locals() + init_logging('find_headerlet_HDUs', level=logging, + mode=logmode, **kwargs) + get_all = False if hdrext is None and hdrname is None and distname is None: if not strict: get_all = True else: - print '=====================================================' - print 'No valid Headerlet extension specified.' - print ' Either "hdrname", "hdrext", or "distname" needs to be specified.' - print '=====================================================' + mess = """\n + ===================================================== + No valid Headerlet extension specified. + Either "hdrname", "hdrext", or "distname" needs to be specified. + ===================================================== + """ + logger.critical(mess) raise ValueError fobj, fname, open_fobj = parse_filename(fobj) @@ -242,10 +258,13 @@ def find_headerlet_HDUs(fobj, hdrext=None, hdrname=None, distname=None, else: kwerr = 'distname' kwval = distname - print '=====================================================' - print 'No valid Headerlet extension found!' - print ' "%s" = %s not found in %s.' % (kwerr, kwval, fname) - print '=====================================================' + message = """\n + ===================================================== + No valid Headerlet extension found!' + "%s" = %s not found in %s.' % (kwerr, kwval, fname) + ===================================================== + """ + logger.critical(message) raise ValueError return hdrlets @@ -272,7 +291,7 @@ def verify_hdrname_is_unique(fobj, hdrname): return unique -def is_wcs_identical(scifile, file2, scikey=" ", file2key=" ", verbose=False): +def is_wcs_identical(scifile, file2, scikey=" ", file2key=" ", logging=False): """ Compares the WCS solution of 2 files. @@ -288,9 +307,8 @@ def is_wcs_identical(scifile, file2, scikey=" ", file2key=" ", verbose=False): alternate WCS key in scifile file2key: string alternate WCS key in file2 - verbose: False or a python logging level - (one of 'INFO', 'DEBUG' logging levels) - (an integer representing a logging level) + logging: boolean + True: enable file logging Notes ----- @@ -306,7 +324,7 @@ def is_wcs_identical(scifile, file2, scikey=" ", file2key=" ", verbose=False): - Velocity aberation """ - init_logging('isWCSIdentical', level=100, verbose=False) + init_logging('is_wcs_identical', level=logging) fname, extname = fu.parseFilename(scifile) scifile = fname if extname is not None: @@ -325,15 +343,14 @@ def is_wcs_identical(scifile, file2, scikey=" ", file2key=" ", verbose=False): numsci2 = max(countExtn(file2), countExtn(file2, 'SIPWCS')) if numsci1 == 0 or numsci2 == 0 or numsci1 != numsci2: - modulelogger.info( - "Number of SCI and SIPWCS extensions do not match.") + logger.info("Number of SCI and SIPWCS extensions do not match.") result = False else: numsci1 = None numsci2 = None if get_rootname(scifile) != get_rootname(file2): - modulelogger.info('Rootnames do not match.') + logger.info('Rootnames do not match.') result = False try: extname1 = pyfits.getval(scifile, 'EXTNAME', ext=('SCI', 1)) @@ -358,40 +375,40 @@ def is_wcs_identical(scifile, file2, scikey=" ", file2key=" ", verbose=False): not np.allclose(w1.wcs.crpix, w2.wcs.crpix, rtol=1e-7) or \ not np.allclose(w1.wcs.cd, w2.wcs.cd, rtol=1e-7) or \ not (np.array(w1.wcs.ctype) == np.array(w2.wcs.ctype)).all(): - modulelogger.info('Primary WCSs do not match') + logger.info('Primary WCSs do not match') result = False if w1.sip or w2.sip: if (w2.sip and not w1.sip) or (w1.sip and not w2.sip) or \ not np.allclose(w1.sip.a, w2.sip.a, rtol=1e-7) or \ not np.allclose(w1.sip.b, w2.sip.b, rtol=1e-7): - modulelogger.info('SIP coefficients do not match') + logger.info('SIP coefficients do not match') result = False if w1.cpdis1 or w2.cpdis1: if w1.cpdis1 and not w2.cpdis1 or \ w2.cpdis1 and not w1.cpdis1 or \ not np.allclose(w1.cpdis1.data, w2.cpdis1.data): - modulelogger.info('NPOL distortions do not match') + logger.info('NPOL distortions do not match') result = False if w1.cpdis2 or w2.cpdis2: if w1.cpdis2 and not w2.cpdis2 or \ w2.cpdis2 and not w1.cpdis2 or \ not np.allclose(w1.cpdis2.data, w2.cpdis2.data): - modulelogger.info('NPOL distortions do not match') + logger.info('NPOL distortions do not match') result = False if w1.det2im1 or w2.det2im1: if w1.det2im1 and not w2.det2im1 or \ w2.det2im1 and not w1.det2im1 or\ not np.allclose(w1.det2im1.data, w2.det2im1.data): - modulelogger.info('Det2Im corrections do not match') + logger.info('Det2Im corrections do not match') result = False if w1.det2im2 or w2.det2im2: if w1.det2im2 and not w2.det2im2 or \ w2.det2im2 and not w1.det2im2 or\ not np.allclose(w1.det2im2.data, w2.det2im2.data): - modulelogger.info('Det2Im corrections do not match') + logger.info('Det2Im corrections do not match') result = False if w1.vafactor != w2.vafactor: - modulelogger.info('VA factors do not match') + logger.info('VA factors do not match') result = False return result @@ -406,7 +423,7 @@ def update_ref_files(source, dest): source: pyfits.Header dest: pyfits.Header """ - modulelogger.info("Updating reference files") + logger.info("Updating reference files") phdukw = {'IDCTAB': True, 'NPOLFILE': True, 'D2IMFILE': True} @@ -563,7 +580,7 @@ def _create_primary_HDU(destim, hdrname, distname, wcsname, #### Public Interface functions def extract_headerlet(filename, output, extnum=None, hdrname=None, - clobber=False, verbose=100): + clobber=False, logging=True): """ Finds a headerlet extension in a science file and writes it out as a headerlet FITS file. @@ -595,12 +612,12 @@ def extract_headerlet(filename, output, extnum=None, hdrname=None, clobber: bool If output file already exists, this parameter specifies whether or not to overwrite that file [Default: False] - verbose: int - python logging level + logging: boolean + enable logging to a file """ - init_logging('extract_headerlet', verbose=verbose) + init_logging('extract_headerlet', level=logging) if isinstance(filename, pyfits.HDUList): filename = [filename] else: @@ -612,20 +629,21 @@ def extract_headerlet(filename, output, extnum=None, hdrname=None, if hdrname in ['', ' ', None, 'INDEF'] and extnum is None: if close_fobj: fobj.close() - raise ValueError("Expected a valid extnum or hdrname parameter") + logger.critical("Expected a valid extnum or hdrname parameter") + raise ValueError if hdrname is not None: extn_from_hdrname = find_headerlet_HDUs(fobj, hdrname=hdrname)[0] if extn_from_hdrname != extnum: - raise ValueError( - "hdrname and extnmu should refer to the same FITS extension" - ) + logger.critical("hdrname and extnmu should refer to the same FITS extension") + raise ValueError else: hdrhdu = fobj[extn_from_hdrname] else: hdrhdu = fobj[extnum] if not isinstance(hdrhdu, HeaderletHDU): - raise ValueError("Specified extension is not a headerlet") + logger.critical("Specified extension is not a headerlet") + raise ValueError hdrlet = hdrhdu.headerlet @@ -647,7 +665,7 @@ def write_headerlet(filename, hdrname, output=None, sciext='SCI', sipname=None, npolfile=None, d2imfile=None, author=None, descrip=None, history=None, rms_ra=None, rms_dec=None, nmatch=None, catalog=None, - attach=True, clobber=False): + attach=True, clobber=False, logging=False): """ Save a WCS as a headerlet FITS file. @@ -728,8 +746,10 @@ def write_headerlet(filename, hdrname, output=None, sciext='SCI', clobber: bool If output file already exists, this parameter specifies whether or not to overwrite that file [Default: False] + logging: boolean + enable file logging """ - init_logging('write_headerlet') + init_logging('write_headerlet', logging=logging) if isinstance(filename, pyfits.HDUList): filename = [filename] @@ -743,12 +763,12 @@ def write_headerlet(filename, hdrname, output=None, sciext='SCI', fname = f.filename() if wcsname in [None, ' ', '', 'INDEF'] and wcskey is None: - print '='*60 - print '[write_headerlet]' - print 'No valid WCS found found in %s.' % fname - print ' A valid value for either "wcsname" or "wcskey" ' - print ' needs to be specified. ' - print '='*60 + message = """\n + No valid WCS found found in %s.' % fname + A valid value for either "wcsname" or "wcskey" ' + needs to be specified. + """ + logger.critical(message) raise ValueError # Translate 'wcskey' value for PRIMARY WCS to valid altwcs value of ' ' @@ -785,7 +805,7 @@ def write_headerlet(filename, hdrname, output=None, sciext='SCI', descrip=descrip, history=history, rms_ra=rms_ra, rms_dec=rms_dec, nmatch=nmatch, catalog=catalog, - verbose=False) + logging=False) if attach: # Check to see whether or not a HeaderletHDU with @@ -805,11 +825,12 @@ def write_headerlet(filename, hdrname, output=None, sciext='SCI', fobj.flush() else: - print 'WARNING:' - print ' Headerlet with hdrname ', hdrname, ' already archived for WCS ', wname - print ' No new headerlet appended to ', fname, '.' - - + message = """ + Headerlet with hdrname ', hdrname, ' already archived for WCS ', wname + No new headerlet appended to ', fname, '.' + """ + logger.critical(message) + if close_fobj: fobj.close() @@ -823,25 +844,16 @@ def write_headerlet(filename, hdrname, output=None, sciext='SCI', outname = '%s_%s_hlet.fits' % (frootname, outname) # If user specifies an output filename for headerlet, write it out - write_hdrlet = True - if os.path.exists(outname): - if clobber: - os.remove(outname) - else: - print 'WARNING:' - print ' Headerlet file ', outname, ' already written out!' - print ' This headerlet file will not be created now.' - write_hdrlet = False - if write_hdrlet: - hdrletobj.writeto(outname) - print 'Created Headerlet file: ', outname + + hdrletobj.tofile(outname, clobber=clobber) + logger.critical( 'Created Headerlet file %s ' % outname) def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, wcskey=" ", wcsname=None, sipname=None, npolfile=None, d2imfile=None, author=None, descrip=None, history=None, rms_ra=None, rms_dec = None, nmatch=None, catalog=None, - verbose=100, logmode='w'): + logging=False, logmode='w'): """ Create a headerlet from a WCS in a science file If both wcskey and wcsname are given they should match, if not @@ -908,8 +920,8 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, to the headerlet PRIMARY header If filename is specified, it will format and attach all text from that file as the history. - verbose: int - python logging level + logging: boolean + enable file logging logmode: 'w' or 'a' log file open mode @@ -917,11 +929,11 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, ------- Headerlet object """ - - init_logging('createHeaderlet', verbose=verbose) - + kwargs = locals() + init_logging('create_headerlet', level=logging, mode=logmode, **kwargs) + logger.info("%s: cr_h starting with arguments:\n\t %s" % + (time.asctime(), kwargs)) fobj, fname, close_file = parse_filename(filename) - # Define extension to evaluate for verification of input parameters wcsext = 1 if fu.isFits(fname)[1] == 'simple': @@ -929,6 +941,7 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, # Translate 'wcskey' value for PRIMARY WCS to valid altwcs value of ' ' if wcskey == 'PRIMARY': wcskey = ' ' + logger.info("wcskey reset from 'PRIMARY' to ' '") wcskey = wcskey.upper() wcsnamekw = "".join(["WCSNAME", wcskey.upper()]).rstrip() hdrnamekw = "".join(["HDRNAME", wcskey.upper()]).rstrip() @@ -938,6 +951,7 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, if wcsnamekw in fobj[wcsext].header: #check if there's a WCSNAME for this wcskey in the header wcsname = fobj[wcsext].header[wcsnamekw] + logger.info("Setting wcsname from header[%s] to %s" % (wcsnamekw, wcsname)) else: if hdrname not in ['', ' ', None, "INDEF"]: """ @@ -947,43 +961,43 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, use hdrname as WCSNAME for the headerlet. """ wcsname = hdrname + logger.debug("Setting wcsname from hdrname to %s" % hdrname) else: if hdrnamekw in fobj[wcsext].header: wcsname = fobj[wcsext].header[hdrnamekw] + logger.debug("Setting wcsname from header[%s] to %s" % (hdrnamekw, wcsname)) else: message = "Required keywords 'HDRNAME' or 'WCSNAME' not found!\n" message += "Please specify a value for parameter 'hdrname',\n" message += " or update header with 'WCSNAME' keyword." - print message - modulelogger.critical(message) - raise KeyError,"Required keywords 'HDRNAME' or 'WCSNAME' not found!" + logger.critical(message) + raise KeyError else: # Verify that 'wcsname' and 'wcskey' values specified by user reference # the same WCS wname = fobj[wcsext].header[wcsnamekw] if wcsname != wname: - message = "Inconsistent values for 'wcskey' and 'wcsname' specified!\n" + message = "\tInconsistent values for 'wcskey' and 'wcsname' specified!\n" message += " 'wcskey' = %s and 'wcsname' = %s. \n" % (wcskey, wcsname) message += "Actual value of %s found to be %s. \n" % (wcsnamekw, wname) - print message - raise KeyError,"Inconsistent values for 'wcskey' and 'wcsname' parameters" - + logger.critical(message) + raise KeyError wkeys = altwcs.wcskeys(fname, ext=wcsext) if wcskey != ' ': if wcskey not in wkeys: - if verbose > 100: - modulelogger.debug('No WCS with wcskey=%s found in extension %s. Skipping...' % (wcskey, str(wcsext))) - raise ValueError(' No WCS with wcskey=%s found in extension %s.Skipping...' % (wcskey, str(wcsext))) + logger.critical('No WCS with wcskey=%s found in extension %s. Skipping...' % (wcskey, str(wcsext))) + raise ValueError # get remaining required keywords if destim is None: if 'ROOTNAME' in fobj[0].header: destim = fobj[0].header['ROOTNAME'] + logger.info("Setting destim to rootname of the science file") else: destim = fname - modulelogger.info('DESTIM not provided') - modulelogger.info('Keyword "ROOTNAME" not found') - modulelogger.info('Using file name as DESTIM') + logger.info('DESTIM not provided') + logger.info('Keyword "ROOTNAME" not found') + logger.info('Using file name as DESTIM') if not hdrname: # check if HDRNAME<wcskey> is in header @@ -992,25 +1006,29 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, else: if wcsnamekw in fobj[wcsext].header: hdrname = fobj[wcsext].header[wcsnamekw] - print 'Using default value for HDRNAME of "%s"' % (hdrname), - print ' derived from %s.' % (wcsnamekw) + message = """ + Using default value for HDRNAME of "%s"' % (hdrname), + derived from %s.' % (wcsnamekw) + """ + logger.info(message) + logger.info("Setting hdrname to %s from header[%s]" + % (hdrname, wcsnamekw)) else: message = "Required keywords 'HDRNAME' or 'WCSNAME' not found" - modulelogger.critical(message) - print message - raise KeyError, message + logger.critical(message) + raise KeyError if not sipname: sipname = utils.build_sipname(fobj) - + logger.info("Setting sipname value to %s" % sipname) if not npolfile: npolfile = utils.build_npolname(fobj) - + logger.info("Setting npolfile value to %s" % npolfile) if not d2imfile: d2imfile = utils.build_d2imname(fobj) - + logger.info("Setting d2imfile value to %s" % d2imfile) distname = utils.build_distname(sipname, npolfile, d2imfile) - + logger.info("Setting distname to %s" % distname) rms_ra = get_header_kw_vals(fobj[wcsext].header, ("RMS_RA"+wcskey).rstrip(), rms_ra, default=0) rms_dec = get_header_kw_vals(fobj[wcsext].header, @@ -1042,12 +1060,12 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, else: errstr = "Expected sciext to be a list of FITS extensions with science data\n"+\ " a valid EXTNAME string, or an integer." - raise ValueError(errstr) + logger.critical(errstr) + raise ValueError if wcskey is 'O': message = "Warning: 'O' is a reserved key for the original WCS. Quitting..." - modulelogger.info(message) - print message + logger.info(message) return # open file and parse comments @@ -1056,7 +1074,7 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, history = f.readlines() f.close() - modulelogger.debug("Data extensions form which to create headerlet:\n\t %s" + logger.debug("Data extensions from which to create headerlet:\n\t %s" % (str(sciext))) hdul = pyfits.HDUList() phdu = _create_primary_HDU(destim, hdrname, distname, wcsname, @@ -1068,7 +1086,6 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, orient_comment = "positions angle of image y axis (deg. e of n)" wcsdvarr_extns = [] if fu.isFits(fobj)[1] is not 'simple': - for e in sciext: try: fext = int(e) @@ -1077,18 +1094,12 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, wkeys = altwcs.wcskeys(fname, ext=fext) if wcskey != ' ': if wcskey not in wkeys: - if verbose > 100: - modulelogger.debug('No WCS with wcskey=%s found in extension %s. Skipping...' % (wcskey, str(e))) + logger.debug('No WCS with wcskey=%s found in extension %s. Skipping...' % (wcskey, str(e))) continue # skip any extension which does not have this wcskey # This reads in full model: alternate WCS keywords plus SIP hwcs = HSTWCS(fname, ext=fext, wcskey=' ') - #if hwcs.wcs.is_unity(): - # # This extension does not contain a valid WCS, so - # # skip on to the next - # continue - h = hwcs.wcs2header(sip2hdr=True) if hasattr(hwcs, 'orientat'): h.update('ORIENTAT', hwcs.orientat, comment=orient_comment) @@ -1163,12 +1174,9 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, try: h.append(fhdr['AXISCORR']) except KeyError: - print ("'D2IMFILE' kw exists but keyword 'AXISCORR' was not found in " - "%s['SCI',%d]" % (fname, val)) - modulelogger.exception("'D2IMFILE' kw exists but keyword 'AXISCORR' was not found in " + logger.critical("'D2IMFILE' kw exists but keyword 'AXISCORR' was not found in " "%s['SCI',%d]" % (fname, val)) raise - try: h.append(fhdr['D2IMERR']) except KeyError: @@ -1188,11 +1196,11 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, if close_file: fobj.close() - return Headerlet(hdul, verbose=verbose, logmode='a') + return Headerlet(hdul, logging=logging, logmode='a') def apply_headerlet_as_primary(filename, hdrlet, attach=True, archive=True, - force=False, verbose=False): + force=False, logging=False, logmode='a'): """ Apply headerlet 'hdrfile' to a science observation 'destfile' as the primary WCS @@ -1210,17 +1218,20 @@ def apply_headerlet_as_primary(filename, hdrlet, attach=True, archive=True, force: boolean If True, this will cause the headerlet to replace the current PRIMARY WCS even if it has a different distortion model. [Default: False] - verbose: False or a python logging level - (one of 'INFO', 'DEBUG' logging levels) - (an integer representing a logging level) + logging: boolean + enable file logging + logmode: 'w' or 'a' + log file open mode """ - init_logging('apply_headerlet_as_primary', verbose=verbose) + kwargs = locals() + init_logging('apply_headerlet_as_primary', level=logging, + mode=logmode, **kwargs) - hlet = Headerlet(hdrlet, verbose=verbose, logmode='a') + hlet = Headerlet(hdrlet, logging=logging) hlet.apply_as_primary(filename, attach=attach, archive=archive, force=force) -def apply_headerlet_as_alternate(filename, hdrlet, attach=True, - wcskey=None, wcsname=None, verbose=False): +def apply_headerlet_as_alternate(filename, hdrlet, attach=True, wcskey=None, + wcsname=None, logging=False, logmode='w'): """ Apply headerlet to a science observation as an alternate WCS @@ -1241,17 +1252,19 @@ def apply_headerlet_as_alternate(filename, hdrlet, attach=True, Name to be assigned to this alternate WCS WCSNAME is a required keyword in a Headerlet but this allows the user to change it as desired. - verbose: False or a python logging level - (one of 'INFO', 'DEBUG' logging levels) - (an integer representing a logging level) + logging: boolean + enable file logging + logmode: 'a' or 'w' """ - init_logging('apply_headerlet_as_alternate', verbose=verbose) + kwargs = locals() + init_logging('apply_headerlet_as_alternate', level=logging, + mode=logmode, **kwargs) - hlet = Headerlet(hdrlet, verbose=verbose, logmode='a') + hlet = Headerlet(hdrlet, logging=logging, logmode=logmode) hlet.apply_as_alternate(filename, attach=attach, wcsname=wcsname, wcskey=wcskey) -def attach_headerlet(filename, hdrlet, verbose=False): +def attach_headerlet(filename, hdrlet, logging=False, logmode='a'): """ Attach Headerlet as an HeaderletHDU to a science file @@ -1261,13 +1274,19 @@ def attach_headerlet(filename, hdrlet, verbose=False): science file to which the headerlet should be applied hdrlet: string or Headerlet object string representing a headerlet file + logging: boolean + enable file logging + logmode: 'a' or 'w' """ - init_logging('attach_headerlet', verbose=verbose) + kwargs = locals() + init_logging('attach_headerlet', level=logging, + mode=logmode, **kwargs) - hlet = Headerlet(hdrlet, verbose=verbose, logmode='a') + hlet = Headerlet(hdrlet, logging=logging, logmode='a') hlet.attach_to_file(filename) -def delete_headerlet(filename, hdrname=None, hdrext=None, distname=None): +def delete_headerlet(filename, hdrname=None, hdrext=None, distname=None, + logging=False, logmode='w'): """ Deletes HeaderletHDU(s) from a science file @@ -1292,17 +1311,25 @@ def delete_headerlet(filename, hdrname=None, hdrext=None, distname=None): tuple has the form ('HDRLET', 1) distname: string or None distortion model as specified in the DISTNAME keyword + logging: boolean + enable file logging + logmode: 'a' or 'w' """ - init_logging('delete_headerlet') + kwargs = locals() + init_logging('delete_headerlet', level=logging, + mode=logmode, **kwargs) + hdrlet_ind = find_headerlet_HDUs(filename, hdrname=hdrname, hdrext=hdrext, - distname=distname) + distname=distname, logging=logging, logmode='a') if len(hdrlet_ind) == 0: - print 'ERROR: ' - print 'No HDUs deleted... No Headerlet HDUs found with ' - print ' hdrname = ', hdrname - print ' hdrext = ', hdrext - print ' distname = ', distname - print 'Please review input parameters and try again. ' + message = """ + No HDUs deleted... No Headerlet HDUs found with ' + hdrname = %s + hdrext = %s + distname = %s + Please review input parameters and try again. + """ % (hdrname, str(hdrext), distname) + logger.critical(message) return fobj, fname, close_fobj = parse_filename(filename, mode='update') @@ -1327,7 +1354,7 @@ def delete_headerlet(filename, hdrname=None, hdrext=None, distname=None): # close file, if was opened by this function if close_fobj: fobj.close() - print 'Deleted headerlet from extension(s): ', hdrlet_ind + logger.critical('Deleted headerlet from extension(s) %s ' % str(hdrlet_ind)) def headerlet_summary(filename, columns=None, pad=2, maxwidth=None, output=None, clobber=True, quiet=False): @@ -1399,8 +1426,8 @@ def headerlet_summary(filename, columns=None, pad=2, maxwidth=None, idcol=extnums_col, output=output, clobber=clobber, quiet=quiet) -def restore_from_headerlet(filename, hdrname=None, hdrext=None, - archive=True, force=False): +def restore_from_headerlet(filename, hdrname=None, hdrext=None, archive=True, + force=False, logging=False, logmode='w'): """ Restores a headerlet as a primary WCS @@ -1423,8 +1450,13 @@ def restore_from_headerlet(filename, hdrname=None, hdrext=None, force: boolean (default:False) When the distortion models of the headerlet and the primary do not match, and archive is False, this flag forces an update of the primary. + logging: boolean + enable file logging + logmode: 'a' or 'w' """ - init_logging('restore_from_headerlet') + kwargs = locals() + init_logging('restore_from_headerlet', level=logging, + mode=logmode, **kwargs) hdrlet_ind = find_headerlet_HDUs(filename, hdrext=hdrext, hdrname=hdrname) @@ -1437,14 +1469,13 @@ def restore_from_headerlet(filename, hdrname=None, hdrext=None, else: kwerr = 'hdrname' kwval = hdrname - print '=====================================================' - print '[restore_from_headerlet]' - print 'Multiple Headerlet extensions found with the same name.' - print ' %d Headerlets with "%s" = %s found in %s.' % ( - len(hdrlet_ind), kwerr, kwval, fname) - print '=====================================================' + message = """ + Multiple Headerlet extensions found with the same name. + %d Headerlets with "%s" = %s found in %s. + """% (len(hdrlet_ind), kwerr, kwval, fname) if close_fobj: fobj.close() + logger.critical(message) raise ValueError hdrlet_indx = hdrlet_ind[0] @@ -1470,12 +1501,12 @@ def restore_from_headerlet(filename, hdrname=None, hdrext=None, if not archive and not force: if close_fobj: fobj.close() - print '=====================================================' - print '[restore_from_headerlet]' - print 'Headerlet does not have the same distortion as image!' - print ' Set "archive"=True to save old distortion model, or' - print ' set "force"=True to overwrite old model with new.' - print '=====================================================' + message = """ + Headerlet does not have the same distortion as image! + Set "archive"=True to save old distortion model, or + set "force"=True to overwrite