def waiver2mef(sciname, newname=None, convert_dq=True, writefits=True):
"""
Converts a GEIS science file and its corresponding
data quality file (if present) to MEF format
Writes out both files to disk.
Returns the new name of the science image.
"""
if isinstance(sciname, fits.HDUList):
filename = sciname.filename()
else:
filename = sciname
try:
clobber = True
fimg = convertwaiveredfits.convertwaiveredfits(filename)
#check for the existence of a data quality file
_dqname = fileutil.buildNewRootname(filename, extn='_c1f.fits')
dqexists = os.path.exists(_dqname)
if convert_dq and dqexists:
try:
dqfile = convertwaiveredfits.convertwaiveredfits(_dqname)
dqfitsname = fileutil.buildNewRootname(_dqname,
extn='_c1h.fits')
except Exception:
print("Could not read data quality file %s" % _dqname)
if writefits:
# User wants to make a FITS copy and update it
# using the filename they have provided
rname = fileutil.buildNewRootname(filename)
fitsname = fileutil.buildNewRootname(rname, extn='_c0h.fits')
# Write out GEIS image as multi-extension FITS.
fexists = os.path.exists(fitsname)
if (fexists and clobber) or not fexists:
print('Writing out WAIVERED as MEF to ', fitsname)
if ASTROPY_VER_GE13:
fimg.writeto(fitsname, overwrite=clobber)
else:
fimg.writeto(fitsname, clobber=clobber)
if dqexists:
print('Writing out WAIVERED as MEF to ', dqfitsname)
if ASTROPY_VER_GE13:
dqfile.writeto(dqfitsname, overwrite=clobber)
else:
dqfile.writeto(dqfitsname, clobber=clobber)
# Now close input GEIS image, and open writable
# handle to output FITS image instead...
fimg.close()
del fimg
fimg = fits.open(fitsname, mode='update', memmap=False)
return fimg
except IOError:
print('Warning: File %s could not be found' % sciname)
return None
def waiver2mef(sciname, newname=None, convert_dq=True, writefits=True):
"""
Converts a GEIS science file and its corresponding
data quality file (if present) to MEF format
Writes out both files to disk.
Returns the new name of the science image.
"""
if isinstance(sciname, fits.HDUList):
filename = sciname.filename()
else:
filename = sciname
try:
clobber = True
fimg = convertwaiveredfits.convertwaiveredfits(filename)
#check for the existence of a data quality file
_dqname = fileutil.buildNewRootname(filename, extn='_c1f.fits')
dqexists = os.path.exists(_dqname)
if convert_dq and dqexists:
try:
dqfile = convertwaiveredfits.convertwaiveredfits(_dqname)
dqfitsname = fileutil.buildNewRootname(_dqname, extn='_c1h.fits')
except Exception:
print("Could not read data quality file %s" % _dqname)
if writefits:
# User wants to make a FITS copy and update it
# using the filename they have provided
rname = fileutil.buildNewRootname(filename)
fitsname = fileutil.buildNewRootname(rname, extn='_c0h.fits')
# Write out GEIS image as multi-extension FITS.
fexists = os.path.exists(fitsname)
if (fexists and clobber) or not fexists:
print('Writing out WAIVERED as MEF to ', fitsname)
if ASTROPY_VER_GE13:
fimg.writeto(fitsname, overwrite=clobber)
else:
fimg.writeto(fitsname, clobber=clobber)
if dqexists:
print('Writing out WAIVERED as MEF to ', dqfitsname)
if ASTROPY_VER_GE13:
dqfile.writeto(dqfitsname, overwrite=clobber)
else:
dqfile.writeto(dqfitsname, clobber=clobber)
# Now close input GEIS image, and open writable
# handle to output FITS image instead...
fimg.close()
del fimg
fimg = fits.open(fitsname, mode='update', memmap=False)
return fimg
except IOError:
print('Warning: File %s could not be found' % sciname)
return None
def process_input(input,
output=None,
ivmlist=None,
updatewcs=True,
prodonly=False,
wcskey=None,
**workinplace):
"""
Create the full input list of filenames after verifying and converting
files as needed.
"""
newfilelist, ivmlist, output, oldasndict, origflist = buildFileListOrig(
input,
output=output,
ivmlist=ivmlist,
wcskey=wcskey,
updatewcs=updatewcs,
**workinplace)
if not newfilelist:
buildEmptyDRZ(input, output)
return None, None, output
# run all WCS updating -- Now done in buildFileList
#pydr_input = _process_input_wcs(newfilelist, wcskey, updatewcs)
pydr_input = newfilelist
# AsnTable will handle the case when output==None
if not oldasndict: # and output is not None:
oldasndict = asnutil.ASNTable(pydr_input, output=output)
oldasndict.create()
asndict = update_member_names(oldasndict, pydr_input)
asndict['original_file_names'] = origflist
# Build output filename
drz_extn = '_drz.fits'
for img in newfilelist:
# special case logic to automatically recognize when _flc.fits files
# are provided as input and produce a _drc.fits file instead
if '_flc.fits' in img:
drz_extn = '_drc.fits'
break
if output in [None, '']:
output = fileutil.buildNewRootname(asndict['output'], extn=drz_extn)
else:
if '.fits' in output.lower():
pass
elif drz_extn[:4] not in output.lower():
output = fileutil.buildNewRootname(output, extn=drz_extn)
log.info('Setting up output name: %s' % output)
return asndict, ivmlist, output
def process_input(input, output=None, ivmlist=None, updatewcs=True,
prodonly=False, wcskey=None, **workinplace):
"""
Create the full input list of filenames after verifying and converting
files as needed.
"""
newfilelist, ivmlist, output, oldasndict, origflist = buildFileListOrig(
input, output=output, ivmlist=ivmlist, wcskey=wcskey,
updatewcs=updatewcs, **workinplace)
if not newfilelist:
buildEmptyDRZ(input, output)
return None, None, output
# run all WCS updating -- Now done in buildFileList
#pydr_input = _process_input_wcs(newfilelist, wcskey, updatewcs)
pydr_input = newfilelist
# AsnTable will handle the case when output==None
if not oldasndict:# and output is not None:
oldasndict = asnutil.ASNTable(pydr_input, output=output)
oldasndict.create()
asndict = update_member_names(oldasndict, pydr_input)
asndict['original_file_names'] = origflist
# Build output filename
drz_extn = '_drz.fits'
for img in newfilelist:
# special case logic to automatically recognize when _flc.fits files
# are provided as input and produce a _drc.fits file instead
if '_flc.fits' in img:
drz_extn = '_drc.fits'
break
if output in [None,'']:
output = fileutil.buildNewRootname(asndict['output'],
extn=drz_extn)
else:
if '.fits' in output.lower():
pass
elif drz_extn[:4] not in output.lower():
output = fileutil.buildNewRootname(output, extn=drz_extn)
log.info('Setting up output name: %s' % output)
return asndict, ivmlist, output
def update_member_names(oldasndict, pydr_input):
"""
Update names in a member dictionary.
Given an association dictionary with rootnames and a list of full
file names, it will update the names in the member dictionary to
contain '_*' extension. For example a rootname of 'u9600201m' will
be replaced by 'u9600201m_c0h' making sure that a MEf file is passed
as an input and not the corresponding GEIS file.
"""
omembers = oldasndict['members'].copy()
nmembers = {}
translated_names = [f.split('.fits')[0] for f in pydr_input]
newkeys = [fileutil.buildNewRootname(file) for file in pydr_input]
keys_map = list(zip(newkeys, pydr_input))
for okey, oval in list(omembers.items()):
if okey in newkeys:
nkey = pydr_input[newkeys.index(okey)]
nmembers[nkey.split('.fits')[0]] = oval
oldasndict.pop('members')
# replace should be always True to cover the case when flt files were removed
# and the case when names were translated
oldasndict.update(members=nmembers, replace=True)
oldasndict['order'] = translated_names
return oldasndict
def waiver2mef(sciname, newname=None, convert_dq=True):
"""
Converts a GEIS science file and its corresponding
data quality file (if present) to MEF format
Writes out both files to disk.
Returns the new name of the science image.
"""
def convert(file):
newfilename = fileutil.buildNewRootname(file, extn='_c0h.fits')
try:
newimage = fileutil.openImage(file,
writefits=True,
fitsname=newfilename,
clobber=True)
del newimage
return newfilename
except IOError:
print('Warning: File %s could not be found' % file)
return None
newsciname = convert(sciname)
if convert_dq:
dq_name = convert(fileutil.buildNewRootname(sciname, extn='_c1h.fits'))
return newsciname
def extract_rootname(kwvalue,suffix=""):
""" Returns the rootname from a full reference filename
If a non-valid value (any of ['','N/A','NONE','INDEF',None]) is input,
simply return a string value of 'NONE'
This function will also replace any 'suffix' specified with a blank.
"""
# check to see whether a valid kwvalue has been provided as input
if kwvalue.strip() in ['','N/A','NONE','INDEF',None]:
return 'NONE' # no valid value, so return 'NONE'
# for a valid kwvalue, parse out the rootname
# strip off any environment variable from input filename, if any are given
if '$' in kwvalue:
fullval = kwvalue[kwvalue.find('$')+1:]
else:
fullval = kwvalue
# Extract filename without path from kwvalue
fname = os.path.basename(fullval).strip()
# Now, rip out just the rootname from the full filename
rootname = fileutil.buildNewRootname(fname)
# Now, remove any known suffix from rootname
rootname = rootname.replace(suffix,'')
return rootname.strip()
def update_member_names(oldasndict, pydr_input):
"""
Update names in a member dictionary.
Given an association dictionary with rootnames and a list of full
file names, it will update the names in the member dictionary to
contain '_*' extension. For example a rootname of 'u9600201m' will
be replaced by 'u9600201m_c0h' making sure that a MEf file is passed
as an input and not the corresponding GEIS file.
"""
omembers = oldasndict['members'].copy()
nmembers = {}
translated_names = [f.split('.fits')[0] for f in pydr_input]
newkeys = [fileutil.buildNewRootname(file) for file in pydr_input]
keys_map = list(zip(newkeys, pydr_input))
for okey, oval in list(omembers.items()):
if okey in newkeys:
nkey = pydr_input[newkeys.index(okey)]
nmembers[nkey.split('.fits')[0]] = oval
oldasndict.pop('members')
# replace should be always True to cover the case when flt files were removed
# and the case when names were translated
oldasndict.update(members=nmembers, replace=True)
oldasndict['order'] = translated_names
return oldasndict
def extract_rootname(kwvalue, suffix=""):
""" Returns the rootname from a full reference filename
If a non-valid value (any of ['','N/A','NONE','INDEF',None]) is input,
simply return a string value of 'NONE'
This function will also replace any 'suffix' specified with a blank.
