diff options
25 files changed, 307 insertions, 330 deletions
diff --git a/lib/stwcs/distortion/coeff_converter.py b/lib/stwcs/distortion/coeff_converter.py index 6d9a754..aace72f 100644 --- a/lib/stwcs/distortion/coeff_converter.py +++ b/lib/stwcs/distortion/coeff_converter.py @@ -1,18 +1,18 @@ from __future__ import division # confidence high import numpy as np -from astropy.io import fits as pyfits -#import pywcs +from astropy.io import fits from astropy import wcs as pywcs def sip2idc(wcs): """ Converts SIP style coefficients to IDCTAB coefficients. - :Parameters: - `wcs`: pyfits.Header or pywcs.WCS object + Parameters + ---------- + wcs : `astropy.io.fits.Header` or `astropy.wcs.WCS` object """ - if isinstance(wcs,pyfits.Header): + if isinstance(wcs, fits.Header): ocx10 = wcs.get('OCX10', None) ocx11 = wcs.get('OCX11', None) ocy10 = wcs.get('OCY10', None) @@ -22,7 +22,7 @@ def sip2idc(wcs): if None in [ocx10, ocx11, ocy10, ocy11, sipa, sipb]: print 'Cannot convert SIP to IDC coefficients.\n' return None, None - elif isinstance(wcs,pywcs.WCS): + elif isinstance(wcs, pywcs.WCS): try: ocx10 = wcs.ocx10 ocx11 = wcs.ocx11 diff --git a/lib/stwcs/distortion/utils.py b/lib/stwcs/distortion/utils.py index 69b24a5..5e0bf79 100644 --- a/lib/stwcs/distortion/utils.py +++ b/lib/stwcs/distortion/utils.py @@ -1,7 +1,6 @@ from __future__ import division # confidence high import os import numpy as np -#import pywcs from astropy import wcs as pywcs from stwcs import wcsutil from numpy import sqrt, arctan2 @@ -24,7 +23,7 @@ def output_wcs(list_of_wcsobj, ref_wcs=None, owcs=None, undistort=True): undistort: boolean (default-True) a flag whether to create an undistorted output WCS """ - fra_dec = np.vstack([w.calcFootprint() for w in list_of_wcsobj]) + fra_dec = np.vstack([w.calc_footprint() for w in list_of_wcsobj]) wcsname = list_of_wcsobj[0].wcs.name # This new algorithm may not be strictly necessary, but it may be more diff --git a/lib/stwcs/gui/apply_headerlet.py b/lib/stwcs/gui/apply_headerlet.py index 8d8daf9..9f51029 100644 --- a/lib/stwcs/gui/apply_headerlet.py +++ b/lib/stwcs/gui/apply_headerlet.py @@ -1,8 +1,5 @@ import os import string - -#import pyfits -from astropy.io import fits as pyfits from stsci.tools import teal, parseinput import stwcs diff --git a/lib/stwcs/gui/archive_headerlet.py b/lib/stwcs/gui/archive_headerlet.py index 65e133a..70dbc89 100644 --- a/lib/stwcs/gui/archive_headerlet.py +++ b/lib/stwcs/gui/archive_headerlet.py @@ -1,8 +1,7 @@ import os import string -#import pyfits -from astropy.io import fits as pyfits +from astropy.io import fits from stsci.tools import teal import stwcs diff --git a/lib/stwcs/gui/attach_headerlet.py b/lib/stwcs/gui/attach_headerlet.py index 5a3bdc8..873c549 100644 --- a/lib/stwcs/gui/attach_headerlet.py +++ b/lib/stwcs/gui/attach_headerlet.py @@ -1,7 +1,5 @@ import os -#import pyfits -from astropy.io import fits as pyfits from stsci.tools import teal import stwcs diff --git a/lib/stwcs/gui/delete_headerlet.py b/lib/stwcs/gui/delete_headerlet.py index f25c545..96d3ed1 100644 --- a/lib/stwcs/gui/delete_headerlet.py +++ b/lib/stwcs/gui/delete_headerlet.py @@ -1,7 +1,5 @@ import os -#import pyfits -from astropy.io import fits as pyfits from stsci.tools import teal from stsci.tools import parseinput diff --git a/lib/stwcs/gui/extract_headerlet.py b/lib/stwcs/gui/extract_headerlet.py index 16a0aee..972f5c7 100644 --- a/lib/stwcs/gui/extract_headerlet.py +++ b/lib/stwcs/gui/extract_headerlet.py @@ -1,7 +1,5 @@ import os -#import pyfits -from astropy.io import fits as pyfits from stsci.tools import teal import stwcs diff --git a/lib/stwcs/gui/headerlet_summary.py b/lib/stwcs/gui/headerlet_summary.py index 7772a95..82a3e0c 100644 --- a/lib/stwcs/gui/headerlet_summary.py +++ b/lib/stwcs/gui/headerlet_summary.py @@ -1,7 +1,4 @@ import os - -#import pyfits -from astropy.io import fits as pyfits from stsci.tools import teal import stwcs diff --git a/lib/stwcs/gui/restore_headerlet.py b/lib/stwcs/gui/restore_headerlet.py index 46575db..2f46bb7 100644 --- a/lib/stwcs/gui/restore_headerlet.py +++ b/lib/stwcs/gui/restore_headerlet.py @@ -1,8 +1,6 @@ import os import string -#import pyfits -from astropy.io import fits as pyfits from stsci.tools import teal import stwcs diff --git a/lib/stwcs/gui/updatewcs.py b/lib/stwcs/gui/updatewcs.py index 1e5b9d9..f8f10d7 100644 --- a/lib/stwcs/gui/updatewcs.py +++ b/lib/stwcs/gui/updatewcs.py @@ -1,7 +1,6 @@ import os -#import pyfits -from astropy.io import fits as pyfits +from astropy.io import fits from stsci.tools import parseinput from stsci.tools import fileutil from stsci.tools import teal @@ -67,7 +66,7 @@ def run(configObj=None): # for file in input: # Check to insure that there is a valid reference file to be used - idctab = pyfits.getval(file,'idctab') + idctab = fits.getval(file, 'idctab') if not os.path.exists(fileutil.osfn(idctab)): print 'No valid distortion reference file ',idctab,' found in ',file,'!' raise ValueError @@ -78,7 +77,7 @@ def run(configObj=None): # for file in input: # get instrument name from input file - instr = pyfits.getval(file,'INSTRUME') + instr = fits.getval(file,'INSTRUME') # make copy of input parameters dict for this file fdict = cdict.copy() # Remove any parameter that is not part of this instrument's allowed corrections diff --git a/lib/stwcs/gui/write_headerlet.py b/lib/stwcs/gui/write_headerlet.py index 9ba0639..353e32b 100644 --- a/lib/stwcs/gui/write_headerlet.py +++ b/lib/stwcs/gui/write_headerlet.py @@ -1,7 +1,5 @@ import os -#import pyfits -from astropy.io import fits as pyfits from stsci.tools import teal from stsci.tools import parseinput diff --git a/lib/stwcs/updatewcs/__init__.py b/lib/stwcs/updatewcs/__init__.py index d8acb17..aca33f7 100644 --- a/lib/stwcs/updatewcs/__init__.py +++ b/lib/stwcs/updatewcs/__init__.py @@ -1,12 +1,11 @@ from __future__ import division # confidence high import os -from astropy.io import fits as pyfits +from astropy.io import fits import numpy as np from stwcs import wcsutil from stwcs.wcsutil import HSTWCS import stwcs -#import pywcs from astropy import wcs as pywcs import astropy @@ -24,8 +23,6 @@ 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, verbose=False): """ @@ -46,8 +43,8 @@ def updatewcs(input, vacorr=True, tddcorr=True, npolcorr=True, d2imcorr=True, Dependencies ------------ `stsci.tools` - `pyfits` - `pywcs` + `astropy.io.fits` + `astropy.wcs` Parameters ---------- @@ -114,7 +111,7 @@ def makecorr(fname, allowed_corr): list of corrections to be applied """ logger.info("Allowed corrections: {0}".format(allowed_corr)) - f = pyfits.open(fname, mode='update') + f = fits.open(fname, mode='update') #Determine the reference chip and create the reference HSTWCS object nrefchip, nrefext = getNrefchip(f) wcsutil.restoreWCS(f, nrefext, wcskey='O') @@ -181,7 +178,7 @@ def makecorr(fname, allowed_corr): f[0].header.set('UPWCSVER', value=stwcs.