old model with new. + """ + logger.critical(message) raise ValueError # check whether primary WCS has been archived already @@ -1513,8 +1544,8 @@ def restore_from_headerlet(filename, hdrname=None, hdrext=None, if close_fobj: fobj.close() -def restore_all_with_distname(filename, distname, primary, - archive=True, sciext='SCI'): +def restore_all_with_distname(filename, distname, primary, archive=True, + sciext='SCI', logging=False, logmode='w'): """ Restores all HeaderletHDUs with a given distortion model as alternate WCSs and a primary @@ -1535,22 +1566,30 @@ def restore_all_with_distname(filename, distname, primary, flag indicating if HeaderletHDUs should be created from the primary and alternate WCSs in fname before restoring all matching headerlet extensions + logging: boolean + enable file logging + logmode: 'a' or 'w' """ - init_logging('restore_all_with_distname') + kwargs = locals() + init_logging('restore_all_with_distname', level=logging, + mode=logmode, **kwargs) fobj, fname, close_fobj = parse_filename(filename, mode='update') hdrlet_ind = find_headerlet_HDUs(fobj, distname=distname) if len(hdrlet_ind) == 0: - print '=====================================================' - print '[restore_all_with_distname]' - print 'No Headerlet extensions found with ' - print ' "DISTNAME" = %s in %s.' % (distname, fname) - print 'Full list of DISTNAMEs found in all headerlet extensions: ' - print get_headerlet_kw_names(fobj, kw='DISTNAME') - print '=====================================================' + message = """ + No Headerlet extensions found with + + DISTNAME = %s in %s. + + For a full list of DISTNAMEs found in all headerlet extensions: + + get_headerlet_kw_names(fobj, kw='DISTNAME') + """ % (distname, fname) if close_fobj: fobj.close() + logger.critical(message) raise ValueError # Interpret 'primary' parameter input into extension number @@ -1567,11 +1606,11 @@ def restore_all_with_distname(filename, distname, primary, if primary_ind is None: if close_fobj: fobj.close() - print '=====================================================' - print '[restore_all_from_distname]' - print 'No Headerlet extensions found with ' - print ' "DISTNAME" = %s in %s.' % (primary, fname) - print '=====================================================' + message = """ + No Headerlet extensions found with + print ' "DISTNAME" = %s in %s. + """ % (primary, fname) + logger.critical(message) raise ValueError # Check to see whether 'primary' HeaderletHDU has same distname as user # specified on input @@ -1585,13 +1624,13 @@ def restore_all_with_distname(filename, distname, primary, if pri_distname != distname: if close_fobj: fobj.close() - print '=====================================================' - print '[restore_all_from_distname]' - print 'Headerlet extension to be used as PRIMARY WCS ' - print ' has "DISTNAME" = %s while %s.' % (pri_distname) - print ' "DISTNAME" = %s was specified on input.' % (distname) - print ' All updated WCSs must have same DISTNAME. Quitting...' - print '=====================================================' + message = """ + Headerlet extension to be used as PRIMARY WCS + has "DISTNAME" = %s + "DISTNAME" = %s was specified on input. + All updated WCSs must have same DISTNAME. Quitting...' + """ % (pri_distname, distname) + logger.critical(message) raise ValueError # read in the names of the WCSs which the HeaderletHDUs will update @@ -1623,7 +1662,8 @@ def archive_as_headerlet(filename, hdrname, sciext='SCI', wcsname=None, wcskey=None, destim=None, sipname=None, npolfile=None, d2imfile=None, author=None, descrip=None, history=None, - rms_ra=None, rms_dec=None, nmatch=None, catalog=None): + rms_ra=None, rms_dec=None, nmatch=None, catalog=None, + logging=False, logmode='w'): """ Save a WCS as a headerlet extension and write it out to a file. @@ -1685,19 +1725,26 @@ def archive_as_headerlet(filename, hdrname, sciext='SCI', to the headerlet PRIMARY header If filename is specified, it will format and attach all text from that file as the history. + logging: boolean + enable file folling + logmode: 'w' or 'a' + log file open mode """ - init_logging('archive_as_headerlet') + kwargs = locals() + init_logging('archive_as_headerlet', level=logging, + mode=logmode, **kwargs) + fobj, fname, close_fobj = parse_filename(filename, mode='update') if wcsname in [None, ' ', '', 'INDEF'] and wcskey is None: - print '='*60 - print '[archive_as_headerlet]' - print 'No valid WCS found found in %s.' % fname - print ' A valid value for either "wcsname" or "wcskey" ' - print ' needs to be specified. ' - print '='*60 + message = """ + No valid WCS found found in %s. + A valid value for either "wcsname" or "wcskey" + needs to be specified. + """ % fname if close_fobj: fobj.close() + logger.critical(message) raise ValueError # Translate 'wcskey' value for PRIMARY WCS to valid altwcs value of ' ' @@ -1726,7 +1773,7 @@ def