diff options
Diffstat (limited to 'lib/stwcs/wcsutil/headerlet.py')
| -rw-r--r-- | lib/stwcs/wcsutil/headerlet.py | 1934 |
1 files changed, 1686 insertions, 248 deletions
diff --git a/lib/stwcs/wcsutil/headerlet.py b/lib/stwcs/wcsutil/headerlet.py index 4c29234..194e16b 100644 --- a/lib/stwcs/wcsutil/headerlet.py +++ b/lib/stwcs/wcsutil/headerlet.py @@ -1,6 +1,9 @@ from __future__ import division import logging import os +import string +import textwrap +import copy import tarfile import tempfile import time @@ -14,14 +17,26 @@ import altwcs import wcscorr from hstwcs import HSTWCS from mappings import basic_wcs +from stwcs.updatewcs import utils + from stsci.tools.fileutil import countExtn from stsci.tools import fileutil as fu +#### Logging support functions module_logger = logging.getLogger('headerlet') import atexit atexit.register(logging.shutdown) +FITS_STD_KW = ['XTENSION', 'BITPIX', 'NAXIS', 'PCOUNT', + 'GCOUNT','EXTNAME', 'EXTVER', 'ORIGIN', + 'INHERIT', 'DATE', 'IRAF-TLM'] + +DEFAULT_SUMMARY_COLS = ['HDRNAME','WCSNAME','DISTNAME','AUTHOR','DATE', + 'SIPNAME','NPOLFILE','D2IMFILE','DESCRIP'] +COLUMN_DICT = {'vals':[],'width':[]} +COLUMN_FMT = '{:<{width}}' + def setLogger(logger, level, mode='w'): formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s") log_filename = 'headerlet.log' @@ -30,18 +45,212 @@ def setLogger(logger, level, mode='w'): fh.setFormatter(formatter) logger.addHandler(fh) logger.setLevel(level) + +def initLogging(function_name, logger = None, level=100, verbose=False, logmode='w'): + """ Initialize logging for a function + + Parameters + ---------- + function_name: 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 + """ + if logger is None: + logger = module_logger + + if verbose: + setLogger(logger, verbose, mode=logmode) + else: + logger.setLevel(level) + + logger.info("Starting %s: %s" % (function_name, time.asctime())) + -def hdrnames(fobj): +#### Utility functions +def is_par_blank(par): + return par in ['',' ','INDEF',"None",None] + +def parseFilename(fname,mode='readonly'): """ - Returns a list of HDRNAME keywords from all HeaderletHDU - extensions in a science file. + Interprets the input as either a filename of a file that needs to be opened + or a PyFITS object. + + Parameters + ---------- + fname: string, pyfits.HDUList + Input pointing to a file or PyFITS object. An input filename (str) will + be expanded as necessary to interpret any environmental variables + included in the filename. + mode: string + Specifies what PyFITS mode to use when opening the file, if it needs + to open the file at all [Default: 'readonly'] + + Returns + ------- + fobj: pyfits.HDUList + PyFITS handle for input file + fname: string + Name of input file + close_fobj: bool + Flag specifying whether or not fobj needs to be closed since it was + opened by this function. This allows a program to know whether they + need to worry about closing the PyFITS object as opposed to letting + the higher level interface close the object. + """ + close_fobj = False + if not isinstance(fname,list): + if isinstance(fname,str): + fname = fu.osfn(fname) + fobj = pyfits.open(fname,mode=mode) + close_fobj = True + else: + fobj = fname + if hasattr(fobj,'filename'): + fname = fobj.filename() + else: + fname = '' + return fobj,fname,close_fobj +def getHeaderletKwNames(fobj,kw='HDRNAME'): + """ + Returns a list of specified keywords from all HeaderletHDU + extensions in a science file. + Parameters ---------- fobj: string, pyfits.HDUList + kw: str + Name of keyword to be read and reported """ + fobj,fname,open_fobj = parseFilename(fobj) + + hdrnames = [] + for ext in fobj: + if isinstance(ext,pyfits.hdu.base.NonstandardExtHDU): + hdrnames.append(ext.header[kw]) + if open_fobj: + fobj.close() + + return hdrnames + + + +def findHeaderletHDUs(fobj, hdrext=None, hdrname=None, distname=None, strict=True): + """ + Returns all HeaderletHDU extensions in a science file that matches + the inputs specified by the user. If no hdrext, hdrname or distname are + specified, this function will return a list of all HeaderletHDU objects. + + Parameters + ---------- + fobj: string, pyfits.HDUList + Name of FITS file or open pyfits object (pyfits.HDUList instance) + hdrext: int, tuple or None + index number(EXTVER) or extension tuple of HeaderletHDU to be returned + hdrname: string + value of HDRNAME for HeaderletHDU to be returned + distname: string + value of DISTNAME for HeaderletHDUs to be returned + strict: bool [Default: True] + Specifies whether or not at least one parameter needs to be provided + 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. + + Returns + ------- + hdrlets: list + A list of all matching HeaderletHDU extension indices (could be just one) + """ + 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 '=====================================================' + raise ValueError + + fobj,fname,open_fobj = parseFilename(fobj) + + hdrlets = [] + if hdrext is not None and isinstance(hdrext,int): + if hdrext in range(len(fobj)): # insure specified hdrext is in fobj + if isinstance(fobj[hdrext],pyfits.hdu.base.NonstandardExtHDU) and \ + fobj[hdrext].header['EXTNAME'] == 'HDRLET': + hdrlets.append(hdrext) + else: + for ext in fobj: + if isinstance(ext,pyfits.hdu.base.NonstandardExtHDU): + if get_all: + hdrlets.append(fobj.index(ext)) + else: + if hdrext is not None: + if isinstance(hdrext,tuple): + hdrextname = hdrext[0] + hdrextnum = hdrext[1] + else: + hdrextname = 'HDRLET' + hdrextnum = hdrext + hdrext_match = ((hdrext is not None) and + (hdrextnum == ext.header['EXTVER']) and + (hdrextname == ext.header['EXTNAME'])) + hdrname_match = ((hdrname is not None) and + (hdrname == ext.header['HDRNAME'])) + distname_match = ((distname is not None) and + (distname == ext.header['DISTNAME'])) + if hdrext_match or hdrname_match or distname_match: + hdrlets.append(fobj.index(ext)) + + if open_fobj: + fobj.close() + + if len(hdrlets) == 0: + if hdrname: + kwerr = 'hdrname' + kwval = hdrname + elif hdrext: + kwerr = 'hdrext' + kwval = hdrext + else: + kwerr = 'distname' + kwval = distname + print '=====================================================' + print 'No valid Headerlet extension found!' + print ' "%s" = %s not found in %s.'%(kwerr,kwval,fname) + print '=====================================================' + raise ValueError + + return hdrlets + +def verifyHdrnameIsUnique(fobj,hdrname): + """ + Verifies that no other HeaderletHDU extension has the specified hdrname. + + Parameters + ---------- + fobj: string, pyfits.HDUList + Name of FITS file or open pyfits object (pyfits.HDUList instance) + hdrname: string + value of HDRNAME for HeaderletHDU to be compared as unique + + Returns + ------- + unique: bool + If True, no other HeaderletHDU has the specified HDRNAME value + """ + hdrnames_list = getHeaderletKwNames(fobj) + unique = not(hdrname in hdrnames_list) + + return unique + def isWCSIdentical(scifile, file2, verbose=False): """ Compares the WCS solution of 2 files. @@ -68,12 +277,7 @@ def isWCSIdentical(scifile, file2, verbose=False): - Velocity aberation """ - if verbose: - setLogger(module_logger, verbose) - else: - module_logger.setLevel(100) - - module_logger.info("Starting isWCSIdentical: %s" % time.asctime()) + initLogging('isWCSIdentical', level=100, verbose=False) result = True numsci1 = max(countExtn(scifile), countExtn(scifile, 'SIPWCS')) @@ -140,37 +344,447 @@ def isWCSIdentical(scifile, file2, verbose=False): return result +def updateRefFiles(source, dest, verbose=False): + """ + Update the reference files name in the primary header of 'dest' + using values from 'source' -def create_headerlet(fname, sciext=None, hdrname=None, destim=None, wcskey=" ", wcsname=None, - sipname=None, npolfile=None, d2imfile=None, - verbose=100, logmode='w'): + Parameters + ---------- + source: pyfits.Header.ascardlist + dest: pyfits.Header.ascardlist + """ + module_logger.info("Updating reference files") + phdukw = {'IDCTAB': True, + 'NPOLFILE': True, + 'D2IMFILE': True} + + try: + wind = dest.index_of('HISTORY') + except KeyError: + wind = len(dest) + for key in phdukw.keys(): + try: + value = source[key] + dest.insert(wind, value) + except KeyError: + # TODO: I don't understand what the point of this is. Is it meant + # for logging purposes? Right now it isn't used. + phdukw[key] = False + return phdukw + +def getRootname(fname): + """ + returns the value of ROOTNAME or DESTIM + """ + + try: + rootname = pyfits.getval(fname, 'ROOTNAME') + except KeyError: + rootname = pyfits.getval(fname, 'DESTIM') + return rootname + +def