"""
# check to see whether a valid kwvalue has been provided as input
if kwvalue.strip() in ['', 'N/A', 'NONE', 'INDEF', None]:
return 'NONE' # no valid value, so return 'NONE'
# for a valid kwvalue, parse out the rootname
# strip off any environment variable from input filename, if any are given
if '$' in kwvalue:
fullval = kwvalue[kwvalue.find('$') + 1:]
else:
fullval = kwvalue
# Extract filename without path from kwvalue
fname = os.path.basename(fullval).strip()
# Now, rip out just the rootname from the full filename
rootname = fileutil.buildNewRootname(fname)
# Now, remove any known suffix from rootname
rootname = rootname.replace(suffix, '')
return rootname.strip()
def geis2mef(sciname, convert_dq=True):
"""
Converts a GEIS science file and its corresponding
data quality file (if present) to MEF format
Writes out both files to disk.
Returns the new name of the science image.
"""
clobber = True
mode = 'update'
memmap = True
# Input was specified as a GEIS image, but no FITS copy
# exists. Read it in with 'readgeis' and make a copy
# then open the FITS copy...
try:
# Open as a GEIS image for reading only
fimg = readgeis.readgeis(sciname)
except Exception:
raise IOError("Could not open GEIS input: %s" % sciname)
#check for the existence of a data quality file
_dqname = fileutil.buildNewRootname(sciname, extn='.c1h')
dqexists = os.path.exists(_dqname)
if dqexists:
try:
dqfile = readgeis.readgeis(_dqname)
dqfitsname = fileutil.buildFITSName(_dqname)
except Exception:
print("Could not read data quality file %s" % _dqname)
# Check to see if user wanted to update GEIS header.
# or write out a multi-extension FITS file and return a handle to it
# User wants to make a FITS copy and update it
# using the filename they have provided
fitsname = fileutil.buildFITSName(sciname)
# Write out GEIS image as multi-extension FITS.
fexists = os.path.exists(fitsname)
if (fexists and clobber) or not fexists:
print('Writing out GEIS as MEF to ', fitsname)
if ASTROPY_VER_GE13:
fimg.writeto(fitsname, overwrite=clobber)
else:
fimg.writeto(fitsname, clobber=clobber)
if dqexists:
print('Writing out GEIS as MEF to ', dqfitsname)
if ASTROPY_VER_GE13:
dqfile.writeto(dqfitsname, overwrite=clobber)
else:
dqfile.writeto(dqfitsname, clobber=clobber)
# Now close input GEIS image, and open writable
# handle to output FITS image instead...
fimg.close()
del fimg
fimg = fits.open(fitsname, mode=mode, memmap=memmap)
return fimg
def geis2mef(sciname, convert_dq=True):
"""
Converts a GEIS science file and its corresponding
data quality file (if present) to MEF format
Writes out both files to disk.
Returns the new name of the science image.
"""
clobber = True
mode = 'update'
memmap = True
# Input was specified as a GEIS image, but no FITS copy
# exists. Read it in with 'readgeis' and make a copy
# then open the FITS copy...
try:
# Open as a GEIS image for reading only
fimg = readgeis.readgeis(sciname)
except Exception:
raise IOError("Could not open GEIS input: %s" % sciname)
#check for the existence of a data quality file
_dqname = fileutil.buildNewRootname(sciname, extn='.c1h')
dqexists = os.path.exists(_dqname)
if dqexists:
try:
dqfile = readgeis.readgeis(_dqname)
dqfitsname = fileutil.buildFITSName(_dqname)
except Exception:
print("Could not read data quality file %s" % _dqname)
# Check to see if user wanted to update GEIS header.
# or write out a multi-extension FITS file and return a handle to it
# User wants to make a FITS copy and update it
# using the filename they have provided
fitsname = fileutil.buildFITSName(sciname)
# Write out GEIS image as multi-extension FITS.
fexists = os.path.exists(fitsname)
if (fexists and clobber) or not fexists:
print('Writing out GEIS as MEF to ', fitsname)
if ASTROPY_VER_GE13:
fimg.writeto(fitsname, overwrite=clobber)
else:
fimg.writeto(fitsname, clobber=clobber)
if dqexists:
print('Writing out GEIS as MEF to ', dqfitsname)
if ASTROPY_VER_GE13:
dqfile.writeto(dqfitsname, overwrite=clobber)
else:
dqfile.writeto(dqfitsname, clobber=clobber)
# Now close input GEIS image, and open writable
# handle to output FITS image instead...
fimg.close()
del fimg
fimg = fits.open(fitsname, mode=mode, memmap=memmap)
return fimg
def convert(file):
newfilename = fileutil.buildNewRootname(file, extn='_c0h.fits')
try:
newimage = fileutil.openImage(file,writefits=True,
fitsname=newfilename,clobber=True)
del newimage
return newfilename
except IOError:
print('Warning: File %s could not be found' % file)
return None
def addMembers(self,filename):
# The PC chip defines the orientation of the metachip, so use
# it for the PARITY as well.
self.detector = 'WFPC'
_chip1_rot = None
# Build rootname here for each SCI extension...
if self.pars['section'] == None:
self.pars['section'] = [None] * self.nmembers
group_indx = list(range(1,self.nmembers+1))
else:
group_indx = self.pars['section']
for i in range(self.nmembers):
_extname = self.imtype.makeSciName(i+1,section=self.pars['section'][i])
_detnum = fileutil.getKeyword(_extname,self.DETECTOR_NAME)
# Start by looking for the corresponding WFPC2 'c1h' files
_dqfile, _dqextn = self._findDQFile()
# Reset dqfile name in ImType class to point to new file
self.imtype.dqfile = _dqfile
self.imtype.dq_extn = _dqextn
# Build mask file for this member chip
_dqname = self.imtype.makeDQName(extver=group_indx[i])
_masklist = []
_masknames = []
if _dqname != None:
_maskname = buildmask.buildMaskName(fileutil.buildNewRootname(_dqname),_detnum)
else:
_maskname = None
_masknames.append(_maskname)
outmask = buildmask.buildShadowMaskImage(_dqname,_detnum,group_indx[i],_maskname, bitvalue=self.bitvalue[0], binned=self.binned)
_masklist.append(outmask)
_maskname = _maskname.replace('final_mask','single_mask')
_masknames.append(_maskname)
outmask = buildmask.buildShadowMaskImage(_dqname,_detnum,group_indx[i],_maskname, bitvalue=self.bitvalue[1], binned=self.binned)
_masklist.append(outmask)
_masklist.append(_masknames)
self.members.append(Exposure(_extname, idckey=self.idckey, dqname=_dqname,
mask=_masklist, parity=self.PARITY[str(i+1)],
idcdir=self.pars['idcdir'], group_indx = i+1,
rot=_chip1_rot, handle=self.image_handle, extver=_detnum,
exptime=self.exptime[0], ref_pscale=self.REFDATA['1']['psize'], binned=self.binned))
if self.idckey != 'idctab':
_chip1_rot = self.members[0].geometry.def_rot
def setNames(self,filename,output):
"""
Define standard name attibutes:
outname - Default final output name
outdata - Name for drizzle science output
outsingle - Name for output for single image
"""
self.rootname = filename
self.outname = output
# Define FITS output filenames for intermediate products
# to be used when 'build=no'
self.outdata = fileutil.buildNewRootname(output,extn='_sci.fits')
self.outweight = fileutil.buildNewRootname(output,extn='_weight.fits')
self.outcontext = fileutil.buildNewRootname(output,extn='_context.fits')
# Define output file names for separate output for each input
self.outsingle = fileutil.buildNewRootname(filename,extn='_single_sci.fits')
self.outsweight = fileutil.buildNewRootname(filename,extn='_single_wht.fits')
self.outscontext = None
def convert(file):
newfilename = fileutil.buildNewRootname(file, extn='_c0h.fits')
try:
newimage = fileutil.openImage(file,
writefits=True,
fitsname=newfilename,
clobber=True)
del newimage
return newfilename
except IOError:
print('Warning: File %s could not be found' % file)
return None
def init_logging(logfile=DEFAULT_LOGNAME, default=None, level=logging.INFO):
"""
Set up logger for capturing stdout/stderr messages.
Must be called prior to writing any messages that you want to log.
"""
if logfile == "INDEF":
if not is_blank(default):
logname = fileutil.buildNewRootname(default, '.log')
else:
logname = DEFAULT_LOGNAME
elif logfile not in [None, "", " "]:
if logfile.endswith('.log'):
logname = logfile
else:
logname = logfile + '.log'
else:
logname = None
if logname is not None:
logutil.setup_global_logging()
# Don't use logging.basicConfig since it can only be called once in a
# session
# TODO: Would be fine to use logging.config.dictConfig, but it's not
# available in Python 2.5
global _log_file_handler
root_logger = logging.getLogger()
if _log_file_handler:
root_logger.removeHandler(_log_file_handler)
# Default mode is 'a' which is fine
_log_file_handler = logging.FileHandler(logname)
# TODO: Make the default level configurable in the task parameters
_log_file_handler.setLevel(level)
# Insure file handler has '.name' set so calling code can get it.
_log_file_handler.set_name(logname)
_log_file_handler.setFormatter(
logging.Formatter('[%(levelname)-8s] %(message)s'))
root_logger.setLevel(level)
root_logger.addHandler(_log_file_handler)
print('Setting up logfile : ', logname)
else:
print('No trailer file created...')
return logname
def init_logging(logfile=DEFAULT_LOGNAME, default=None, level=logging.INFO):
"""
Set up logger for capturing stdout/stderr messages.
Must be called prior to writing any messages that you want to log.
