from __future__ import division # confidence high import pyfits from pytools import fileutil import utils import numpy as np class DGEOCorr(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 extension and add it to the file object. - Add record-valued keywords which describe the lookup tables to the science extension header - Add a keyword 'NPOLEXT' to the science extension header, whose value is the reference file used to create the WCSDVARR extension If WCSDVARR extensions exist, subsequent updates will overwrite them. If not, they will be added to the file object. 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 """ assert isinstance(fobj, pyfits.HDUList) 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 DGEOEXT 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 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 dgeo 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 DGEO files Make sure 'CCDCHIP' in the dgeo file 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 DGEO 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: print 'First order IDCTAB coefficients are not available.\n' print 'Cannot convert SIP to IDC coefficients.\n' return None try: idcscale = header['IDCSCALE'] except KeyError: 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 DGEO 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 dgeo 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: #for i in range(len(dgf)): try: nplextname = ext.header['EXTNAME'] nplextver = ext.header['EXTVER'] except KeyError: continue #dgccdchip = ext.header.get('CCDCHIP', 0) 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 #dgeo_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 dgeo 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)