diff options
Diffstat (limited to 'updatewcs')
| -rw-r--r-- | updatewcs/__init__.py | 396 | ||||
| -rw-r--r-- | updatewcs/apply_corrections.py | 223 | ||||
| -rw-r--r-- | updatewcs/corrections.py | 230 | ||||
| -rw-r--r-- | updatewcs/det2im.py | 200 | ||||
| -rw-r--r-- | updatewcs/makewcs.py | 251 | ||||
| -rw-r--r-- | updatewcs/npol.py | 319 | ||||
| -rw-r--r-- | updatewcs/utils.py | 28 |
7 files changed, 0 insertions, 1647 deletions
diff --git a/updatewcs/__init__.py b/updatewcs/__init__.py deleted file mode 100644 index ab852d0..0000000 --- a/updatewcs/__init__.py +++ /dev/null @@ -1,396 +0,0 @@ -from __future__ import division # confidence high - -import os -import pyfits -import numpy as np -from stwcs import wcsutil -from stwcs.wcsutil import HSTWCS -from stwcs import __version__ as stwcsversion -import pywcs - -import utils, corrections, makewcs -import npol, det2im -from pytools import parseinput, fileutil -import apply_corrections - -import time -import logging -logger = logging.getLogger('stwcs.updatewcs') - -import atexit -atexit.register(logging.shutdown) - -#Note: The order of corrections is important - -__docformat__ = 'restructuredtext' - -def updatewcs(input, vacorr=True, tddcorr=True, npolcorr=True, d2imcorr=True, - checkfiles=True, wcskey=" ", wcsname=" ", clobber=False, verbose=False): - """ - - Updates HST science files with the best available calibration information. - This allows users to retrieve from the archive self contained science files - which do not require additional reference files. - - Basic WCS keywords are updated in the process and new keywords (following WCS - Paper IV and the SIP convention) as well as new extensions are added to the science files. - - - Example - ------- - >>>from stwcs import updatewcs - >>>updatewcs.updatewcs(filename) - - Dependencies - ------------ - `pytools` - `pyfits` - `pywcs` - - Parameters - ---------- - input: a python list of file names or a string (wild card characters allowed) - input files may be in fits, geis or waiver fits format - vacorr: boolean - If True, vecocity aberration correction will be applied - tddcorr: boolean - If True, time dependent distortion correction will be applied - npolcorr: boolean - If True, a Lookup table distortion will be applied - d2imcorr: boolean - If True, detector to image correction will be applied - checkfiles: boolean - If True, the format of the input files will be checked, - geis and waiver fits files will be converted to MEF format. - Default value is True for standalone mode. - wcskey: None, one character string A-Z or an empty string of length 1 - If None - the primary WCS is not archived - If an empty string - the next available wcskey is used for the archive - A-Z - use this key to archive the WCS - wcsname: a string - The name under which the primary WCS is archived after it is updated. - If an empty string (default), the name of the idctable is used as - a base. - clobber: boolean - a flag for reusing the wcskey when archiving the primary WCS - """ - if verbose == False: - logger.setLevel(100) - else: - formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s") - log_filename = 'stwcs.log' - fh = logging.FileHandler(log_filename, mode='w') - fh.setLevel(logging.DEBUG) - fh.setFormatter(formatter) - logger.addHandler(fh) - logger.setLevel(verbose) - args = "vacorr=%s, tddcorr=%s, npolcorr=%s, d2imcorr=%s, checkfiles=%s, \ - wcskey=%s, wcsname=%s, clobber=%s" % (str(vacorr), str(tddcorr), str(npolcorr), - str(d2imcorr), str(checkfiles), str(wcskey), - str(wcsname), str(clobber)) - logger.info('\n\tStarting UPDATEWCS: %s', time.asctime()) - - files = parseinput.parseinput(input)[0] - logger.info("\n\tInput files: %s, " % [i for i in files]) - logger.info("\n\tInput arguments: %s" %args) - if checkfiles: - files = checkFiles(files) - if not files: - print 'No valid input, quitting ...\n' - return - - for f in files: - acorr = apply_corrections.setCorrections(f, vacorr=vacorr, \ - tddcorr=tddcorr,npolcorr=npolcorr, d2imcorr=d2imcorr) - if 'MakeWCS' in acorr and newIDCTAB(f): - logger.warning("\n\tNew IDCTAB file detected. All current WCSs will be deleted") - cleanWCS(f) - - #restore the original WCS keywords - makecorr(f, acorr, wkey=wcskey, wname=wcsname, clobber=False) - return files - -def makecorr(fname, allowed_corr, wkey=" ", wname=" ", clobber=False): - """ - Purpose - ======= - Applies corrections to the WCS of a single file - - :Parameters: - `fname`: string - file name - `acorr`: list - list of corrections to be applied - `wkey`: None, one character string A-Z or an empty string of length 1 - If None - the primary WCS is not archived - If an empty string - the next available wcskey is used for the archive - A-Z - use this key to archive the WCS - `wname`: a string - The name under which the primary WCS is archived after it is updated. - If an empty string (default), the name of the idctable is used as - a base. - `clobber`: boolean - a flag for reusing the wcskey when archiving the primary WCS - """ - f = pyfits.open(fname, mode='update') - #restore the original WCS keywords - #wcsutil.restoreWCS(f, ext=[], wcskey='O', clobber=True) - #Determine the reference chip and create the reference HSTWCS object - nrefchip, nrefext = getNrefchip(f) - wcsutil.restoreWCS(f, nrefext, wcskey='O', clobber=True) - rwcs = HSTWCS(fobj=f, ext=nrefext) - rwcs.readModel(update=True,header=f[nrefext].header) - - wcsutil.archiveWCS(f, nrefext, 'O', wcsname='OPUS', clobber=True) - - if 'DET2IMCorr' in allowed_corr: - det2im.DET2IMCorr.updateWCS(f) - - # get a wcskey and wcsname from the first extension header - idcname = fileutil.osfn(rwcs.idctab) - key, name = getKeyName(f[1].header, wkey, wname, idcname) - - for i in range(len(f))[1:]: - extn = f[i] - - if extn.header.has_key('extname'): - extname = extn.header['extname'].lower() - if extname == 'sci': - wcsutil.restoreWCS(f, ext=i, wcskey='O', clobber=True) - sciextver = extn.header['extver'] - ref_wcs = rwcs.deepcopy() - hdr = extn.header - ext_wcs = HSTWCS(fobj=f, ext=i) - wcsutil.archiveWCS(f, ext=i, wcskey="O", wcsname="OPUS", clobber=True) - ext_wcs.readModel(update=True,header=hdr) - for c in allowed_corr: - if c != 'NPOLCorr' and c != 'DET2IMCorr': - corr_klass = corrections.