"""
if logfile == "INDEF":
if not is_blank(default):
logname = fileutil.buildNewRootname(default, '.log')
else:
logname = DEFAULT_LOGNAME
elif logfile not in [None, "" , " "]:
if logfile.endswith('.log'):
logname = logfile
else:
logname = logfile + '.log'
else:
logname = None
if logname is not None:
logutil.setup_global_logging()
# Don't use logging.basicConfig since it can only be called once in a
# session
# TODO: Would be fine to use logging.config.dictConfig, but it's not
# available in Python 2.5
global _log_file_handler
root_logger = logging.getLogger()
if _log_file_handler:
root_logger.removeHandler(_log_file_handler)
# Default mode is 'a' which is fine
_log_file_handler = logging.FileHandler(logname)
# TODO: Make the default level configurable in the task parameters
_log_file_handler.setLevel(level)
_log_file_handler.setFormatter(
logging.Formatter('[%(levelname)-8s] %(message)s'))
root_logger.setLevel(level)
root_logger.addHandler(_log_file_handler)
print('Setting up logfile : ', logname)
#stdout_logger = logging.getLogger('stsci.tools.logutil.stdout')
# Disable display of prints to stdout from all packages except
# drizzlepac
#stdout_logger.addFilter(logutil.EchoFilter(include=['drizzlepac']))
else:
print('No trailer file created...')
def find_gsc_offset(image, input_catalog='GSC1', output_catalog='GAIA'):
"""Find the GSC to GAIA offset based on guide star coordinates
Parameters
----------
image : str
filename of image to be processed
Returns
-------
delta_ra,delta_dec : tuple of floats
Offset in decimal degrees of image based on correction to guide star
coordinates relative to GAIA
"""
serviceType = "GSCConvert/GSCconvert.aspx"
spec_str = "TRANSFORM={}-{}&IPPPSSOOT={}"
if 'rootname' in pf.getheader(image):
ippssoot = pf.getval(image, 'rootname').upper()
else:
ippssoot = fu.buildNewRootname(image).upper()
spec = spec_str.format(input_catalog, output_catalog, ippssoot)
serviceUrl = "{}/{}?{}".format(SERVICELOCATION, serviceType,spec)
rawcat = requests.get(serviceUrl)
if not rawcat.ok:
log.info("Problem accessing service with:\n{{}".format(serviceUrl))
raise ValueError
delta_ra = delta_dec = None
tree = BytesIO(rawcat.content)
for _,element in etree.iterparse(tree):
if element.tag == 'deltaRA':
delta_ra = float(element.text)
elif element.tag == 'deltaDEC':
delta_dec = float(element.text)
return delta_ra,delta_dec
def find_gsc_offset(image, input_catalog='GSC1', output_catalog='GAIA'):
"""Find the GSC to GAIA offset based on guide star coordinates
Parameters
----------
image : str
filename of image to be processed
Returns
-------
delta_ra,delta_dec : tuple of floats
Offset in decimal degrees of image based on correction to guide star
coordinates relative to GAIA
"""
serviceType = "GSCConvert/GSCconvert.aspx"
spec_str = "TRANSFORM={}-{}&IPPPSSOOT={}"
if 'rootname' in pf.getheader(image):
ippssoot = pf.getval(image, 'rootname').upper()
else:
ippssoot = fu.buildNewRootname(image).upper()
spec = spec_str.format(input_catalog, output_catalog, ippssoot)
serviceUrl = "{}/{}?{}".format(SERVICELOCATION, serviceType, spec)
rawcat = requests.get(serviceUrl)
if not rawcat.ok:
print("Problem accessing service with:\n{{}".format(serviceUrl))
raise ValueError
delta_ra = delta_dec = None
tree = BytesIO(rawcat.content)
for _, element in etree.iterparse(tree):
if element.tag == 'deltaRA':
delta_ra = float(element.text)
elif element.tag == 'deltaDEC':
delta_dec = float(element.text)
return delta_ra, delta_dec
def waiver2mef(sciname, newname=None, convert_dq=True):
"""
Converts a GEIS science file and its corresponding
data quality file (if present) to MEF format
Writes out both files to disk.
Returns the new name of the science image.
"""
def convert(file):
newfilename = fileutil.buildNewRootname(file, extn='_c0h.fits')
try:
newimage = fileutil.openImage(file,writefits=True,
fitsname=newfilename,clobber=True)
del newimage
return newfilename
except IOError:
print('Warning: File %s could not be found' % file)
return None
newsciname = convert(sciname)
if convert_dq:
dq_name = convert(fileutil.buildNewRootname(sciname, extn='_c1h.fits'))
return newsciname
def splitStis(stisfile, sci_count):
"""
:Purpose: Split a STIS association file into multiple imset MEF files.
Split the corresponding spt file if present into single spt files.
If an spt file can't be split or is missing a Warning is printed.
Returns
-------
names: list
a list with the names of the new flt files.
"""
newfiles = []
f = fits.open(stisfile)
hdu0 = f[0].copy()
for count in range(1, sci_count + 1):
fitsobj = fits.HDUList()
fitsobj.append(hdu0)
hdu = f[('sci', count)].copy()
fitsobj.append(hdu)
rootname = hdu.header['EXPNAME']
newfilename = fileutil.buildNewRootname(rootname, extn='_flt.fits')
try:
# Verify error array exists
if f[('err', count)].data == None:
raise ValueError
# Verify dq array exists
if f[('dq', count)].data == None:
raise ValueError
# Copy the err extension
hdu = f[('err', count)].copy()
fitsobj.append(hdu)
# Copy the dq extension
hdu = f[('dq', count)].copy()
fitsobj.append(hdu)
fitsobj[1].header['EXTVER'] = 1
fitsobj[2].header['EXTVER'] = 1
fitsobj[3].header['EXTVER'] = 1
except ValueError:
print('\nWarning:')
print('Extension version %d of the input file %s does not' %
(count, stisfile))
print('contain all required image extensions. Each must contain')
print('populates SCI, ERR and DQ arrays.')
continue
# Determine if the file you wish to create already exists on the disk.
# If the file does exist, replace it.
if (os.path.exists(newfilename)):
os.remove(newfilename)
print(" Replacing " + newfilename + "...")
# Write out the new file
fitsobj.writeto(newfilename)
newfiles.append(newfilename)
f.close()
sptfilename = fileutil.buildNewRootname(stisfile, extn='_spt.fits')
try:
sptfile = fits.open(sptfilename)
except IOError:
print('SPT file not found %s \n' % sptfilename)
return newfiles
if sptfile:
hdu0 = sptfile[0].copy()
try:
for count in range(1, sci_count + 1):
fitsobj = fits.HDUList()
fitsobj.append(hdu0)
hdu = sptfile[count].copy()
fitsobj.append(hdu)
rootname = hdu.header['EXPNAME']
newfilename = fileutil.buildNewRootname(rootname,
extn='_spt.fits')
fitsobj[1].header['EXTVER'] = 1
if (os.path.exists(newfilename)):
os.remove(newfilename)
print(" Replacing " + newfilename + "...")
# Write out the new file
fitsobj.writeto(newfilename)
except:
print("Warning: Unable to split spt file %s " % sptfilename)
sptfile.close()
return newfiles
def compare_sub_to_full_sci(subarray,full_sci,output=False,update=True):
from stsci.tools import fileutil
from stwcs import updatewcs
if update:
# update input SCI file to be consistent with reference files in header
print('Updating input file ',subarray,' to be consistent with reference files listed in header...')
updatewcs.updatewcs(subarray)
print('Updating input file ',full_sci,' to be consistent with reference files listed in header...')
updatewcs.updatewcs(full_sci)
fulldgeofile = fileutil.osfn(pyfits.getval(subarray,'ODGEOFIL'))
# parse out rootname from input file if user wants results written to file
if output:
soutroot = fileutil.buildNewRootname(subarray)
foutroot = fileutil.buildNewRootname(full_sci)
hdulist = pyfits.open(fulldgeofile)
detector = pyfits.getval(fulldgeofile,'DETECTOR')
filter_names = fileutil.getFilterNames(pyfits.getheader(subarray))
# count the number of chips in subarray image
xyfile = pyfits.open(subarray)
numchips = 0
ccdchip = []
extname = xyfile[1].header['EXTNAME']
for extn in xyfile:
if 'extname' in extn.header and extn.header['extname'] == extname:
numchips += 1
if 'ccdchip' in extn.header:
ccdchip.append([extn.header['ccdchip'],extn.header['extver']])
else:
ccdchip.append([1,1])
snx = xyfile['sci',1].header['NAXIS1']
sny = xyfile['sci',1].header['NAXIS2']
ltv1 = xyfile['sci',1].header['ltv1']
ltv2 = xyfile['sci',1].header['ltv2']
xyfile.close()
# build grid of points for full-size image for
# chips corresponding to subarray
xyfile = pyfits.open(full_sci)
fullchip = []
for extn in xyfile:
if ('extname' in extn.header and extn.header['extname'] == extname) and \
extn.header['ccdchip'] == ccdchip[0][0]:
fullchip.append([extn.header['ccdchip'],extn.header['extver']])
xyfile.close()
sxarr,syarr = build_grid_arrays(snx,sny,1)
full_range = [slice(-ltv2,-ltv2+sny),slice(-ltv1,-ltv1+snx)]
fnx = pyfits.getval(full_sci,'NAXIS1','sci',1)
fny = pyfits.getval(full_sci,'NAXIS2','sci',1)
fxarr,fyarr = build_grid_arrays(fnx,fny,1)
# initialize plot here
if has_matplotlib:
pl.clf()
pl.gray()
for chip,det,fext in zip(list(range(1,numchips+1)),ccdchip,fullchip):
# Compute the correction imposed by the D2IM+DGEO corrections
# on the subarray
sxout,syout = transform_d2im_dgeo(subarray,det[1],sxarr,syarr)
sdx= (sxout-sxarr).reshape(sny,snx)
sdy= (syout-syarr).reshape(sny,snx)
# Compute the correction imposed by the D2IM+DGEO corrections
# on the full sized SCI image
fxout,fyout = transform_d2im_dgeo(full_sci,fext[1],fxarr,fyarr)
fdx= (fxout-fxarr).reshape(fny,fnx)
fdy= (fyout-fyarr).reshape(fny,fnx)
# determine the difference
diffx = (sdx - fdx[full_range[0],full_range[1]]).astype(np.float32)
if has_matplotlib:
pl.imshow(diffx)
pl.title('sub_dx-full_x: %s %s[%d:%d,%d:%d] with %g +/- %g' %
(filter_names, detector, full_range[0].start,
full_range[0].stop, full_range[1].start,
full_range[1].stop, diffx.mean(),diffx.std()))
pl.colorbar()
if sys.version_info[0] < 3:
raw_input("Press 'ENTER' to close figure and plot DY...")