mapFitsExt2HDUListInd(fname, extname): + """ + Map FITS extensions with 'EXTNAME' to HDUList indexes. + """ + + f,fname,close_fobj = parseFilename(fname) + + d = {} + for hdu in f: + if 'EXTNAME' in hdu.header and hdu.header['EXTNAME'] == extname: + extver = hdu.header['EXTVER'] + d[(extname, extver)] = f.index_of((extname, extver)) + if close_fobj: + f.close() + return d + +def getHeaderletObj(fname, sciext='SCI', wcskey=' ',wcsname=None,hdrname=None, + sipname=None, npolfile=None, d2imfile=None, + author=None, descrip=None, history=None, + rms_ra = None, rms_dec = None, nmatch=None, catalog=None, + hdrletnum=1, verbose=100): + """ + Generate and return a HeaderletHDU with EXTVER and HDRNAME set + + """ + fobj,fname,open_fobj = parseFilename(fname) + + # Translate 'wcskey' value for PRIMARY WCS to valid altwcs value of ' ' + if wcskey == 'PRIMARY': wcskey = ' ' + + hlt = create_headerlet(fobj, sciext=sciext, + wcskey=wcskey, wcsname=wcsname, hdrname=hdrname, + sipname=sipname, npolfile=npolfile, d2imfile=d2imfile, + author=author, descrip=descrip, history=history, + rms_ra=rms_ra, rms_dec=rms_dec, nmatch=nmatch, + catalog=catalog, verbose=verbose, logmode='a') + if open_fobj: + fobj.close() + + return hlt + +def print_summary(summary_cols, summary_dict, pad=2, maxwidth=None, idcol=None, + output=None, clobber=True, quiet=False ): + """ + Print out summary dictionary to STDOUT, and possibly an output file + + """ + nrows = None + if idcol: + nrows = len(idcol['vals']) + + # Find max width of each column + column_widths = {} + for kw in summary_dict: + colwidth = np.array(summary_dict[kw]['width']).max() + if maxwidth: + colwidth = min(colwidth,maxwidth) + column_widths[kw] = colwidth + pad + if nrows is None: + nrows = len(summary_dict[kw]['vals']) + + # print rows now + outstr = '' + # Start with column names + if idcol: + outstr += COLUMN_FMT.format(idcol['name'],width=idcol['width']+pad) + for kw in summary_cols: + outstr += COLUMN_FMT.format(kw,width=column_widths[kw]) + outstr += '\n' + # Now, add a row for each headerlet + for row in range(nrows): + if idcol: + outstr += COLUMN_FMT.format(idcol['vals'][row],width=idcol['width']+pad) + for kw in summary_cols: + val = summary_dict[kw]['vals'][row][:(column_widths[kw]-pad)] + outstr += COLUMN_FMT.format(val, width=column_widths[kw]) + outstr += '\n' + if not quiet: + print outstr + + # If specified, write info to separate text file + write_file = False + if output: + output = fu.osfn(output) # Expand any environment variables in filename + write_file = True + if os.path.exists(output): + if clobber: + os.remove(output) + else: + print 'WARNING: Not writing results to file!' + print ' Output text file ',output,' already exists.' + print ' Set "clobber" to True or move file before trying again.' + write_file = False + if write_file: + fout = open(output,mode='w') + fout.write(outstr) + fout.close() + +#### Private utility functions +def _createPrimaryHDU(destim, hdrname, distname, wcsname, + sipname, npolfile, d2imfile, upwcsver, pywcsver, + author, descrip, history): + if author is None: author = '' + if descrip is None: descrip = '' + if history is None: history = '' + phdu = pyfits.PrimaryHDU() + phdu.header.update('DESTIM', destim, + comment='Destination observation root name') + phdu.header.update('HDRNAME', hdrname, comment='Headerlet name') + fmt="%Y-%m-%dT%H:%M:%S" + phdu.header.update('DATE', time.strftime(fmt), + comment='Date FITS file was generated') + phdu.header.update('WCSNAME', wcsname, comment='WCS name') + phdu.header.update('DISTNAME', distname, comment='Distortion model name') + phdu.header.update('SIPNAME', sipname, comment='origin of SIP polynomial distortion model') + phdu.header.update('NPOLFILE', npolfile, comment='origin of non-polynmial distortion model') + phdu.header.update('D2IMFILE', d2imfile, comment='origin of detector to image correction') + phdu.header.update('AUTHOR', author, comment='headerlet created by this user') + phdu.header.update('DESCRIP', descrip, comment='Short description of headerlet solution') + + # clean up history string in order to remove whitespace characters that + # would cause problems with FITS + if isinstance(history,list): + history_str = '' + for line in history: + history_str += line + else: + history_str = history + history_lines = textwrap.wrap(history_str,width=70) + for hline in history_lines: + phdu.header.add_history(hline) + + phdu.header.ascard.append(upwcsver) + phdu.header.ascard.append(pywcsver) + return phdu + + +#### Public Interface functions +def extract_headerlet(filename, output, extnum=None, hdrname=None, + clobber=False, verbose=100): """ - Create a headerlet from a WCS in a science file - If both wcskey and wcsname are given they should match, if not + Finds a headerlet extension in a science file and writes it out as + a headerlet FITS file. + + If both hdrname and extnum are given they should match, if not raise an Exception + + Parameters + ---------- + filename: string or HDUList + Either a filename or PyFITS HDUList object for the input science file + An input filename (str) will be expanded as necessary to interpret + any environmental variables included in the filename. + output: string + Filename or just rootname of output headerlet FITS file + If string does not contain '.fits', it will create a filename with + '_hlet.fits' suffix + extnum: int + Extension number which contains the headerlet to be written out + hdrname: string + Unique name for headerlet, stored as the HDRNAME keyword + It stops if a value is not provided and no extnum has been specified + clobber: bool + If output file already exists, this parameter specifies whether or not + to overwrite that file [Default: False] + verbose: int + python logging level + + """ + + initLogging('extract_headerlet', verbose=verbose) + fobj,fname,close_fobj = parseFilename(filename) + + if hdrname in ['',' ',None, 'INDEF']: + if extnum is None: + print 'No valid headerlet specified! Quitting...' + if close_fobj: fobj.close() + else: + hdrhdu = fobj[extnum] + else: + extnum = findHeaderletHDUs(fobj,hdrname=hdrname)[0] + hdrhdu = fobj[extnum] + hdrlet = hdrhdu.headerlet + + if '.fits' in output: + outname = output + else: + outname = '%s_hlet.fits'%(output) + hdrlet.write_to(outname) + + if close_fobj: + fobj.close() + +def write_headerlet(filename, hdrname, output=None, 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, + attach=True, clobber=False): + + """ + Save a WCS as a headerlet FITS file. + + This function will create a headerlet, write out the headerlet to a + separate headerlet file, then, optionally, attach it as an extension + to the science image (if it has not already been archived) + + Either wcsname or wcskey must be provided; if both are given, they must + match a valid WCS. + + Updates wcscorr if necessary. Parameters ---------- - fname: string or HDUList - science file + filename: string or HDUList + Either a filename or PyFITS HDUList object for the input science file + An input filename (str) will be expanded as necessary to interpret + any environmental variables included in the filename. + hdrname: string + Unique name for this headerlet, stored as HDRNAME keyword + output: string or None + Filename or just rootname of output headerlet FITS file + If string does not contain '.fits', it will create a filename with + '_hlet.fits' suffix + If None, a default filename based on the input filename will be + generated for the headerlet FITS filename + sciext: string + name (EXTNAME) of extension that contains WCS to be saved + wcsname: string + name of WCS to be archived, if " ": stop + wcskey: one of A...Z or " " or "PRIMARY" + if " " or "PRIMARY" - archive the primary WCS + destim: string + DESTIM keyword + if NOne, use ROOTNAME or science file name + sipname: string or None (default) + Name of unique file where the polynomial distortion coefficients were + read from. If None, the behavior is: + The code looks for a keyword 'SIPNAME' in the science header + If not found, for HST it defaults to 'IDCTAB' + If there is no SIP model the value is 'NOMODEL' + If there is a SIP model but no SIPNAME, it is set to 'UNKNOWN' + npolfile: string or None (default) + Name of a unique file where the non-polynomial distortion was stored. + If None: + The code looks for 'NPOLFILE' in science header. + If 'NPOLFILE' was not found and there is no npol model, it is set to 'NOMODEL' + If npol model exists, it is set to 'UNKNOWN' + d2imfile: string + Name of a unique file where the detector to image correction was + stored. If