__getattribute__(c) - kw2update = corr_klass.updateWCS(ext_wcs, ref_wcs) - for kw in kw2update: - hdr.update(kw, kw2update[kw]) - #if wkey is None, do not archive the primary WCS - if key is not None: - wcsutil.archiveWCS(f, ext=i, wcskey=key, wcsname=name, clobber=True) - elif extname in ['err', 'dq', 'sdq', 'samp', 'time']: - cextver = extn.header['extver'] - if cextver == sciextver: - hdr = f[('SCI',sciextver)].header - w = pywcs.WCS(hdr, f) - copyWCS(w, extn.header, key, name) - else: - continue - - if 'NPOLCorr' in allowed_corr: - kw2update = npol.NPOLCorr.updateWCS(f) - for kw in kw2update: - f[1].header.update(kw, kw2update[kw]) - # Finally record the version of the software which updated the WCS - if f[0].header.has_key('HISTORY'): - f[0].header.update(key='UPWCSVER', value=stwcsversion, - comment="Version of STWCS used to updated the WCS", before='HISTORY') - elif f[0].header.has_key('ASN_MTYP'): - f[0].header.update(key='UPWCSVER', value=stwcsversion, - comment="Version of STWCS used to updated the WCS", after='ASN_MTYP') - else: - # Find index of last non-blank card, and insert this new keyword after that card - for i in range(len(f[0].header.ascard)-1,0,-1): - if f[0].header[i].strip() != '': break - - f[0].header.update(key='UPWCSVER', value=stwcsversion, - comment="Version of STWCS used to updated the WCS",after=i) - f.close() - -def getKeyName(hdr, wkey, wname, idcname): - if wkey is not None: # archive the primary WCS - if wkey == " ": - if wname == " " : - # get the next available key and use the IDCTABLE name as WCSNAME - idcname = os.path.split(idcname)[1] - name = ''.join(['IDC_',idcname.split('_idc.fits')[0]]) - key = wcsutil.getKeyFromName(hdr, name) - if not key: - key = wcsutil.next_wcskey(hdr) - else: - #try to get a key from WCSNAME - # if not - get the next availabble key - name = wname - key = wcsutil.getKeyFromName(hdr, wname) - if not key: - key = wcsutil.next_wcskey(hdr) - else: - key = wkey - name = wname - return key, name - -def copyWCS(w, hdr, wkey, wname): - """ - This is a convenience function to copy a WCS object - to a header as a primary WCS. It is used only to copy the - WCS of the 'SCI' extension to the headers of 'ERR', 'DQ', 'SDQ', - 'TIME' or 'SAMP' extensions. - """ - hwcs = w.to_header() - - if w.wcs.has_cd(): - wcsutil.pc2cd(hwcs) - for k in hwcs.keys(): - key = k[:7] + wkey - hdr.update(key=key, value=hwcs[k]) - norient = np.rad2deg(np.arctan2(hwcs['CD1_2'],hwcs['CD2_2'])) - okey = 'ORIENT%s' % wkey - hdr.update(key=okey, value=norient) - -def getNrefchip(fobj): - """ - - Finds which FITS extension holds the reference chip. - - The reference chip has EXTNAME='SCI', can be in any extension and - is instrument specific. This functions provides mappings between - sci extensions, chips and fits extensions. - In the case of a subarray when the reference chip is missing, the - first 'SCI' extension is the reference chip. - - Parameters - ---------- - fobj: pyfits HDUList object - """ - nrefext = 1 - nrefchip = 1 - instrument = fobj[0].header['INSTRUME'] - - if instrument == 'WFPC2': - chipkw = 'DETECTOR' - extvers = [("SCI",img.header['EXTVER']) for img in - fobj[1:] if img.header['EXTNAME'].lower()=='sci'] - detectors = [img.header[chipkw] for img in fobj[1:] if - img.header['EXTNAME'].lower()=='sci'] - fitsext = [i for i in range(len(fobj))[1:] if - fobj[i].header['EXTNAME'].lower()=='sci'] - det2ext=dict(map(None, detectors,extvers)) - ext2det=dict(map(None, extvers, detectors)) - ext2fitsext=dict(map(None, extvers, fitsext)) - - if 3 not in detectors: - nrefchip = ext2det.pop(extvers[0]) - nrefext = ext2fitsext.pop(extvers[0]) - else: - nrefchip = 3 - extname = det2ext.pop(nrefchip) - nrefext = ext2fitsext.pop(extname) - - elif (instrument == 'ACS' and fobj[0].header['DETECTOR'] == 'WFC') or \ - (instrument == 'WFC3' and fobj[0].header['DETECTOR'] == 'UVIS'): - chipkw = 'CCDCHIP' - extvers = [("SCI",img.header['EXTVER']) for img in - fobj[1:] if img.header['EXTNAME'].lower()=='sci'] - detectors = [img.header[chipkw] for img in fobj[1:] if - img.header['EXTNAME'].lower()=='sci'] - fitsext = [i for i in range(len(fobj))[1:] if - fobj[i].header['EXTNAME'].lower()=='sci'] - det2ext=dict(map(None, detectors,extvers)) - ext2det=dict(map(None, extvers, detectors)) - ext2fitsext=dict(map(None, extvers, fitsext)) - - if 2 not in detectors: - nrefchip = ext2det.pop(extvers[0]) - nrefext = ext2fitsext.pop(extvers[0]) - else: - nrefchip = 2 - extname = det2ext.pop(nrefchip) - nrefext = ext2fitsext.pop(extname) - else: - for i in range(len(fobj)): - extname = fobj[i].header.get('EXTNAME', None) - if extname != None and extname.lower == 'sci': - nrefext = i - break - - return nrefchip, nrefext - -def checkFiles(input): - """ - Checks that input files are in the correct format. - Converts geis and waiver fits files to multiextension fits. - """ - from pytools.check_files import geis2mef, waiver2mef, checkFiles - logger.info("\n\tChecking files %s" % input) - removed_files = [] - newfiles = [] - if not isinstance(input, list): - input=[input] - - for file in input: - try: - imgfits,imgtype = fileutil.isFits(file) - except IOError: - logger.warning( "\n\tFile %s could not be found, removing it from the input list.\n" %file) - removed_files.append(file) - continue - # Check for existence of waiver FITS input, and quit if found. - # Or should we print a warning and continue but not use that file - if imgfits: - if imgtype == 'waiver': - newfilename = waiver2mef(file, convert_dq=True) - if newfilename == None: - logger.warning("\n\tRemoving file %s from input list - could not convert waiver to mef" %file) - removed_files.append(file) - else: - newfiles.append(newfilename) - else: - newfiles.append(file) - - # If a GEIS image is provided as input, create a new MEF file with - # a name generated using 'buildFITSName()' - # Convert the corresponding data quality file if present - if not imgfits: - newfilename = geis2mef(file, convert_dq=True) - if newfilename == None: - logger.warning("\n\tRemoving file %s from input list - could not convert geis to mef" %file) - removed_files.append(file) - else: - newfiles.append(newfilename) - if removed_files: - logger.warning('\n\tThe following files will be removed from the list of files to be processed %s' % removed_files) - #for f in removed_files: - # print f - - newfiles = checkFiles(newfiles)[0] - logger.info("\n\tThese files passed the input check and will be processed: %s" % newfiles) - return newfiles - -def newIDCTAB(fname): - #When this is called we know there's a kw IDCTAB in the header - idctab = fileutil.osfn(pyfits.getval(fname, 'IDCTAB')) - try: - #check for the presence of IDCTAB in the first extension - oldidctab = fileutil.osfn(pyfits.getval(fname, 'IDCTAB', ext=1)) - except KeyError: - return False - if idctab == oldidctab: - return False - else: - return True - -def cleanWCS(fname): - # A new IDCTAB means all previously computed WCS's are invalid - # We are deleting all of them except the original OPUS WCS.nvalidates all WCS's. - keys = wcsutil.wcskeys(pyfits.getheader(fname, ext=1)) - f = pyfits.open(fname, mode='update') - fext = range(len(f)) - for key in keys: - wcsutil.deleteWCS(fname, ext=fext,wcskey=key) - -def getCorrections(instrument): - """ - Print corrections available for an instrument - - :Parameters: - `instrument`: string, one of 'WFPC2', 'NICMOS', 'STIS', 'ACS', 'WFC3' - """ - acorr = apply_corrections.allowed_corrections[instrument] - - print "The following corrections will be performed for instrument %s\n" % instrument - for c in acorr: print c,': ' , apply_corrections.cnames[c] - diff --git a/updatewcs/apply_corrections.py b/updatewcs/apply_corrections.py deleted file mode 100644 index 881e5d1..0000000 --- a/updatewcs/apply_corrections.py +++ /dev/null @@ -1,223 +0,0 @@ -from __future__ import division # confidence high - -import os -import pyfits -import time -from pytools import fileutil -import os.path -from stwcs.wcsutil import altwcs - -import logging -logger = logging.getLogger("stwcs.updatewcs.apply_corrections") - -#Note: The order of corrections is important - -__docformat__ = 'restructuredtext' - -# A dictionary which lists the allowed corrections for each instrument. -# These are the default corrections applied also in the pipeline. - -allowed_corrections={'WFPC2': ['DET2IMCorr', 'MakeWCS','CompSIP', 'VACorr'], - 'ACS': ['DET2IMCorr', 'TDDCorr', 'MakeWCS', 'CompSIP','VACorr', 'NPOLCorr'], - 'STIS': ['MakeWCS', 'CompSIP','VACorr'], - 'NICMOS': ['MakeWCS', 'CompSIP','VACorr'], - 'WFC3': ['MakeWCS', 'CompSIP','VACorr'], - } - -cnames = {'DET2IMCorr': 'Detector to Image Correction', - 'TDDCorr': 'Time Dependent Distortion Correction', - 'MakeWCS': 'Recalculate basic WCS keywords based on the distortion model', - 'CompSIP': 'Given IDCTAB distortion model calculate the SIP coefficients', - 'VACorr': 'Velocity Aberration Correction', - 'NPOLCorr': 'Lookup Table Distortion' - } - -def setCorrections(fname, vacorr=True, tddcorr=True, npolcorr=True, d2imcorr=True): - """ - Creates a list of corrections to be applied to a file - based on user input paramters and allowed corrections - for the instrument. - """ - instrument = pyfits.getval(fname, 'INSTRUME') - # make a copy of this list ! - acorr = allowed_corrections[instrument][:] - - # Check if idctab is present on disk - # If kw IDCTAB is present in the header but the file is - # not found on disk, do not run TDDCorr, MakeCWS and CompSIP - if not foundIDCTAB(fname): - if 'TDDCorr' in acorr: acorr.remove('TDDCorr') - if 'MakeWCS' in acorr: acorr.remove('MakeWCS') - if 'CompSIP' in acorr: acorr.remove('CompSIP') - - if 'VACorr' in acorr and vacorr==False: acorr.remove('VACorr') - if 'TDDCorr' in acorr: - tddcorr = applyTDDCorr(fname, tddcorr) - if tddcorr == False: acorr.remove('TDDCorr') - - if 'NPOLCorr' in acorr: - npolcorr = applyNpolCorr(fname, npolcorr) - if npolcorr == False: acorr.remove('NPOLCorr') - if 'DET2IMCorr' in acorr: - d2imcorr = applyD2ImCorr(fname, d2imcorr) - if d2imcorr == False: acorr.remove('DET2IMCorr') - logger.info("\n\tCorrections to be applied to %s: %s " % (fname, str(acorr))) - return acorr - -def foundIDCTAB(fname): - try: - idctab = fileutil.osfn(pyfits.getval(fname, 'IDCTAB')) - except KeyError: - return False - if idctab == 'N/A' or idctab == "": - return False - if os.path.exists(idctab): - return True - else: - return False - -def applyTDDCorr(fname, utddcorr): - """ - The default value of tddcorr for all ACS images is True. - This correction will be performed if all conditions below are True: - - the user did not turn it off on the command line - - the detector is WFC - - the idc table specified in the primary header is available. - """ - instrument = pyfits.getval(fname, 'INSTRUME') - try: - detector = pyfits.getval(fname, 'DETECTOR') - except KeyError: - detector = None - try: - tddswitch = pyfits.getval(fname, 'TDDCORR') - except KeyError: - tddswitch = 'PERFORM' - - if instrument == 'ACS' and detector == 'WFC' and utddcorr == True and tddswitch == 'PERFORM': - tddcorr = True - try: - idctab = pyfits.getval(fname, 'IDCTAB') - except KeyError: - tddcorr = False - #print "***IDCTAB keyword not found - not applying TDD correction***\n" - if os.path.exists(fileutil.osfn(idctab)): - tddcorr = True - else: - tddcorr = False - #print "***IDCTAB file not found - not applying TDD correction***\n" - else: - tddcorr = False - - return tddcorr - -def applyNpolCorr(fname, unpolcorr): - """ - Determines whether non-polynomial distortion lookup tables should be added - as extensions to the science file based on the 'NPOLFILE' keyword in the - primary header and NPOLEXT kw in the first extension. - This is a default correction and will always run in the pipeline. - The file used to generate the extensions is - recorded in the NPOLEXT keyword in the first science extension. - If 'NPOLFILE' in the primary header is different from 'NPOLEXT' in the - extension header and the file exists on disk and is a 'new type' npolfile, - then the lookup tables will be updated as 'WCSDVARR' extensions. - """ - applyNPOLCorr = True - try: - # get NPOLFILE kw from primary header - fnpol0 = pyfits.getval(fname, 'NPOLFILE') - if fnpol0 == 'N/A': - return False - fnpol0 = fileutil.osfn(fnpol0) - if not fileutil.findFile(fnpol0): - msg = """\n\tKw "NPOLFILE" exists in primary header but file %s not found - Non-polynomial distortion correction will not be applied\n - """ % fnpol0 - logger.critical(msg) - applyNPOLCorr = False - return applyNPOLCorr - try: - # get NPOLEXT kw from first extension header - fnpol1 = pyfits.getval(fname, 'NPOLEXT', ext=1) - fnpol1 = fileutil.osfn(fnpol1) - if fnpol1 and fileutil.findFile(fnpol1): - if fnpol0 != fnpol1: - applyNPOLCorr = True - else: - msg = """\n\tNPOLEXT with the same value as NPOLFILE found in first extension. - NPOL correction will not be applied.""" - logger.info(msg) - applyNPOLCorr = False - else: - # npl file defined in first extension may not be found - # but if a valid kw exists in the primary header, non-polynomial - #distortion correction should be applied. - applyNPOLCorr = True - except KeyError: - # the case of "NPOLFILE" kw present in primary header but "NPOLEXT" missing - # in first extension header - applyNPOLCorr = True - except KeyError: - logger.info('\n\t"NPOLFILE" keyword not found in primary header') - applyNPOLCorr = False - return applyNPOLCorr - - if isOldStyleDGEO(fname, fnpol0): - applyNPOLCorr = False - return (applyNPOLCorr and unpolcorr) - -def isOldStyleDGEO(fname, dgname): - # checks if the file defined in a NPOLFILE kw is a full size - # (old style) image - - sci_naxis1 = pyfits.getval(fname, 'NAXIS1', ext=1) - sci_naxis2 = pyfits.getval(fname, 'NAXIS2', ext=1) - dg_naxis1 = pyfits.getval(dgname, 'NAXIS1', ext=1) - dg_naxis2 = pyfits.getval(dgname, 'NAXIS2', ext=1) - if sci_naxis1 <= dg_naxis1 or sci_naxis2 <= dg_naxis2: - msg = """\n\tOnly full size (old style) DGEO file was found.