diff options
| -rw-r--r-- | lib/stwcs/wcsutil/headerlet.py | 179 |
1 files changed, 73 insertions, 106 deletions
diff --git a/lib/stwcs/wcsutil/headerlet.py b/lib/stwcs/wcsutil/headerlet.py index 0318bf2..2888e28 100644 --- a/lib/stwcs/wcsutil/headerlet.py +++ b/lib/stwcs/wcsutil/headerlet.py @@ -29,7 +29,7 @@ def setLogger(logger, level, mode='w'): fh.setFormatter(formatter) logger.addHandler(fh) logger.setLevel(level) - + def isWCSIdentical(scifile, file2, verbose=False): """ Compares the WCS solution of 2 files. @@ -181,20 +181,20 @@ def createHeaderlet(fname, hdrname, destim=None, output=None, verbose=False, log module_logger.critical("Required keyword 'HDRNAME' not given") raise ValueError("Please provide a name for the headerlet, HDRNAME is " "a required parameter.") - + # get the version of STWCS used to create the WCS of the science file. try: upwcsver = fobj[0].header.ascard['STWCSVER'] except KeyError: upwcsver = pyfits.Card("STWCSVER", " ", "Version of STWCS used to update the WCS") - + # get all keys for alternate WCSs altkeys = altwcs.wcskeys(fobj[('SCI', 1)].header) - + if 'O' in altkeys: altkeys.remove('O') - + numsci = countExtn(fname, 'SCI') module_logger.debug("Number of 'SCI' extensions in file %s is %s" % (fname, numsci)) @@ -208,7 +208,8 @@ def createHeaderlet(fname, hdrname, destim=None, output=None, verbose=False, log comment='Date FITS file was generated') phdu.header.ascard.append(upwcsver) - refs = updateRefFiles(fobj[0].header.ascard, phdu.header.ascard, verbose=verbose) + refs = updateRefFiles(fobj[0].header.ascard, phdu.header.ascard, + verbose=verbose) phdukw.update(refs) phdu.header.update(key='VAFACTOR', value=fobj[('SCI',1)].header.get('VAFACTOR', 1.)) @@ -220,7 +221,7 @@ def createHeaderlet(fname, hdrname, destim=None, output=None, verbose=False, log for ak in altkeys: awcs = HSTWCS(fname,ext=('SCI', e), wcskey=ak) h.extend(awcs.wcs2header(idc2hdr=False).ascard) - h.append(pyfits.Card(key='VAFACTOR', value=hwcs.vafactor, + h.append(pyfits.Card(key='VAFACTOR', value=hwcs.vafactor, comment='Velocity aberration plate scale factor')) h.insert(0, pyfits.Card(key='EXTNAME', value='SIPWCS', comment='Extension name')) @@ -265,20 +266,14 @@ def createHeaderlet(fname, hdrname, destim=None, output=None, verbose=False, log comment='Maximum error of D2IMARR')) hdu = pyfits.ImageHDU(header=pyfits.Header(h)) - # temporary fix for pyfits ticket # 48 - hdu._extver = e hdul.append(hdu) numwdvarr = countExtn(fname, 'WCSDVARR') numd2im = countExtn(fname, 'D2IMARR') for w in range(1, numwdvarr + 1): hdu = fobj[('WCSDVARR', w)].copy() - # temporary fix for pyfits ticket # 48 - hdu._extver = w hdul.append(hdu) for d in range(1, numd2im + 1): hdu = fobj[('D2IMARR', d)].copy() - # temporary fix for pyfits ticket # 48 - hdu._extver = d hdul.append(hdu) if output is not None: # write the headerlet to a file @@ -372,9 +367,7 @@ def mapFitsExt2HDUListInd(fname, extname): close_file = False d = {} for hdu in f: - # TODO: Replace calls to header.has_key() with `in header` once - # pyfits refactoring branch is in production use - if hdu.header.has_key('EXTNAME') and hdu.header['EXTNAME'] == extname: + if 'EXTNAME' in hdu.header and hdu.header['EXTNAME'] == extname: extver = hdu.header['EXTVER'] d[(extname, extver)] = f.index_of((extname, extver)) if close_file: @@ -388,7 +381,8 @@ 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, logmode='w'): + def __init__(self, fobj, wcskeys=[], mode='copyonwrite', verbose=False, + logmode='w'): """ Parameters ---------- @@ -426,11 +420,12 @@ 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, attach=True, createsummary=True): + + def apply(self, dest, createheaderlet=True, hdrname=None, attach=True, + createsummary=True): """ Apply this headerlet to a file. - + Parameters ---------- dest: string @@ -438,10 +433,10 @@ class Headerlet(pyfits.HDUList): hdrname: string A unique name for the headerlet createheaderlet: boolean - A flag which indicates if a headerlet should be created + A flag which indicates if a headerlet should be created from the old WCS and attached to the science file (default: True) attach: boolean, default: True - By default the headerlet being applied will be attached + By default the headerlet being applied will be attached as an extension to the science file. Set 'attach' to False to disable this. createsummary: boolean, default: True @@ -500,8 +495,7 @@ class Headerlet(pyfits.HDUList): except KeyError: wind = len(fhdr) 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(): + for k in siphdr: if k not in ['XTENSION', 'BITPIX', 'NAXIS', 'PCOUNT', 'GCOUNT','EXTNAME', 'EXTVER', 'ORIGIN', 'INHERIT', 'DATE', 'IRAF-TLM']: @@ -525,7 +519,7 @@ class Headerlet(pyfits.HDUList): # Append the original headerlet if createheaderlet and orig_hlt_hdu: fobj.append(orig_hlt_hdu) - + if attach: # Finally, append an HDU for this headerlet new_hlt = HeaderletHDU.fromheaderlet(self) @@ -543,11 +537,10 @@ class Headerlet(pyfits.HDUList): def hverify(self): self.verify() - assert(self[0].header.has_key('DESTIM') and - self[0].header['DESTIM'].strip()) - assert(self[0].header.has_key('HDRNAME') and - self[0].header['HDRNAME'].strip()) - assert(self[0].header.has_key('STWCSVER')) + header = self[0].header + assert('DESTIM' in header and header['DESTIM'].strip()) + assert('HDRNAME' in header and header['HDRNAME'].strip()) + assert('STWCSVER' in header) def verify_dest(self, dest): @@ -588,7 +581,8 @@ class Headerlet(pyfits.HDUList): for idx in range(numext): # Only delete WCS from extensions which may have WCS keywords - if dest[idx].__dict__.has_key('_xtn') and "IMAGE" in dest[idx]._xtn: + if ('XTENSION' in dest[idx].header and + dest[idx].header['XTENSION'] == 'IMAGE'): self._removeD2IM(dest[idx]) self._removeSIP(dest[idx]) self._removeLUT(dest[idx]) @@ -598,7 +592,7 @@ class Headerlet(pyfits.HDUList): del dest[idx].header.ascard['VAFACTOR'] except KeyError: pass - + self._removeRefFiles(dest[0]) self._removeAltWCS(dest, ext=range(numext)) numwdvarr = countExtn(dest, 'WCSDVARR') @@ -607,7 +601,7 @@ class Headerlet(pyfits.HDUList): del dest[('WCSDVARR', idx)] for idx in range(1, numd2im + 1): del dest[('D2IMARR', idx)] - + def _removeRefFiles(self, phdu): """ phdu: Primary HDU @@ -618,7 +612,7 @@ class Headerlet(pyfits.HDUList): del phdu.header.ascard[kw] except KeyError: pass - + def _removeSIP(self, ext): """ Remove the SIP distortion of a FITS extension @@ -724,7 +718,7 @@ class Headerlet(pyfits.HDUList): pass -class HeaderletHDU(pyfits.core._NonstandardExtHDU): +class HeaderletHDU(pyfits.hdu.base.NonstandardExtHDU): """ A non-standard extension HDU for encapsulating Headerlets in a file. These HDUs have an extension type of HDRLET and their EXTNAME is derived from the @@ -739,64 +733,46 @@ class HeaderletHDU(pyfits.core._NonstandardExtHDU): `headerlet` attribute. """ - _xtn = _extension = 'HDRLET' - - def __init__(self, data=None, header=None): - super(HeaderletHDU, self).__init__(data=data, header=header) - # TODO: This can be removed after the next pyfits release, but for now - # the _ExtensionHDU base class sets self._xtn = '' in its __init__(). - self._xtn = self._extension - # For some reason _NonstandardExtHDU.__init__ sets self.name = None, - # even if it's already been set by the EXTNAME keyword in - # _ExtensionHDU.__init__() -_-; - if header and header.has_key('EXTNAME') and not self.name: - self.name = header['EXTNAME'] - # self._extver, if set, is still preserved. From - # _ExtensionHDU.__init__()...totally inconsistent. - - def __getattr__(self, attr): - if attr == 'data': - size = self.size() - self._file.seek(self._datLoc) - self.