diff options
Diffstat (limited to 'wcsutil/headerlet.py')
| -rw-r--r-- | wcsutil/headerlet.py | 144 |
1 files changed, 80 insertions, 64 deletions
diff --git a/wcsutil/headerlet.py b/wcsutil/headerlet.py index e528184..5941189 100644 --- a/wcsutil/headerlet.py +++ b/wcsutil/headerlet.py @@ -16,9 +16,20 @@ from hstwcs import HSTWCS from mappings import basic_wcs from pytools.fileutil import countExtn -logger = logging.getLogger(__name__) - - +module_logger = logging.getLogger('headerlet') + +import atexit +atexit.register(logging.shutdown) + +def setLogger(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 isWCSIdentical(scifile, file2, verbose=False): """ Compares the WCS solution of 2 files. @@ -46,22 +57,22 @@ def isWCSIdentical(scifile, file2, verbose=False): """ if verbose: - logger.setLevel(verbose) + setLogger(module_logger, verbose) else: - logger.setLevel(100) + module_logger.setLevel(100) - logger.info("Starting isWCSIdentical: %s" % time.asctime()) + module_logger.info("Starting isWCSIdentical: %s" % time.asctime()) result = True numsci1 = max(countExtn(scifile), countExtn(scifile, 'SIPWCS')) numsci2 = max(countExtn(file2), countExtn(file2, 'SIPWCS')) if numsci1 == 0 or numsci2 == 0 or numsci1 != numsci2: - logger.info("Number of SCI and SIPWCS extensions do not match.") + module_logger.info("Number of SCI and SIPWCS extensions do not match.") result = False if getRootname(scifile) != getRootname(file2): - logger.info('Rootnames do not match.') + module_logger.info('Rootnames do not match.') result = False try: extname1 = pyfits.getval(scifile, 'EXTNAME', ext=('SCI', 1)) @@ -75,44 +86,44 @@ def isWCSIdentical(scifile, file2, verbose=False): for i in range(1, numsci1 + 1): w1 = HSTWCS(scifile, ext=(extname1, i)) w2 = HSTWCS(file2, ext=(extname2, i)) - if not (w1.wcs.crval == w2.wcs.crval).all() or \ - not (w1.wcs.crpix == w2.wcs.crpix).all() or \ - not (w1.wcs.cd == w2.wcs.cd).all() or \ - not (np.array(w1.wcs.ctype) == np.array(w2.wcs.ctype)).all(): - logger.info('Primary WCSs do not match') + if not np.allclose(w1.wcs.crval, w2.wcs.crval, rtol=1e-7) or \ + 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(): + module_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 (w1.sip.a == w2.sip.a).all() or \ - not (w1.sip.b == w2.sip.b).all(): - logger.info('SIP coefficients do not match') + 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): + module_logger.info('SIP coefficients do not match') result = False - if w1.cpdis1 or w2.cipdis1: + if w1.cpdis1 or w2.cpdis1: if w1.cpdis1 and not w2.cpdis1 or \ w2.cpdis1 and not w1.cpdis1 or \ - not (w1.cpdis1.data == w2.cpdis1.data).all(): - logger.info('NPOL distortions do not match') + not np.allclose(w1.cpdis1.data, w2.cpdis1.data): + module_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 (w1.cpdis2.data == w2.cpdis2.data).all(): - logger.info('NPOL distortions do not match') + not np.allclose(w1.cpdis2.data, w2.cpdis2.data): + module_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 (w1.det2im1.data == w2.det2im1.data).all(): - logger.info('Det2Im corrections do not match') + not np.allclose(w1.det2im1.data, w2.det2im1.data): + module_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 (w1.det2im2.data == w2.det2im2.data).all(): - logger.info('Det2Im