None: + The code looks for 'D2IMFILE' in the science header. + If 'D2IMFILE' is not found and there is no d2im correction, + it is set to 'NOMODEL' + If d2im correction exists, but 'D2IMFILE' is missing from science + header, it is set to 'UNKNOWN' + author: string + Name of user who created the headerlet, added as 'AUTHOR' keyword + to headerlet PRIMARY header + descrip: string + Short description of the solution provided by the headerlet + This description will be added as the single 'DESCRIP' keyword + to the headerlet PRIMARY header + history: filename, string or list of strings + Long (possibly multi-line) description of the solution provided + by the headerlet. These comments will be added as 'HISTORY' cards + to the headerlet PRIMARY header + If filename is specified, it will format and attach all text from + that file as the history. + attach: bool + Specify whether or not to attach this headerlet as a new extension + It will verify that no other headerlet extension has been created with + the same 'hdrname' value. + clobber: bool + If output file already exists, this parameter specifies whether or not + to overwrite that file [Default: False] + """ + initLogging('write_headerlet') + + 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 + raise ValueError + + if hdrname in [None, ' ','']: + print '='*60 + print '[write_headerlet]' + print 'No valid name for this headerlet was provided for %s.'%fname + print ' A valid value for "hdrname" needs to be specified. ' + print '='*60 + raise ValueError + + # Translate 'wcskey' value for PRIMARY WCS to valid altwcs value of ' ' + if wcskey == 'PRIMARY': wcskey = ' ' + + if attach: umode = 'update' + else: umode='readonly' + + fobj,fname,close_fobj = parseFilename(filename,mode=umode) + + # Insure that WCSCORR table has been created with all original + # WCS's recorded prior to adding the headerlet WCS + wcscorr.init_wcscorr(fobj) + + numhlt = countExtn(fobj, 'HDRLET') + + if wcsname is None: + scihdr = fobj[sciext,1].header + wcsname = scihdr['wcsname'+wcskey] + + hdrletobj = getHeaderletObj(fobj,sciext=sciext, + wcsname=wcsname, wcskey=wcskey, + hdrname=hdrname, + sipname=sipname, npolfile=npolfile, + d2imfile=d2imfile, author=author, + descrip=descrip, history=history, + rms_ra=rms_ra, rms_dec=rms_dec, nmatch=nmatch, + catalog=catalog, + hdrletnum=numhlt + 1, verbose=False) + + if attach: + # Check to see whether or not a HeaderletHDU with this hdrname already + # exists + hdrnames = getHeaderletKwNames(fobj) + if hdrname not in hdrnames: + hdrlet_hdu = HeaderletHDU.fromheaderlet(hdrletobj) + + if destim is not None: + hdrlet_hdu[0].header['destim'] = destim + + fobj.append(hdrlet_hdu) + + # Update the WCSCORR table with new rows from the headerlet's WCSs + wcscorr.update_wcscorr(fobj, hdrletobj, 'SIPWCS') + + fobj.flush() + else: + print 'WARNING:' + print ' Headerlet with hdrname ',hdrname,' already archived for WCS ',wcsname + print ' No new headerlet appended to ',fname,'.' + + + if close_fobj: + fobj.close() + + if output is None: + # Generate default filename for headerlet FITS file + output = fname[:fname.find('.fits')] + if '.fits' not in output: + output = output+'_hlet.fits' + + # If user specifies an output filename for headerlet, write it out + if os.path.exists(output): + if clobber: + os.remove(output) + else: + print 'WARNING:' + print ' Headerlet file ',output,' already written out!' + print ' This headerlet file will not be created now.' + + hdrletobj.writeto(output) + print 'Create Headerlet file: ',output + +def create_headerlet(filename, sciext=None, 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'): + """ + Create a headerlet from a WCS in a science file + If both wcskey and wcsname are given they should match, if not + raise an Exception + + Parameters + ---------- + filename: string or HDUList + Either a filename or PyFITS HDUList object for the input science file + An input filename (str) will be expanded as necessary to interpret + any environmental variables included in the filename. sciext: string or python list - Extension in which the science data is. The headerlet will be created + Extension in which the science data is. The headerlet will be created from these extensions. If string - a valid EXTNAME is expected If list - a list of FITS extension numbers or extension tuples ('SCI', 1) is expected. - If None, loops over all extensions in the file, including the primary + If None, loops over all extensions in the file, including the primary [BROKEN-22Sept2011] hdrname: string value of HDRNAME keyword Takes the value from the HDRNAME<wcskey> keyword, if not available from WCSNAME<wcskey> - It stops if neither is found in the science file and a value is not provided + It stops if neither is found in the science file and a value is not provided destim: string or None name of file this headerlet can be applied to if None, use ROOTNAME keyword - wcskey: char (A...Z) or " " or None + wcskey: char (A...Z) or " " or "PRIMARY" or None a char representing an alternate WCS to be used for the headerlet - if " ", use the primary (default) - if None use wcsname + if " ", use the primary (default) + if None use wcsname wcsname: string or None if wcskey is None use wcsname specified here to choose an alternate WCS for the headerlet sipname: string or None (default) @@ -194,33 +808,39 @@ def create_headerlet(fname, sciext=None, hdrname=None, destim=None, wcskey=" ", it is set to 'NOMODEL' If d2im correction exists, but 'D2IMFILE' is missing from science header, it is set to 'UNKNOWN' + author: string + Name of user who created the headerlet, added as 'AUTHOR' keyword + to headerlet PRIMARY header + descrip: string + Short description of the solution provided by the headerlet + This description will be added as the single 'DESCRIP' keyword + to the headerlet PRIMARY header + history: filename, string or list of strings + Long (possibly multi-line) description of the solution provided + by the headerlet. These comments will be added as 'HISTORY' cards + 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 logmode: 'w' or 'a' log file open mode - + Returns ------- Headerlet object """ + + initLogging('createHeaderlet', verbose=verbose) - - if verbose: - setLogger(module_logger, verbose, mode=logmode) - else: - module_logger.setLevel(100) - - module_logger.info("Starting createHeaderlet: %s" % time.asctime()) phdukw = {'IDCTAB': True, 'NPOLFILE': True, 'D2IMFILE': True} - if not isinstance(fname, pyfits.HDUList): - fobj = pyfits.open(fname) - close_file = True - else: - fobj = fname - close_file = False + fobj,fname,close_file = parseFilename(filename) + # Translate 'wcskey' value for PRIMARY WCS to valid altwcs value of ' ' + if wcskey == 'PRIMARY': wcskey = ' ' + # get all required keywords if destim is None: try: @@ -230,7 +850,7 @@ def create_headerlet(fname, sciext=None, hdrname=None, destim=None, wcskey=" ", module_logger.info('DESTIM not provided') module_logger.info('Keyword "ROOTNAME" not found') module_logger.info('Using file name as DESTIM') - + if not hdrname: # check if HDRNAME<wcskey> is in header hdrname = "".join(["HDRNAME",wcskey.upper()]) @@ -238,53 +858,34 @@ def create_headerlet(fname, sciext=None, hdrname=None, destim=None, wcskey=" ", hdrname = fobj[1].header['HDRNAME'] except KeyError: try: - hdrname = fobj[1].header['WCSNAME'] + hdrname = fobj[1].header['WCSNAME'+wcskey] + print 'Using default value for HDRNAME of "%d"', + print ' derived from WCSNAME%d.'