\n - Non-polynomial distortion correction will not be applied.""" - logger.critical(msg) - return True - else: - return False - -def applyD2ImCorr(fname, d2imcorr): - applyD2IMCorr = True - try: - # get D2IMFILE kw from primary header - fd2im0 = pyfits.getval(fname, 'D2IMFILE') - if fd2im0 == 'N/A': - return False - fd2im0 = fileutil.osfn(fd2im0) - if not fileutil.findFile(fd2im0): - msg = """\n\tKw D2IMFILE exists in primary header but file %s not found\n - Detector to image correction will not be applied\n""" % fd2im0 - logger.critical(msg) - print msg - applyD2IMCorr = False - return applyD2IMCorr - try: - # get D2IMEXT kw from first extension header - fd2imext = pyfits.getval(fname, 'D2IMEXT', ext=1) - fd2imext = fileutil.osfn(fd2imext) - if fd2imext and fileutil.findFile(fd2imext): - if fd2im0 != fd2imext: - applyD2IMCorr = True - else: - applyD2IMCorr = False - else: - # D2IM file defined in first extension may not be found - # but if a valid kw exists in the primary header, - # detector to image correction should be applied. - applyD2IMCorr = True - except KeyError: - # the case of D2IMFILE kw present in primary header but D2IMEXT missing - # in first extension header - applyD2IMCorr = True - except KeyError: - print 'D2IMFILE keyword not found in primary header' - applyD2IMCorr = False - return applyD2IMCorr - diff --git a/updatewcs/corrections.py b/updatewcs/corrections.py deleted file mode 100644 index 2bbdfb1..0000000 --- a/updatewcs/corrections.py +++ /dev/null @@ -1,230 +0,0 @@ -from __future__ import division # confidence high - -import datetime -import numpy as np -from numpy import linalg -from pytools import fileutil -from utils import diff_angles -import makewcs, npol - -import logging, time -logger=logging.getLogger('stwcs.updatewcs.corrections') - -MakeWCS = makewcs.MakeWCS -NPOLCorr = npol.NPOLCorr - -class TDDCorr(object): - """ - Apply time dependent distortion correction to distortion coefficients and basic - WCS keywords. This correction **must** be done before any other WCS correction. - - Parameters - ---------- - ext_wcs: HSTWCS object - An HSTWCS object to be modified - ref_wcs: HSTWCS object - A reference HSTWCS object - - Notes - ----- - Compute the ACS/WFC time dependent distortion terms as described - in [1]_ and apply the correction to the WCS of the observation. - - The model coefficients are stored in the primary header of the IDCTAB. - :math:`D_{ref}` is the reference date. The computed corrections are saved - in the science extension header as TDDALPHA and TDDBETA keywords. - - .. math:: TDDALPHA = A_{0} + {A_{1}*(obsdate - D_{ref})} - - .. math:: TDDBETA = B_{0} + B_{1}*(obsdate - D_{ref}) - - - The time dependent distortion affects the IDCTAB coefficients, and the - relative location of the two chips. Because the linear order IDCTAB - coefficients ar eused in the computatuion of the NPOL extensions, - the TDD correction affects all components of the distortion model. - - Application of TDD to the IDCTAB polynomial coefficients: - The TDD model is computed in Jay's frame, while the IDCTAB coefficients - are in the HST V2/V3 frame. The coefficients are transformed to Jay's frame, - TDD is applied and they are transformed back to the V2/V3 frame. This - correction is performed in this class. - - Application of TDD to the relative location of the two chips is - done in `makewcs`. - - References - ---------- - .. [1] Jay Anderson, "Variation of the Distortion Solution of the WFC", ACS ISR 2007-08. - - """ - def updateWCS(cls, ext_wcs, ref_wcs): - """ - - Calculates alpha and beta for ACS/WFC data. - - Writes 2 new kw to the extension header: TDDALPHA and TDDBETA - """ - logger.info("\n\tStarting TDDCorr: %s" % time.asctime()) - alpha, beta = cls.compute_alpha_beta(ext_wcs) - cls.apply_tdd2idc(ref_wcs, alpha, beta) - cls.apply_tdd2idc(ext_wcs, alpha, beta) - ext_wcs.idcmodel.refpix['TDDALPHA'] = alpha - ext_wcs.idcmodel.refpix['TDDBETA'] = beta - ref_wcs.idcmodel.refpix['TDDALPHA'] = alpha - ref_wcs.idcmodel.refpix['TDDBETA'] = beta - - newkw = {'TDDALPHA': alpha, 'TDDBETA':beta, 'OCX10':ext_wcs.idcmodel.cx[1,0], - 'OCX11':ext_wcs.idcmodel.cx[1,1],'OCY10':ext_wcs.idcmodel.cy[1,0], - 'OCY11':ext_wcs.idcmodel.cy[1,1],} - - return newkw - updateWCS = classmethod(updateWCS) - - def apply_tdd2idc(cls, hwcs, alpha, beta): - """ - Applies TDD to the idctab coefficients of a ACS/WFC observation. - This should be always the first correction. - """ - theta_v2v3 = 2.234529 - mrotp = fileutil.buildRotMatrix(theta_v2v3) - mrotn = fileutil.buildRotMatrix(-theta_v2v3) - tdd_mat = np.array([[1+(beta/2048.), alpha/2048.],[alpha/2048.,1-(beta/2048.)]],np.float64) - abmat1 = np.dot(tdd_mat, mrotn) - abmat2 = np.dot(mrotp,abmat1) - xshape, yshape = hwcs.idcmodel.cx.shape, hwcs.idcmodel.cy.shape - icxy = np.dot(abmat2,[hwcs.idcmodel.cx.ravel(), hwcs.idcmodel.cy.ravel()]) - hwcs.idcmodel.cx = icxy[0] - hwcs.idcmodel.cy = icxy[1] - hwcs.idcmodel.cx.shape = xshape - hwcs.idcmodel.cy.shape = yshape - - apply_tdd2idc = classmethod(apply_tdd2idc) - - def compute_alpha_beta(cls, ext_wcs): - """ - Compute the ACS time dependent distortion skew terms - as described in ACS ISR 07-08 by J. Anderson. - - Jay's code only computes the alpha/beta values based on a decimal year - with only 3 digits, so this line reproduces that when needed for comparison - with his results. - rday = float(('%0.3f')%rday) - - The zero-point terms account for the skew accumulated between - 2002.0 and 2004.5, when the latest IDCTAB was delivered. - alpha = 0.095 + 0.090*(rday-dday)/2.5 - beta = -0.029 - 0.030*(rday-dday)/2.5 - """ - if not isinstance(ext_wcs.date_obs,float): - year,month,day = ext_wcs.date_obs.split('-') - rdate = datetime.datetime(int(year),int(month),int(day)) - rday = float(rdate.strftime("%j"))/365.25 + rdate.year - else: - rday = ext_wcs.date_obs - - skew_coeffs = ext_wcs.idcmodel.refpix['skew_coeffs'] - if skew_coeffs is None: - # Only print out warning for post-SM4 data where this may matter - if rday > 2009.0: - err_str = "------------------------------------------------------------------------ \n" - err_str += "WARNING: the IDCTAB geometric distortion file specified in the image \n" - err_str += " header did not have the time-dependent distortion coefficients. \n" - err_str += " The pre-SM4 time-dependent skew solution will be used by default.