corrections do not match') + not np.allclose(w1.det2im2.data, w2.det2im2.data): + module_logger.info('Det2Im corrections do not match') result = False if w1.vafactor != w2.vafactor: - logger.info('VA factors do not match') + module_logger.info('VA factors do not match') result = False return result @@ -120,7 +131,7 @@ def isWCSIdentical(scifile, file2, verbose=False): # TODO: It would be logical for this to be part of the Headerlet class, perhaps # as a classmethod -def createHeaderlet(fname, hdrname, destim=None, output=None, verbose=False): +def createHeaderlet(fname, hdrname, destim=None, output=None, verbose=False, logmode='w'): """ Create a headerlet from a science observation @@ -143,11 +154,11 @@ def createHeaderlet(fname, hdrname, destim=None, output=None, verbose=False): """ if verbose: - logger.setLevel(verbose) + setLogger(module_logger, verbose, mode=logmode) else: - logger.setLevel(100) + module_logger.setLevel(100) - logger.info("Starting createHeaderlet: %s" % time.asctime()) + module_logger.info("Starting createHeaderlet: %s" % time.asctime()) fmt="%Y-%m-%dT%H:%M:%S" phdukw = {'IDCTAB': True, 'NPOLFILE': True, @@ -162,16 +173,15 @@ def createHeaderlet(fname, hdrname, destim=None, output=None, verbose=False): try: destim = fobj[0].header['ROOTNAME'] except KeyError: - logger.exception('Required keyword "DESTIM" not found') + module_logger.exception('Required keyword "DESTIM" not found') print 'Please provide a value for the DESTIM keyword' raise if hdrname is None: - logger.critical("Required keyword 'HDRNAME' not given") + module_logger.critical("Required keyword 'HDRNAME' not given") raise ValueError("Please provide a name for the headerlet, HDRNAME is " "a required parameter.") - - - + + # get all keys for alternate WCSs altkeys = altwcs.wcskeys(fobj[('SCI', 1)].header) try: upwcsver = fobj[0].header.ascard['STWCSVER'] @@ -181,7 +191,7 @@ def createHeaderlet(fname, hdrname, destim=None, output=None, verbose=False): if 'O' in altkeys: altkeys.remove('O') numsci = countExtn(fname) - logger.debug("Number of 'SCI' extensions in file %s is %s" + module_logger.debug("Number of 'SCI' extensions in file %s is %s" % (fname, numsci)) hdul = pyfits.HDUList() phdu = pyfits.PrimaryHDU() @@ -192,7 +202,7 @@ def createHeaderlet(fname, hdrname, destim=None, output=None, verbose=False): comment='Date FITS file was generated') phdu.header.ascard.append(upwcsver) - updateRefFiles(fobj[0].header.ascard, phdu.header.ascard) + updateRefFiles(fobj[0].header.ascard, phdu.header.ascard, verbose=verbose) phdu.header.update(key='VAFACTOR', value=fobj[('SCI',1)].header.get('VAFACTOR', 1.)) hdul.append(phdu) @@ -235,7 +245,7 @@ def createHeaderlet(fname, hdrname, destim=None, output=None, verbose=False): try: h.append(fhdr['AXISCORR']) except KeyError: - logger.exception("Required keyword AXISCORR was not found in " + module_logger.exception("Required keyword AXISCORR was not found in " "%s['SCI',%d]" % (fname, e)) raise @@ -268,7 +278,7 @@ def createHeaderlet(fname, hdrname, destim=None, output=None, verbose=False): hdul.writeto(output, clobber=True) if close_file: fobj.close() - return Headerlet(hdul) + return Headerlet(hdul,verbose=verbose, logmode='a') def applyHeaderlet(hdrfile, destfile, createheaderlet=True, hdrname=None, verbose=False): @@ -292,12 +302,15 @@ def applyHeaderlet(hdrfile, destfile, createheaderlet=True, hdrname=None, (one of 'INFO', 'DEBUG' logging levels) (an integer representing a logging level) """ - - logger.info("Starting applyHeaderlet: %s" % time.asctime()) - hlet = Headerlet(hdrfile) + if verbose: + setLogger(module_logger, verbose) + else: + module_logger.setLevel(100) + module_logger.info("Starting applyHeaderlet: %s" % time.asctime()) + hlet = Headerlet(hdrfile, verbose=verbose, logmode='a') hlet.apply(destfile, createheaderlet=createheaderlet, hdrname=hdrname) -def updateRefFiles(source, dest): +def updateRefFiles(source, dest, verbose=False): """ Update the reference files name in the primary header of 'dest' using values from 'source' @@ -307,8 +320,7 @@ def updateRefFiles(source, dest): source: pyfits.Header.ascardlist dest: pyfits.Header.ascardlist """ - - logger.info("Updating reference files") + module_logger.info("Updating reference files") phdukw = {'IDCTAB': True, 'NPOLFILE': True, 'D2IMFILE': True} @@ -366,7 +378,7 @@ class Headerlet(pyfits.HDUList): Ref: http://stsdas.stsci.edu/stsci_python_sphinxdocs/stwcs/headerlet_def.html """ - def __init__(self, fobj, wcskeys=[], mode='copyonwrite', verbose=False): + def __init__(self, fobj, wcskeys=[], mode='copyonwrite', verbose=False, logmode='w'): """ Parameters ---------- @@ -381,8 +393,14 @@ class Headerlet(pyfits.HDUList): mode: string, optional Mode with which to open the given file object """ + self.verbose = verbose + self.hdr_logger = logging.getLogger('headerlet.Headerlet') + if self.verbose: + setLogger(self.hdr_logger, self.verbose, mode=logmode) + else: + self.hdr_logger.setLevel(100) - logger.info("Creating a Headerlet object from wcskeys %s" % wcskeys) + self.hdr_logger.info("Creating a Headerlet object from wcskeys %s" % wcskeys) self.wcskeys = wcskeys if not isinstance(fobj, list): fobj = pyfits.open(fobj, mode=mode) @@ -398,12 +416,11 @@ class Headerlet(pyfits.HDUList): self.vafactor = self[1].header.get("VAFACTOR", 1) #None instead of 1? self.d2imerr = 0 self.axiscorr = 1 - + def apply(self, dest, createheaderlet=True, hdrname=None): """ Apply this headerlet to a file. """ - self.hverify() if self.verify_dest(dest): if not isinstance(dest, pyfits.HDUList): @@ -432,13 +449,13 @@ class Headerlet(pyfits.HDUList): # the file if not hdrname: hdrname = fobj[0].header['ROOTNAME'] + '_orig' - orig_hlt = createHeaderlet(fobj, hdrname) + orig_hlt = createHeaderlet(fobj, hdrname, verbose=self.verbose, logmode='a') orig_hlt_hdu = HeaderletHDU.fromheaderlet(orig_hlt) orig_hlt_hdu.update_ext_version(numhlt + 1) numhlt += 1 self._delDestWCS(fobj) - updateRefFiles(self[0].header.ascard, fobj[0].header.ascard) + updateRefFiles(self[0].header.ascard, fobj[0].header.ascard, verbose=self.verbose) numsip = countExtn(self, 'SIPWCS') for idx in range(1, numsip + 1): fhdr = fobj[('SCI', idx)].header.ascard @@ -454,7 +471,7 @@ class Headerlet(pyfits.HDUList): wind = fhdr.index_of('HISTORY') except KeyError: wind = len(fhdr) - logger.debug("Inserting WCS keywords at index %s" % wind) + self.hdr_logger.debug("Inserting WCS keywords at index %s" % wind) # TODO: Drop .keys() when refactored pyfits comes into use for k in siphdr.keys(): if k not