__version__, comment="Version of STWCS used to updated the WCS", after='ASN_MTYP') - f[0].header.set('PYWCSVER', value=pywcs.__version__, + f[0].header.set('PYWCSVER', value=astropy.__version__, comment="Version of PYWCS used to updated the WCS", after='ASN_MTYP') else: @@ -192,7 +189,7 @@ def makecorr(fname, allowed_corr): f[0].header.set('UPWCSVER', stwcs.__version__, "Version of STWCS used to updated the WCS", after=i) - f[0].header.set('PYWCSVER', pywcs.__version__, + f[0].header.set('PYWCSVER', astropy.__version__, "Version of PYWCS used to updated the WCS", after=i) # add additional keywords to be used by headerlets @@ -231,7 +228,7 @@ def getNrefchip(fobj): Parameters ---------- - fobj: pyfits HDUList object + fobj: `astropy.io.fits.HDUList` object """ nrefext = 1 nrefchip = 1 @@ -337,7 +334,7 @@ def checkFiles(input): def newIDCTAB(fname): #When this is called we know there's a kw IDCTAB in the header - hdul = pyfits.open(fname) + hdul = fits.open(fname) idctab = fileutil.osfn(hdul[0].header['IDCTAB']) try: #check for the presence of IDCTAB in the first extension @@ -352,7 +349,7 @@ def newIDCTAB(fname): 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. - f = pyfits.open(fname, mode='update') + f = fits.open(fname, mode='update') keys = wcsutil.wcskeys(f[1].header) # Remove the primary WCS from the list try: diff --git a/lib/stwcs/updatewcs/apply_corrections.py b/lib/stwcs/updatewcs/apply_corrections.py index fa56db6..b7e41b2 100644 --- a/lib/stwcs/updatewcs/apply_corrections.py +++ b/lib/stwcs/updatewcs/apply_corrections.py @@ -1,7 +1,7 @@ from __future__ import division # confidence high import os -from astropy.io import fits as pyfits +from astropy.io import fits import time from stsci.tools import fileutil import os.path @@ -38,7 +38,7 @@ def setCorrections(fname, vacorr=True, tddcorr=True, npolcorr=True, d2imcorr=Tru based on user input paramters and allowed corrections for the instrument. """ - instrument = pyfits.getval(fname, 'INSTRUME') + instrument = fits.getval(fname, 'INSTRUME') # make a copy of this list ! acorr = allowed_corrections[instrument][:] @@ -66,7 +66,7 @@ def setCorrections(fname, vacorr=True, tddcorr=True, npolcorr=True, d2imcorr=Tru def foundIDCTAB(fname): try: - idctab = fileutil.osfn(pyfits.getval(fname, 'IDCTAB')) + idctab = fileutil.osfn(fits.getval(fname, 'IDCTAB')) except KeyError: return False if idctab == 'N/A' or idctab == "": @@ -85,7 +85,7 @@ def applyTDDCorr(fname, utddcorr): - the idc table specified in the primary header is available. """ - phdr = pyfits.getheader(fname) + phdr = fits.getheader(fname) instrument = phdr['INSTRUME'] try: detector = phdr['DETECTOR'] @@ -127,7 +127,7 @@ def applyNpolCorr(fname, unpolcorr): applyNPOLCorr = True try: # get NPOLFILE kw from primary header - fnpol0 = pyfits.getval(fname, 'NPOLFILE') + fnpol0 = fits.getval(fname, 'NPOLFILE') if fnpol0 == 'N/A': return False fnpol0 = fileutil.osfn(fnpol0) @@ -140,7 +140,7 @@ def applyNpolCorr(fname, unpolcorr): return applyNPOLCorr try: # get NPOLEXT kw from first extension header - fnpol1 = pyfits.getval(fname, 'NPOLEXT', ext=1) + fnpol1 = fits.getval(fname, 'NPOLEXT', ext=1) fnpol1 = fileutil.osfn(fnpol1) if fnpol1 and fileutil.findFile(fnpol1): if fnpol0 != fnpol1: @@ -172,8 +172,8 @@ def isOldStyleDGEO(fname, dgname): # checks if the file defined in a NPOLFILE kw is a full size # (old style) image - sci_hdr = pyfits.getheader(fname, ext=1) - dgeo_hdr = pyfits.getheader(dgname, ext=1) + sci_hdr = fits.getheader(fname, ext=1) + dgeo_hdr = fits.getheader(dgname, ext=1) sci_naxis1 = sci_hdr['NAXIS1'] sci_naxis2 = sci_hdr['NAXIS2'] dg_naxis1 = dgeo_hdr['NAXIS1'] @@ -190,7 +190,7 @@ def applyD2ImCorr(fname, d2imcorr): applyD2IMCorr = True try: # get D2IMFILE kw from primary header - fd2im0 = pyfits.getval(fname, 'D2IMFILE') + fd2im0 = fits.getval(fname, 'D2IMFILE') if fd2im0 == 'N/A': return False fd2im0 = fileutil.osfn(fd2im0) @@ -203,7 +203,7 @@ def applyD2ImCorr(fname, d2imcorr): return applyD2IMCorr try: # get D2IMEXT kw from first extension header - fd2imext = pyfits.getval(fname, 'D2IMEXT', ext=1) + fd2imext = fits.getval(fname, 'D2IMEXT', ext=1) fd2imext = fileutil.osfn(fd2imext) if fd2imext and fileutil.findFile(fd2imext): if fd2im0 != fd2imext: diff --git a/lib/stwcs/updatewcs/det2im.py b/lib/stwcs/updatewcs/det2im.py index a783c88..902deaa 100644 --- a/lib/stwcs/updatewcs/det2im.py +++ b/lib/stwcs/updatewcs/det2im.py @@ -1,6 +1,6 @@ from __future__ import division # confidence high -from astropy.io import fits as pyfits +from astropy.io import fits from stsci.tools import fileutil import utils import numpy as np @@ -33,15 +33,15 @@ class DET2IMCorr(object): """ Parameters ---------- - fobj: pyfits object + fobj: `astropy.io.fits.HDUList` object Science file, for which a distortion correction in a NPOLFILE is available """ logger.info("\n\tStarting DET2IM: %s" %time.asctime()) try: - assert isinstance(fobj, pyfits.HDUList) + assert isinstance(fobj, fits.HDUList) except AssertionError: - logger.exception('\n\tInput must be a pyfits.HDUList object') + logger.exception('\n\tInput must be a fits.HDUList object') raise cls.applyDet2ImCorr(fobj) @@ -54,7 +54,7 @@ class DET2IMCorr(object): def applyDet2ImCorr(cls, fobj): """ - For each science extension in a pyfits file object: + For each science extension in a fits file object: - create a WCSDVARR extension - update science header - add/update D2IMEXT keyword @@ -159,7 +159,7 @@ class DET2IMCorr(object): Make sure 'CCDCHIP' in the npolfile matches "CCDCHIP' in the science file. """ xdata, ydata = (None, None) - d2im = pyfits.open(d2imfile) + d2im = fits.open(d2imfile) for ext in d2im: d2imextname = ext.header.get('EXTNAME',"") d2imccdchip = ext.header.get('CCDCHIP',1) @@ -183,7 +183,7 @@ class DET2IMCorr(object): hdr = cls.createD2ImHdr(sciheader, d2imfile=d2imfile, wdvarr_ver=wdvarr_ver, d2im_extname=d2im_extname, ccdchip=ccdchip) - hdu=pyfits.ImageHDU(header=hdr, data=data) + hdu = fits.ImageHDU(header=hdr, data=data) return hdu createD2ImHDU = classmethod(createD2ImHDU) @@ -196,7 +196,7 @@ class DET2IMCorr(object): is such that a full size d2im table is created and then shifted or scaled if the science image is a subarray or binned image. """ - d2im = pyfits.open(d2imfile) + d2im = fits.open(d2imfile) d2im_phdr = d2im[0].header for ext in d2im: try: @@ -272,7 +272,7 @@ class DET2IMCorr(object): for card in d2im_phdr.cards[start_indx:end_indx]: cdl.append(card) - hdr = pyfits.Header(cards=cdl) + hdr = fits.Header(cards=cdl) return hdr diff --git a/lib/stwcs/updatewcs/npol.py b/lib/stwcs/updatewcs/npol.py index 0427b61..cee7b9b 100644 --- a/lib/stwcs/updatewcs/npol.py +++ b/lib/stwcs/updatewcs/npol.py @@ -1,6 +1,6 @@ from __future__ import division # confidence high -from astropy.io import fits as pyfits +from astropy.io import fits from stsci.tools import fileutil import utils import numpy as np @@ -37,15 +37,15 @@ class NPOLCorr(object): """ Parameters ---------- - fobj: pyfits object - Science file, for which a distortion correction in a NPOLFILE is available + fobj : `astropy.io.fits.HDUList` object + Science file, for which a distortion correction in a NPOLFILE is available """ logger.info("\n\tStarting NPOL: %s" %time.asctime()) try: - assert isinstance(fobj, pyfits.HDUList) + assert isinstance(fobj, fits.HDUList) except AssertionError: - logger.exception('\n\tInput must be a pyfits.HDUList object') + logger.exception('\n\tInput must be a fits.HDUList object') raise cls.applyNPOLCorr(fobj) @@ -58,7 +58,7 @@ class NPOLCorr(object): def applyNPOLCorr(cls, fobj): """ - For each science extension in a pyfits file object: + For each science extension in a fits file object: - create a WCSDVARR extension - update science header - add/update NPOLEXT keyword @@ -168,7 +168,7 @@ class NPOLCorr(object): 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) + npl = fits.open(nplfile) for ext in npl: nplextname = ext.header.get('EXTNAME',"") nplccdchip = ext.header.get('CCDCHIP',1) @@ -224,7 +224,7 @@ class NPOLCorr(object): 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) - hdu=pyfits.ImageHDU(header=hdr, data=data) + hdu = fits.ImageHDU(header=hdr, data=data) return hdu createNpolHDU = classmethod(createNpolHDU) @@ -237,7 +237,7 @@ class NPOLCorr(object): 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) + npl = fits.open(npolfile) npol_phdr = npl[0].header for ext in npl: try: @@ -315,7 +315,7 @@ class NPOLCorr(object): for card in npol_phdr.cards[start_indx:end_indx]: cdl.append(card) - hdr = pyfits.Header(cards=cdl) + hdr = fits.Header(cards=cdl) return hdr diff --git a/lib/stwcs/updatewcs/utils.py b/lib/stwcs/updatewcs/utils.py index 550ce56..7bdd6fe 100644 --- a/lib/stwcs/updatewcs/utils.py +++ b/lib/stwcs/updatewcs/utils.py @@ -35,8 +35,8 @@ def updateNEXTENDKw(fobj): Parameters ----------- - fobj : pyfits.HDUList - PyFITS object for file opened in update mode + fobj : `astropy.io.fits.HDUList` + The FITS object for file opened in `update` mode """ if 'nextend' in fobj[0].header: @@ -124,11 +124,11 @@ def build_sipname(fobj, fname=None, sipname=None): Parameters ---------- - fobj: HDUList - pyfits file object - fname: string - science file name (to be used if ROOTNAMe is not present - sipname: string + fobj : `astropy.io.fits.HDUList` + file object + fname : string + science file name (to be used if ROOTNAME is not present + sipname : string user supplied SIPNAME keyword Returns @@ -169,10 +169,10 @@ def build_npolname(fobj, npolfile=None): Parameters ---------- - fobj: HDUList - pyfits file object - npolfile: string - user supplied NPOLFILE keyword + fobj : `astropy.io.fits.HDUList` + file object + npolfile : string + user supplied NPOLFILE keyword Returns ------- @@ -202,10 +202,10 @@ def build_d2imname(fobj, d2imfile=None): Parameters ---------- - fobj: HDUList - pyfits file object - d2imfile: string - user supplied NPOLFILE keyword + fobj : `astropy.io.fits.HDUList` + file object + d2imfile : string + user supplied NPOLFILE keyword Returns ------- diff --git a/lib/stwcs/wcsutil/__init__.py b/lib/stwcs/wcsutil/__init__.py index 9b7ed8c..b92299e 100644 --- a/lib/stwcs/wcsutil/__init__.py +++ b/lib/stwcs/wcsutil/__init__.py @@ -3,16 +3,14 @@ from __future__ import division # confidence high from altwcs import * from hstwcs import HSTWCS -__docformat__ = 'restructuredtext' - def help(): print 'How to create an HSTWCS object:\n\n' print """ \ - 1. Using a pyfits HDUList object and an extension number \n + 1. Using a `astropy.io.fits.HDUList` object and an extension number \n Example:\n - - fobj = pyfits.open('some_file.fits')\n + from astropy.io improt fits + fobj = fits.open('some_file.fits')\n w = wcsutil.HSTWCS(fobj, 3)\n\n 2. Create an HSTWCS object using a qualified file name. \n diff --git a/lib/stwcs/wcsutil/altwcs.py b/lib/stwcs/wcsutil/altwcs.py index a8f1cc1..71588f4 100644 --- a/lib/stwcs/wcsutil/altwcs.py +++ b/lib/stwcs/wcsutil/altwcs.py @@ -3,10 +3,8 @@ import os import string import numpy as np -#import pywcs from astropy import wcs as pywcs -from astropy.io import fits as pyfits -#import pyfits +from astropy.io import fits from stsci.tools import fileutil as fu altwcskw = ['WCSAXES', 'CRVAL', 'CRPIX', 'PC', 'CDELT', 'CD', 'CTYPE', 'CUNIT', @@ -21,19 +19,19 @@ def archiveWCS(fname, ext, wcskey=" ", wcsname=" ", reusekey=False): Parameters ---------- - fname: string or pyfits.HDUList - a file name or a file object - ext: an int, a tuple, string, or list of integers or tuples (e.g.('sci',1)) - fits extensions to work with - If a string is provided, it should specify the EXTNAME of extensions - with WCSs to be archived - wcskey: string "A"-"Z" or " " - if " ": get next available key if wcsname is also " " or try - to get a key from WCSNAME value - wcsname: string - Name of alternate WCS description - reusekey: boolean - if True - overwrites a WCS with the same key + fname : string or `astropy.io.fits.HDUList` + file name or a file object + ext : int, tuple, str, or list of integers or tuples (e.g.