%(hdrname,wcskey) except KeyError, detail: - message = "Required keyword 'HDRNAME' not given" + message = "Required keywords 'HDRNAME' or 'WCSNAME' not found" module_logger.critical(message) print message, detail - + if not wcsname: wname = "".join(["WCSNAME",wcskey.upper()]) - try: + if wname in fobj[1].header: wcsname = fobj[1].header[wname] - except KeyError, detail: + else: message = "Missing required keyword 'WCSNAME'." module_logger.critical(message) print message, detail - + if not sipname: - try: - sipname = fobj[0].header["SIPNAME"] - except KeyError: - try: - sipname = fobj[0].header["IDCTAB"] - except KeyError: - if 'A_ORDER' in fobj[1].header or 'B_ORDER' in fobj[1].header: - sipname = 'UNKNOWN' - else: - sipname = 'NOMODEL' - + sipname = utils.build_sipname(fobj) + if not npolfile: - try: - npolfile = fobj[0].header["NPOLFILE"] - except KeyError: - if countExtn(f, 'WCSDVARR'): - npolfile = 'UNKNOWN' - else: - npolfile = 'NOMODEL' - + npolfile = utils.build_npolname(fobj) + if not d2imfile: - try: - d2imfile = fobj[0].header["D2IMFILE"] - except KeyError: - if countExtn(f, 'D2IMARR'): - npolfile = 'UNKNOWN' - else: - npolfile = 'NOMODEL' - - distname = "_".join([sipname, npolfile, d2imfile]) - + d2imfile = utils.build_d2imname(fobj) + + distname = utils.build_distname(sipname, npolfile, d2imfile) + # get the version of STWCS used to create the WCS of the science file. try: upwcsver = fobj[0].header.ascard['STWCSVER'] @@ -298,7 +899,7 @@ def create_headerlet(fname, sciext=None, hdrname=None, destim=None, wcskey=" ", "Version of PYWCS used to update the WCS") if not sciext: - sciext = range(fobj) + sciext = range(len(fobj)) elif isinstance(sciext, str): numsciext = countExtn(fobj, sciext) sciext = [(sciext, i) for i in range(1, numsciext+1)] @@ -308,69 +909,107 @@ def create_headerlet(fname, sciext=None, hdrname=None, destim=None, wcskey=" ", raise ValueError("Expected sciext to be a list of FITS extensions with science data or a string of valid EXTNAME") if wcskey is 'O': - message = "Warning: 'O' is a reserved key for the original WCS" + message = "Warning: 'O' is a reserved key for the original WCS. Quitting..." module_logger.info(message) print message + return + + # open file and parse comments + if history not in ['',' ',None,'INDEF'] and os.path.isfile(history): + f = open(fu.osfn(history)) + history = f.readlines() + f.close() module_logger.debug("Data extensions form which to create headerlet:\n\t %s" % (str(sciext))) hdul = pyfits.HDUList() - phdu = _createPrimaryHDU(destim, hdrname, distname, wcsname, - sipname, npolfile, d2imfile, upwcsver, pywcsver) + phdu = _createPrimaryHDU(destim, hdrname, distname, wcsname, + sipname, npolfile, d2imfile, upwcsver, pywcsver, + author, descrip, history) hdul.append(phdu) - + orient_comment = "positions angle of image y axis (deg. e of n)" + if fu.isFits(fobj)[1] is not 'simple': - + for e in sciext: - hwcs = HSTWCS(fname, ext=e, wcskey=wcskey) - h = hwcs.wcs2header(sip2hdr=True).ascard + wkeys = altwcs.wcskeys(fname,ext=e) + if wcskey != ' ' and wkeys > 0: + if wcskey not in wkeys: + if verbose > 100: + module_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=e,wcskey=' ') + h = hwcs.wcs2header(sip2hdr=True) + h.update('ORIENTAT',hwcs.orientat, comment=orient_comment) + if wcskey != ' ': + # Now read in specified linear WCS terms from alternate WCS + try: + althdr = altwcs.convertAltWCS(fname,e,oldkey=wcskey,newkey=" ") + althdrwcs = HSTWCS(fname,e,wcskey=wcskey) + alt_orient = althdrwcs.orientat + except KeyError: + continue # Skip over any extension which does not have a WCS + althdr = althdr.ascard + # Update full WCS with values from alternate WCS + for card in althdr: + h.update(card.key,card.value) + h.update('ORIENTAT',alt_orientat, comment=orient_comment) + h = h.ascard 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')) - if isinstance(e, int): val = e + if isinstance(e, int): + if 'extver' in fobj[e].header: + val = fobj[e].header['extver'] + else: + val = e else: val = e[1] h.insert(1, pyfits.Card(key='EXTVER', value=val, comment='Extension version')) - h.append(pyfits.Card("SCIEXT", str(e), + h.append(pyfits.Card("SCIEXT", str(e), "Target science data extension")) fhdr = fobj[e].header.ascard if npolfile is not 'NOMODEL': cpdis = fhdr['CPDIS*...'] for c in range(1, len(cpdis) + 1): h.append(cpdis[c - 1]) - dp = fhdr['DP%s.*...' % c] + dp = fhdr['DP%s*' % c] h.extend(dp) - + try: h.append(fhdr['CPERROR%s' % c]) except KeyError: pass - + try: h.append(fhdr['NPOLEXT']) except KeyError: pass - + if d2imfile is not 'NOMODEL': try: h.append(fhdr['D2IMEXT']) except KeyError: pass - + try: h.append(fhdr['AXISCORR']) except KeyError: + print ("'D2IMFILE' kw exists but keyword 'AXISCORR' was not found in " + "%s['SCI',%d]" % (fname, val)) module_logger.exception("'D2IMFILE' kw exists but keyword 'AXISCORR' was not found in " - "%s['SCI',%d]" % (fname, e)) + "%s['SCI',%d]" % (fname, val)) raise - + try: h.append(fhdr['D2IMERR']) except KeyError: h.append(pyfits.Card(key='DPERROR', value=0, comment='Maximum error of D2IMARR')) - + hdu = pyfits.ImageHDU(header=pyfits.Header(h)) hdul.append(hdu) numwdvarr = countExtn(fname, 'WCSDVARR') @@ -386,116 +1025,557 @@ def create_headerlet(fname, sciext=None, hdrname=None, destim=None, wcskey=" ", fobj.close() return Headerlet(hdul,verbose=verbose, logmode='a') -def _createPrimaryHDU(destim, hdrname, distname, wcsname, - sipname, npolfile, d2imfile, upwcsver, pywcsver): - phdu = pyfits.PrimaryHDU() - phdu.header.update('DESTIM', destim, - comment='Destination observation root name') - phdu.header.update('HDRNAME', hdrname, comment='Headerlet name') - fmt="%Y-%m-%dT%H:%M:%S" - phdu.header.update('DATE', time.strftime(fmt), - comment='Date FITS file was generated') - phdu.header.update('WCSNAME', wcsname, comment='WCS name') - phdu.header.update('DISTNAME', distname, comment='Distortion model name') - phdu.header.update('SIPNAME', sipname, comment='origin of SIP polynomial distortion model') - phdu.header.update('NPOLFILE', npolfile, comment='origin of non-polynmial distortion model') - phdu.header.update('D2IMFILE', d2imfile, comment='origin of detector to image correction') - - phdu.header.ascard.append(upwcsver) - phdu.header.ascard.append(pywcsver) - return phdu -def applyHeaderlet(hdrfile, destfile, createheaderlet=True, hdrname=None, - verbose=False): +def apply_headerlet_as_primary(filename, hdrlet, attach=True,archive=True, + force=False, verbose=False): """ - Apply headerlet 'hdrfile' to a science observation 'destfile' + Apply headerlet 'hdrfile' to a science observation 'destfile' as the primary WCS Parameters ---------- - hdrfile: string - Headerlet file - destfile: string + filename: string File name of science observation whose WCS solution will be updated - createheaderlet: boolean + hdrlet: string + Headerlet file + attach: boolean + True (default): append headerlet to FITS file as a new extension. + archive: boolean True (default): before updating, create a headerlet with the WCS old solution. - hdrname: string or None (default) - will be the value of the HDRNAME keyword in the headerlet generated - for the old WCS solution. If not specified, a sensible default - will be used. Not required if createheaderlet is False + 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) """ - 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) + initLogging('apply_headerlet_as_primary', verbose=verbose) + + hlet = Headerlet(hdrlet, verbose=verbose, logmode='a') + hlet.apply_as_primary(filename, attach=attach, archive=archive, force=force) -def updateRefFiles(source, dest, verbose=False): +def apply_headerlet_as_alternate(filename, hdrlet, attach=True, + wcskey=None, wcsname=None, verbose=False): """ - Update the reference files name in the primary header of 'dest' - using values from 'source' + Apply headerlet to a science observation as an alternate WCS Parameters ---------- - source: pyfits.Header.ascardlist - dest: pyfits.Header.ascardlist + filename: string + File name of science observation whose WCS solution will be updated + hdrlet: string + Headerlet file + attach: boolean + flag indicating if the headerlet should be attached as a + HeaderletHDU to fobj. If True checks that HDRNAME is unique + in the fobj and stops if not. + wcskey: string + Key value (A-Z, except O) for this alternate WCS + If None, the next available key will be used + wcsname: string + 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) """ - module_logger.info("Updating reference files") - phdukw = {'IDCTAB': True, - 'NPOLFILE': True, - 'D2IMFILE': True} + initLogging('apply_headerlet_as_alternate', verbose=verbose) + + hlet = Headerlet(hdrlet, verbose=verbose, logmode='a') + hlet.apply_as_alternate(filename, attach=attach, wcsname=wcsname, wcskey=wcskey) - try: - wind = dest.index_of('HISTORY') - except KeyError: - wind = len(dest) - for key in phdukw.keys(): - try: - value = source[key] - dest.insert(wind, value) - except KeyError: - # TODO: I don't understand what the point of this is. Is it meant - # for logging purposes? Right now it isn't used. - phdukw[key] = False - return phdukw +def attach_headerlet(filename, hdrlet, verbose=False): + """ + Attach Headerlet as an HeaderletHDU to a science file -def getRootname(fname): + Parameters + ---------- + filename: string, HDUList + science file to which the headerlet should be applied + hdrlet: string or Headerlet object + string representing a headerlet file """ - returns the value of ROOTNAME or DESTIM + initLogging('attach_headerlet', verbose=verbose) + + hlet = Headerlet(hdrlet, verbose=verbose, logmode='a') + hlet.attach_to_file(filename) + +def