__dict__[attr] = self._file.read(size) - elif attr == 'headerlet': - self._file.seek(self._datLoc) - s = StringIO() - # Read the data into a StringIO--reading directly from the file - # won't work (at least for gzipped files) due to problems deep - # within the gzip module that make it difficult to read gzip files - # embedded in another file - s.write(self._file.read(self.size())) - s.seek(0) - if self._header['COMPRESS']: - mode = 'r:gz' - else: - mode = 'r' - t = tarfile.open(mode=mode, fileobj=s) - members = t.getmembers() - if not len(members): - raise ValueError('The Headerlet contents are missing.') - elif len(members) > 1: - warnings.warn('More than one file is contained in this ' - 'only the headerlet file should be present.') - hlt_name = self._header['HDRNAME'] + '_hdr.fits' - try: - hlt_info = t.getmember(hlt_name) - except KeyError: - warnings.warn('The file %s was missing from the HDU data. ' - 'Assuming that the first file in the data is ' - 'headerlet file.' % hlt_name) - hlt_info = members[0] - hlt_file = t.extractfile(hlt_info) - # hlt_file is a file-like object - hlt = Headerlet(hlt_file, mode='readonly') - self.__dict__[attr] = hlt + _extension = 'HDRLET' + + @pyfits.util.lazyproperty + def data(self): + size = self.size() + self._file.seek(self._datLoc) + return self._file.readarray(size) + + @pyfits.util.lazyproperty + def headerlet(self): + self._file.seek(self._datLoc) + s = StringIO() + # Read the data into a StringIO--reading directly from the file + # won't work (at least for gzipped files) due to problems deep + # within the gzip module that make it difficult to read gzip files + # embedded in another file + s.write(self._file.read(self.size())) + s.seek(0) + if self._header['COMPRESS']: + mode = 'r:gz' else: - return pyfits.core._ValidHDU.__getattr__(self, attr) + mode = 'r' + t = tarfile.open(mode=mode, fileobj=s) + members = t.getmembers() + if not len(members): + raise ValueError('The Headerlet contents are missing.') + elif len(members) > 1: + warnings.warn('More than one file is contained in this ' + 'only the headerlet file should be present.') + hlt_name = self._header['HDRNAME'] + '_hdr.fits' try: - return self.__dict__[attr] + hlt_info = t.getmember(hlt_name) except KeyError: - raise AttributeError(attr) + warnings.warn('The file %s was missing from the HDU data. ' + 'Assuming that the first file in the data is ' + 'headerlet file.' % hlt_name) + hlt_info = members[0] + hlt_file = t.extractfile(hlt_info) + # hlt_file is a file-like object + return Headerlet(hlt_file, mode='readonly') @classmethod def fromheaderlet(cls, headerlet, compress=False): @@ -857,7 +833,10 @@ class HeaderletHDU(pyfits.core._NonstandardExtHDU): header = pyfits.Header(pyfits.CardList(cards)) hdu = cls(data=pyfits.DELAYED, header=header) - hdu._file = s + # TODO: These hacks are a necessary evil, but should be removed once + # the pyfits API is improved to better support specifying a backing + # file object for an HDU + hdu._file = pyfits.file._File(s) hdu._datLoc = 0 return hdu @@ -881,18 +860,6 @@ class HeaderletHDU(pyfits.core._NonstandardExtHDU): def _summary(self): # TODO: Perhaps make this more descriptive... - return '%-10s %-12s %4d' % (self.name, self.__class__.__name__, - len(self._header.ascard)) - -# Monkey-patch pyfits to add minimal support for HeaderletHDUs -# TODO: Get rid of this ASAP!!! (it won't be necessary with the pyfits -# refactoring branch) -if not hasattr(pyfits.Header._updateHDUtype, '_patched'): - __old_updateHDUtype = pyfits.Header._updateHDUtype - def __updateHDUtype(self): - if HeaderletHDU.match_header(self): - self._hdutype = HeaderletHDU - else: - __old_updateHDUtype(self) - __updateHDUtype._patched = True - pyfits.Header._updateHDUtype = __updateHDUtype + return (self.name, self.__class__.__name__, len(self._header.ascard)) + +pyfits.register_hdu(HeaderletHDU) |