else:
input("Press 'ENTER' to close figure and plot DY...")
pl.close()
# determine the difference
diffy = (sdy - fdy[full_range[0],full_range[1]]).astype(np.float32)
if has_matplotlib:
pl.imshow(diffy)
pl.title('sub_dy-full_y: %s %s[%d:%d,%d:%d] with %g +/- %g' %
(filter_names, detector, full_range[0].start,
full_range[0].stop, full_range[1].start,
full_range[1].stop, diffy.mean(), diffy.std()))
pl.colorbar()
if sys.version_info[0] < 3:
raw_input("Press 'ENTER' to close figure and exit...")
else:
input("Press 'ENTER' to close figure and exit...")
pl.close()
if output:
outname = foutroot+'_sci'+str(chip)+'_newfull_dxy.fits'
if os.path.exists(outname): os.remove(outname)
hdulist['dx',chip].data = fdx
hdulist['dy',chip].data = fdy
hdulist.writeto(outname)
outname = soutroot+'_sci'+str(chip)+'_newsub_dxy.fits'
if os.path.exists(outname): os.remove(outname)
hdulist['dx',chip].data = sdx
hdulist['dy',chip].data = sdy
hdulist.writeto(outname)
"""
outname = outroot+'_sci'+str(chip)+'_diff_dxy.fits'
if os.path.exists(outname): os.remove(outname)
hdulist['dx',chip].data = diffx
hdulist['dy',chip].data = diffy
hdulist.writeto(outname)
"""
print('Created output file with differences named: ',outname)
if output:
hdulist.close()
def process(inFile,force=False,newpath=None, inmemory=False, num_cores=None,
headerlets=True, align_to_gaia=True):
""" Run astrodrizzle on input file/ASN table
using default values for astrodrizzle parameters.
"""
# We only need to import this package if a user run the task
import drizzlepac
from drizzlepac import processInput # used for creating new ASNs for _flc inputs
from stwcs import updatewcs
from drizzlepac import alignimages
# interpret envvar variable, if specified
if envvar_compute_name in os.environ:
val = os.environ[envvar_compute_name].lower()
if val not in envvar_bool_dict:
msg = "ERROR: invalid value for {}.".format(envvar_compute_name)
msg += " \n Valid Values: on, off, yes, no, true, false"
raise ValueError(msg)
align_to_gaia = envvar_bool_dict[val]
if envvar_new_apriori_name in os.environ:
# Reset ASTROMETRY_STEP_CONTROL based on this variable
# This provides backward-compatibility until ASTROMETRY_STEP_CONTROL
# gets removed entirely.
val = os.environ[envvar_new_apriori_name].lower()
if val not in envvar_dict:
msg = "ERROR: invalid value for {}.".format(envvar_new_apriori_name)
msg += " \n Valid Values: on, off, yes, no, true, false"
raise ValueError(msg)
os.environ[envvar_old_apriori_name] = envvar_dict[val]
if headerlets or align_to_gaia:
from stwcs.wcsutil import headerlet
# Open the input file
try:
# Make sure given filename is complete and exists...
inFilename = fileutil.buildRootname(inFile,ext=['.fits'])
if not os.path.exists(inFilename):
print("ERROR: Input file - %s - does not exist." % inFilename)
return
except TypeError:
print("ERROR: Inappropriate input file.")
return
#If newpath was specified, move all files to that directory for processing
if newpath:
orig_processing_dir = os.getcwd()
new_processing_dir = _createWorkingDir(newpath,inFilename)
_copyToNewWorkingDir(new_processing_dir,inFilename)
os.chdir(new_processing_dir)
# Initialize for later use...
_mname = None
_new_asn = None
_calfiles = []
# Identify WFPC2 inputs to account for differences in WFPC2 inputs
wfpc2_input = fits.getval(inFilename, 'instrume') == 'WFPC2'
cal_ext = None
# Check input file to see if [DRIZ/DITH]CORR is set to PERFORM
if '_asn' in inFilename:
# We are working with an ASN table.
# Use asnutil code to extract filename
inFilename = _lowerAsn(inFilename)
_new_asn = [inFilename]
_asndict = asnutil.readASNTable(inFilename,None,prodonly=False)
_cal_prodname = _asndict['output'].lower()
#_fname = fileutil.buildRootname(_cal_prodname,ext=['_drz.fits'])
# Retrieve the first member's rootname for possible use later
_fimg = fits.open(inFilename, memmap=False)
for name in _fimg[1].data.field('MEMNAME'):
if name[-1] != '*':
_mname = name.split('\0', 1)[0].lower()
break
_fimg.close()
del _fimg
else:
# Check to see if input is a _RAW file
# If it is, strip off the _raw.fits extension...
_indx = inFilename.find('_raw')
if _indx < 0: _indx = len(inFilename)
# ... and build the CALXXX product rootname.
if wfpc2_input:
# force code to define _c0m file as calibrated product to be used
cal_ext = ['_c0m.fits']
_mname = fileutil.buildRootname(inFilename[:_indx], ext=cal_ext)
_cal_prodname = inFilename[:_indx]
# Reset inFilename to correspond to appropriate input for
# drizzle: calibrated product name.
inFilename = _mname
if _mname is None:
errorMsg = 'Could not find calibrated product!'
raise Exception(errorMsg)
# Create trailer filenames based on ASN output filename or
# on input name for single exposures
if '_raw' in inFile:
# Output trailer file to RAW file's trailer
_trlroot = inFile[:inFile.find('_raw')]
elif '_asn' in inFile:
# Output trailer file to ASN file's trailer, not product's trailer
_trlroot = inFile[:inFile.find('_asn')]
else:
# Default: trim off last suffix of input filename
# and replacing with .tra
_indx = inFile.rfind('_')
if _indx > 0:
_trlroot = inFile[:_indx]
else:
_trlroot = inFile
_trlfile = _trlroot + '.tra'
# Open product and read keyword value
# Check to see if product already exists...
dkey = 'DRIZCORR'
# ...if product does NOT exist, interrogate input file
# to find out whether 'dcorr' has been set to PERFORM
# Check if user wants to process again regardless of DRIZCORR keyword value
if force:
dcorr = 'PERFORM'
else:
if _mname :
_fimg = fits.open(fileutil.buildRootname(_mname,ext=['_raw.fits']), memmap=False)
_phdr = _fimg['PRIMARY'].header
if dkey in _phdr:
dcorr = _phdr[dkey]
else:
dcorr = None
_fimg.close()
del _fimg
else:
dcorr = None
time_str = _getTime()
_tmptrl = _trlroot + '_tmp.tra'
_drizfile = _trlroot + '_pydriz'
_drizlog = _drizfile + ".log" # the '.log' gets added automatically by astrodrizzle
_alignlog = _trlroot + '_align.log'
if dcorr == 'PERFORM':
if '_asn.fits' not in inFilename:
# Working with a singleton
# However, we always want to make sure we always use
# a calibrated product as input, if available.
_infile = fileutil.buildRootname(_cal_prodname, ext=cal_ext)
_infile_flc = fileutil.buildRootname(_cal_prodname,ext=['_flc.fits'])
_cal_prodname = _infile
_inlist = _calfiles = [_infile]
# Add CTE corrected filename as additional input if present
if os.path.exists(_infile_flc) and _infile_flc != _infile:
_inlist.append(_infile_flc)
else:
# Working with an ASN table...
_infile = inFilename
flist,duplist = processInput.checkForDuplicateInputs(_asndict['order'])
_calfiles = flist
if len(duplist) > 0:
origasn = processInput.changeSuffixinASN(inFilename,'flt')
dupasn = processInput.changeSuffixinASN(inFilename,'flc')
_inlist = [origasn,dupasn]
else:
_inlist = [_infile]
# We want to keep the original specification of the calibration
# product name, though, not a lower-case version...
_cal_prodname = inFilename
_new_asn.extend(_inlist) # kept so we can delete it when finished
# check to see whether FLC files are also present, and need to be updated
# generate list of FLC files
align_files = None
_calfiles_flc = [f.replace('_flt.fits','_flc.fits') for f in _calfiles]
# insure these files exist, if not, blank them out
# Also pick out what files will be used for additional alignment to GAIA
if not os.path.exists(_calfiles_flc[0]):
_calfiles_flc = None
align_files = _calfiles
align_update_files = None
else:
align_files = _calfiles_flc
align_update_files = _calfiles
# Run updatewcs on each list of images
updatewcs.updatewcs(_calfiles)
if _calfiles_flc:
updatewcs.updatewcs(_calfiles_flc)
if align_to_gaia:
# Perform additional alignment on the FLC files, if present
###############
#
# call hlapipeline code here on align_files list of files
#
###############
# Create trailer marker message for start of align_to_GAIA processing
_trlmsg = _timestamp("Align_to_GAIA started ")
print(_trlmsg)
ftmp = open(_tmptrl,'w')
ftmp.writelines(_trlmsg)
ftmp.close()
_appendTrlFile(_trlfile,_tmptrl)
_trlmsg = ""
# Create an empty astropy table so it can be used as input/output for the perform_align function
#align_table = Table()
try:
align_table = alignimages.perform_align(align_files,update_hdr_wcs=True, runfile=_alignlog)
for row in align_table:
if row['status'] == 0:
trlstr = "Successfully aligned {} to {} astrometric frame\n"
_trlmsg += trlstr.format(row['imageName'], row['catalog'])
else:
trlstr = "Could not align {} to absolute astrometric frame\n"
_trlmsg += trlstr.format(row['imageName'])
except Exception:
# Something went wrong with alignment to GAIA, so report this in
# trailer file
_trlmsg = "EXCEPTION encountered in alignimages...\n"
_trlmsg += " No correction to absolute astrometric frame applied!\n"
# Write the perform_align log to the trailer file...(this will delete the _alignlog)
_appendTrlFile(_trlfile,_alignlog)
# Append messages from this calling routine post-perform_align
ftmp = open(_tmptrl,'w')
ftmp.writelines(_trlmsg)
ftmp.close()
_appendTrlFile(_trlfile,_tmptrl)
_trlmsg = ""
#Check to see whether there are any additional input files that need to
# be aligned (namely, FLT images)
if align_update_files and align_table:
# Apply headerlets from alignment to FLT version of the files
for fltfile, flcfile in zip(align_update_files, align_files):
row = align_table[align_table['imageName']==flcfile]
headerletFile = row['headerletFile'][0]
if headerletFile != "None":
headerlet.apply_headerlet_as_primary(fltfile, headerletFile,
attach=True, archive=True)
# append log file contents to _trlmsg for inclusion in trailer file
_trlstr = "Applying headerlet {} as Primary WCS to {}\n"
_trlmsg += _trlstr.format(headerletFile, fltfile)
else:
_trlmsg += "No absolute astrometric headerlet applied to {}\n".format(fltfile)
# Finally, append any further messages associated with alignement from this calling routine
_trlmsg += _timestamp('Align_to_GAIA completed ')
print(_trlmsg)
ftmp = open(_tmptrl,'w')
ftmp.writelines(_trlmsg)
ftmp.close()
_appendTrlFile(_trlfile,_tmptrl)
# Run astrodrizzle and send its processing statements to _trlfile
_pyver = drizzlepac.astrodrizzle.__version__
for _infile in _inlist: # Run astrodrizzle for all inputs
# Create trailer marker message for start of astrodrizzle processing
_trlmsg = _timestamp('astrodrizzle started ')
_trlmsg += __trlmarker__
_trlmsg += '%s: Processing %s with astrodrizzle Version %s\n' % (time_str,_infile,_pyver)
print(_trlmsg)
