diff options
| -rw-r--r-- | lib/stwcs/wcsutil/headerlet.py | 61 | ||||
| -rw-r--r-- | lib/stwcs/wcsutil/wcscorr.py | 82 |
2 files changed, 89 insertions, 54 deletions
diff --git a/lib/stwcs/wcsutil/headerlet.py b/lib/stwcs/wcsutil/headerlet.py index fe26393..557057f 100644 --- a/lib/stwcs/wcsutil/headerlet.py +++ b/lib/stwcs/wcsutil/headerlet.py @@ -797,14 +797,31 @@ def write_headerlet(filename, hdrname, output=None, sciext='SCI', umode = 'readonly' fobj, fname, close_fobj = parse_filename(f, mode=umode) - wnames = altwcs.wcsnames(fobj,ext=('sci',1)) + # Interpret sciext input for this file + if isinstance(sciext, int): + sciextlist = [sciext] # allow for specification of simple FITS header + elif isinstance(sciext, str): + numsciext = countExtn(fobj, sciext) + if numsciext > 0: + sciextlist = [tuple((sciext,i)) for i in range(1, numsciext+1)] + else: + sciextlist = [0] + elif isinstance(sciext, list): + sciextlist = sciext + else: + errstr = "Expected sciext to be a list of FITS extensions with science data\n"+\ + " a valid EXTNAME string, or an integer." + logger.critical(errstr) + raise ValueError + + wnames = altwcs.wcsnames(fobj,ext=sciextlist[0]) # Insure that WCSCORR table has been created with all original # WCS's recorded prior to adding the headerlet WCS wcscorr.init_wcscorr(fobj) if wcsname is None: - scihdr = fobj[sciext, 1].header + scihdr = fobj[sciextlist[0]].header wname = scihdr['wcsname'+wcskey] else: wname = wcsname @@ -812,7 +829,7 @@ def write_headerlet(filename, hdrname, output=None, sciext='SCI', hdrname = wcsname logger.critical('Creating the headerlet from image %s' % fname) - hdrletobj = create_headerlet(fobj, sciext=sciext, + hdrletobj = create_headerlet(fobj, sciext=sciextlist, wcsname=wname, wcskey=wcskey, hdrname=hdrname, sipname=sipname, npolfile=npolfile, @@ -829,7 +846,7 @@ def write_headerlet(filename, hdrname, output=None, sciext='SCI', hdrlet_hdu = HeaderletHDU.fromheaderlet(hdrletobj) if destim is not None: - hdrlet_hdu[0].header['destim'] = destim + hdrlet_hdu.header['destim'] = destim fobj.append(hdrlet_hdu) @@ -846,6 +863,7 @@ def write_headerlet(filename, hdrname, output=None, sciext='SCI', logger.critical(message) if close_fobj: + logger.info('Closing image in write_headerlet()...') fobj.close() frootname = fu.buildNewRootname(fname) @@ -862,6 +880,7 @@ def write_headerlet(filename, hdrname, output=None, sciext='SCI', hdrletobj.tofile(outname, clobber=clobber) logger.critical( 'Created Headerlet file %s ' % outname) + del hdrletobj @with_logging def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, @@ -947,9 +966,18 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, """ fobj, fname, close_file = parse_filename(filename) + + # initial interpretation of sciext value for determination of input file type + sciextn = sciext + if not isinstance(sciext,str): + sciextn = 'SCI' + elif isinstance(sciext,list) and not isinstance(sciext[0],int): + sciextn = sciext[0][0] + numsci = countExtn(fobj,extname=sciextn) + # Define extension to evaluate for verification of input parameters wcsext = 1 - if fu.isFits(fname)[1] == 'simple': + if fu.isFits(fname)[1] == 'simple' or numsci == 0: wcsext = 0 # Translate 'wcskey' value for PRIMARY WCS to valid altwcs value of ' ' if wcskey == 'PRIMARY': @@ -960,7 +988,6 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, hdrnamekw = "".join(["HDRNAME", wcskey.upper()]).rstrip() wnames = altwcs.wcsnames(fobj,ext=wcsext) - if not wcsname: # User did not specify a value for 'wcsname' if wcsnamekw in fobj[wcsext].header: @@ -1068,7 +1095,7 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, sciext = [sciext] # allow for specification of simple FITS header elif isinstance(sciext, str): numsciext = countExtn(fobj, sciext) - sciext = [(sciext + ", " + str(i)) for i in range(1, numsciext+1)] + sciext = [tuple((sciext,i)) for i in range(1, numsciext+1)] elif isinstance(sciext, list): pass else: @@ -1101,10 +1128,11 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, wcsdvarr_extns = [] if fu.isFits(fobj)[1] is not 'simple': for e in sciext: - try: - fext = int(e) - except ValueError: - fext = fu.parseExtn(e) + fext = e + if not isinstance(e,int): + if isinstance(e,str): + fext = fu.parseExtn(e) + fext = fu.findExtname(fobj,fext[0],extver=fext[1]) wkeys = altwcs.wcskeys(fobj, ext=fext) if wcskey != ' ': if wcskey not in wkeys: @@ -1148,7 +1176,7 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, val = fext else: val = fext[1] h.insert(1, ('EXTVER', val, 'Extension version')) - h.append(('SCIEXT', e, 'Target science data extension')) + h.append(('SCIEXT', fext, 'Target science data extension')) fhdr = fobj[fext].header if npolfile is not 'NOMODEL': cpdis = fhdr['CPDIS*...'] @@ -2018,7 +2046,10 @@ class Headerlet(pyfits.HDUList): (not dist_models_equal and c.keyword not in FITS_STD_KW)): if 'DP' not in c.keyword: - fhdr.set(c.keyword, c.value, c.comment, + if c.keyword in fhdr: + fhdr[c.keyword] = c.value + else: + fhdr.set(c.keyword, c.value, c.comment, after=akeywd, before=bkeywd) else: update_cpdis = True @@ -2215,8 +2246,8 @@ class Headerlet(pyfits.HDUList): new_hlt = HeaderletHDU.fromheaderlet(self) new_hlt.header.update('extver', numhlt + 1) fobj.append(new_hlt) - if archive: - wcscorr.update_wcscorr(fobj, self, 'SIPWCS', active=False) + #if archive: + #wcscorr.update_wcscorr(fobj, self, 'SIPWCS', active=False) else: message = "Observation %s cannot be updated with headerlet" % (fname) diff --git a/lib/stwcs/wcsutil/wcscorr.py b/lib/stwcs/wcsutil/wcscorr.py index c767e09..d716f89 100644 --- a/lib/stwcs/wcsutil/wcscorr.py +++ b/lib/stwcs/wcsutil/wcscorr.py @@ -28,7 +28,7 @@ def init_wcscorr(input, force=False): This function will NOT overwrite any rows already present. This function works on all SCI extensions at one time. - """ + """ # TODO: Create some sort of decorator or (for Python2.5) context for # opening a FITS file and closing it when done, if necessary if not isinstance(input, pyfits.HDUList): @@ -42,8 +42,8 @@ def init_wcscorr(input, force=False): # Do not try to generate a WCSCORR table for a simple FITS file numsci = fileutil.countExtn(fimg) if len(fimg) == 1 or numsci == 0: - return - + return + enames = [] for e in fimg: enames.append(e.name) if 'WCSCORR' in enames: @@ -54,11 +54,11 @@ def init_wcscorr(input, force=False): print 'Initializing new WCSCORR table for ',fimg.filename() used_wcskeys = altwcs.wcskeys(fimg['SCI', 1].header) - + # define the primary columns of the WCSEXT table with initial rows for each # SCI extension for the original OPUS solution - numsci = fileutil.countExtn(fimg) numwcs = len(used_wcskeys) + if numwcs == 0: numwcs = 1 # create new table with more rows than needed initially to make it easier to # add new rows later @@ -82,7 +82,7 @@ def init_wcscorr(input, force=False): pri_funcs = {'SIPNAME':stwcs.updatewcs.utils.build_sipname, 'NPOLNAME':stwcs.updatewcs.utils.build_npolname, 'D2IMNAME':stwcs.updatewcs.utils.build_d2imname} - + # Now copy original OPUS values into table for extver in xrange(1, numsci + 1): rowind = find_wcscorr_row(wcsext.data, @@ -142,7 +142,7 @@ def init_wcscorr(input, force=False): wcsid = wcshdr['WCSNAME' + uwkey] # identify next empty row - rowind = find_wcscorr_row(wcsext.data, + rowind = find_wcscorr_row(wcsext.data, selections={'wcs_id':['','0.0']}) rows = np.where(rowind) if len(rows[0]) > 0: @@ -194,10 +194,10 @@ def find_wcscorr_row(wcstab, selections): mask = None for i in selections: icol = wcstab.field(i) - if isinstance(icol,np.chararray): icol = icol.rstrip() + if isinstance(icol,np.chararray): icol = icol.rstrip() selecti = selections[i] if not isinstance(selecti,list): - if