('sci',1)) + fits extensions to work with + If a string is provided, it should specify the EXTNAME of extensions + with WCSs to be archived + wcskey : string "A"-"Z" or " " + if " ": get next available key if wcsname is also " " or try + to get a key from WCSNAME value + wcsname : string + Name of alternate WCS description + reusekey : boolean + if True - overwrites a WCS with the same key Examples -------- @@ -55,7 +53,7 @@ def archiveWCS(fname, ext, wcskey=" ", wcsname=" ", reusekey=False): """ if isinstance(fname, str): - f = pyfits.open(fname, mode='update') + f = fits.open(fname, mode='update') else: f = fname @@ -151,7 +149,7 @@ def restore_from_to(f, fromext=None, toext=None, wcskey=" ", wcsname=" "): Parameters ---------- - f: string or pyfits.HDUList object + f: string or `astropy.io.fits.HDUList` a file name or a file object fromext: string extname from which to read in the alternate WCS, for example 'SCI' @@ -171,7 +169,7 @@ def restore_from_to(f, fromext=None, toext=None, wcskey=" ", wcsname=" "): """ if isinstance(f, str): - fobj = pyfits.open(f, mode='update') + fobj = fits.open(f, mode='update') else: fobj = f @@ -232,17 +230,17 @@ def restoreWCS(f, ext, wcskey=" ", wcsname=" "): Parameters ---------- - f: string or pyfits.HDUList object - a file name or a file object - ext: an int, a tuple, string, or list of integers or tuples (e.g.('sci',1)) - fits extensions to work with - If a string is provided, it should specify the EXTNAME of extensions - with WCSs to be archived - wcskey: a charater - "A"-"Z" - Used for one of 26 alternate WCS definitions. - or " " - find a key from WCSNAMe value - wcsname: string (optional) - if given and wcskey is " ", will try to restore by WCSNAME value + f : str or `astropy.io.fits.HDUList` + file name or a file object + ext : int, tuple, str, or list of integers or tuples (e.g.('sci',1)) + fits extensions to work with + If a string is provided, it should specify the EXTNAME of extensions + with WCSs to be archived + wcskey : str + "A"-"Z" - Used for one of 26 alternate WCS definitions. + or " " - find a key from WCSNAMe value + wcsname : str + (optional) if given and wcskey is " ", will try to restore by WCSNAME value See Also -------- @@ -251,7 +249,7 @@ def restoreWCS(f, ext, wcskey=" ", wcsname=" "): """ if isinstance(f, str): - fobj = pyfits.open(f, mode='update') + fobj = fits.open(f, mode='update') else: fobj = f @@ -301,17 +299,18 @@ def deleteWCS(fname, ext, wcskey=" ", wcsname=" "): Parameters ---------- - fname: sting or a pyfits.HDUList object - ext: an int, a tuple, string, or list of integers or tuples (e.g.('sci',1)) - fits extensions to work with - If a string is provided, it should specify the EXTNAME of extensions - with WCSs to be archived - wcskey: one of 'A'-'Z' or " " - wcsname: string - Name of alternate WCS description + fname : str or a `astropy.io.fits.HDUList` + ext : int, tuple, str, or list of integers or tuples (e.g.('sci',1)) + fits extensions to work with + If a string is provided, it should specify the EXTNAME of extensions + with WCSs to be archived + wcskey : str + one of 'A'-'Z' or " " + wcsname : str + Name of alternate WCS description """ if isinstance(fname, str): - fobj = pyfits.open(fname, mode='update') + fobj = fits.open(fname, mode='update') else: fobj = fname @@ -436,19 +435,19 @@ def _restore(fobj, ukey, fromextnum, #header operations def _check_headerpars(fobj, ext): - if not isinstance(fobj, pyfits.Header) and not isinstance(fobj, pyfits.HDUList) \ + if not isinstance(fobj, fits.Header) and not isinstance(fobj, fits.HDUList) \ and not isinstance(fobj, str): raise ValueError("Expected a file name, a file object or a header\n") - if not isinstance(fobj, pyfits.Header): + if not isinstance(fobj, fits.Header): #raise ValueError("Expected a valid ext parameter when input is a file") if not isinstance(ext, int) and not isinstance(ext, tuple): raise ValueError("Expected ext to be a number or a tuple, e.g. ('SCI', 1)\n") def _getheader(fobj, ext): if isinstance(fobj, str): - hdr = pyfits.getheader(fobj,ext) - elif isinstance(fobj, pyfits.Header): + hdr = fits.getheader(fobj,ext) + elif isinstance(fobj, fits.Header): hdr = fobj else: hdr = fobj[ext].header @@ -459,21 +458,22 @@ def readAltWCS(fobj, ext, wcskey=' ',verbose=False): Parameters ---------- - fobj: string, pyfits.HDUList - fits filename or pyfits file object + fobj : str, `astropy.io.fits.HDUList` + fits filename or fits file object containing alternate/primary WCS(s) to be converted - wcskey: string [" ",A-Z] + wcskey : str + [" ",A-Z] alternate/primary WCS key that will be replaced by the new key - ext: int - extension number + ext : int + fits extension number Returns ------- - hdr: pyfits.Header + hdr: fits.Header header object with ONLY the keywords for specified alternate WCS """ if isinstance(fobj, str): - fobj = pyfits.open(fobj) + fobj = fits.open(fobj) hdr = _getheader(fobj,ext) try: @@ -497,19 +497,21 @@ def convertAltWCS(fobj,ext,oldkey=" ",newkey=' '): Parameters ---------- - fobj: string, pyfits.HDUList, or pyfits.Header - fits filename, pyfits file object or pyfits header + fobj : str, `astropy.io.fits.HDUList`, or `astropy.io.fits.Header` + fits filename, fits file object or fits header containing alternate/primary WCS(s) to be converted - ext: int + ext : int extension number - oldkey: string [" ",A-Z] + oldkey : str + [" ",A-Z] alternate/primary WCS key that will be replaced by the new key - newkey: string [" ",A-Z] + newkey : str + [" ",A-Z] new alternate/primary WCS key Returns ------- - hdr: pyfits.Header + hdr: `astropy.io.fits.Header` header object with keywords renamed from oldkey to newkey """ hdr = readAltWCS(fobj,ext,wcskey=oldkey) @@ -532,9 +534,9 @@ def wcskeys(fobj, ext=None): Parameters ---------- - fobj: string, pyfits.HDUList or pyfits.Header - fits file name, pyfits file object or pyfits header - ext: int or None + fobj : str, `astropy.io.fits.HDUList` or `astropy.io.fits.Header` + fits file name, fits file object or fits header + ext : int or None extension number if None, fobj must be a header """ @@ -554,9 +556,9 @@ def wcsnames(fobj, ext=None): Parameters ---------- - fobj: string, pyfits.HDUList or pyfits.Header - fits file name, pyfits file object or pyfits header - ext: int or None + fobj : stri, `astropy.io.fits.HDUList` or `astropy.io.fits.Header` + fits file name, fits file object or fits header + ext : int or None extension number if None, fobj must be a header @@ -579,11 +581,11 @@ def available_wcskeys(fobj, ext=None): Parameters ---------- - fobj: string, pyfits.HDUList or pyfits.Header - fits file name, pyfits file object or pyfits header - ext: int or None - extension number - if None, fobj must be a header + fobj : str, `astropy.io.fits.HDUList` or `astropy.io.fits.Header` + fits file name, fits file object or fits header + ext : int or None + extension number + if None, fobj must be a header """ _check_headerpars(fobj, ext) hdr = _getheader(fobj, ext) @@ -602,11 +604,11 @@ def next_wcskey(fobj, ext=None): Parameters ---------- - fobj: string, pyfits.HDUList or pyfits.Header - fits file name, pyfits file object or pyfits header - ext: int or None - extension number - if None, fobj must be a header + fobj : str, `astropy.io.fits.HDUList` or `astropy.io.fits.Header` + fits file name, fits file object or fits header + ext : int or None + extension number + if None, fobj must be a header """ _check_headerpars(fobj, ext) hdr = _getheader(fobj, ext) @@ -624,9 +626,9 @@ def getKeyFromName(header, wcsname): Parameters ---------- - header: pyfits.Header - wcsname: str - Value of WCSNAME + header : `astropy.io.fits.Header` + wcsname : str + value of WCSNAME """ wkey = None names = wcsnames(header) @@ -648,7 +650,7 @@ def pc2cd(hdr, key=' '): Parameters ---------- - hdr: pyfits.Header + hdr: `astropy.io.fits.Header` """ for c in ['1_1', '1_2', '2_1', '2_2']: @@ -668,19 +670,20 @@ def _parpasscheck(fobj, ext, wcskey, fromext=None, toext=None, reusekey=False): """ Check input parameters to altwcs functions - fobj: string or pyfits.HDUList object - a file name or a file object - ext: an int, a tuple, a python list of integers or a python list - of tuples (e.g.('sci',1)) - fits extensions to work with - wcskey: a charater - "A"-"Z" or " "- Used for one of 26 alternate WCS definitions - wcsname: string (optional) - if given and wcskey is " ", will try to restore by WCSNAME value - reusekey: boolean - A flag which indicates whether to reuse a wcskey in the header - """ - if not isinstance(fobj,pyfits.HDUList): + fobj : str or `astropy.io.fits.HDUList` object + a file name or a file object + ext : int, a tuple, a python list of integers or a python list + of tuples (e.g.('sci',1)) + fits extensions to work with + wcskey : str + "A"-"Z" or " "- Used for one of 26 alternate WCS definitions + wcsname : str + (optional) + if given and wcskey is " ", will try to restore by WCSNAME value + reusekey : bool + A flag which indicates whether to reuse a wcskey in the header + """ + if not isinstance(fobj, fits.HDUList): print "First parameter must be a fits file object or a file name." return False @@ -730,8 +733,8 @@ def mapFitsExt2HDUListInd(fname, extname): Map FITS extensions with 'EXTNAME' to HDUList indexes. """ - if not isinstance(fname, pyfits.HDUList): - f = pyfits.open(fname) + if not isinstance(fname, fits.HDUList): + f = fits.open(fname) close_file = True else: f = fname diff --git a/lib/stwcs/wcsutil/convertwcs.py b/lib/stwcs/wcsutil/convertwcs.py index 6f9f0bf..7ece2a0 100644 --- a/lib/stwcs/wcsutil/convertwcs.py +++ b/lib/stwcs/wcsutil/convertwcs.py @@ -1,5 +1,4 @@ -from astropy.io import fits as pyfits - +from astropy.io import fits try: import stwcs from stwcs import wcsutil @@ -19,8 +18,8 @@ def archive_prefix_OPUS_WCS(fobj,extname='SCI'): Parameters ---------- - fobj: string or pyfits.HDUList - Filename or pyfits object of a file + fobj : str or `astropy.io.fits.HDUList` + Filename or fits object of a file """ if stwcs is None: @@ -33,7 +32,7 @@ def archive_prefix_OPUS_WCS(fobj,extname='SCI'): closefits = False if isinstance(fobj,str): # A filename was provided as input - fobj = pyfits.open(fobj,mode='update') + fobj = fits.open(fobj,mode='update') closefits=True # Define the header @@ -79,13 +78,13 @@ def create_prefix_OPUS_WCS(fobj,extname='SCI'): Parameters ---------- - fobj: string or pyfits.HDUList - Filename or pyfits object of a file + fobj : str or `astropy.io.fits.HDUList` + Filename or fits object of a file Raises ------ IOError: - if input PyFITS object was not opened in 'update' mode + if input FITS object was not opened in 'update' mode """ # List of O-prefix keywords to create @@ -94,7 +93,7 @@ def create_prefix_OPUS_WCS(fobj,extname='SCI'): closefits = False if isinstance(fobj,str): # A filename was provided as input - fobj = pyfits.open(fobj,mode='update') + fobj = fits.open(fobj, mode='update') closefits=True else: # check to make sure this FITS obj has been opened in update mode diff --git a/lib/stwcs/wcsutil/getinput.py b/lib/stwcs/wcsutil/getinput.py index b5a5df7..dbd240f 100644 --- a/lib/stwcs/wcsutil/getinput.py +++ b/lib/stwcs/wcsutil/getinput.py @@ -1,4 +1,4 @@ -from astropy.io import fits as pyfits +from astropy.io import fits from stsci.tools import irafglob, fileutil, parseinput def parseSingleInput(f=None, ext=None): @@ -20,14 +20,14 @@ def parseSingleInput(f=None, ext=None): extnum = int(ext[1]) #handle ext=('',extnum) else: extnum = ext - phdu = pyfits.open(filename) + phdu = fits.open(filename) hdr0 = phdu[0].header try: ehdr = phdu[extnum].header except (IndexError, KeyError), e: raise e.__class__('Unable to get extension %s.' % extnum) - elif isinstance(f, pyfits.HDUList): + elif isinstance(f, fits.HDUList): phdu = f if ext == None: extnum = 0 @@ -38,8 +38,8 @@ def parseSingleInput(f=None, ext=None): filename = hdr0.get('FILENAME', "") else: - raise ValueError('Input must be a file name string or a pyfits file ' - 'object') + raise ValueError('Input must be a file name string or a' + '`astropy.io.fits.HDUList` object') return filename, hdr0, ehdr, phdu diff --git a/lib/stwcs/wcsutil/headerlet.py b/lib/stwcs/wcsutil/headerlet.py index 3ab53f5..a314cc0 100644 --- a/lib/stwcs/wcsutil/headerlet.py +++ b/lib/stwcs/wcsutil/headerlet.py @@ -19,7 +19,7 @@ import copy import time import numpy as np -from astropy.io import fits as pyfits +from astropy.io import fits #import pywcs from astropy import wcs as pywcs from astropy.utils import lazyproperty @@ -125,27 +125,28 @@ def parse_filename(fname, mode='readonly'): 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 + fname : str, `astropy.io.fits.HDUList` + Input pointing to a file or `astropy.io.fits.HDUList` 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 + mode : string + Specifies what 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 + fobj : `astropy.io.fits.HDUList` + FITS file handle for input - fname: string + fname : str Name of input file - close_fobj: bool + 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 + need to worry about closing the FITS object as opposed to letting the higher level interface close the object. """ @@ -153,7 +154,7 @@ def parse_filename(fname, mode='readonly'): if not isinstance(fname, list): if isinstance(fname, basestring): fname = fu.osfn(fname) - fobj = pyfits.open(fname, mode=mode) + fobj = fits.open(fname, mode=mode) close_fobj = True else: fobj = fname @@ -170,8 +171,8 @@ def get_headerlet_kw_names(fobj, kw='HDRNAME'): Parameters ---------- - fobj: string, pyfits.HDUList - kw: str + fobj : str, `astropy.io.fits.HDUList` + kw : str Name of keyword to be read and reported """ @@ -179,7 +180,7 @@ def get_headerlet_kw_names(fobj, kw='HDRNAME'): hdrnames = [] for ext in fobj: - if isinstance(ext, pyfits.hdu.base.NonstandardExtHDU): + if isinstance(ext, fits.hdu.base.NonstandardExtHDU): hdrnames.append(ext.header[kw]) if open_fobj: @@ -205,27 +206,27 @@ def find_headerlet_HDUs(fobj, hdrext=None, hdrname=None, distname=None, Parameters ---------- - fobj: string, pyfits.HDUList - Name of FITS file or open pyfits object (pyfits.HDUList instance) - hdrext: int, tuple or None + fobj : str, `astropy.io.fits.HDUList` + Name of FITS file or open fits object (`astropy.io.fits.HDUList` instance) + hdrext : int, tuple or None index number(EXTVER) or extension tuple of HeaderletHDU to be returned - hdrname: string + hdrname : string value of HDRNAME for HeaderletHDU to be returned - distname: string + distname : string value of DISTNAME for HeaderletHDUs to be returned - strict: bool [Default: True] + 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. - logging: boolean + logging : boolean enable logging to a file called headerlet.log - logmode: 'w' or 'a' + logmode : 'w' or 'a' log file open mode Returns ------- - hdrlets: list + hdrlets : list A list of all matching HeaderletHDU extension indices (could be just one) """ @@ -249,12 +250,12 @@ def find_headerlet_HDUs(fobj, hdrext=None, hdrname=None, distname=None, 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 \ + if isinstance(fobj[hdrext], fits.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 isinstance(ext, fits.hdu.base.NonstandardExtHDU): if get_all: hdrlets.append(fobj.index(ext)) else: @@ -305,9 +306,9 @@ def verify_hdrname_is_unique(fobj, hdrname): Parameters ---------- - fobj: string, pyfits.HDUList - Name of FITS file or open pyfits object (pyfits.HDUList instance) - hdrname: string + fobj : str, `astropy.io.fits.HDUList` + Name of FITS file or open fits file object + hdrname : str value of HDRNAME for HeaderletHDU to be compared as unique Returns @@ -340,8 +341,8 @@ def update_ref_files(source, dest): Parameters ---------- - source: pyfits.Header - dest: pyfits.Header + source : `astropy.io.fits.Header` + dest : `astropy.io.fits.Header` """ logger.info("Updating reference files") phdukw = {'NPOLFILE': True, @@ -470,7 +471,7 @@ def _create_primary_HDU(fobj, fname, wcsext, destim, hdrname, wcsname, upwcsver = fobj[0].header.get('UPWCSVER', "") pywcsver = fobj[0].header.get('PYWCSVER', "") # build Primary HDU - phdu = pyfits.PrimaryHDU() + phdu = fits.PrimaryHDU() phdu.header['DESTIM'] = (destim, 'Destination observation root name') phdu.header['HDRNAME'] = (hdrname, 'Headerlet name') fmt = "%Y-%m-%dT%H:%M:%S" @@ -555,7 +556,7 @@ def extract_headerlet(filename, output, extnum=None, hdrname=None, """ - if isinstance(filename, pyfits.HDUList): + if isinstance(filename, fits.HDUList): filename = [filename] else: filename, oname = parseinput.parseinput(filename) @@ -689,7 +690,7 @@ def write_headerlet(filename, hdrname, output=None, sciext='SCI', enable file logging """ - if isinstance(filename, pyfits.HDUList): + if isinstance(filename, fits.HDUList): filename = [filename] else: filename, oname = parseinput.parseinput(filename) @@ -1021,7 +1022,7 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, hwcs = HSTWCS(fobj, ext=ext, wcskey=wcskey) - whdul = hwcs.to_fits(relax=True, wkey=" ") + whdul = hwcs.to_fits(relax=True, key=" ") if hasattr(hwcs, 'orientat'): orient_comment = "positions angle of image y axis (deg. e of n)" whdul[0].header['ORIENTAT'] = (wcs.orientat, orient_comment) @@ -1064,7 +1065,7 @@ def create_headerlet(filename, sciext='SCI', hdrname=None, destim=None, whdul[0].header['DP1.EXTVER'] = fobj[ext].header['DP1.EXTVER'] if 'DP2.EXTVER' in whdul[0].header: whdul[0].header['DP2.EXTVER'] = fobj[ext].header['DP2.EXTVER'] - ihdu = pyfits.ImageHDU(header=whdul[0].header, name='SIPWCS') + ihdu = fits.ImageHDU(header=whdul[0].header, name='SIPWCS') if ext[0] != "PRIMARY": ihdu.update_ext_version(fobj[ext].header['EXTVER'], comment='Extension version') @@ -1761,7 +1762,7 @@ def archive_as_headerlet(filename, hdrname, sciext='SCI', fobj.close() #### Headerlet Class definitions -class Headerlet(pyfits.HDUList): +class Headerlet(fits.HDUList): """ A Headerlet class Ref: http://mediawiki.stsci.edu/mediawiki/index.php/Telescopedia:Headerlets @@ -2133,7 +2134,7 @@ class Headerlet(pyfits.HDUList): fhdr = fobj[tg_ext].header hwcs = pywcs.WCS(siphdr, self) - hwcs_header = hwcs.to_header(wkey=wkey) + hwcs_header = hwcs.to_header(key=wkey) _idc2hdr(siphdr, fhdr, towkey=wkey) if hwcs.wcs.has_cd(): hwcs_header = altwcs.pc2cd(hwcs_header, key=wkey) @@ -2144,7 +2145,7 @@ class Headerlet(pyfits.HDUList): for kw in self.fit_kws: #fhdr.insert(wind, pyfits.Card(kw + wkey, # self[0].header[kw])) - fhdr.append(pyfits.Card(kw + wkey, self[0].header[kw])) + fhdr.append(fits.Card(kw + wkey, self[0].header[kw])) # Update the WCSCORR table with new rows from the headerlet's WCSs wcscorr.update_wcscorr(fobj, self, 'SIPWCS') @@ -2301,8 +2302,8 @@ class Headerlet(pyfits.HDUList): model/reference files. """ destim_opened = False - if not isinstance(dest, pyfits.HDUList): - destim = pyfits.open(dest) + if not isinstance(dest, fits.HDUList): + destim = fits.open(dest) destim_opened = True else: destim = dest @@ -2333,8 +2334,8 @@ class Headerlet(pyfits.HDUList): of the science file (or the name of the destination file) """ try: - if not isinstance(dest, pyfits.HDUList): - droot = pyfits.getval(dest, 'ROOTNAME') + if not isinstance(dest, fits.HDUList): + droot = fits.getval(dest, 'ROOTNAME') else: droot = dest[0].header['ROOTNAME'] except KeyError: @@ -2660,7 +2661,7 @@ def get_extname_extver_list(fobj, sciext): return extlist -class HeaderletHDU(pyfits.hdu.nonstandard.FitsHDU): +class HeaderletHDU(fits.hdu.nonstandard.FitsHDU): """ A non-standard extension HDU for encapsulating Headerlets in a file. These HDUs have an extension type of HDRLET and their EXTNAME is derived from the @@ -2740,4 +2741,4 @@ class HeaderletHDU(pyfits.hdu.nonstandard.FitsHDU): return hlet -pyfits.register_hdu(HeaderletHDU) +fits.register_hdu(HeaderletHDU) diff --git a/lib/stwcs/wcsutil/hstwcs.py b/lib/stwcs/wcsutil/hstwcs.py index b9983e6..4c2c140 100644 --- a/lib/stwcs/wcsutil/hstwcs.py +++ b/lib/stwcs/wcsutil/hstwcs.py @@ -1,10 +1,8 @@ from __future__ import division # confidence high import os -#from pywcs import WCS from