in ['XTENSION', 'BITPIX', 'NAXIS', 'PCOUNT', @@ -488,7 +505,7 @@ class Headerlet(pyfits.HDUList): if close_dest: fobj.close() else: - logger.critical("Observation %s cannot be updated with headerlet " + self.hdr_logger.critical("Observation %s cannot be updated with headerlet " "%s" % (fobj.filename(), self.hdrname)) print "Observation %s cannot be updated with headerlet %s" \ % (fobj.filename(), self.hdrname) @@ -517,13 +534,13 @@ class Headerlet(pyfits.HDUList): else: droot = dest[0].header['ROOTNAME'] except KeyError: - logger.debug("Keyword 'ROOTNAME' not found in destination file") + self.hdr_logger.debug("Keyword 'ROOTNAME' not found in destination file") droot = dest.split('.fits')[0] if droot == self.destim: - logger.debug("verify_destim() returned True") + self.hdr_logger.debug("verify_destim() returned True") return True else: - logger.debug("verify_destim() returned False") + self.hdr_logger.debug("verify_destim() returned False") return False def tofile(self, fname, destim=None, hdrname=None, clobber=False): @@ -536,7 +553,7 @@ class Headerlet(pyfits.HDUList): Delete the WCS of a science file """ - logger.info("Deleting all WCSs of file %s" % dest.filename()) + self.hdr_logger.info("Deleting all WCSs of file %s" % dest.filename()) numext = len(dest) for idx in range(numext): @@ -565,7 +582,7 @@ class Headerlet(pyfits.HDUList): Remove the SIP distortion of a FITS extension """ - logger.debug("Removing SIP distortion from (%s, %s)" + self.hdr_logger.debug("Removing SIP distortion from (%s, %s)" % (ext.name, ext._extver)) for prefix in ['A', 'B', 'AP', 'BP']: try: @@ -590,7 +607,7 @@ class Headerlet(pyfits.HDUList): Remove the Lookup Table distortion of a FITS extension """ - logger.debug("Removing LUT distortion from (%s, %s)" + self.hdr_logger.debug("Removing LUT distortion from (%s, %s)" % (ext.name, ext._extver)) try: cpdis = ext.header['CPDIS*'] @@ -611,7 +628,7 @@ class Headerlet(pyfits.HDUList): Remove the Detector to Image correction of a FITS extension """ - logger.debug("Removing D2IM correction from (%s, %s)" + self.hdr_logger.debug("Removing D2IM correction from (%s, %s)" % (ext.name, ext._extver)) d2imkeys = ['D2IMFILE', 'AXISCORR', 'D2IMEXT', 'D2IMERR'] for k in d2imkeys: @@ -625,9 +642,8 @@ class Headerlet(pyfits.HDUList): Remove Alternate WCSs of a FITS extension. A WCS with wcskey 'O' is never deleted. """ - dkeys = altwcs.wcskeys(dest[('SCI', 1)].header) - logger.debug("Removing alternate WCSs with keys %s from %s" + self.hdr_logger.debug("Removing alternate WCSs with keys %s from %s" % (dkeys, dest.filename())) for k in dkeys: altwcs.deleteWCS(dest, ext=ext, wcskey=k) @@ -637,7 +653,7 @@ class Headerlet(pyfits.HDUList): Remove the primary WCS of a FITS extension """ - logger.debug("Removing Primary WCS from (%s, %s)" + self.hdr_logger.debug("Removing Primary WCS from (%s, %s)" % (ext.name, ext._extver)) naxis = ext.header.ascard['NAXIS'].value for key in basic_wcs: @@ -656,7 +672,7 @@ class Headerlet(pyfits.HDUList): Remove IDC coefficients of a FITS extension """ - logger.debug("Removing IDC coefficient from (%s, %s)" + self.hdr_logger.debug("Removing IDC coefficient from (%s, %s)" % (ext.name, ext._extver)) coeffs = ['OCX10', 'OCX11', 'OCY10', 'OCY11', 'IDCSCALE'] for k in coeffs: |