# Write out trailer comments to trailer file...
ftmp = open(_tmptrl,'w')
ftmp.writelines(_trlmsg)
ftmp.close()
_appendTrlFile(_trlfile,_tmptrl)
_pyd_err = _trlroot+'_pydriz.stderr'
try:
b = drizzlepac.astrodrizzle.AstroDrizzle(input=_infile,runfile=_drizfile,
configobj='defaults',in_memory=inmemory,
num_cores=num_cores, **pipeline_pars)
except Exception as errorobj:
_appendTrlFile(_trlfile,_drizlog)
_appendTrlFile(_trlfile,_pyd_err)
_ftrl = open(_trlfile,'a')
_ftrl.write('ERROR: Could not complete astrodrizzle processing of %s.\n' % _infile)
_ftrl.write(str(sys.exc_info()[0])+': ')
_ftrl.writelines(str(errorobj))
_ftrl.write('\n')
_ftrl.close()
print('ERROR: Could not complete astrodrizzle processing of %s.' % _infile)
raise Exception(str(errorobj))
# Now, append comments created by PyDrizzle to CALXXX trailer file
print('Updating trailer file %s with astrodrizzle comments.' % _trlfile)
_appendTrlFile(_trlfile,_drizlog)
# Save this for when astropy.io.fits can modify a file 'in-place'
# Update calibration switch
_fimg = fits.open(_cal_prodname, mode='update', memmap=False)
_fimg['PRIMARY'].header[dkey] = 'COMPLETE'
_fimg.close()
del _fimg
# Enforce pipeline convention of all lower-case product
# names
_prodlist = glob.glob('*drz.fits')
for _prodname in _prodlist:
_plower = _prodname.lower()
if _prodname != _plower: os.rename(_prodname,_plower)
else:
# Create default trailer file messages when astrodrizzle is not
# run on a file. This will typically apply only to BIAS,DARK
# and other reference images.
# Start by building up the message...
_trlmsg = _timestamp('astrodrizzle skipped ')
_trlmsg = _trlmsg + __trlmarker__
_trlmsg = _trlmsg + '%s: astrodrizzle processing not requested for %s.\n' % (time_str,inFilename)
_trlmsg = _trlmsg + ' astrodrizzle will not be run at this time.\n'
print(_trlmsg)
# Write message out to temp file and append it to full trailer file
ftmp = open(_tmptrl,'w')
ftmp.writelines(_trlmsg)
ftmp.close()
_appendTrlFile(_trlfile,_tmptrl)
# Append final timestamp to trailer file...
_final_msg = '%s: Finished processing %s \n' % (time_str,inFilename)
_final_msg += _timestamp('astrodrizzle completed ')
_trlmsg += _final_msg
ftmp = open(_tmptrl,'w')
ftmp.writelines(_trlmsg)
ftmp.close()
_appendTrlFile(_trlfile,_tmptrl)
# If we created a new ASN table, we need to remove it
if _new_asn is not None:
for _name in _new_asn: fileutil.removeFile(_name)
# Clean up any generated OrIg_files directory
if os.path.exists("OrIg_files"):
# check to see whether this directory is empty
flist = glob.glob('OrIg_files/*.fits')
if len(flist) == 0:
os.rmdir("OrIg_files")
else:
print('OrIg_files directory NOT removed as it still contained images...')
# If headerlets have already been written out by alignment code,
# do NOT write out this version of the headerlets
if headerlets:
# Generate headerlets for each updated FLT image
hlet_msg = _timestamp("Writing Headerlets started")
for fname in _calfiles:
frootname = fileutil.buildNewRootname(fname)
hname = "%s_flt_hlet.fits"%frootname
# Write out headerlet file used by astrodrizzle, however,
# do not overwrite any that was already written out by alignimages
if not os.path.exists(hname):
hlet_msg += "Created Headerlet file %s \n"%hname
try:
headerlet.write_headerlet(fname,'OPUS',output='flt', wcskey='PRIMARY',
author="OPUS",descrip="Default WCS from Pipeline Calibration",
attach=False,clobber=True,logging=False)
except ValueError:
hlet_msg += _timestamp("SKIPPED: Headerlet not created for %s \n"%fname)
# update trailer file to log creation of headerlet files
hlet_msg += _timestamp("Writing Headerlets completed")
ftrl = open(_trlfile,'a')
ftrl.write(hlet_msg)
ftrl.close()
# If processing was done in a temp working dir, restore results to original
# processing directory, return to original working dir and remove temp dir
if newpath:
_restoreResults(new_processing_dir,orig_processing_dir)
os.chdir(orig_processing_dir)
_removeWorkingDir(new_processing_dir)
# Provide feedback to user
print(_final_msg)
def __init__(self,expname, handle=None, dqname=None, idckey=None,
new=no,wcs=None,mask=None,pa_key=None, parity=None,
idcdir=None, rot=None, extver=1, exptime=None,
ref_pscale=1.0, binned=1, mt_wcs=None, group_indx = None):
# This name should be formatted for use in image I/O
self.name = fileutil.osfn(expname)
# osfn() will expand '.' unnecessarily, potentially
# creating a string-length problem for 'drizzle', which
# is limited to strings of 80 chars.
_path,_name = os.path.split(self.name)
# if path for this filename is the same as the current dir,
# then there is no need to pass along the path.
if _path == os.getcwd(): self.name = _name
# Keep track of any associated mask file created for
# this exposure from its DQ file, or other mask file.
_fname,_extn = fileutil.parseFilename(expname)
_open = False
# Make sure we have an open file handle to use for getting the
# header and data arrays.
if not handle and not new:
handle = fileutil.openImage(expname)
_open = True
# If no extension was specified, try to interrogate the file
# to find whether the SCI array is in the Primary
# (as in Simple FITS) or first extension (as in MEF).
if handle and _extn == None:
if handle[0].data == None:
# Primary extension specified and no data present.
# Try looking for data in next extension.
if len(handle) > 1 and handle[1].data != None:
_extn = 1
expname += '[1]'
else:
raise IOError("No valid image data in %s.\n"%expname)
else:
_extn = 0
self.dgeoname = None
self.xgeoim = ""
self.ygeoim = ""
self.exptime = exptime
self.group_indx = group_indx
if not new:
# Read in a copy of the header for this exposure/group/extension
_header = fileutil.getHeader(expname,handle=handle)
_chip = drutil.getChipId(_header)
self.chip = str(_chip)
# Keep track of any distortion correction images provided
# for this chip
self.dgeoname = fileutil.getKeyword(expname,'DGEOFILE',handle=handle)
self.xgeoim,self.ygeoim = self.getDGEOExtn()
if self.exptime == None:
self.exptime = float(_header['EXPTIME'])
if self.exptime == 0.: self.exptime = 1.0
#
# Extract photometric transformation keywords
# If they do not exist, use default values of 0 and 1
#
self.plam = float(fileutil.getKeyword(expname,'PHOTPLAM',handle=handle)) / 10.
if self.plam == None:
# Setup a default value in case this keyword does not exist
self.plam = 555.
self.photzpt = float(fileutil.getKeyword(expname,'PHOTZPT',handle=handle))
if self.photzpt == None: self.photzpt = 0.0
self.photflam = float(fileutil.getKeyword(expname,'PHOTFLAM',handle=handle))
if self.photflam == None: self.photflam = 1.0
# Read in date-obs from primary header
if _header:
if 'date-obs' in _header:
self.dateobs = _header['date-obs']
elif 'date_obs' in _header:
self.dateobs = _header['date_obs']
else:
self.dateobs = None
else:
self.dateobs = None
# Initialize the value of BUNIT based on the header information, if
# the header has the keyword
if 'BUNIT' in _header and _header['BUNIT'].find('ergs') < 0:
self.bunit = _header['BUNIT']
else:
self.bunit = 'ELECTRONS'
else:
_chip = 1
_header = None
self.chip = str(_chip)
# Set a default value for pivot wavelength
self.plam = 555.
self.photzpt = 0.0
self.photflam = 1.0
self.dateobs = None
if self.exptime == None:
self.exptime = 1.