astropy.wcs import WCS -from astropy.io import fits as pyfits -#import pyfits +from astropy.io import fits import instruments from stwcs.distortion import models, coeff_converter import altwcs @@ -113,22 +111,22 @@ class HSTWCS(WCS): Parameters ---------- - fobj: string or PyFITS HDUList object or None - a file name, e.g j9irw4b1q_flt.fits - a fully qualified filename[EXTNAME,EXTNUM], e.g. j9irw4b1q_flt.fits[sci,1] - a pyfits file object, e.g pyfits.open('j9irw4b1q_flt.fits'), in which case the - user is responsible for closing the file object. - ext: int, tuple or None - extension number - if ext is tuple, it must be ("EXTNAME", EXTNUM), e.g. ("SCI", 2) - if ext is None, it is assumed the data is in the primary hdu - minerr: float - minimum value a distortion correction must have in order to be applied. - If CPERRja, CQERRja are smaller than minerr, the corersponding - distortion is not applied. - wcskey: str - A one character A-Z or " " used to retrieve and define an - alternate WCS description. + fobj : str or `astropy.io.fits.HDUList` object or None + file name, e.g j9irw4b1q_flt.fits + fully qualified filename[EXTNAME,EXTNUM], e.g. j9irw4b1q_flt.fits[sci,1] + `astropy.io.fits` file object, e.g fits.open('j9irw4b1q_flt.fits'), in which case the + user is responsible for closing the file object. + ext : int, tuple or None + extension number + if ext is tuple, it must be ("EXTNAME", EXTNUM), e.g. ("SCI", 2) + if ext is None, it is assumed the data is in the primary hdu + minerr : float + minimum value a distortion correction must have in order to be applied. + If CPERRja, CQERRja are smaller than minerr, the corersponding + distortion is not applied. + wcskey : str + A one character A-Z or " " used to retrieve and define an + alternate WCS description. """ self.inst_kw = ins_spec_kw @@ -146,9 +144,9 @@ class HSTWCS(WCS): self.instrument = instrument_name WCS.__init__(self, ehdr, fobj=phdu, minerr=self.minerr, key=self.wcskey) - # If input was a pyfits HDUList object, it's the user's + # If input was a `astropy.io.fits.HDUList` object, it's the user's # responsibility to close it, otherwise, it's closed here. - if not isinstance(fobj, pyfits.HDUList): + if not isinstance(fobj, fits.HDUList): phdu.close() self.setInstrSpecKw(hdr0, ehdr) self.readIDCCoeffs(ehdr) @@ -197,10 +195,10 @@ class HSTWCS(WCS): Parameters ---------- - prim_hdr: pyfits.Header - primary header - ext_hdr: pyfits.Header - extension header + prim_hdr : `astropy.io.fits.Header` + primary header + ext_hdr : `astropy.io.fits.Header` + extension header """ if self.instrument in inst_mappings.keys(): @@ -270,12 +268,12 @@ class HSTWCS(WCS): Parameters ---------- - header: pyfits.Header - fits extension header - update: boolean (False) - if True - record the following IDCTAB quantities as header keywords: - CX10, CX11, CY10, CY11, IDCSCALE, IDCTHETA, IDCXREF, IDCYREF, - IDCV2REF, IDCV3REF + header : `astropy.io.fits.Header` + fits extension header + update : bool (False) + if True - record the following IDCTAB quantities as header keywords: + CX10, CX11, CY10, CY11, IDCSCALE, IDCTHETA, IDCXREF, IDCYREF, + IDCV2REF, IDCV3REF """ if self.idctab in [None, '', ' ','N/A']: #Keyword idctab is not present in header - check for sip coefficients @@ -321,12 +319,12 @@ class HSTWCS(WCS): Parameters ---------- - header: pyfits.Header - fits extension header - update: boolean (False) - if True - save teh following as header keywords: - CX10, CX11, CY10, CY11, IDCSCALE, IDCTHETA, IDCXREF, IDCYREF, - IDCV2REF, IDCV3REF + header : `astropy.io.fits.Header` + fits extension header + update : booln (False) + if True - save teh following as header keywords: + CX10, CX11, CY10, CY11, IDCSCALE, IDCTHETA, IDCXREF, IDCYREF, + IDCV2REF, IDCV3REF """ if self.date_obs == None: @@ -373,15 +371,15 @@ class HSTWCS(WCS): def wcs2header(self, sip2hdr=False, idc2hdr=True, wcskey=None, relax=False): """ - Create a pyfits.Header object from WCS keywords. + Create a `astropy.io.fits.Header` object from WCS keywords. If the original header had a CD matrix, return a CD matrix, otherwise return a PC matrix. Parameters ---------- - sip2hdr: boolean - If True - include SIP coefficients + sip2hdr : bool + If True - include SIP coefficients """ h = self.to_header(key=wcskey, relax=relax) @@ -399,7 +397,7 @@ class HSTWCS(WCS): if idc2hdr: for card in self._idc2hdr(): - h[card.key+wcskey] = (card.value, card.comment) + h[card.keyword + wcskey] = (card.value, card.comment) try: del h['RESTFRQ'] del h['RESTWAV'] @@ -407,9 +405,9 @@ class HSTWCS(WCS): if sip2hdr and self.sip: for card in self._sip2hdr('a'): - h[card.key] = (card.value, card.comment) + h[card.keyword] = (card.value, card.comment) for card in self._sip2hdr('b'): - h[card.key] = (card.value, card.comment) + h[card.keyword] = (card.value, card.comment) try: ap = self.sip.ap @@ -422,41 +420,41 @@ class HSTWCS(WCS): if ap: for card in self._sip2hdr('ap'): - h[card.key] = (card.value, card.comment) + h[card.keyword] = (card.value, card.comment) if bp: for card in self._sip2hdr('bp'): - h[card.key] = (card.value, card.comment) + h[card.keyword] = (card.value, card.comment) return h def _sip2hdr(self, k): """ Get a set of SIP coefficients in the form of an array - and turn them into a pyfits.Cardlist. + and turn them into a `astropy.io.fits.Cardlist`. k - one of 'a', 'b', 'ap', 'bp' """ - cards = pyfits.CardList() + cards = fits.CardList() korder = self.sip.__getattribute__(k+'_order') - cards.append(pyfits.Card(key=k.upper()+'_ORDER', value=korder)) + cards.append(fits.Card(keyword=k.upper()+'_ORDER', value=korder)) coeffs = self.sip.__getattribute__(k) ind = coeffs.nonzero() for i in range(len(ind[0])): - card = pyfits.Card(key=k.upper()+'_'+str(ind[0][i])+'_'+str(ind[1][i]), - value=coeffs[ind[0][i], ind[1][i]]) + card = fits.Card(keyword=k.upper()+'_'+str(ind[0][i])+'_'+str(ind[1][i]), + value=coeffs[ind[0][i], ind[1][i]]) cards.append(card) return cards def _idc2hdr(self): # save some of the idc coefficients coeffs = ['ocx10', 'ocx11', 'ocy10', 'ocy11', 'idcscale'] - cards = pyfits.CardList() + cards = fits.CardList() for c in coeffs: try: val = self.