\n" - err_str += " Please update IDCTAB with new reference file from HST archive. \n" - err_str += "------------------------------------------------------------------------ \n" - print err_str - # Using default pre-SM4 coefficients - skew_coeffs = {'TDD_A':[0.095,0.090/2.5], - 'TDD_B':[-0.029,-0.030/2.5], - 'TDD_DATE':2004.5,'TDDORDER':1} - - alpha = 0 - beta = 0 - # Compute skew terms, allowing for non-linear coefficients as well - for c in range(skew_coeffs['TDDORDER']+1): - alpha += skew_coeffs['TDD_A'][c]* np.power((rday-skew_coeffs['TDD_DATE']),c) - beta += skew_coeffs['TDD_B'][c]*np.power((rday-skew_coeffs['TDD_DATE']),c) - - return alpha,beta - compute_alpha_beta = classmethod(compute_alpha_beta) - - -class VACorr(object): - """ - Apply velocity aberation correction to WCS keywords. - - Notes - ----- - Velocity Aberration is stored in the extension header keyword 'VAFACTOR'. - The correction is applied to the CD matrix and CRVALs. - - """ - def updateWCS(cls, ext_wcs, ref_wcs): - logger.info("\n\tStarting VACorr: %s" % time.asctime()) - if ext_wcs.vafactor != 1: - ext_wcs.wcs.cd = ext_wcs.wcs.cd * ext_wcs.vafactor - crval0 = ref_wcs.wcs.crval[0] + ext_wcs.vafactor*diff_angles(ext_wcs.wcs.crval[0], - ref_wcs.wcs.crval[0]) - crval1 = ref_wcs.wcs.crval[1] + ext_wcs.vafactor*diff_angles(ext_wcs.wcs.crval[1], - ref_wcs.wcs.crval[1]) - crval = np.array([crval0,crval1]) - ext_wcs.wcs.crval = crval - ext_wcs.wcs.set() - else: - pass - kw2update={'CD1_1': ext_wcs.wcs.cd[0,0], 'CD1_2':ext_wcs.wcs.cd[0,1], - 'CD2_1':ext_wcs.wcs.cd[1,0], 'CD2_2':ext_wcs.wcs.cd[1,1], - 'CRVAL1':ext_wcs.wcs.crval[0], 'CRVAL2':ext_wcs.wcs.crval[1]} - return kw2update - - updateWCS = classmethod(updateWCS) - - -class CompSIP(object): - """ - Compute Simple Imaging Polynomial (SIP) coefficients as defined in [2]_ - from IDC table coefficients. - - This class transforms the TDD corrected IDCTAB coefficients into SIP format. - It also applies a binning factor to the coefficients if the observation was - binned. - - References - ---------- - .. [2] David Shupe, et al, "The SIP Convention of representing Distortion - in FITS Image headers", Astronomical Data Analysis Software And Systems, ASP - Conference Series, Vol. 347, 2005 - - """ - def updateWCS(cls, ext_wcs, ref_wcs): - logger.info("\n\tStarting CompSIP: %s" %time.asctime()) - kw2update = {} - order = ext_wcs.idcmodel.norder - kw2update['A_ORDER'] = order - kw2update['B_ORDER'] = order - pscale = ext_wcs.idcmodel.refpix['PSCALE'] - - cx = ext_wcs.idcmodel.cx - cy = ext_wcs.idcmodel.cy - - matr = np.array([[cx[1,1],cx[1,0]], [cy[1,1],cy[1,0]]], dtype=np.float64) - imatr = linalg.inv(matr) - akeys1 = np.zeros((order+1,order+1), dtype=np.float64) - bkeys1 = np.zeros((order+1,order+1), dtype=np.float64) - for n in range(order+1): - for m in range(order+1): - if n >= m and n>=2: - idcval = np.array([[cx[n,m]],[cy[n,m]]]) - sipval = np.dot(imatr, idcval) - akeys1[m,n-m] = sipval[0] - bkeys1[m,n-m] = sipval[1] - Akey="A_%d_%d" % (m,n-m) - Bkey="B_%d_%d" % (m,n-m) - kw2update[Akey] = sipval[0,0] * ext_wcs.binned - kw2update[Bkey] = sipval[1,0] * ext_wcs.binned - kw2update['CTYPE1'] = 'RA---TAN-SIP' - kw2update['CTYPE2'] = 'DEC--TAN-SIP' - return kw2update - - updateWCS = classmethod(updateWCS) - - diff --git a/updatewcs/det2im.py b/updatewcs/det2im.py deleted file mode 100644 index b59ca17..0000000 --- a/updatewcs/det2im.py +++ /dev/null @@ -1,200 +0,0 @@ -from __future__ import division # confidence high - -import time -import pyfits -from pytools import fileutil -import utils - -import logging -logger = logging.getLogger('stwcs.updatewcs.Det2IM') - -class DET2IMCorr(object): - """ - Stores a small correction to the detector coordinates as a d2imarr - extension in the science file. - - Notes - ----- - For the case of ACS/WFC every 68th column is wider than the rest. - To compensate for this a small correction needs to be applied to the - detector coordinates. We call this a detector to image transformation. - The so obtained image coordinates are the input to all other distortion - corrections. The correction is originally stored in an external - reference file pointed to by 'D2IMFILE' keyword in the primary header. - This class attaches the correction array as an extension to the science - file with extname = `d2imarr`. - - Other keywords used in this correction are: - - `AXISCORR`: integer (1 or 2) - axis to which the detector to image - correction is applied - - `D2IMEXT`: string = name of reference file which was used to create - the lookup table extension - - `D2IMERR`: float, optional - maximum value of the correction - - """ - def updateWCS(cls, fobj): - """ - Parameters - ---------- - fobj: pyfits object - Science file, for which a detector to image correction - is available - - Notes - ----- - Uses the file pointed to in the primary header keyword 'D2IMFILE' - to create an extension with a detector to image correction. - """ - logger.info("\n\tStarting Det2IM Correction: %s" % time.asctime()) - try: - assert isinstance(fobj, pyfits.HDUList) - except AssertionError: - logger.exception('\n\tInput must be a pyfits.HDUList object') - raise - - d2imfile = fileutil.osfn(fobj[0].header['D2IMFILE']) - axiscorr = cls.getAxisCorr(d2imfile) - d2imerr = pyfits.getdata(d2imfile, ext=1).max() - if axiscorr == None: - new_kw = {} - else: - new_kw = {'D2IMEXT': d2imfile, 'AXISCORR': axiscorr, 'D2IMERR': d2imerr} - cls.applyDet2ImCorr(fobj,axiscorr) - cls.updatehdr(fobj, new_kw) - - updateWCS = classmethod(updateWCS) - - def getAxisCorr(cls, refname): - try: - direction = pyfits.getval(refname, ext=1, key='EXTNAME') - if direction == 'DX': return 1 - elif direction == 'DY': return 2 - else: - logger.warning('\n\tDET2IM correction expects the reference file to have \ - an EXTNAME keyword of value "DX" or "DY", EXTNAMe %s detected' % direction) - return None - except KeyError: - logger.exception("\n\tD2IMFILE %s is missing EXTNAME keyword. Unable to determine axis \ - to which to apply the correction." % refname) - direction = None - return direction - getAxisCorr = classmethod(getAxisCorr) - - def applyDet2ImCorr(cls,fobj, axiscorr): - binned = utils.getBinning(fobj) - hdu = cls.createDgeoHDU(fobj, axiscorr, binned) - d2imarr_ind = cls.getD2imIndex(fobj) - if d2imarr_ind: - fobj[d2imarr_ind] = hdu - else: - fobj.append(hdu) - applyDet2ImCorr = classmethod(applyDet2ImCorr) - - def getD2imIndex(cls,fobj): - index = None - for e in range(len(fobj)): - try: - ename = fobj[e].header['EXTNAME'] - except KeyError: - continue - if ename == 'D2IMARR': - index = e - return index - getD2imIndex = classmethod(getD2imIndex) - - def createDgeoHDU(cls, fobj, axiscorr, binned=1): - d2imfile = fileutil.osfn(fobj[0].header['D2IMFILE']) - d2im_data = pyfits.getdata(d2imfile, ext=1) - sci_hdr = fobj['sci',1].header - d2im_hdr = cls.createDet2ImHdr(fobj, binned) - hdu = pyfits.ImageHDU(header=d2im_hdr, data=d2im_data) - - return hdu - - createDgeoHDU = classmethod(createDgeoHDU) - - def createDet2ImHdr(cls, fobj, binned=1): - """ - Creates a header for the D2IMARR extension based on the - reference file recorded in D2IMFILE keyword in the primary header. - fobj - the science file - - """ - d2imfile = fileutil.osfn(fobj[0].header['D2IMFILE']) - axiscorr = cls.getAxisCorr(d2imfile) - sci_hdr = fobj[1].header - data_shape = pyfits.getdata(d2imfile, ext=1).shape - naxis = pyfits.getval(d2imfile, ext=1, key='NAXIS') - - kw = { 'NAXIS': 'Size of the axis', - 'CRPIX': 'Coordinate system reference pixel', - 'CRVAL': 'Coordinate system value at reference pixel', - 'CDELT': 'Coordinate increment along axis'} - - kw_comm1 = {} - kw_val1 = {} - for key in kw.keys(): - for i in range(1, naxis+1): - si = str(i) - kw_comm1[key+si] = kw[key] - - for i in range(1, naxis+1): - si = str(i) - kw_val1['NAXIS'+si] = data_shape[i-1] - kw_val1['CRPIX'+si] = data_shape[i-1]/2. - kw_val1['CDELT'+si] = 1./binned - kw_val1['CRVAL'+si] = (sci_hdr.get('NAXIS'+si, 1)/2. + \ - sci_hdr.get('LTV'+si, 0.)) / binned - - - kw_comm0 = {'XTENSION': 'Image extension', - 'BITPIX': 'IEEE floating point', - 'NAXIS': 'Number of axes', - 'EXTNAME': 'WCS distortion array', - 'EXTVER': 'Distortion array version number', - 'PCOUNT': 'Special data area of size 0', - 'GCOUNT': 'One data group', - 'AXISCORR': 'Direction in which the det2im correction is applied'} - - kw_val0 = { 'XTENSION': 'IMAGE', - 'BITPIX': -32, - 'NAXIS': naxis, - 'EXTNAME': 'D2IMARR', - 'EXTVER': 1, - 'PCOUNT': 0, - 'GCOUNT': 1, - 'AXISCORR': axiscorr - } - - - cdl = pyfits.CardList() - for key in kw_comm0.keys(): - cdl.append(pyfits.Card(key=key, value=kw_val0[key], comment=kw_comm0[key])) - for key in kw_comm1.keys(): - cdl.append(pyfits.Card(key=key, value=kw_val1[key], comment=kw_comm1[key])) - - hdr = pyfits.Header(cards=cdl) - return hdr - - createDet2ImHdr = classmethod(createDet2ImHdr) - - def updatehdr(cls, fobj, kwdict): - """ - Update extension headers to keep record of the files used for the - detector to image correction. - """ - for ext in fobj: - try: - extname = ext.header['EXTNAME'].lower() - except KeyError: - continue - if extname == 'sci': - for kw in kwdict: - ext.header.update(kw, kwdict[kw]) - else: - continue - updatehdr = classmethod(updatehdr) - diff --git a/updatewcs/makewcs.py b/updatewcs/makewcs.py deleted file mode 100644 index f23da7e..0000000 --- a/updatewcs/makewcs.py +++ /dev/null @@ -1,251 +0,0 @@ -from __future__ import division # confidence high - -from stwcs import DEGTORAD, RADTODEG -import numpy as np -from math import sin, sqrt, pow, cos, asin, atan2,pi -import utils -from pytools import fileutil - -import logging, time -logger = logging.getLogger("stwcs.updatewcs.makewcs") - -class MakeWCS(object): - """ - Recompute basic WCS keywords based on PA_V3 and distortion model. - - Notes - ----- - - Compute the reference chip WCS: - - -- CRVAL: transform the model XREF/YREF to the sky - -- PA_V3 is calculated at the target position and adjusted - for each chip orientation - -- CD: PA_V3 and the model scale are used to cnstruct a CD matrix - - - Compute the second chip WCS: - - -- CRVAL: - the distance between the zero points of the two - chip models on the sky - -- CD matrix: first order coefficients are added to the components - of this distance and transfered on the sky. The difference - between CRVAL and these vectors is the new CD matrix for each chip. - -- CRPIX: chip's model zero point in pixel space (XREF/YREF) - - - Time dependent distortion correction is applied to both chips' V2/V3 values. - - """ - tdd_xyref = {1: [2048, 3072], 2:[2048, 1024]} - def updateWCS(cls, ext_wcs, ref_wcs): - """ - recomputes the basic WCS kw - """ - logger.info("\n\tStarting MakeWCS: %s" % time.asctime()) - ltvoff, offshift = cls.getOffsets(ext_wcs) - - v23_corr = cls.zero_point_corr(ext_wcs) - rv23_corr = cls.zero_point_corr(ref_wcs) - - cls.uprefwcs(ext_wcs, ref_wcs, rv23_corr, ltvoff, offshift) - cls.upextwcs(ext_wcs, ref_wcs, v23_corr, rv23_corr, ltvoff, offshift) - - kw2update = {'CD1_1': ext_wcs.wcs.cd[0,0], - 'CD1_2': ext_wcs.wcs.cd[0,1], - 'CD2_1': ext_wcs.wcs.cd[1,0], - 'CD2_2': ext_wcs.wcs.cd[1,1], - 'CRVAL1': ext_wcs.wcs.crval[0], - 'CRVAL2': ext_wcs.wcs.crval[1], - 'CRPIX1': ext_wcs.wcs.crpix[0], - 'CRPIX2': ext_wcs.wcs.crpix[1], - 'IDCTAB': ext_wcs.idctab, - } - return kw2update - - updateWCS = classmethod(updateWCS) - - def upextwcs(cls, ext_wcs, ref_wcs, v23_corr, rv23_corr, loff, offsh): - """ - updates an extension wcs - """ - ltvoffx, ltvoffy = loff[0], loff[1] - offshiftx, offshifty = offsh[0], offsh[1] - ltv1 = ext_wcs.ltv1 - ltv2 = ext_wcs.ltv2 - if ltv1 != 0. or ltv2 != 0.: - offsetx = ext_wcs.wcs.crpix[0] - ltv1 - ext_wcs.idcmodel.refpix['XREF'] - offsety = ext_wcs.wcs.crpix[1] - ltv2 - ext_wcs.idcmodel.refpix['YREF'] - fx,fy = ext_wcs.idcmodel.shift(ext_wcs.idcmodel.cx,ext_wcs.idcmodel.cy,offsetx,offsety) - else: - fx, fy = ext_wcs.idcmodel.cx, ext_wcs.idcmodel.cy - - tddscale = (ref_wcs.pscale/fx[1,1]) - v2 = ext_wcs.idcmodel.refpix['V2REF'] + v23_corr[0,0] * tddscale - v3 = ext_wcs.idcmodel.refpix['V3REF'] - v23_corr[1,0] * tddscale - v2ref = ref_wcs.idcmodel.refpix['V2REF'] + rv23_corr[0,0] * tddscale - v3ref = ref_wcs.idcmodel.refpix['V3REF'] - rv23_corr[1,0] * tddscale - - R_scale = ref_wcs.idcmodel.refpix['PSCALE']/3600.0 - off = sqrt((v2-v2ref)**2 + (v3-v3ref)**2)/(R_scale*3600.0) - - if v3 == v3ref: - theta=0.0 - else: - theta = atan2(ext_wcs.parity[0][0]*(v2-v2ref), ext_wcs.parity[1][1]*(v3-v3ref)) - - if ref_wcs.idcmodel.refpix['THETA']: theta += ref_wcs.idcmodel.refpix['THETA']*pi/180.0 - - dX=(off*sin(theta)) + offshiftx - dY=(off*cos(theta)) + offshifty - - px = np.array([[dX,dY]]) - newcrval = ref_wcs.wcs.p2s(px, 1)['world'][0] - newcrpix = np.array([ext_wcs.idcmodel.refpix['XREF'] + ltvoffx, - ext_wcs.idcmodel.refpix['YREF'] + ltvoffy]) - ext_wcs.wcs.crval = newcrval - ext_wcs.wcs.crpix = newcrpix - ext_wcs.wcs.set() - - # Create a small vector, in reference image pixel scale - delmat = np.array([[fx[1,1], fy[1,1]], \ - [fx[1,0], fy[1,0]]]) / R_scale/3600. - - # Account for subarray offset - # Angle of chip relative to chip - if ext_wcs.idcmodel.refpix['THETA']: - dtheta = ext_wcs.idcmodel.refpix['THETA'] - ref_wcs.idcmodel.refpix['THETA'] - else: - dtheta = 0.0 - - rrmat = fileutil.buildRotMatrix(dtheta) - # Rotate the vectors - dxy = np.dot(delmat, rrmat) - wc = ref_wcs.wcs.p2s((px + dxy), 1)['world'] - - # Calculate the new CDs and convert to degrees - cd11 = utils.diff_angles(wc[0,0],newcrval[0])*cos(newcrval[1]*pi/180.0) - cd12 = utils.diff_angles(wc[1,0],newcrval[0])*cos(newcrval[1]*pi/180.0) - cd21 = utils.diff_angles(wc[0,1],newcrval[1]) - cd22 = utils.diff_angles(wc[1,1],newcrval[1]) - cd = np.array([[cd11, cd12], [cd21, cd22]]) - ext_wcs.wcs.cd = cd - ext_wcs.wcs.set() - - upextwcs = classmethod(upextwcs) - - def uprefwcs(cls, ext_wcs, ref_wcs, rv23_corr_tdd, loff, offsh): - """ - Updates the reference chip - """ - ltvoffx, ltvoffy = loff[0], loff[1] - offshift = offsh - dec = ref_wcs.wcs.crval[1] - tddscale = (ref_wcs.pscale/ext_wcs.idcmodel.cx[1,1]) - rv23 = [ref_wcs.idcmodel.refpix['V2REF'] + (rv23_corr_tdd[0,0] *tddscale), - ref_wcs.idcmodel.refpix['V3REF'] - (rv23_corr_tdd[1,0] * tddscale)] - # Get an approximate reference position on the sky - rref = np.array([[ref_wcs.idcmodel.refpix['XREF']+ltvoffx , - ref_wcs.idcmodel.refpix['YREF']+ltvoffy]]) - - crval = ref_wcs.wcs.p2s(rref, 1)['world'][0] - # Convert the PA_V3 orientation to the orientation at the aperture - # This is for the reference chip only - we use this for the - # reference tangent plane definition - # It has the same orientation as the reference chip - pv = troll(ext_wcs.pav3,dec,rv23[0], rv23[1]) - # Add the chip rotation angle - if ref_wcs.idcmodel.refpix['THETA']: - pv += ref_wcs.idcmodel.refpix['THETA'] - - - # Set