archive_as_headerlet(filename, hdrname, sciext='SCI', descrip=descrip, history=history, rms_ra=rms_ra, rms_dec=rms_dec, nmatch=nmatch, catalog=catalog, - verbose=False) + logging=False) hlt_hdu = HeaderletHDU.fromheaderlet(hdrletobj) if destim is not None: @@ -1736,9 +1783,11 @@ def archive_as_headerlet(filename, hdrname, sciext='SCI', fobj.flush() else: - print 'WARNING:' - print ' Headerlet with hdrname ', hdrname, ' already archived for WCS ', wcsname - print ' No new headerlet appended to ', fname, '.' + message = """ + Headerlet with hdrname %s already archived for WCS %s + No new headerlet appended to %s . + """ % (hdrname, wcsname, fname) + logger.critical(message) if close_fobj: fobj.close() @@ -1750,7 +1799,7 @@ class Headerlet(pyfits.HDUList): Ref: http://mediawiki.stsci.edu/mediawiki/index.php/Telescopedia:Headerlets """ - def __init__(self, fobj, mode='copyonwrite', verbose=False, logmode='w'): + def __init__(self, fobj, mode='copyonwrite', logging=False, logmode='w'): """ Parameters ---------- @@ -1759,16 +1808,14 @@ class Headerlet(pyfits.HDUList): instances, or an HDUList instance mode: string, optional Mode with which to open the given file object - verbose: int - python logging level, higher numbers trigger more output + logging: boolean + enable file logging logmode: 'w' or 'a' for internal use only, indicates whether the log file should be open in attach or write mode """ - self.verbose = verbose - self.hdr_logger = logging.getLogger('headerlet.Headerlet') - init_logging('class Headerlet', logger=self.hdr_logger, level=100, - verbose=self.verbose, logmode=logmode) + self.logging = logging + init_logging('class Headerlet', level=logging, mode=logmode) fobj, fname, close_file = parse_filename(fobj) @@ -1828,10 +1875,13 @@ class Headerlet(pyfits.HDUList): # matches the distortion model in the headerlet being applied dist_models_equal = True if self[0].header['DISTNAME'] != fobj[0].header['DISTNAME']: - if self.verbose: - print 'Distortion model in headerlet not the same as destination model' - print ' Headerlet model : ', self[0].header['DISTNAME'] - print ' Destination model: ', fobj[0].header['DISTNAME'] + if self.logging: + message = """ + Distortion model in headerlet not the same as destination model + Headerlet model : %s + Destination model: %s + """ % (self[0].header['DISTNAME'], fobj[0].header['DISTNAME']) + logger.critical(message) dist_models_equal = False if not dist_models_equal and not force: @@ -1875,7 +1925,7 @@ class Headerlet(pyfits.HDUList): hdrname=hdrname, sipname=None, npolfile=None, d2imfile=None, author=None, descrip=None, history=None, - verbose=self.verbose) + logging=self.logging) orig_hlt_hdu = HeaderletHDU.fromheaderlet(orig_hlt) numhlt += 1 orig_hlt_hdu.header.update('EXTVER', numhlt) @@ -1913,7 +1963,7 @@ class Headerlet(pyfits.HDUList): hdrname=hname, sipname=None, npolfile=None, d2imfile=None, author=None, descrip=None, history=None, - verbose=self.verbose) + logging=self.logging) numhlt += 1 alt_hlet_hdu = HeaderletHDU.fromheaderlet(alt_hlet) alt_hlet_hdu.header.update('EXTVER', numhlt) @@ -1952,7 +2002,7 @@ class Headerlet(pyfits.HDUList): else: if 'HISTORY' in fhdr: bkeywd = 'HISTORY' - self.hdr_logger.debug( + logger.debug( "Updating WCS keywords after %s and/or before %s " % (akeywd,bkeywd)) update_cpdis = False @@ -1999,10 +2049,8 @@ class Headerlet(pyfits.HDUList): if close_dest: fobj.close() else: - self.hdr_logger.critical("Observation %s cannot be updated with headerlet " + logger.critical("Observation %s cannot be updated with headerlet " "%s" % (fname, self.hdrname)) - print "Observation %s cannot be updated with headerlet %s" \ - % (fname, self.hdrname) def apply_as_alternate(self, fobj, attach=True, wcskey=None, wcsname=None): """ @@ -2039,17 +2087,14 @@ class Headerlet(pyfits.HDUList): distname = 'UNKNOWN' if distname == 'UNKNOWN' or self.distname != distname: - self.hdr_logger.critical("Observation %s cannot be updated with headerlet %s"\ - % (fname, self.hdrname)) - print ("Observation %s cannot be updated with headerlet %s"\ - % (fname, self.hdrname)) - self.hdr_logger.critical(" Distortion in image: %s \n did not match \n headerlet distortion: %s" - % (distname, self.distname)) - print ( " Distortion in image: %s \n did not match \n headerlet distortion: %s" - % (distname, self.distname)) - print ("The method .attach_to_file() can be used to append this headerlet to %s"\ - % (fname)) - if close_dest: fobj.close() + message = """ + Observation %s cannot be updated with headerlet %s + Distortion in image: %s \n did not match \n headerlet distortion: %s + The method .attach_to_file() can be used to append this headerlet to %s" + """ % (fname, self.hdrname, distname, self.distname, fname) + if close_dest: + fobj.close() + logger.critical(message) raise ValueError # Insure that WCSCORR table has been created with all original @@ -2076,7 +2121,7 @@ class Headerlet(pyfits.HDUList): wkey = wcskey else: mess = "Observation %s already contains alternate WCS with key %s" % (fname, wcskey) - self.hdr_logger.critical(mess) + logger.critical(mess) if close_dest: fobj.close() raise ValueError(mess) @@ -2089,12 +2134,9 @@ class Headerlet(pyfits.HDUList): sciext = int(sciext) except ValueError: sciext = fu.parseExtn(sciext) - #fhdr = fobj[('SCI', idx)].header fhdr = fobj[sciext].header siphdr = self[('SIPWCS', idx)].header.ascard - - # a minimal attempt to get the position of the WCS keywords group # in the header by looking for the PA_APER kw. # at least make sure the WCS kw are written before the HISTORY kw @@ -2103,7 +2145,7 @@ class Headerlet(pyfits.HDUList): wind = fhdr.ascard.index_of('HISTORY') except KeyError: wind = len(fhdr) - self.hdr_logger.debug("Inserting WCS keywords at index %s" % wind) + logger.debug("Inserting WCS keywords at index %s" % wind) for k in siphdr: for akw in altwcs.altwcskw: @@ -2127,7 +2169,7 @@ class Headerlet(pyfits.HDUList): self.attach_to_file(fobj) else: mess = "Observation %s cannot be updated with headerlet %s" % (fname, self.hdrname) - self.hdr_logger.critical(mess) + logger.critical(mess) print mess if close_dest: fobj.close() @@ -2171,8 +2213,7 @@ class Headerlet(pyfits.HDUList): if not hdrver: message += " * Image %s already has headerlet " % (fname) message += "with HDRNAME='%s'\n" % (self.hdrname) - self.hdr_logger.critical(message) - print message + logger.critical(message) if close_dest: fobj.close() @@ -2269,7 +2310,7 @@ class Headerlet(pyfits.HDUList): HDRNAME. """ unique = verify_hdrname_is_unique(dest, self.hdrname) - self.hdr_logger.debug("verify_hdrname() returned %s"%unique) + logger.debug("verify_hdrname() returned %s"%unique) return unique def verify_dest(self, dest): @@ -2286,13 +2327,13 @@ class Headerlet(pyfits.HDUList): else: droot = dest[0].header['ROOTNAME'] except KeyError: - self.hdr_logger.debug("Keyword 'ROOTNAME' not found in destination file") + logger.debug("Keyword 'ROOTNAME' not found in destination file") droot = dest.split('.fits')[0] if droot == self.destim: - self.hdr_logger.debug("verify_destim() returned True") + logger.debug("verify_destim() returned True") return True else: - self.hdr_logger.debug("verify_destim() returned False") + logger.debug("verify_destim() returned False") return False def tofile(self, fname, destim=None, hdrname=None, clobber=False): @@ -2319,7 +2360,7 @@ class Headerlet(pyfits.HDUList): Delete the WCS of a science file """ - self.hdr_logger.info("Deleting all WCSs of file %s" % dest.filename()) + logger.info("Deleting all WCSs of file %s" % dest.filename()) numext = len(dest) for idx in range(numext): @@ -2362,7 +2403,7 @@ class Headerlet(pyfits.HDUList): Remove the any existing astrometric fit values from a FITS extension """ - self.hdr_logger.debug("Removing astrometric fit values from (%s, %s)"% + logger.debug("Removing astrometric fit values from (%s, %s)"% (ext.name, ext._extver)) dkeys = altwcs.wcskeys(ext.header) if 'O' in dkeys: dkeys.remove('O') # Do not remove wcskey='O' values @@ -2377,7 +2418,7 @@ class Headerlet(pyfits.HDUList): Remove the SIP distortion of a FITS extension """ - self.hdr_logger.debug("Removing SIP distortion from (%s, %s)" + logger.debug("Removing SIP distortion from (%s, %s)" % (ext.name, ext._extver)) for prefix in ['A', 'B', 'AP', 'BP']: try: @@ -2402,7 +2443,7 @@ class Headerlet(pyfits.HDUList): Remove the Lookup Table distortion of a FITS extension """ - self.hdr_logger.debug("Removing LUT distortion from (%s, %s)" + logger.debug("Removing LUT distortion from (%s, %s)" % (ext.name, ext._extver)) try: cpdis = ext.header['CPDIS*'] @@ -2423,7 +2464,7 @@ class Headerlet(pyfits.HDUList): Remove the Detector to Image correction of a FITS extension """ - self.hdr_logger.debug("Removing D2IM correction from (%s, %s)" + logger.debug("Removing D2IM correction from (%s, %s)" % (ext.name, ext._extver)) d2imkeys = ['D2IMFILE', 'AXISCORR', 'D2IMEXT', 'D2IMERR'] for k in d2imkeys: @@ -2442,7 +2483,7 @@ class Headerlet(pyfits.HDUList): if val in dkeys: dkeys.remove(val) # Never delete WCS with wcskey='O' - self.hdr_logger.debug("Removing alternate WCSs with keys %s from %s" + logger.debug("Removing alternate WCSs with keys %s from %s" % (dkeys, dest.filename())) for k in dkeys: altwcs.deleteWCS(dest, ext=ext, wcskey=k) @@ -2452,7 +2493,7 @@ class Headerlet(pyfits.HDUList): Remove the primary WCS of a FITS extension """ - self.hdr_logger.debug("Removing Primary WCS from (%s, %s)" + hdr_logger.debug("Removing Primary WCS from (%s, %s)" % (ext.name, ext._extver)) naxis = ext.header.ascard['NAXIS'].value for key in basic_wcs: @@ -2471,7 +2512,7 @@ class Headerlet(pyfits.HDUList): Remove IDC coefficients of a FITS extension """ - self.hdr_logger.debug("Removing IDC coefficient from (%s, %s)" + ogger.debug("Removing IDC coefficient from (%s, %s)" % (ext.name, ext._extver)) coeffs = ['OCX10', 'OCX11', 'OCY10', 'OCY11', 'IDCSCALE'] for k in coeffs: |