self.parity = parity
self.header = _header
self.extver = extver
# Create a pointer to the mask file's data array
# and the name of the original input DQ file
self.maskname = None
self.singlemaskname = None
self.masklist = None
if mask != None:
# Specifies filenames to be used if created.
self.maskname = mask[0]
self.singlemaskname = mask[1]
self.masklist = mask[2]
self.dqname = dqname
# Remember the name of the coeffs file generated for this chip
self.coeffs = self.buildCoeffsName()
# Read the name of idcfile from image header if not explicitly
# provided by user.
if idckey != None and idckey.lower() != 'wcs':
_indx = expname.find('[')
if _indx > -1:
_idc_fname = expname[:_indx]+'[0]'
else: _idc_fname = expname+'[0]'
idcfile, idctype = drutil.getIDCFile(self.header,keyword=idckey,
directory=idcdir)
else:
idcfile = None
idctype = None
if (idckey != None) and (idckey.lower() == 'header'):
idckey = idctype
# Get distortion model and WCS info.
self.geometry = ObsGeometry(expname, idcfile, idckey=idckey,
chip=_chip, new=new, header=self.header,
pa_key=pa_key, rot=rot, date=self.dateobs,
ref_pscale=ref_pscale, binned=binned, mt_wcs=mt_wcs)
# Remember the name and type of the IDC file used...
self.idcfile = idcfile
self.idctype = idctype
# Remember the names of the filters used for the exposure
self.filters = self.geometry.filter1+','+self.geometry.filter2
# Define shape here...
# nx,ny,pixel scale
#
if wcs != None:
# We have been passed a WCS to use
self.geometry.wcs = wcs
self.geometry.model.pscale = wcs.pscale
if expname != None:
self.geometry.wcs.rootname = expname
self.naxis1 = self.geometry.wcs.naxis1
self.naxis2 = self.geometry.wcs.naxis2
self.pscale = self.geometry.wcs.pscale
self.shape = (self.naxis1,self.naxis2,self.pscale)
# Keep track of the positions of the corners of the exposure
# both for the RAW image and the
# distortion-corrected, unscaled, unrotated image
self.corners = {'raw':np.zeros((4,2),dtype=np.float64),'corrected':np.zeros((4,2),dtype=np.float64)}
self.setCorners()
# Generate BLOT output name specific to this Exposure
_blot_extn = '_sci'+repr(extver)+'_blt.fits'
self.outblot = fileutil.buildNewRootname(self.name,extn=_blot_extn)
# Keep track of undistorted frame's position relative to metachip
# Zero-point offset for chip relative to meta-chip product
# These values get computed using 'setSingleOffsets' from 'writeCoeffs'
# to insure that the final XDELTA/YDELTA values have been computed.
self.product_wcs = self.geometry.wcslin
self.xzero = 0.
self.yzero = 0.
self.chip_shape = (0.,0.)
self.xsh2 = 0.
self.ysh2 = 0.
if _open:
handle.close()
del handle
def process(inFile,force=False,newpath=None, inmemory=False, num_cores=None,
headerlets=True):
""" Run astrodrizzle on input file/ASN table
using default values for astrodrizzle parameters.
"""
# We only need to import this package if a user run the task
import drizzlepac
from drizzlepac import processInput # used for creating new ASNs for _flc inputs
import stwcs
if headerlets:
from stwcs.wcsutil import headerlet
# Open the input file
try:
# Make sure given filename is complete and exists...
inFilename = fileutil.buildRootname(inFile,ext=['.fits'])
if not os.path.exists(inFilename):
print("ERROR: Input file - %s - does not exist." % inFilename)
return
except TypeError:
print("ERROR: Inappropriate input file.")
return
#If newpath was specified, move all files to that directory for processing
if newpath:
orig_processing_dir = os.getcwd()
new_processing_dir = _createWorkingDir(newpath,inFilename)
_copyToNewWorkingDir(new_processing_dir,inFilename)
os.chdir(new_processing_dir)
# Initialize for later use...
_mname = None
_new_asn = None
_calfiles = []
# Identify WFPC2 inputs to account for differences in WFPC2 inputs
wfpc2_input = fits.getval(inFilename, 'instrume') == 'WFPC2'
cal_ext = None
# Check input file to see if [DRIZ/DITH]CORR is set to PERFORM
if '_asn' in inFilename:
# We are working with an ASN table.
# Use asnutil code to extract filename
inFilename = _lowerAsn(inFilename)
_new_asn = [inFilename]
_asndict = asnutil.readASNTable(inFilename,None,prodonly=False)
_cal_prodname = _asndict['output'].lower()
_fname = fileutil.buildRootname(_cal_prodname,ext=['_drz.fits'])
# Retrieve the first member's rootname for possible use later
_fimg = fits.open(inFilename, memmap=False)
for name in _fimg[1].data.field('MEMNAME'):
if name[-1] != '*':
_mname = name.split('\0', 1)[0].lower()
break
_fimg.close()
del _fimg
else:
# Check to see if input is a _RAW file
# If it is, strip off the _raw.fits extension...
_indx = inFilename.find('_raw')
if _indx < 0: _indx = len(inFilename)
# ... and build the CALXXX product rootname.
if wfpc2_input:
# force code to define _c0m file as calibrated product to be used
cal_ext = ['_c0m.fits']
_mname = fileutil.buildRootname(inFilename[:_indx], ext=cal_ext)
_cal_prodname = inFilename[:_indx]
# Reset inFilename to correspond to appropriate input for
# drizzle: calibrated product name.
inFilename = _mname
if _mname is None:
errorMsg = 'Could not find calibrated product!'
raise Exception(errorMsg)
# Create trailer filenames based on ASN output filename or
# on input name for single exposures
if '_raw' in inFile:
# Output trailer file to RAW file's trailer
_trlroot = inFile[:inFile.find('_raw')]
elif '_asn' in inFile:
# Output trailer file to ASN file's trailer, not product's trailer
_trlroot = inFile[:inFile.find('_asn')]
else:
# Default: trim off last suffix of input filename
# and replacing with .tra
_indx = inFile.rfind('_')
if _indx > 0:
_trlroot = inFile[:_indx]
else:
_trlroot = inFile
_trlfile = _trlroot + '.tra'
# Open product and read keyword value
# Check to see if product already exists...
dkey = 'DRIZCORR'
# ...if product does NOT exist, interrogate input file
# to find out whether 'dcorr' has been set to PERFORM
# Check if user wants to process again regardless of DRIZCORR keyword value
if force:
dcorr = 'PERFORM'
else:
if _mname :
_fimg = fits.open(fileutil.buildRootname(_mname,ext=['_raw.fits']), memmap=False)
_phdr = _fimg['PRIMARY'].header
if dkey in _phdr:
dcorr = _phdr[dkey]
else:
dcorr = None
_fimg.close()
del _fimg
else:
dcorr = None
time_str = _getTime()
_tmptrl = _trlroot + '_tmp.tra'
_drizfile = _trlroot + '_pydriz'
_drizlog = _drizfile + ".log" # the '.log' gets added automatically by astrodrizzle
if dcorr == 'PERFORM':
if '_asn.fits' not in inFilename:
# Working with a singleton
# However, we always want to make sure we always use
# a calibrated product as input, if available.
_infile = fileutil.buildRootname(_cal_prodname, ext=cal_ext)
_infile_flc = fileutil.buildRootname(_cal_prodname,ext=['_flc.fits'])
_cal_prodname = _infile
_inlist = _calfiles = [_infile]
# Add CTE corrected filename as additional input if present
if os.path.exists(_infile_flc) and _infile_flc != _infile:
_inlist.append(_infile_flc)
else:
# Working with an ASN table...
_infile = inFilename
flist,duplist = processInput.checkForDuplicateInputs(_asndict['order'])
_calfiles = flist
if len(duplist) > 0:
origasn = processInput.changeSuffixinASN(inFilename,'flt')
dupasn = processInput.changeSuffixinASN(inFilename,'flc')
_inlist = [origasn,dupasn]
else:
_inlist = [_infile]
# We want to keep the original specification of the calibration
# product name, though, not a lower-case version...
_cal_prodname = inFilename
_new_asn.extend(_inlist) # kept so we can delete it when finished
# Run astrodrizzle and send its processing statements to _trlfile
_pyver = drizzlepac.astrodrizzle.__version__
for _infile in _inlist: # Run astrodrizzle for all inputs
# Create trailer marker message for start of astrodrizzle processing
_trlmsg = _timestamp('astrodrizzle started ')
_trlmsg = _trlmsg+ __trlmarker__
_trlmsg = _trlmsg + '%s: Processing %s with astrodrizzle Version %s\n' % (time_str,_infile,_pyver)
print(_trlmsg)
# Write out trailer comments to trailer file...
ftmp = open(_tmptrl,'w')
ftmp.writelines(_trlmsg)
ftmp.close()
_appendTrlFile(_trlfile,_tmptrl)
_pyd_err = _trlroot+'_pydriz.stderr'
try:
b = drizzlepac.astrodrizzle.AstroDrizzle(input=_infile,runfile=_drizfile,
configobj='defaults',in_memory=inmemory,
num_cores=num_cores, **pipeline_pars)
except Exception as errorobj:
_appendTrlFile(_trlfile,_drizlog)
_appendTrlFile(_trlfile,_pyd_err)
_ftrl = open(_trlfile,'a')
_ftrl.write('ERROR: Could not complete astrodrizzle processing of %s.\n' % _infile)
_ftrl.write(str(sys.exc_info()[0])+': ')
_ftrl.writelines(str(errorobj))
_ftrl.write('\n')
_ftrl.close()
print('ERROR: Could not complete astrodrizzle processing of %s.' % _infile)
raise Exception(str(errorobj))
# Now, append comments created by PyDrizzle to CALXXX trailer file
print('Updating trailer file %s with astrodrizzle comments.' % _trlfile)
_appendTrlFile(_trlfile,_drizlog)
# Save this for when astropy.io.fits can modify a file 'in-place'
# Update calibration switch
_fimg = fits.open(_cal_prodname, mode='update', memmap=False)
_fimg['PRIMARY'].header[dkey] = 'COMPLETE'
_fimg.close()
del _fimg
# Enforce pipeline convention of all lower-case product
# names
_prodlist = glob.glob('*drz.fits')
for _prodname in _prodlist:
_plower = _prodname.lower()
if _prodname != _plower: os.rename(_prodname,_plower)
else:
# Create default trailer file messages when astrodrizzle is not
# run on a file. This will typically apply only to BIAS,DARK
# and other reference images.
# Start by building up the message...
_trlmsg = _timestamp('astrodrizzle skipped ')
_trlmsg = _trlmsg + __trlmarker__
_trlmsg = _trlmsg + '%s: astrodrizzle processing not requested for %s.\n' % (time_str,inFilename)
_trlmsg = _trlmsg + ' astrodrizzle will not be run at this time.\n'
print(_trlmsg)
# Write message out to temp file and append it to full trailer file
ftmp = open(_tmptrl,'w')
ftmp.writelines(_trlmsg)
ftmp.close()
_appendTrlFile(_trlfile,_tmptrl)
_fmsg = None
# Append final timestamp to trailer file...
_final_msg = '%s: Finished processing %s \n' % (time_str,inFilename)
_final_msg += _timestamp('astrodrizzle completed ')
_trlmsg += _final_msg
ftmp = open(_tmptrl,'w')
ftmp.writelines(_trlmsg)
ftmp.close()
_appendTrlFile(_trlfile,_tmptrl)
# If we created a new ASN table, we need to remove it
if _new_asn is not None:
for _name in _new_asn: fileutil.removeFile(_name)
# Clean up any generated OrIg_files directory
if os.path.exists("OrIg_files"):
# check to see whether this directory is empty
flist = glob.glob('OrIg_files/*.fits')
if len(flist) == 0:
os.rmdir("OrIg_files")
else:
print('OrIg_files directory NOT removed as it still contained images...')