delete_headerlet(filename, hdrname=None, hdrext=None, distname=None): """ + Deletes HeaderletHDU(s) from a science file - try: - rootname = pyfits.getval(fname, 'ROOTNAME') - except KeyError: - rootname = pyfits.getval(fname, 'DESTIM') - return rootname + Notes + ----- + One of hdrname, hdrext or distname should be given. + If hdrname is given - delete a HeaderletHDU with a name HDRNAME from fobj. + If hdrext is given - delete HeaderletHDU in extension. + If distname is given - deletes all HeaderletHDUs with a specific distortion model from fobj. + Updates wcscorr -def mapFitsExt2HDUListInd(fname, extname): + Parameters + ---------- + filename: string or HDUList + Either a filename or PyFITS HDUList object for the input science file + An input filename (str) will be expanded as necessary to interpret + any environmental variables included in the filename. + hdrname: string or None + HeaderletHDU primary header keyword HDRNAME + hdrext: int, tuple or None + HeaderletHDU FITS extension number + tuple has the form ('HDRLET', 1) + distname: string or None + distortion model as specified in the DISTNAME keyword + """ + initLogging('delete_headerlet') + hdrlet_ind = findHeaderletHDUs(filename,hdrname=hdrname, hdrext=hdrext, + distname=distname) + 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. ' + return + + fobj,fname,close_fobj = parseFilename(filename,mode='update') + + # delete row(s) from WCSCORR table now... + # + # + if hdrname not in ['',' ',None,'INDEF']: + selections = {'hdrname':hdrname} + elif hdrname in ['',' ',None,'INDEF'] and hdrext is not None: + selections = {'hdrname':fobj[hdrext].header['hdrname']} + else: + selections = {'distname':distname} + wcscorr.delete_wcscorr_row(fobj['WCSCORR'].data,selections) + + # delete the headerlet extension now + for hdrind in hdrlet_ind: + del fobj[hdrind] + + # Update file object with changes + fobj.flush() + # close file, if was opened by this function + if close_fobj: + fobj.close() + print 'Deleted headerlet from extension(s): ',hdrlet_ind + +def headerlet_summary(filename,columns=None,pad=2,maxwidth=None, + output=None,clobber=True,quiet=False): """ - Map FITS extensions with 'EXTNAME' to HDUList indexes. + Print a summary of all HeaderletHDUs in a science file to STDOUT, and + optionally to a text file + The summary includes: + HDRLET_ext_number HDRNAME WCSNAME DISTNAME SIPNAME NPOLFILE D2IMFILE + + Parameters + ---------- + filename: string or HDUList + Either a filename or PyFITS HDUList object for the input science file + An input filename (str) will be expanded as necessary to interpret + any environmental variables included in the filename. + columns: list + List of headerlet PRIMARY header keywords to report in summary + By default (set to None), it will use the default set of keywords + defined as the global list DEFAULT_SUMMARY_COLS + pad: int + Number of padding spaces to put between printed columns + [Default: 2] + maxwidth: int + Maximum column width(not counting padding) for any column in summary + By default (set to None), each column's full width will be used + output: string (optional) + Name of optional output file to record summary. This filename + can contain environment variables. + [Default: None] + clobber: bool + If True, will overwrite any previous output file of same name + quiet: bool + If True, will NOT report info to STDOUT + """ + if columns is None: + summary_cols = DEFAULT_SUMMARY_COLS + else: + summary_cols = columns + + summary_dict = {} + for kw in summary_cols: + summary_dict[kw] = copy.deepcopy(COLUMN_DICT) + + # Define Extension number column + extnums_col = copy.deepcopy(COLUMN_DICT) + extnums_col['name'] = 'EXTN' + extnums_col['width'] = 6 + + fobj,fname,close_fobj = parseFilename(filename) + # find all HDRLET extensions and combine info into a single summary + for extn in fobj: + if 'extname' in extn.header and extn.header['extname'] == 'HDRLET': + hdrlet_indx = fobj.index_of(('hdrlet',extn.header['extver'])) + try: + ext_cols, ext_summary = extn.headerlet.summary(columns=summary_cols) + extnums_col['vals'].append(hdrlet_indx) + for kw in summary_cols: + for key in COLUMN_DICT: + summary_dict[kw][key].extend(ext_summary[kw][key]) + except: + print 'Skipping headerlet...Could not read Headerlet from extension ',hdrlet_indx + + if close_fobj: + fobj.close() + + # Print out the summary dictionary + print_summary(summary_cols, summary_dict, pad=pad, maxwidth=maxwidth, + idcol=extnums_col, output=output, + clobber=clobber, quiet=quiet) + +def restore_from_headerlet(filename, hdrname=None, hdrext=None, archive=True, force=False): """ + Restores a headerlet as a primary WCS + + Parameters + ---------- + filename: string or HDUList + Either a filename or PyFITS HDUList object for the input science file + An input filename (str) will be expanded as necessary to interpret + any environmental variables included in the filename. + hdrname: string + HDRNAME keyword of HeaderletHDU + hdrext: int or tuple + Headerlet extension number of tuple ('HDRLET',2) + archive: boolean (default: True) + When the distortion model in the headerlet is the same as the distortion model of + the science file, this flag indicates if the primary WCS should be saved as an alternate + nd a headerlet extension. + When the distortion models do not match this flag indicates if the current primary and + alternate WCSs should be archived as headerlet extensions and alternate WCS. + 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. + """ + initLogging('restore_from_headerlet') + + hdrlet_ind = findHeaderletHDUs(filename,hdrext=hdrext,hdrname=hdrname) - if not isinstance(fname, pyfits.HDUList): - f = pyfits.open(fname) - close_file = True + fobj,fname,close_fobj = parseFilename(filename,mode='update') + + if len(hdrlet_ind) > 1: + if hdrext: + kwerr = 'hdrext' + kwval = hdrext + 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 '=====================================================' + if close_fobj: + fobj.close() + raise ValueError + + hdrlet_indx = hdrlet_ind[0] + + # read headerlet from HeaderletHDU into memory + if hasattr(fobj[hdrlet_ind[0]], 'hdulist'): + hdrlet = fobj[hdrlet_indx].hdulist else: - f = fname - close_file = False - d = {} - for hdu in f: - 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: - f.close() - return d + hdrlet = fobj[hdrlet_indx].headerlet # older convention in PyFITS + + # read in the names of the extensions which HeaderletHDU updates + extlist = [] + for ext in hdrlet: + if 'extname' in ext.header and ext.header['extname'] == 'SIPWCS': + # convert from string to tuple or int + sciext = eval(ext.header['sciext']) + extlist.append(fobj[sciext]) + # determine whether distortion is the same + current_distname = hdrlet[0].header['distname'] + same_dist = True + if current_distname != fobj[0].header['distname']: + same_dist = False + 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 '=====================================================' + raise ValueError + + # check whether primary WCS has been archived already + # Use information from first 'SCI' extension + priwcs_name = None + + scihdr = extlist[0].header + sci_wcsnames = altwcs.wcsnames(scihdr).values() + if 'hdrname' in scihdr: + priwcs_hdrname = scihdr['hdrname'] + else: + if 'wcsname' in scihdr: + priwcs_hdrname = priwcs_name = scihdr['wcsname'] + else: + if 'idctab' in scihdr: + priwcs_hdrname = ''.join(['IDC_', + utils.extract_rootname(scihdr['idctab'])]) + else: + priwcs_hdrname = 'UNKNOWN' + priwcs_name = priwcs_hdrname + scihdr.update('WCSNAME',priwcs_name) + + priwcs_unique = verifyHdrnameIsUnique(fobj,priwcs_hdrname) + if archive and priwcs_unique: + if priwcs_unique: + newhdrlet = create_headerlet(fobj,sciext=scihdr['extname'], + hdrname=priwcs_hdrname) + newhdrlet.attach_to_file(fobj) + # + # copy hdrlet as a primary + # + hdrlet.apply_as_primary(fobj,attach=False, archive=archive,force=force) + + fobj.flush() + if close_fobj: + fobj.close() + +def restore_all_with_distname(filename, distname, primary, archive=True, sciext='SCI'): + """ + Restores all HeaderletHDUs with a given distortion model as alternate WCSs and a primary + + Parameters + -------------- + filename: string or HDUList + Either a filename or PyFITS HDUList object for the input science file + An input filename (str) will be expanded as necessary to interpret + any environmental variables included in the filename. + distname: string + distortion model as represented by a DISTNAME keyword + primary: int or string or None + HeaderletHDU to be restored as primary + if int - a fits extension + if string - HDRNAME + if None - use first HeaderletHDU + archive: boolean (default True) + flag indicating if HeaderletHDUs should be created from the + primary and alternate WCSs in fname before restoring all matching + headerlet extensions + """ + initLogging('restore_all_with_distname') + + fobj,fname,close_fobj = parseFilename(filename,mode='update') + + hdrlet_ind = findHeaderletHDUs(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.'