isinstance(selecti,str): + if isinstance(selecti,str): selecti = selecti.rstrip() bmask = (icol == selecti) if mask is None: @@ -207,7 +207,7 @@ def find_wcscorr_row(wcstab, selections): del bmask else: for si in selecti: - if isinstance(si,str): + if isinstance(si,str): si = si.rstrip() bmask = (icol == si) if mask is None: @@ -215,7 +215,7 @@ def find_wcscorr_row(wcstab, selections): else: mask = np.logical_or(mask,bmask) del bmask - + return mask @@ -281,11 +281,15 @@ def update_wcscorr(dest, source=None, extname='SCI', wcs_id=None, active=True): % extname) # Initialize the WCSCORR table extension in dest if not already present init_wcscorr(dest) + try: + dest.index_of('WCSCORR') + except KeyError: + return # check to see whether or not this is an up-to-date table # replace with newly initialized table with current format old_table = dest['WCSCORR'] - wcscorr_cols = ['WCS_ID','EXTVER', 'SIPNAME', + wcscorr_cols = ['WCS_ID','EXTVER', 'SIPNAME', 'HDRNAME', 'NPOLNAME', 'D2IMNAME'] for colname in wcscorr_cols: @@ -294,7 +298,7 @@ def update_wcscorr(dest, source=None, extname='SCI', wcs_id=None, active=True): outdated_table = old_table.copy() del dest['WCSCORR'] init_wcscorr(dest) - old_table = dest['WCSCORR'] + old_table = dest['WCSCORR'] break # Current implementation assumes the same WCS keywords are in each @@ -303,7 +307,7 @@ def update_wcscorr(dest, source=None, extname='SCI', wcs_id=None, active=True): wcs_keys = altwcs.wcskeys(source[(extname, 1)].header) wcs_keys = filter(None, wcs_keys) if ' ' not in wcs_keys: wcs_keys.append(' ') # Insure that primary WCS gets used - # apply logic for only updating WCSCORR table with specified keywords + # apply logic for only updating WCSCORR table with specified keywords # corresponding to the WCS with WCSNAME=wcs_id if wcs_id is not None: wnames = altwcs.wcsnames(source[(extname, 1)].header) @@ -314,17 +318,17 @@ def update_wcscorr(dest, source=None, extname='SCI', wcs_id=None, active=True): if len(wkeys) > 1 and ' ' in wkeys: wkeys.remove(' ') wcs_keys = wkeys - + wcshdr = stwcs.wcsutil.HSTWCS(source, ext=(extname, 1)).wcs2header() wcs_keywords = wcshdr.keys() if 'O' in wcs_keys: wcs_keys.remove('O') # 'O' is reserved for original OPUS WCS - + # create new table for hdr and populate it with the newly updated values new_table = create_wcscorr(descrip=True,numrows=0, padding=len(wcs_keys)*numext) prihdr = source[0].header - + # Get headerlet related keywords here sipname = utils.build_sipname(source) npolname = utils.build_npolname(source) @@ -333,7 +337,7 @@ def update_wcscorr(dest, source=None, extname='SCI', wcs_id=None, active=True): hdrname = prihdr['hdrname'] else: hdrname = '' - + idx = -1 for wcs_key in wcs_keys: for extver in range(1, numext + 1): @@ -352,7 +356,7 @@ def update_wcscorr(dest, source=None, extname='SCI', wcs_id=None, active=True): 'SIPNAME':sipname, 'HDRNAME': hdrname, 'NPOLNAME': npolname, 'D2IMNAME':d2imname } - + # Ensure that an entry for this WCS is not already in the dest # table; if so just skip it rowind = find_wcscorr_row(old_table.data, selection) @@ -363,11 +367,11 @@ def update_wcscorr(dest, source=None, extname='SCI', wcs_id=None, active=True): wcs = stwcs.wcsutil.HSTWCS(source, ext=extn, wcskey=wcs_key) wcshdr = wcs.wcs2header() - + # Update selection column values for key, val in selection.iteritems(): if key in new_table.data.names: - new_table.data.field(key)[idx] = val + new_table.data.field(key)[idx] = val for key in wcs_keywords: if key in new_table.data.names: @@ -376,21 +380,21 @@ def update_wcscorr(dest, source=None, extname='SCI', wcs_id=None, active=True): for key in DEFAULT_PRI_KEYS: if key in new_table.data.names and key in prihdr: new_table.data.field(key)[idx] = prihdr[key] - # Now look for additional, non-WCS-keyword table column data + # Now look