if headerlets:
# Generate headerlets for each updated FLT image
hlet_msg = _timestamp("Writing Headerlets started")
for fname in _calfiles:
frootname = fileutil.buildNewRootname(fname)
hname = "%s_flt_hlet.fits"%frootname
hlet_msg += "Created Headerlet file %s \n"%hname
try:
headerlet.write_headerlet(fname,'OPUS',output='flt', wcskey='PRIMARY',
author="OPUS",descrip="Default WCS from Pipeline Calibration",
attach=False,clobber=True,logging=False)
except ValueError:
hlet_msg += _timestamp("SKIPPED: Headerlet not created for %s \n"%fname)
# update trailer file to log creation of headerlet files
hlet_msg += _timestamp("Writing Headerlets completed")
ftrl = open(_trlfile,'a')
ftrl.write(hlet_msg)
ftrl.close()
# If processing was done in a temp working dir, restore results to original
# processing directory, return to original working dir and remove temp dir
if newpath:
_restoreResults(new_processing_dir,orig_processing_dir)
os.chdir(orig_processing_dir)
_removeWorkingDir(new_processing_dir)
# Provide feedback to user
print(_final_msg)
def buildEmptyDRZ(input, output):
"""
Create an empty DRZ file.
This module creates an empty DRZ file in a valid FITS format so that the HST
pipeline can handle the Multidrizzle zero expossure time exception
where all data has been excluded from processing.
Parameters
----------
input : str
filename of the initial input to process_input
output : str
filename of the default empty _drz.fits file to be generated
"""
# Identify the first input image
inputfile = parseinput.parseinput(input)[0]
if not inputfile:
print('\n******* ERROR *******', file=sys.stderr)
print(
'No input file found! Check specification of parameter '
'"input". ', file=sys.stderr)
print('Quitting...', file=sys.stderr)
print('******* ***** *******\n', file=sys.stderr)
return # raise IOError, "No input file found!"
# Set up output file here...
if output is None:
if len(input) == 1:
oname = fileutil.buildNewRootname(input[0])
else:
oname = 'final'
output = fileutil.buildNewRootname(oname, extn='_drz.fits')
else:
if 'drz' not in output:
output = fileutil.buildNewRootname(output, extn='_drz.fits')
log.info('Setting up output name: %s' % output)
# Open the first image (of the excludedFileList?) to use as a template to build
# the DRZ file.
try :
log.info('Building empty DRZ file from %s' % inputfile[0])
img = fits.open(inputfile[0], memmap=False)
except:
raise IOError('Unable to open file %s \n' % inputfile)
# Create the fitsobject
fitsobj = fits.HDUList()
# Copy the primary header
hdu = img[0].copy()
fitsobj.append(hdu)
# Modify the 'NEXTEND' keyword of the primary header to 3 for the
#'sci, wht, and ctx' extensions of the newly created file.
fitsobj[0].header['NEXTEND'] = 3
# Create the 'SCI' extension
hdu = fits.ImageHDU(header=img['sci', 1].header.copy())
hdu.header['EXTNAME'] = 'SCI'
fitsobj.append(hdu)
# Create the 'WHT' extension
hdu = fits.ImageHDU(header=img['sci', 1].header.copy())
hdu.header['EXTNAME'] = 'WHT'
fitsobj.append(hdu)
# Create the 'CTX' extension
hdu = fits.ImageHDU(header=img['sci', 1].header.copy())
hdu.header['EXTNAME'] = 'CTX'
fitsobj.append(hdu)
# Add HISTORY comments explaining the creation of this file.
fitsobj[0].header.add_history("** AstroDrizzle has created this empty "
"DRZ product because**")
fitsobj[0].header.add_history("** all input images were excluded from "
"processing.**")
# Change the filename in the primary header to reflect the name of the output
# filename.
fitsobj[0].header['FILENAME'] = str(output) # +"_drz.fits"
# Change the ROOTNAME keyword to the ROOTNAME of the output PRODUCT
fitsobj[0].header['ROOTNAME'] = str(output.split('_drz.fits')[0])
# Modify the ASN_MTYP keyword to contain "PROD-DTH" so it can be properly
# ingested into the archive catalog.
# stis has this keyword in the [1] header, so I am directing the code
#t o first look in the primary, then the 1
try:
fitsobj[0].header['ASN_MTYP'] = 'PROD-DTH'
except:
fitsobj[1].header['ASN_MTYP'] = 'PROD-DTH'
# If the file is already on disk delete it and replace it with the
# new file
dirfiles = os.listdir(os.curdir)
if dirfiles.count(output) > 0:
os.remove(output)
log.info(" Replacing %s..." % output)
# Write out the empty DRZ file
fitsobj.writeto(output)
print(textutil.textbox(
'ERROR:\nAstroDrizzle has created an empty DRZ product because all '
'input images were excluded from processing or a user requested the '
'program to stop.') + '\n', file=sys.stderr)
return
def processFilenames(input=None,output=None,infilesOnly=False):
"""Process the input string which contains the input file information and
return a filelist,output
"""
ivmlist = None
oldasndict = None
if input is None:
print("No input files provided to processInput")
raise ValueError
if not isinstance(input, list) and ('_asn' in input or '_asc' in input):
# Input is an association table
# Get the input files, and run makewcs on them
oldasndict = asnutil.readASNTable(input, prodonly=infilesOnly)
if not infilesOnly:
if output in ["",None,"None"]:
output = oldasndict['output'].lower() # insure output name is lower case
asnhdr = fits.getheader(input, memmap=False)
# Only perform duplication check if not already completed...
dupcheck = asnhdr.get('DUPCHECK',default="PERFORM") == "PERFORM"
#filelist = [fileutil.buildRootname(fname) for fname in oldasndict['order']]
filelist = buildASNList(oldasndict['order'],input,check_for_duplicates=dupcheck)
elif (not isinstance(input, list)) and \
(input[0] == '@') :
# input is an @ file
f = open(input[1:])
# Read the first line in order to determine whether
# IVM files have been specified in a second column...
line = f.readline()
f.close()
# Parse the @-file with irafglob to extract the input filename
filelist = irafglob.irafglob(input, atfile=util.atfile_sci)
# If there is a second column...
if len(line.split()) == 2:
# ...parse out the names of the IVM files as well
ivmlist = irafglob.irafglob(input, atfile=util.atfile_ivm)
if output in ['',None,"None"]:
if len(filelist) == 1:
output = fileutil.buildNewRootname(filelist[0])
else:
output = 'final'
else:
#input is a string or a python list
try:
filelist, output = parseinput.parseinput(input, outputname=output)
if output in ['',None,"None"]:
if len(filelist) == 1:
output = fileutil.buildNewRootname(filelist[0])
else:
output = 'final'
if not isinstance(input, list):
filelist.sort()
except IOError: raise
# sort the list of input files
# this ensures the list of input files has the same order on all platforms
# it can have ifferent order because listdir() uses inode order, not unix type order
#filelist.sort()
return filelist, output, ivmlist, oldasndict
def splitStis(stisfile, sci_count):
"""
Purpose
=======
Split a STIS association file into multiple imset MEF files.
Split the corresponding spt file if present into single spt files.
If an spt file can't be split or is missing a Warning is printed.
Output: a list with the names of the new flt files.
"""
newfiles = []
f = pyfits.open(stisfile)
hdu0 = f[0].copy()
for count in range(1,sci_count+1):
#newfilename = rootname+str(count)+'.fits'
fitsobj = pyfits.HDUList()
fitsobj.append(hdu0)
hdu = f['sci',count].copy()
fitsobj.append(hdu)
rootname = hdu.header['EXPNAME']
newfilename = fileutil.buildNewRootname(rootname, extn='_flt.fits')
try:
# Verify error array exists
if f['err',count].data == None:
raise ValueError
# Verify dq array exists
if f['dq',count].data == None:
raise ValueError
# Copy the err extension
hdu = f['err',count].copy()
fitsobj.append(hdu)
# Copy the dq extension
hdu = f['dq',count].copy()
fitsobj.append(hdu)
except:
errorstr = "\n###############################\n"
errorstr += "# #\n"
errorstr += "# ERROR: #\n"
errorstr += "# The input image: #\n"
errorstr += " " + str(stisfile) +"\n"
errorstr += "# does not contain required #\n"
errorstr += "# image extensions. Each #\n"
errorstr += "# must contain populated sci,#\n"
errorstr += "# dq, and err arrays. #\n"
errorstr += "# #\n"
errorstr += "###############################\n"
raise ValueError(errorstr)
# Update the 'EXTNER' keyword to indicate the new extnesion number
# for the single exposure files.
fitsobj[1].header['EXTVER'] = 1
fitsobj[2].header['EXTVER'] = 1
fitsobj[3].header['EXTVER'] = 1
# Determine if the file you wish to create already exists on the disk.
# If the file does exist, replace it.
if (os.path.exists(newfilename)):
os.remove(newfilename)
print(" Replacing "+newfilename+"...")
# Write out the new file
fitsobj.writeto(newfilename)
newfiles.append(newfilename)
f.close()
sptfilename = fileutil.buildNewRootname(stisfile, extn='_spt.fits')
try:
sptfile = pyfits.open(sptfilename)
except IOError:
print('SPT file not found %s \n' % sptfilename)
sptfile=None
if sptfile:
hdu0 = sptfile[0].copy()
try:
for count in range(1,sci_count+1):
fitsobj = pyfits.HDUList()
fitsobj.append(hdu0)
hdu = sptfile[count].copy()
fitsobj.append(hdu)
rootname = hdu.header['EXPNAME']
newfilename = fileutil.buildNewRootname(rootname, extn='_spt.fits')
fitsobj[1].header['EXTVER'] = 1
if (os.path.exists(newfilename)):
os.remove(newfilename)
print(" Replacing "+newfilename+"...")