%(kwval,fname) + print 'Full list of DISTNAMEs found in all headerlet extensions: ' + print getHeaderletKwNames(fobj,kw='DISTNAME') + print '=====================================================' + if close_fobj: + fobj.close() + raise ValueError + + # Interpret 'primary' parameter input into extension number + if primary is None: + primary_ind = hdrlet_ind[0] + elif isinstance(primary, int): + primary_ind = primary + else: + primary_ind = None + for ind in hdrlet_ind: + if fobj[ind].header['hdrname'] == primary: + primary_ind = ind + break + 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 '=====================================================' + raise ValueError + # Check to see whether 'primary' HeaderletHDU has same distname as user + # specified on input + + # read headerlet from HeaderletHDU into memory + if hasattr(fobj[primary_ind], 'hdulist'): + primary_hdrlet = fobj[primary_ind].hdulist + else: + primary_hdrlet = fobj[primary_ind].headerlet # older convention in PyFITS + pri_distname = primary_hdrlet[0].header['distname'] + 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 '=====================================================' + raise ValueError + + # read in the names of the WCSs which the HeaderletHDUs will update + wnames = altwcs.wcsnames(fobj[sciext,1].header) + + # work out how many HeaderletHDUs will be used to update the WCSs + numhlt = len(hdrlet_ind) + hdrnames = getHeaderletKwNames(fobj,kw='wcsname') + + # read in headerletHDUs and update WCS keywords + for hlet in hdrlet_ind: + if fobj[hlet].header['distname'] == distname: + if hasattr(fobj[hlet], 'hdulist'): + hdrlet = fobj[hlet].hdulist + else: + hdrlet = fobj[hlet].headerlet # older convention in PyFITS + if hlet == primary_ind: + hdrlet.apply_as_primary(fobj,attach=False,archive=archive,force=True) + else: + hdrlet.apply_as_alternate(fobj,attach=False,wcsname=hdrlet[0].header['wcsname']) + + fobj.flush() + if close_fobj: + fobj.close() +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): + """ + Save a WCS as a headerlet extension and write it out to a file. + This function will create a headerlet, attach it as an extension to the + science image (if it has not already been archived) then, optionally, + write out the headerlet to a separate headerlet file. + + Either wcsname or wcskey must be provided, if both are given, they must match a valid WCS + Updates wcscorr if necessary. + + Parameters + ---------- + filename: string or HDUList + Either a filename or PyFITS HDUList object for the input science file + An input filename (str) will be expanded as necessary to interpret + any environmental variables included in the filename. + hdrname: string + Unique name for this headerlet, stored as HDRNAME keyword + sciext: string + name (EXTNAME) of extension that contains WCS to be saved + wcsname: string + name of WCS to be archived, if " ": stop + wcskey: one of A...Z or " " or "PRIMARY" + if " " or "PRIMARY" - archive the primary WCS + destim: string + DESTIM keyword + if NOne, use ROOTNAME or science file name + sipname: string or None (default) + Name of unique file where the polynomial distortion coefficients were + read from. If None, the behavior is: + The code looks for a keyword 'SIPNAME' in the science header + If not found, for HST it defaults to 'IDCTAB' + If there is no SIP model the value is 'NOMODEL' + If there is a SIP model but no SIPNAME, it is set to 'UNKNOWN' + npolfile: string or None (default) + Name of a unique file where the non-polynomial distortion was stored. + If None: + The code looks for 'NPOLFILE' in science header. + If 'NPOLFILE' was not found and there is no npol model, it is set to 'NOMODEL' + If npol model exists, it is set to 'UNKNOWN' + d2imfile: string + Name of a unique file where the detector to image correction was + stored. If None: + The code looks for 'D2IMFILE' in the science header. + If 'D2IMFILE' is not found and there is no d2im correction, + it is set to 'NOMODEL' + If d2im correction exists, but 'D2IMFILE' is missing from science + header, it is set to 'UNKNOWN' + author: string + Name of user who created the headerlet, added as 'AUTHOR' keyword + to headerlet PRIMARY header + descrip: string + Short description of the solution provided by the headerlet + This description will be added as the single 'DESCRIP' keyword + to the headerlet PRIMARY header + history: filename, string or list of strings + Long (possibly multi-line) description of the solution provided + by the headerlet. These comments will be added as 'HISTORY' cards + to the headerlet PRIMARY header + If filename is specified, it will format and attach all text from + that file as the history. + """ + initLogging('archive_as_headerlet') + + 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 + raise ValueError + + if hdrname in [None, ' ','']: + print '='*60 + print '[archive_as_headerlet]' + print 'No valid name for this headerlet was provided for %s.'%fname + print ' A valid value for "hdrname" needs to be specified. ' + print '='*60 + raise ValueError + + # Translate 'wcskey' value for PRIMARY WCS to valid altwcs value of ' ' + if wcskey == 'PRIMARY': wcskey = ' ' + + fobj,fname,close_fobj = parseFilename(filename,mode='update') + + numhlt = countExtn(fobj, 'HDRLET') + + if wcsname is None: + scihdr = fobj[sciext,1].header + wcsname = scihdr['wcsname'+wcskey] + + + # Check to see whether or not a HeaderletHDU with this hdrname already + # exists + hdrnames = getHeaderletKwNames(fobj) + if hdrname not in hdrnames: + hdrletobj = getHeaderletObj(fobj,sciext=sciext, + wcsname=wcsname, wcskey=wcskey, + hdrname=hdrname, + sipname=sipname, npolfile=npolfile, + d2imfile=d2imfile, author=author, + descrip=descrip, history=history, + rms_ra=rms_ra, rms_dec=rms_dec, nmatch=nmatch, + catalog=catalog, + hdrletnum=numhlt + 1, verbose=False) + hlt_hdu = HeaderletHDU.fromheaderlet(hdrletobj) + + if destim is not None: + hdrlet_hdu[0].header['destim'] = destim + + fobj.append(hdrlet_hdu) + + fobj.flush() + else: + print 'WARNING:' + print ' Headerlet with hdrname ',hdrname,' already archived for WCS ',wcsname + print ' No new headerlet appended to ',fname,'.' + + if close_fobj: + fobj.close() + +#### Headerlet Class definitions class Headerlet(pyfits.HDUList): """ A Headerlet class @@ -511,139 +1591,363 @@ class Headerlet(pyfits.HDUList): instances, or an HDUList instance mode: string, optional Mode with which to open the given file object - verbose: int + verbose: int python logging level, higher numbers trigger more output logmode: 'w' or 'a' - for internal use only, indicates whether the log file + 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') - if self.verbose: - setLogger(self.hdr_logger, self.verbose, mode=logmode) - else: - self.hdr_logger.setLevel(100) - - if not isinstance(fobj, list): - fobj = pyfits.open(fobj, mode=mode) + initLogging('class Headerlet', logger=self.hdr_logger, level=100, + verbose=self.verbose, logmode=logmode) + fobj,fname,close_file = parseFilename(fobj) + super(Headerlet, self).