values for the rest of the reference WCS - ref_wcs.wcs.crval = crval - ref_wcs.wcs.crpix = np.array([0.0,0.0])+offsh - parity = ref_wcs.parity - R_scale = ref_wcs.idcmodel.refpix['PSCALE']/3600.0 - cd11 = parity[0][0] * cos(pv*pi/180.0)*R_scale - cd12 = parity[0][0] * -sin(pv*pi/180.0)*R_scale - cd21 = parity[1][1] * sin(pv*pi/180.0)*R_scale - cd22 = parity[1][1] * cos(pv*pi/180.0)*R_scale - - rcd = np.array([[cd11, cd12], [cd21, cd22]]) - ref_wcs.wcs.cd = rcd - ref_wcs.wcs.set() - - uprefwcs = classmethod(uprefwcs) - - def zero_point_corr(cls,hwcs): - try: - alpha = hwcs.idcmodel.refpix['TDDALPHA'] - beta = hwcs.idcmodel.refpix['TDDBETA'] - except KeyError: - alpha = 0.0 - beta = 0.0 - v23_corr = np.array([[0.],[0.]]) - logger.debug("\n\tTDD Zero point correction for chip %s defaulted to: %s" % (hwcs.chip, v23_corr)) - return v23_corr - - tdd = np.array([[beta, alpha], [alpha, -beta]]) - mrotp = fileutil.buildRotMatrix(2.234529)/2048. - xy0 = np.array([[cls.tdd_xyref[hwcs.chip][0]-2048.], [cls.tdd_xyref[hwcs.chip][1]-2048.]]) - v23_corr = np.dot(mrotp,np.dot(tdd,xy0)) * 0.05 - logger.debug("\n\tTDD Zero point correction for chip %s: %s" % (hwcs.chip, v23_corr)) - return v23_corr - - zero_point_corr = classmethod(zero_point_corr) - - def getOffsets(cls, ext_wcs): - ltv1 = ext_wcs.ltv1 - ltv2 = ext_wcs.ltv2 - - offsetx = ext_wcs.wcs.crpix[0] - ltv1 - ext_wcs.idcmodel.refpix['XREF'] - offsety = ext_wcs.wcs.crpix[1] - ltv2 - ext_wcs.idcmodel.refpix['YREF'] - - shiftx = ext_wcs.idcmodel.refpix['XREF'] + ltv1 - shifty = ext_wcs.idcmodel.refpix['YREF'] + ltv2 - if ltv1 != 0. or ltv2 != 0.: - ltvoffx = ltv1 + offsetx - ltvoffy = ltv2 + offsety - offshiftx = offsetx + shiftx - offshifty = offsety + shifty - else: - ltvoffx = 0. - ltvoffy = 0. - offshiftx = 0. - offshifty = 0. - - ltvoff = np.array([ltvoffx, ltvoffy]) - offshift = np.array([offshiftx, offshifty]) - return ltvoff, offshift - - getOffsets = classmethod(getOffsets) - - -def troll(roll, dec, v2, v3): - """ Computes the roll angle at the target position based on: - the roll angle at the V1 axis(roll), - the dec of the target(dec), and - the V2/V3 position of the aperture (v2,v3) in arcseconds. - - Based on algorithm provided by Colin Cox and used in - Generic Conversion at STScI. - """ - # Convert all angles to radians - _roll = DEGTORAD(roll) - _dec = DEGTORAD(dec) - _v2 = DEGTORAD(v2 / 3600.) - _v3 = DEGTORAD(v3 / 3600.) - - # compute components - sin_rho = sqrt((pow(sin(_v2),2)+pow(sin(_v3),2)) - (pow(sin(_v2),2)*pow(sin(_v3),2))) - rho = asin(sin_rho) - beta = asin(sin(_v3)/sin_rho) - if _v2 < 0: beta = pi - beta - gamma = asin(sin(_v2)/sin_rho) - if _v3 < 0: gamma = pi - gamma - A = pi/2. + _roll - beta - B = atan2( sin(A)*cos(_dec), (sin(_dec)*sin_rho - cos(_dec)*cos(rho)*cos(A))) - - # compute final value - troll = RADTODEG(pi - (gamma+B)) - - return troll - diff --git a/updatewcs/npol.py b/updatewcs/npol.py deleted file mode 100644 index 62c44bd..0000000 --- a/updatewcs/npol.py +++ /dev/null @@ -1,319 +0,0 @@ -from __future__ import division # confidence high - -import pyfits -from pytools import fileutil -import utils -import numpy as np - -import logging, time -logger = logging.getLogger('stwcs.updatewcs.npol') - -class NPOLCorr(object): - """ - Defines a Lookup table prior distortion correction as per WCS paper IV. - It uses a reference file defined by the NPOLFILE (suffix 'NPL') keyword - in the primary header. - - Notes - ----- - - Using extensions in the reference file create a WCSDVARR extensions - and add them to the science file. - - Add record-valued keywords to the science extension header to describe - the lookup tables. - - Add a keyword 'NPOLEXT' to the science extension header to store - the name of the reference file used to create the WCSDVARR extensions. - - If WCSDVARR extensions exist and `NPOLFILE` is different from `NPOLEXT`, - a subsequent update will overwrite the existing extensions. - If WCSDVARR extensions were not found in the science file, they will be added. - - It is assumed that the NPL reference files were created to work with IDC tables - but will be applied with SIP coefficients. A transformation is applied to correct - for the fact that the lookup tables will be applied before the first order coefficients - which are in the CD matrix when the SIP convention is used. - """ - - def updateWCS(cls, fobj): - """ - Parameters - ---------- - fobj: pyfits object - Science file, for which a distortion correction in a NPOLFILE is available - - """ - logger.info("\n\tStarting CompSIP: %s" %time.asctime()) - try: - assert isinstance(fobj, pyfits.HDUList) - except AssertionError: - logger.exception('\n\tInput must be a pyfits.HDUList object') - raise - - cls.applyNPOLCorr(fobj) - nplfile = fobj[0].header['NPOLFILE'] - - new_kw = {'NPOLEXT': nplfile} - return new_kw - - updateWCS = classmethod(updateWCS) - - def applyNPOLCorr(cls, fobj): - """ - For each science extension in a pyfits file object: - - create a WCSDVARR extension - - update science header - - add/update NPOLEXT keyword - """ - nplfile = fileutil.osfn(fobj[0].header['NPOLFILE']) - # Map WCSDVARR EXTVER numbers to extension numbers - wcsdvarr_ind = cls.getWCSIndex(fobj) - for ext in fobj: - try: - extname = ext.header['EXTNAME'].lower() - except KeyError: - continue - if extname == 'sci': - extversion = ext.header['EXTVER'] - ccdchip = cls.get_ccdchip(fobj, extname='SCI', extver=extversion) - binned = utils.getBinning(fobj, extversion) - header = ext.header - # get the data arrays from the reference file and transform them for use with SIP - dx,dy = cls.getData(nplfile, ccdchip) - idccoeffs = cls.getIDCCoeffs(header) - - if idccoeffs != None: - dx, dy = cls.transformData(dx,dy, idccoeffs) - - # Determine EXTVER for the WCSDVARR extension from the NPL file (EXTNAME, EXTVER) kw. - # This is used to populate DPj.EXTVER kw - wcsdvarr_x_version = 2 * extversion -1 - wcsdvarr_y_version = 2 * extversion - - for ename in zip(['DX', 'DY'], [wcsdvarr_x_version,wcsdvarr_y_version],[dx, dy]): - cls.addSciExtKw(header, wdvarr_ver=ename[1], npol_extname=ename[0]) - hdu = cls.createNpolHDU(header, npolfile=nplfile, \ - wdvarr_ver=ename[1], npl_extname=ename[0], data=ename[2],ccdchip=ccdchip, binned=binned) - if wcsdvarr_ind: - fobj[wcsdvarr_ind[ename[1]]] = hdu - else: - fobj.append(hdu) - - - applyNPOLCorr = classmethod(applyNPOLCorr) - - def getWCSIndex(cls, fobj): - - """ - If fobj has WCSDVARR extensions: - returns a mapping of their EXTVER kw to file object extension numbers - if fobj does not have WCSDVARR extensions: - an empty dictionary is returned - """ - wcsd = {} - for e in range(len(fobj)): - try: - ename = fobj[e].header['EXTNAME'] - except KeyError: - continue - if ename == 'WCSDVARR': - wcsd[fobj[e].header['EXTVER']] = e - logger.debug("A map of WSCDVARR externsions %s" % wcsd) - return wcsd - - getWCSIndex = classmethod(getWCSIndex) - - def addSciExtKw(cls, hdr, wdvarr_ver=None, npol_extname=None): - """ - Adds kw to sci extension to define WCSDVARR lookup table extensions - - """ - if npol_extname =='DX': - j=1 - else: - j=2 - - cperror = 'CPERROR%s' %j - cpdis = 'CPDIS%s' %j - dpext = 'DP%s.' %j + 'EXTVER' - dpnaxes = 'DP%s.' %j +'NAXES' - dpaxis1 = 'DP%s.' %j+'AXIS.1' - dpaxis2 = 'DP%s.' %j+'AXIS.2' - keys = [cperror, cpdis, dpext, dpnaxes, dpaxis1, dpaxis2] - values = {cperror: 0.0, cpdis: 'Lookup', dpext: wdvarr_ver, dpnaxes: 2, - dpaxis1: 1, dpaxis2: 2} - - comments = {cperror: 'Maximum error of NPOL correction for axis %s' % j, - cpdis: 'Prior distortion funcion type', - dpext: 'Version number of WCSDVARR extension containing lookup distortion table', - dpnaxes: 'Number of independent variables in distortion function', - dpaxis1: 'Axis number of the jth independent variable in a distortion function', - dpaxis2: 'Axis number of the jth independent variable in a distortion function' - } - - for key in keys: - hdr.update(key=key, value=values[key], comment=comments[key], before='HISTORY') - - addSciExtKw = classmethod(addSciExtKw) - - def getData(cls,nplfile, ccdchip): - """ - Get the data arrays from the reference NPOL files - Make sure 'CCDCHIP' in the npolfile matches "CCDCHIP' in the science file. - """ - npl = pyfits.open(nplfile) - for ext in npl: - nplextname = ext.header.get('EXTNAME',"") - nplccdchip = ext.header.get('CCDCHIP',1) - if nplextname == 'DX' and nplccdchip == ccdchip: - xdata = ext.data.copy() - continue - elif nplextname == 'DY' and nplccdchip == ccdchip: - ydata = ext.data.copy() - continue - else: - continue - npl.close() - return xdata, ydata - getData = classmethod(getData) - - def transformData(cls, dx, dy, coeffs): - """ - Transform the NPOL data arrays for use with SIP - """ - ndx, ndy = np.dot(coeffs, [dx.ravel(), dy.ravel()]) - ndx.shape = dx.shape - ndy.shape=dy.shape - return ndx, ndy - - transformData = classmethod(transformData) - - def getIDCCoeffs(cls, header): - """ - Return a matrix of the scaled first order IDC coefficients. - """ - try: - ocx10 = header['OCX10'] - ocx11 = header['OCX11'] - ocy10 = header['OCY10'] - ocy11 = header['OCY11'] - coeffs = np.array([[ocx11, ocx10], [ocy11,ocy10]], dtype=np.float32) - except KeyError: - logger.exception('\n\tFirst order IDCTAB coefficients are not available. \n\ - Cannot convert SIP to IDC coefficients.') - return None - try: - idcscale = header['IDCSCALE'] - except KeyError: - logger.exception("IDCSCALE not found in header - setting it to 1.") - idcscale = 1 - - return np.linalg.inv(coeffs/idcscale) - - getIDCCoeffs = classmethod(getIDCCoeffs) - - def createNpolHDU(cls, sciheader, npolfile=None, wdvarr_ver=1, npl_extname=None,data = None, ccdchip=1, binned=1): - """ - Creates an HDU to be added to the file object. - """ - hdr = cls.createNpolHdr(sciheader, npolfile=npolfile, wdvarr_ver=wdvarr_ver, npl_extname=npl_extname, ccdchip=ccdchip, binned=binned) - hdu=pyfits.ImageHDU(header=hdr, data=data) - return hdu - - createNpolHDU = classmethod(createNpolHDU) - - def createNpolHdr(cls, sciheader, npolfile, wdvarr_ver, npl_extname, ccdchip, binned): - """ - Creates a header for the WCSDVARR extension based on the NPOL reference file - and sci extension header. The goal is to always work in image coordinates - (also for subarrays and binned images. The WCS for the WCSDVARR extension - i ssuch that a full size npol table is created and then shifted or scaled - if the science image is a subarray or binned image. - """ - npl = pyfits.open(npolfile) - for ext in npl: - try: - nplextname = ext.header['EXTNAME'] - nplextver = ext.header['EXTVER'] - except KeyError: - continue - nplccdchip = cls.get_ccdchip(npl, extname=nplextname, extver=nplextver) - if nplextname == npl_extname and nplccdchip == ccdchip: - npol_header = ext.header - break - else: - continue - npl.close() - - naxis = pyfits.getval(npolfile, ext=1, key='NAXIS') - ccdchip = nplextname #npol_header['CCDCHIP'] - - kw = { 'NAXIS': 'Size of the axis', - 'CDELT': 'Coordinate increment along axis', - 'CRPIX': 'Coordinate system reference pixel', - 'CRVAL': 'Coordinate system value at reference pixel', - } - - kw_comm1 = {} - kw_val1 = {} - for key in kw.keys(): - for i in range(1, naxis+1): - si = str(i) - kw_comm1[key+si] = kw[key] - - for i in range(1, naxis+1): - si = str(i) - kw_val1['NAXIS'+si] = npol_header.get('NAXIS'+si) - kw_val1['CDELT'+si] = npol_header.get('CDELT'+si, 1.0) - kw_val1['CRPIX'+si] = npol_header.get('CRPIX'+si, 0.0) - kw_val1['CRVAL'+si] = npol_header.get('CRVAL'+si, 0.0) - - kw_comm0 = {'XTENSION': 'Image extension', - 'BITPIX': 'IEEE floating point', - 'NAXIS': 'Number of axes', - 'EXTNAME': 'WCS distortion array', - 'EXTVER': 'Distortion array version number', - 'PCOUNT': 'Special data area of size 0', - 'GCOUNT': 'One data group', - } - - kw_val0 = { 'XTENSION': 'IMAGE', - 'BITPIX': -32, - 'NAXIS': naxis, - 'EXTNAME': 'WCSDVARR', - 'EXTVER': wdvarr_ver, - 'PCOUNT': 0, - 'GCOUNT': 1, - 'CCDCHIP': ccdchip, - } - - cdl = pyfits.CardList() - for key in kw_comm0.keys(): - cdl.append(pyfits.Card(key=key, value=kw_val0[key], comment=kw_comm0[key])) - for key in kw_comm1.keys(): - cdl.append(pyfits.Card(key=key, value=kw_val1[key], comment=kw_comm1[key])) - - - hdr = pyfits.Header(cards=cdl) - - return hdr - - createNpolHdr = classmethod(createNpolHdr) - - def get_ccdchip(cls, fobj, extname, extver): - """ - Given a science file or npol file determine CCDCHIP - """ - ccdchip = 1 - if fobj[0].header['INSTRUME'] == 'ACS' and fobj[0].header['DETECTOR'] == 'WFC': - ccdchip = fobj[extname, extver].header['CCDCHIP'] - elif fobj[0].header['INSTRUME'] == 'WFC3' and fobj[0].header['DETECTOR'] == 'UVIS': - ccdchip = fobj[extname, extver].header['CCDCHIP'] - elif fobj[0].header['INSTRUME'] == 'WFPC2': - ccdchip = fobj[extname, extver].header['DETECTOR'] - elif fobj[0].header['INSTRUME'] == 'STIS': - ccdchip = fobj[extname, extver].header['DETECTOR'] - elif fobj[0].header['INSTRUME'] == 'NICMOS': - ccdchip = fobj[extname, extver].header['CAMERA'] - return ccdchip - - get_ccdchip = classmethod(get_ccdchip) -
\ No newline at end of file diff --git a/updatewcs/utils.py b/updatewcs/utils.py deleted file mode 100644 index 29ba5f3..0000000 --- a/updatewcs/utils.py +++ /dev/null @@ -1,28 +0,0 @@ -from __future__ import division # confidence high - -def diff_angles(a,b): - """ - Perform angle subtraction a-b taking into account - small-angle differences across 360degree line. - """ - - diff = a - b - - if diff > 180.0: - diff -= 360.0 - - if diff < -180.0: - diff += 360.0 - - return diff - -def getBinning(fobj, extver=1): - # Return the binning factor - binned = 1 - if fobj[0].header['INSTRUME'] == 'WFPC2': - mode = fobj[0].header.get('MODE', "") - if mode == 'AREA': binned = 2 - else: - binned = fobj['SCI', extver].header.get('BINAXIS',1) - return binned - |