for additional, non-WCS-keyword table column data for key in COL_FITSKW_DICT: fitkw = COL_FITSKW_DICT[key] - # Interpret any 'pri.hdrname' or + # Interpret any 'pri.hdrname' or # 'sci.crpix1' formatted keyword names - if '.' in fitkw: + if '.' in fitkw: srchdr,fitkw = fitkw.split('.') if 'pri' in srchdr.lower(): srchdr = prihdr else: srchdr = source[extn].header else: srchdr = source[extn].header - + if fitkw+wcs_key in srchdr: new_table.data.field(key)[idx] = srchdr[fitkw+wcs_key] - + # If idx was never incremented, no rows were added, so there's nothing else # to do... @@ -421,7 +425,7 @@ def update_wcscorr(dest, source=None, extname='SCI', wcs_id=None, active=True): upd_table.data.field(name)[old_nrows:old_nrows + new_nrows] = \ new_table.data.field(name) upd_table.header.update('TROWS', old_nrows + new_nrows) - + # replace old extension with newly updated table extension dest['WCSCORR'] = upd_table @@ -523,7 +527,7 @@ def create_wcscorr(descrip=False, numrows=1, padding=0): dtype='S')) # create list of remaining columns to be added to table col_list = [id_col, extver_col, wcskey_col] # start with selector columns - + for c in col_names: cdef = copy.deepcopy(c[1]) col_list.append(pyfits.Column(name=c[0], format=cdef['format'], @@ -548,12 +552,12 @@ def create_wcscorr(descrip=False, numrows=1, padding=0): def delete_wcscorr_row(wcstab,selections=None,rows=None): """ Sets all values in a specified row or set of rows to default values - - This function will essentially erase the specified row from the table - without actually removing the row from the table. This avoids the problems - with trying to resize the number of rows in the table while preserving the + + This function will essentially erase the specified row from the table + without actually removing the row from the table. This avoids the problems + with trying to resize the number of rows in the table while preserving the ability to update the table with new rows again without resizing the table. - + Parameters ---------- wcstab: object @@ -565,12 +569,12 @@ def delete_wcscorr_row(wcstab,selections=None,rows=None): If specified, will specify what rows from the table to erase regardless of the value of 'selections' """ - + if selections is None and rows is None: print 'ERROR: Some row selection information must be provided!' print ' Either a row numbers or "selections" must be provided.' raise ValueError - + delete_rows = None if rows is None: if 'wcs_id' in selections and selections['wcs_id'] == 'OPUS': @@ -584,7 +588,7 @@ def delete_wcscorr_row(wcstab,selections=None,rows=None): if not isinstance(rows,list): rows = [rows] delete_rows = rows - + # Insure that rows pointing to OPUS WCS do not get deleted, even by accident for row in delete_rows: if wcstab['WCS_key'][row] == 'O' or wcstab['WCS_ID'][row] == 'OPUS': @@ -596,7 +600,7 @@ def delete_wcscorr_row(wcstab,selections=None,rows=None): # identify next empty row rowind = find_wcscorr_row(wcstab, selections={'wcs_id':['','0.0']}) last_blank_row = np.where(rowind)[0][-1] - + # copy values from blank row into user-specified rows for colname in wcstab.names: wcstab[colname][delete_rows] = wcstab[colname][last_blank_row] @@ -624,7 +628,7 @@ def update_wcscorr_column(wcstab, column, values, selections=None, rows=None): print 'ERROR: Some row selection information must be provided!' print ' Either a row numbers or "selections" must be provided.' raise ValueError - + if not isinstance(values, list): values = [values] @@ -653,7 +657,7 @@ def update_wcscorr_column(wcstab, column, values, selections=None, rows=None): print ' as there are rows to be updated.' print ' Table will not be updated...' raise ValueError - + if len(values) == 1 and len(values) < len(update_rows): values = values * len(update_rows) # copy values from blank row into user-specified rows |