__init__(fobj) self.fname = self.filename() self.hdrname = self[0].header["HDRNAME"] self.wcsname = self[0].header["WCSNAME"] - self.stwcsver = self[0].header.get("STWCSVER", "") - self.stwcsver = self[0].header.get("PYWCSVER", "") + self.upwcsver = self[0].header.get("UPWCSVER", "") + self.pywcsver = self[0].header.get("PYWCSVER", "") self.destim = self[0].header["DESTIM"] - self.idctab = self[0].header["SIPNAME"] + self.sipname = self[0].header["SIPNAME"] self.npolfile = self[0].header["NPOLFILE"] self.d2imfile = self[0].header["D2IMFILE"] self.distname = self[0].header["DISTNAME"] self.vafactor = self[1].header.get("VAFACTOR", 1) #None instead of 1? + self.author = self[0].header["AUTHOR"] + self.descrip = self[0].header["DESCRIP"] + + self.history = '' + for card in self[0].header['HISTORY*']: + self.history += card.value+'\n' + self.d2imerr = 0 self.axiscorr = 1 - def apply_as_primary(fobj, attach=True, archive=True, force=False): + def apply_as_primary(self, fobj, attach=True, archive=True, force=False): """ Copy this headerlet as a primary WCS to fobj - + Parameters ---------- fobj: string, HDUList science file to which the headerlet should be applied attach: boolean - flag indicating if the headerlet should be attached as a - HeaderletHDU to fobj. If True checks that HDRNAME is unique + flag indicating if the headerlet should be attached as a + HeaderletHDU to fobj. If True checks that HDRNAME is unique in the fobj and stops if not. archive: boolean (default is True) - When the distortion model in the headerlet is the same as the - distortion model of the science file, this flag indicates if - the primary WCS should be saved as an alternate and a headerlet + When the distortion model in the headerlet is the same as the + distortion model of the science file, this flag indicates if + the primary WCS should be saved as an alternate and a headerlet extension. - When the distortion models do not match this flag indicates if - the current primary and alternate WCSs should be archived as + When the distortion models do not match this flag indicates if + the current primary and alternate WCSs should be archived as headerlet extensions and alternate WCS. force: boolean (default is False) - When the distortion models of the headerlet and the primary do - not match, and archive is False this flag forces an update + 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 """ self.hverify() - if self.verify_dest(dest): - if not isinstance(dest, pyfits.HDUList): - fobj = pyfits.open(dest, mode='update') + if self.verify_dest(fobj): + if not isinstance(fobj, pyfits.HDUList): + fobj = pyfits.open(fobj, mode='update') close_dest = True else: - fobj = dest close_dest = False - # Create the WCSCORR HDU/table from the existing WCS keywords if - # necessary - if createsummary: - try: - # TODO: in the pyfits refactoring branch if will be easier to - # test whether an HDUList contains a certain extension HDU - # without relying on try/except - wcscorr_table = fobj['WCSCORR'] - except KeyError: - # The WCSCORR table needs to be created - wcscorr.init_wcscorr(fobj) - + # Check to see whether the distortion model in the destination + # 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'] + dist_models_equal = False + + if not dist_models_equal and not force: + raise ValueError + orig_hlt_hdu = None numhlt = countExtn(fobj, 'HDRLET') - if createheaderlet: - # Create a headerlet for the original WCS data in the file, - # create an HDU from the original headerlet, and append it to - # the file - if not hdrname: + hdrlet_extnames = getHeaderletKwNames(fobj) + + # Insure that WCSCORR table has been created with all original + # WCS's recorded prior to adding the headerlet WCS + wcscorr.init_wcscorr(fobj) + + alt_hlethdu = [] + # If archive has been specified + # regardless of whether or not the distortion models are equal... + if archive: + if 'wcsname' in fobj[('SCI',1)].header: + hdrname = fobj[('SCI',1)].header['WCSNAME'] + wcsname = hdrname + else: hdrname = fobj[0].header['ROOTNAME'] + '_orig' - 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 + wcsname = None + wcskey = ' ' + # Check the HDRNAME for all current headerlet extensions + # to see whether this PRIMARY WCS has already been appended + if hdrname not in hdrlet_extnames: + # - if WCS has not been saved, write out WCS as headerlet extension + # Create a headerlet for the original Primary WCS data in the file, + # create an HDU from the original headerlet, and append it to + # the file + orig_hlt = getHeaderletObj(fobj,sciext='SCI', + wcsname=wcsname, wcskey=wcskey, + hdrname=hdrname, sipname=None, + npolfile=None, d2imfile=None, + author=None, descrip=None, history=None, + hdrletnum=numhlt + 1, verbose=self.verbose) + orig_hlt_hdu = HeaderletHDU.fromheaderlet(orig_hlt) + numhlt += 1 + orig_hlt_hdu.header.update('EXTVER',numhlt) + + wcsextn = mapFitsExt2HDUListInd(fobj.filename(),"SCI")[('SCI',1)] + if dist_models_equal: + # Use the WCSNAME to determine whether or not to archive + # Primary WCS as altwcs + # wcsname = hwcs.wcs.name + scihdr = fobj[wcsextn].header + if 'hdrname' in scihdr: + priwcs_name = scihdr['hdrname'] + else: + if 'wcsname' in scihdr: + priwcs_name = scihdr['wcsname'] + else: + if 'idctab' in scihdr: + priwcs_name = ''.join(['IDC_', + utils.extract_rootname(scihdr['idctab'])]) + else: + priwcs_name = 'UNKNOWN' + nextkey = altwcs.next_wcskey(fobj,ext=wcsextn) + numsci = countExtn(fobj,'SCI') + sciext_list = [] + for i in range(1,numsci+1): + sciext_list.append(('SCI',i)) + altwcs.archiveWCS(fobj,ext=sciext_list,wcskey=nextkey,wcsname=priwcs_name) + else: + for hname in altwcs.wcsnames(fobj,ext=wcsextn).values(): + if hname != 'OPUS' and hname not in hdrlet_extnames: + # get HeaderletHDU for alternate WCS as well + alt_hlet = getHeaderletObj(fobj, sciext='SCI', + wcsname=hname, wcskey=wcskey, + hdrname=hname, sipname=None, + npolfile=None, d2imfile=None, + author=None, descrip=None, history=None, + hdrletnum=numhlt + 1, verbose=self.verbose) + numhlt += 1 + alt_hlet_hdu = HeaderletHDU.fromheaderlet(alt_hlet) + alt_hlet_hdu.header.update('EXTVER',numhlt) + alt_hlethdu.append(alt_hlet_hdu) + hdrlet_extnames.append(hname) + + if not dist_models_equal: + self._delDestWCS(fobj) + #! Always attach these extensions last. + # Otherwise their headers may get updated with the other WCS kw. + numwdvar = countExtn(self, 'WCSDVARR') + numd2im = countExtn(self, 'D2IMARR') + for idx in range(1, numwdvar + 1): + fobj.append(self[('WCSDVARR', idx)].copy()) + for idx in range(1, numd2im + 1): + fobj.append(self[('D2IMARR', idx)].copy()) - self._delDestWCS(fobj) refs = 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 + fhdr = fobj[('SCI', idx)].header + siphdr = self[('SIPWCS', idx)].header.ascard + + if dist_models_equal: + hwcs = HSTWCS(fobj,ext=('SCI',idx)) + hwcshdr = hwcs.wcs2header(sip2hdr=not(dist_models_equal)) + + # 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 + # if everything fails, append the kw to the header + akeywd = None + bkeywd = None + if 'PA_APER' in fhdr: + akeywd = 'PA_APER' + else: + if 'HISTORY' in fhdr: + bkeywd = 'HISTORY' + self.hdr_logger.debug( + "Updating WCS keywords after %s and/or before %s " % + (akeywd,bkeywd)) + update_cpdis = False + for k in siphdr[-1::-1]: + # Replace or add WCS keyword from headerlet as PRIMARY WCS + # In the case that the distortion models are not equal, + # this will copy all keywords from headerlet into fobj + # When the distortion models are equal, though, it will + # only copy the primary WCS keywords (CRVAL,CRPIX,...) + if (dist_models_equal and (k.key in hwcshdr)) or \ + (not dist_models_equal and k.key not in FITS_STD_KW): + if 'DP' not in k.key: + fhdr.update(k.key,k.value,comment=k.comment, + after=akeywd,before=bkeywd) + else: + update_cpdis = True + else: + pass + # Update WCS with HDRNAME as well + fhdr.update('HDRNAME',self[0].header['hdrname'],after='WCSNAME') + + # Update header with record-valued keywords here + if update_cpdis: + numdp = len(siphdr['CPDIS*']) + for dpaxis in range(1,numdp+1): + cpdis_indx = fhdr.ascard.index_of('CPDIS%d'%(dpaxis)) + for dpcard in siphdr['DP%d*'%(dpaxis)][-1::-1]: + fhdr.ascard.insert(cpdis_indx,dpcard) + + # Update the WCSCORR table with new rows from the headerlet's WCSs + wcscorr.update_wcscorr(fobj, self, 'SIPWCS') + + # Append the original headerlet + if archive and orig_hlt_hdu: + fobj.append(orig_hlt_hdu) + # Append any alternate WCS Headerlets + if len(alt_hlethdu) > 0: + for ahdu in alt_hlethdu: + fobj.append(ahdu) + if attach: + # Finally, append an HDU for this headerlet + new_hlt = HeaderletHDU.fromheaderlet(self) + new_hlt.update_ext_version(numhlt + 1) + fobj.append(new_hlt) + + if close_dest: + fobj.close() + else: + 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) + + def apply_as_alternate(self, fobj, attach=True, wcskey=None, wcsname=None): + """ + Copy this headerlet as an alternate WCS to fobj + + Parameters + ---------- + fobj: string, HDUList + science file/HDUList to which the headerlet should be applied + attach: boolean + flag indicating if the headerlet should be attached as a + HeaderletHDU to fobj. If True checks that HDRNAME is unique + in the fobj and stops if not. + wcskey: string + Key value (A-Z, except O) for this alternate WCS + If None, the next available key will be used + wcsname: string + 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. + + """ + self.hverify() + if self.verify_dest(fobj): + if not isinstance(fobj, pyfits.HDUList): + fobj = pyfits.open(fobj, mode='update') + close_dest = True + else: + close_dest = False + fname = fobj.filename() + + # Verify