__getattribute__(c) except AttributeError: continue if val: - cards.append(pyfits.Card(key=c, value=val)) + cards.append(fits.Card(keyword=c, value=val)) return cards def pc2cd(self): @@ -606,8 +604,9 @@ detect_divergence=True, quiet=False) Examples -------- - >>> import stwcs, pyfits - >>> hdulist = pyfits.open('j94f05bgq_flt.fits') + >>> import stwcs + >>> from astropy.io import fits + >>> hdulist = fits.open('j94f05bgq_flt.fits') >>> w = stwcs.wcsutil.HSTWCS(hdulist, ext=('sci',1)) >>> hdulist.close() diff --git a/lib/stwcs/wcsutil/mosaic.py b/lib/stwcs/wcsutil/mosaic.py index 5f15f2f..ffdc103 100644 --- a/lib/stwcs/wcsutil/mosaic.py +++ b/lib/stwcs/wcsutil/mosaic.py @@ -1,7 +1,7 @@ from __future__ import division import numpy as np from matplotlib import pyplot as plt -from astropy.io import fits as pyfits +from astropy.io import fits import string from stsci.tools import parseinput, irafglob @@ -83,7 +83,7 @@ def vmosaic(fnames, outwcs=None, ref_wcs=None, ext=None, extname=None, undistort return outwcs def updatehdr(fname, wcsobj, wkey, wcsname, ext=1, clobber=False): - hdr = pyfits.getheader(fname, ext=ext) + hdr = fits.getheader(fname, ext=ext) all_keys = list(string.ascii_uppercase) if wkey.upper() not in all_keys: raise KeyError, "wkey must be one character: A-Z" @@ -92,7 +92,7 @@ def updatehdr(fname, wcsobj, wkey, wcsname, ext=1, clobber=False): raise ValueError, "wkey %s is already in use. Use clobber=True to overwrite it or specify a different key." %wkey else: altwcs.deleteWCS(fname, ext=ext, wcskey='V') - f = pyfits.open(fname, mode='update') + f = fits.open(fname, mode='update') hwcs = wcs2header(wcsobj) wcsnamekey = 'WCSNAME' + wkey @@ -152,7 +152,7 @@ def readWCS(input, exts=None, extname=None): continue elif extname != None: for f in filelist: - fobj = pyfits.open(f) + fobj = fits.open(f) for i in range(len(fobj)): try: ename = fobj[i].header['EXTNAME'] diff --git a/lib/stwcs/wcsutil/wcscorr.py b/lib/stwcs/wcsutil/wcscorr.py index c581e7f..fedc2b2 100644 --- a/lib/stwcs/wcsutil/wcscorr.py +++ b/lib/stwcs/wcsutil/wcscorr.py @@ -1,5 +1,5 @@ import os,copy -from astropy.io import fits as pyfits +from astropy.io import fits import numpy as np from stsci.tools import fileutil @@ -31,9 +31,9 @@ def init_wcscorr(input, force=False): """ # TODO: Create some sort of decorator or (for Python2.5) context for # opening a FITS file and closing it when done, if necessary - if not isinstance(input, pyfits.HDUList): - # input must be a filename, so open as PyFITS object - fimg = pyfits.open(input, mode='update') + if not isinstance(input, fits.HDUList): + # input must be a filename, so open as `astropy.io.fits.HDUList` object + fimg = fits.open(input, mode='update') need_to_close = True else: fimg = input @@ -225,8 +225,8 @@ def archive_wcs_file(image, wcs_id=None): newly updated WCS keyword values. """ - if not isinstance(image, pyfits.HDUList): - fimg = pyfits.open(image, mode='update') + if not isinstance(image, fits.HDUList): + fimg = fits.open(image, mode='update') close_image = True else: fimg = image @@ -265,8 +265,8 @@ def update_wcscorr(dest, source=None, extname='SCI', wcs_id=None, active=True): active WCS information, not just appending the WCS to the file as a headerlet """ - if not isinstance(dest,pyfits.HDUList): - dest = pyfits.open(dest,mode='update') + if not isinstance(dest, fits.HDUList): + dest = fits.open(dest,mode='update') fname = dest.filename() if source is None: @@ -409,7 +409,7 @@ def update_wcscorr(dest, source=None, extname='SCI', wcs_id=None, active=True): if (old_nrows + new_nrows) > old_table.data.shape[0]-1: pad_rows = 2 * new_nrows # if not, create a new table with 'pad_rows' new empty rows - upd_table = pyfits.new_table(old_table.columns,header=old_table.header, + upd_table = fits.new_table(old_table.columns,header=old_table.header, nrows=old_table.data.shape[0]+pad_rows) else: upd_table = old_table @@ -435,8 +435,8 @@ def restore_file_from_wcscorr(image, id='OPUS', wcskey=''): If wcskey is specified, the WCS with that key will be updated instead. """ - if not isinstance(image, pyfits.HDUList): - fimg = pyfits.open(image, mode='update') + if not isinstance(image, fits.HDUList): + fimg = fits.open(image, mode='update') close_image = True else: fimg = image @@ -517,32 +517,32 @@ def create_wcscorr(descrip=False, numrows=1, padding=0): ('NMatch', def_int32_col), ('Catalog', def_str40_col)] # Define selector columns - id_col = pyfits.Column(name='WCS_ID', format='40A', - array=np.array(['OPUS'] * numrows + [''] * padding, - dtype='S24')) - extver_col = pyfits.Column(name='EXTVER', format='I', - array=np.array(range(1, numrows + 1), - dtype=np.int16)) - wcskey_col = pyfits.Column(name='WCS_key', format='A', - array=np.array(['O'] * numrows + [''] * padding, - dtype='S')) + id_col = fits.Column(name='WCS_ID', format='40A', + array=np.array(['OPUS'] * numrows + [''] * padding, + dtype='S24')) + extver_col = fits.Column(name='EXTVER', format='I', + array=np.array(range(1, numrows + 1), + dtype=np.int16)) + wcskey_col = fits.Column(name='WCS_key', format='A', + array=np.array(['O'] * numrows + [''] * padding, + dtype='S')) # create list of remaining columns to be added to table col_list = [id_col, extver_col, wcskey_col] # start with selector columns for c in col_names: cdef = copy.deepcopy(c[1]) - col_list.append(pyfits.Column(name=c[0], format=cdef['format'], + col_list.append(fits.Column(name=c[0], format=cdef['format'], array=cdef['array'])) if descrip: col_list.append( - pyfits.Column(name='DESCRIP', format='128A', - array=np.array( - ['Original WCS computed by OPUS'] * numrows, - dtype='S128'))) + fits.Column(name='DESCRIP', format='128A', + array=np.array( + ['Original WCS computed by OPUS'] * numrows, + dtype='S128'))) # Now create the new table from the column definitions - newtab = pyfits.new_table(pyfits.ColDefs(col_list), nrows=trows) + newtab = fits.new_table(fits.ColDefs(col_list), nrows=trows) # The fact that setting .name is necessary should be considered a bug in # pyfits. # TODO: Make sure this is fixed in pyfits, then remove this diff --git a/lib/stwcs/wcsutil/wcsdiff.py b/lib/stwcs/wcsutil/wcsdiff.py index f027df2..cfc2d66 100644 --- a/lib/stwcs/wcsutil/wcsdiff.py +++ b/lib/stwcs/wcsutil/wcsdiff.py @@ -1,8 +1,7 @@ from __future__ import print_function -#import pywcs from astropy import wcs as pywcs from collections import OrderedDict -from astropy.io import fits as pyfits +from astropy.io import fits from .headerlet import parse_filename import numpy as np @@ -127,10 +126,10 @@ def is_wcs_identical(scifile, file2, sciextlist, fextlist, scikey=" ", def get_rootname(fname): """ - returns the value of ROOTNAME or DESTIM + Returns the value of ROOTNAME or DESTIM """ - hdr = pyfits.getheader(fname) + hdr = fits.getheader(fname) try: rootname = hdr['ROOTNAME'] except KeyError: |