whether this headerlet has the same distortion found in + # the image being updated + if 'DISTNAME' in fobj[0].header: + distname = fobj[0].header['DISTNAME'] + else: + # perhaps call 'updatewcs.utils.construct_distname()' instead + 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() + raise ValueError + + # Insure that WCSCORR table has been created with all original + # WCS's recorded prior to adding the headerlet WCS + wcscorr.init_wcscorr(fobj) + + # determine value of WCSNAME to be used + if wcsname is not None: + wname = wcsname + else: + wname = self[0].header['WCSNAME'] + + numhlt = countExtn(fobj, 'HDRLET') + numsip = countExtn(self, 'SIPWCS') + for idx in range(1, numsip + 1): + fhdr = fobj[('SCI', idx)].header siphdr = self[('SIPWCS', idx)].header.ascard + + # determine what alternate WCS this headerlet will be assigned to + if wcskey is None: + wkey = altwcs.next_wcskey(fobj[('SCI',idx)].header) + else: + available_keys = altwcs.available_wcskeys(fobj[('SCI',idx)].header) + if wcskey in available_keys: + wkey = wcskey + else: + self.hdr_logger.critical("Observation %s already contains alternate WCS with key \ + %s" % (fname, wcskey)) + print ("Observation %s already contains alternate WCS with key \ + %s" % (fname, wcskey)) + if close_dest: fobj.close() + raise ValueError + # 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 befir the HISTORY kw + # at least make sure the WCS kw are written before the HISTORY kw # if everything fails, append the kw to the header try: - wind = fhdr.index_of('PA_APER') + wind = fhdr.ascard.index_of('HISTORY') except KeyError: - try: - wind = fhdr.index_of('HISTORY') - except KeyError: - wind = len(fhdr) + wind = len(fhdr) self.hdr_logger.debug("Inserting WCS keywords at index %s" % wind) + for k in siphdr: + """ if k.key not in ['XTENSION', 'BITPIX', 'NAXIS', 'PCOUNT', 'GCOUNT','EXTNAME', 'EXTVER', 'ORIGIN', 'INHERIT', 'DATE', 'IRAF-TLM']: - fhdr.insert(wind, k) + """ + for akw in altwcs.altwcskw: + if akw in k.key: + fhdr.ascard.insert(wind,pyfits.Card( + key=k.key[:7]+wkey,value=k.value, + comment=k.comment)) else: pass - #! Always attach these extensions last. Otherwise their headers may - # get updated with the other WCS kw. - numwdvar = countExtn(self, 'WCSDVARR') - numd2im = countExtn(self, 'D2IMARR') - for idx in range(1, numwdvar + 1): - fobj.append(self[('WCSDVARR', idx)].copy()) - for idx in range(1, numd2im + 1): - fobj.append(self[('D2IMARR', idx)].copy()) + fhdr.ascard.insert(wind,pyfits.Card('WCSNAME'+wkey,wname)) + # also update with HDRNAME (a non-WCS-standard kw) + fhdr.ascard.insert(wind,pyfits.Card('HDRNAME'+wkey, + self[0].header['hdrname'])) # Update the WCSCORR table with new rows from the headerlet's WCSs - if createsummary: - wcscorr.update_wcscorr(fobj, self, 'SIPWCS') - - # Append the original headerlet - if createheaderlet and orig_hlt_hdu: - fobj.append(orig_hlt_hdu) - + wcscorr.update_wcscorr(fobj, self, 'SIPWCS') + if attach: # Finally, append an HDU for this headerlet new_hlt = HeaderletHDU.fromheaderlet(self) @@ -654,10 +1958,123 @@ class Headerlet(pyfits.HDUList): fobj.close() else: 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) + + def attach_to_file(self,fobj): + """ + Attach Headerlet as an HeaderletHDU to a science file + + Parameters + ---------- + fobj: string, HDUList + science file/HDUList to which the headerlet should be applied + + Notes + ----- + The algorithm used by this method: + - verify headerlet can be applied to this file (based on DESTIM) + - verify that HDRNAME is unique for this file + - attach as HeaderletHDU to fobj + - update wcscorr + """ + self.hverify() + if not isinstance(fobj, pyfits.HDUList): + fobj = pyfits.open(fobj, mode='update') + close_dest = True + else: + close_dest = False + if self.verify_dest(fobj) and self.verify_hdrname(fobj): + + numhlt = countExtn(fobj, 'HDRLET') + new_hlt = HeaderletHDU.fromheaderlet(self) + new_hlt.header.update('extver',numhlt + 1) + fobj.append(new_hlt) + + wcscorr.update_wcscorr(fobj, self, 'SIPWCS',active=False) + + else: + 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) + if close_dest: + fobj.close() + + def info(self, columns=None, pad=2, maxwidth=None, + output=None, clobber=True, quiet=False): + """ + Prints a summary of this headerlet + The summary includes: + HDRNAME WCSNAME DISTNAME SIPNAME NPOLFILE D2IMFILE + + Parameters + ---------- + columns: list + List of headerlet PRIMARY header keywords to report in summary + By default (set to None), it will use the default set of keywords + defined as the global list DEFAULT_SUMMARY_COLS + pad: int + Number of padding spaces to put between printed columns + [Default: 2] + maxwidth: int + Maximum column width(not counting padding) for any column in summary + By default (set to None), each column's full width will be used + output: string (optional) + Name of optional output file to record summary. This filename + can contain environment variables. + [Default: None] + clobber: bool + If True, will overwrite any previous output file of same name + quiet: bool + If True, will NOT report info to STDOUT + + """ + summary_cols, summary_dict = self.summary(columns=columns) + print_summary(summary_cols, summary_dict, pad=pad, maxwidth=maxwidth, + idcol=None, output=output, clobber=clobber, quiet=quiet) + + def summary(self, columns=None): + """ + Returns a summary of this headerlet as a dictionary + + The summary includes a summary of the distortion model as : + HDRNAME WCSNAME DISTNAME SIPNAME NPOLFILE D2IMFILE + + Parameters + ---------- + columns: list + List of headerlet PRIMARY header keywords to report in summary + By default(set to None), it will use the default set of keywords + defined as the global list DEFAULT_SUMMARY_COLS + + Returns + ------- + summary: dict + Dictionary of values for summary + """ + if columns is None: + summary_cols = DEFAULT_SUMMARY_COLS + else: + summary_cols = columns + + # Initialize summary dict based on requested columns + summary = {} + for kw in summary_cols: + summary[kw] = copy.deepcopy(COLUMN_DICT) + + # Populate the summary with headerlet values + for kw in summary_cols: + if kw in self[0].header: + val = self[0].header[kw] + else: + val = 'INDEF' + summary[kw]['vals'].append(val) + summary[kw]['width'].append(max(len(val),len(kw))) + + return summary_cols,summary def hverify(self): self.verify() @@ -665,8 +2082,18 @@ class Headerlet(pyfits.HDUList): assert('DESTIM' in header and header['DESTIM'].strip()) assert('HDRNAME' in header and header['HDRNAME'].strip()) assert('STWCSVER' in header) - - + + def verify_hdrname(self,dest): + """ + Verifies that the headerlet can be applied to the observation + + Reports whether or not this file already has a headerlet with this + HDRNAME. + """ + unique = verifyHdrnameIsUnique(dest,self.hdrname) + self.hdr_logger.debug("verify_hdrname() returned %s"%unique) + return unique + def verify_dest(self, dest): """ verifies that the headerlet can be applied to the observation @@ -775,7 +2202,7 @@ class Headerlet(pyfits.HDUList): return try: for c in range(1, len(cpdis) + 1): - del ext.header['DP%s.*...' % c] + del ext.header['DP%s*...' % c] del ext.header[cpdis[c - 1].key] del ext.header['CPERR*'] del ext.header['NPOLFILE'] @@ -806,7 +2233,8 @@ class Headerlet(pyfits.HDUList): 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) + if k not in ['O',' ','']: # Never delete WCS with wcskey='O' + altwcs.deleteWCS(dest, ext=ext, wcskey=k) def _removePrimaryWCS(self, ext): """ @@ -893,10 +2321,11 @@ class HeaderletHDU(pyfits.hdu.base.NonstandardExtHDU): '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): """ @@ -935,6 +2364,11 @@ class HeaderletHDU(pyfits.hdu.base.NonstandardExtHDU): finally: os.remove(name) + if 'sipname' in headerlet[0].header: + sipname = headerlet[0].header['sipname'] + else: + sipname = headerlet[0].header['wcsname'] + cards = [ pyfits.Card('XTENSION', cls._extension, 'Headerlet extension'), pyfits.Card('BITPIX', 8, 'array data type'), @@ -946,8 +2380,12 @@ class HeaderletHDU(pyfits.hdu.base.NonstandardExtHDU): 'name of the headerlet extension'), phdu.header.ascard['HDRNAME'], phdu.header.ascard['DATE'], - pyfits.Card('SIPNAME', headerlet['SIPWCS', 1].header['WCSNAMEA'], + pyfits.Card('SIPNAME', sipname, 'SIP distortion model name'), + pyfits.Card('WCSNAME', headerlet[0].header['WCSNAME'], + 'WCS name'), + pyfits.Card('DISTNAME', headerlet[0].header['DISTNAME'], + 'Distortion model name'), phdu.header.ascard['NPOLFILE'], phdu.header.ascard['D2IMFILE'], pyfits.Card('COMPRESS', compress, 'Uses gzip compression') |