# Write out the new file
fitsobj.writeto(newfilename)
except:
print("Warning: Unable to split spt file %s " % sptfilename)
sptfile.close()
return newfiles
def run(input,quiet=yes,restore=no,prepend='O', tddcorr=True):
print("+ MAKEWCS Version %s" % __version__)
_prepend = prepend
files = parseinput.parseinput(input)[0]
newfiles = []
if files == []:
print("No valid input files found.\n")
raise IOError
for image in files:
#find out what the input is
imgfits,imgtype = fileutil.isFits(image)
# Check for existence of waiver FITS input, and quit if found.
if imgfits and imgtype == 'waiver':
"""
errormsg = '\n\nPyDrizzle does not support waiver fits format.\n'
errormsg += 'Convert the input files to GEIS or multiextension FITS.\n\n'
raise ValueError, errormsg
"""
newfilename = fileutil.buildNewRootname(image, extn='_c0h.fits')
# Convert GEIS image to MEF file
newimage = fileutil.openImage(image,writefits=True,fitsname=newfilename,clobber=True)
del newimage
# Work with new file
image = newfilename
newfiles.append(image)
# If a GEIS image is provided as input, create a new MEF file with
# a name generated using 'buildFITSName()' and update that new MEF file.
if not imgfits:
# Create standardized name for MEF file
newfilename = fileutil.buildFITSName(image)
# Convert GEIS image to MEF file
newimage = fileutil.openImage(image,writefits=True,fitsname=newfilename,clobber=True)
del newimage
# Work with new file
image = newfilename
newfiles.append(image)
if not quiet:
print("Input files: ",files)
# First get the name of the IDC table
#idctab = drutil.getIDCFile(_files[0][0],keyword='idctab')[0]
idctab = drutil.getIDCFile(image,keyword='idctab')[0]
_found = fileutil.findFile(idctab)
if idctab == None or idctab == '':
print('#\n No IDCTAB specified. No correction can be done for file %s.Quitting makewcs\n' %image)
#raise ValueError
continue
elif not _found:
print('#\n IDCTAB: ',idctab,' could not be found. \n')
print('WCS keywords for file %s will not be updated.\n' %image)
#raise IOError
continue
_phdu = image + '[0]'
_instrument = fileutil.getKeyword(_phdu,keyword='INSTRUME')
if _instrument == 'WFPC2':
Nrefchip, Nrefext = getNrefchip(image)
else:
Nrefchip = None
Nrefext = None
if _instrument not in NUM_PER_EXTN:
raise ValueError("Instrument %s not supported yet. Exiting..." \
%_instrument)
_detector = fileutil.getKeyword(_phdu, keyword='DETECTOR')
_nimsets = get_numsci(image)
for i in range(_nimsets):
if image.find('.fits') > 0:
_img = image+'[sci,'+repr(i+1)+']'
else:
_img = image+'['+repr(i+1)+']'
if not restore:
if not quiet:
print('Updating image: ', _img)
_update(_img,idctab, _nimsets, apply_tdd=False,
quiet=quiet,instrument=_instrument,prepend=_prepend,
nrchip=Nrefchip, nrext = Nrefext)
if _instrument == 'ACS' and _detector == 'WFC':
tddswitch = fileutil.getKeyword(_phdu,keyword='TDDCORR')
# This logic requires that TDDCORR be in the primary header
# and set to PERFORM in order to turn this on at all. It can
# be turned off by setting either tddcorr=False or setting
# the keyword to anything but PERFORM or by deleting the
# keyword altogether. PyDrizzle will rely simply on the
# values of alpha and beta as computed here to apply the
# correction to the coefficients.
if (tddcorr and tddswitch != 'OMIT'):
print('Applying time-dependent distortion corrections...')
_update(_img,idctab, _nimsets, apply_tdd=True, \
quiet=quiet,instrument=_instrument,prepend=_prepend, nrchip=Nrefchip, nrext = Nrefext)
else:
if not quiet:
print('Restoring original WCS values for',_img)
restoreCD(_img,_prepend)
#fimg = fileutil.openImage(image,mode='update')
#if 'TDDCORR' in fimg[0].header and fimg[0].header['TDDCORR'] == 'PERFORM':
# fimg[0].header['TDDCORR'] = 'COMPLETE'
#fimg.close()
if newfiles == []:
return files
else:
return newfiles
def process(inFile,
force=False,
newpath=None,
inmemory=False,
num_cores=None,
headerlets=True):
""" Run astrodrizzle on input file/ASN table
using default values for astrodrizzle parameters.
"""
# We only need to import this package if a user run the task
import drizzlepac
from drizzlepac import processInput # used for creating new ASNs for _flc inputs
import stwcs
if headerlets:
from stwcs.wcsutil import headerlet
# Open the input file
try:
# Make sure given filename is complete and exists...
inFilename = fileutil.buildRootname(inFile, ext=['.fits'])
if not os.path.exists(inFilename):
print("ERROR: Input file - %s - does not exist." % inFilename)
return
except TypeError:
print("ERROR: Inappropriate input file.")
return
#If newpath was specified, move all files to that directory for processing
if newpath:
orig_processing_dir = os.getcwd()
new_processing_dir = _createWorkingDir(newpath, inFilename)
_copyToNewWorkingDir(new_processing_dir, inFilename)
os.chdir(new_processing_dir)
# Initialize for later use...
_mname = None
_new_asn = None
_calfiles = []
# Check input file to see if [DRIZ/DITH]CORR is set to PERFORM
if '_asn' in inFilename:
# We are working with an ASN table.
# Use asnutil code to extract filename
inFilename = _lowerAsn(inFilename)
_new_asn = [inFilename]
_asndict = asnutil.readASNTable(inFilename, None, prodonly=False)
_cal_prodname = _asndict['output'].lower()
_fname = fileutil.buildRootname(_cal_prodname, ext=['_drz.fits'])
# Retrieve the first member's rootname for possible use later
_fimg = fits.open(inFilename)
for name in _fimg[1].data.field('MEMNAME'):
if name[-1] != '*':
_mname = name.split('\0', 1)[0].lower()
break
_fimg.close()
del _fimg
else:
# Check to see if input is a _RAW file
# If it is, strip off the _raw.fits extension...
_indx = inFilename.find('_raw')
if _indx < 0: _indx = len(inFilename)
# ... and build the CALXXX product rootname.
_mname = fileutil.buildRootname(inFilename[:_indx])
_cal_prodname = inFilename[:_indx]
# Reset inFilename to correspond to appropriate input for
# drizzle: calibrated product name.
inFilename = _mname
if _mname == None:
errorMsg = 'Could not find calibrated product!'
raise Exception(errorMsg)
# Create trailer filenames based on ASN output filename or
# on input name for single exposures
if '_raw' in inFile:
# Output trailer file to RAW file's trailer
_trlroot = inFile[:inFile.find('_raw')]
elif '_asn' in inFile:
# Output trailer file to ASN file's trailer, not product's trailer
_trlroot = inFile[:inFile.find('_asn')]
else:
# Default: trim off last suffix of input filename
# and replacing with .tra
_indx = inFile.rfind('_')
if _indx > 0:
_trlroot = inFile[:_indx]
else:
_trlroot = inFile
_trlfile = _trlroot + '.tra'
# Open product and read keyword value
# Check to see if product already exists...
dkey = 'DRIZCORR'
# ...if product does NOT exist, interrogate input file
# to find out whether 'dcorr' has been set to PERFORM
# Check if user wants to process again regardless of DRIZCORR keyword value
if force: dcorr = 'PERFORM'
else:
if _mname:
_fimg = fits.open(fileutil.buildRootname(_mname,
ext=['_raw.fits']))
_phdr = _fimg['PRIMARY'].header
if dkey in _phdr:
dcorr = _phdr[dkey]
else:
dcorr = None
_fimg.close()
del _fimg
else:
dcorr = None
time_str = _getTime()
_tmptrl = _trlroot + '_tmp.tra'
_drizfile = _trlroot + '_pydriz'
_drizlog = _drizfile + ".log" # the '.log' gets added automatically by astrodrizzle
if dcorr == 'PERFORM':
if '_asn.fits' not in inFilename:
# Working with a singleton
# However, we always want to make sure we always use
# a calibrated product as input, if available.
_infile = fileutil.buildRootname(_cal_prodname)
_infile_flc = fileutil.buildRootname(_cal_prodname,
ext=['_flc.fits'])
_cal_prodname = _infile
_inlist = _calfiles = [_infile]
# Add CTE corrected filename as additional input if present
if os.path.exists(_infile_flc) and _infile_flc != _infile:
_inlist.append(_infile_flc)
else:
# Working with an ASN table...
_infile = inFilename
flist, duplist = processInput.checkForDuplicateInputs(
_asndict['order'])
_calfiles = flist
if len(duplist) > 0:
origasn = processInput.changeSuffixinASN(inFilename, 'flt')
dupasn = processInput.changeSuffixinASN(inFilename, 'flc')
_inlist = [origasn, dupasn]
else:
_inlist = [_infile]
# We want to keep the original specification of the calibration
# product name, though, not a lower-case version...
_cal_prodname = inFilename
_new_asn.extend(_inlist) # kept so we can delete it when finished
# Run astrodrizzle and send its processing statements to _trlfile
_pyver = drizzlepac.astrodrizzle.__version__
for _infile in _inlist: # Run astrodrizzle for all inputs
# Create trailer marker message for start of astrodrizzle processing
_trlmsg = _timestamp('astrodrizzle started ')
_trlmsg = _trlmsg + __trlmarker__
_trlmsg = _trlmsg + '%s: Processing %s with astrodrizzle Version %s\n' % (
time_str, _infile, _pyver)
print(_trlmsg)
# Write out trailer comments to trailer file...
ftmp = open(_tmptrl, 'w')
ftmp.writelines(_trlmsg)
ftmp.close()
_appendTrlFile(_trlfile, _tmptrl)
_pyd_err = _trlroot + '_pydriz.stderr'
try:
b = drizzlepac.astrodrizzle.AstroDrizzle(input=_infile,
runfile=_drizfile,
configobj='defaults',
in_memory=inmemory,
num_cores=num_cores,
**pipeline_pars)
except Exception as errorobj:
_appendTrlFile(_trlfile, _drizlog)
_appendTrlFile(_trlfile, _pyd_err)
_ftrl = open(_trlfile, 'a')
_ftrl.write(
'ERROR: Could not complete astrodrizzle processing of %s.\n'
% _infile)
_ftrl.write(str(sys.exc_info()[0]) + ': ')
_ftrl.writelines(str(errorobj))
_ftrl.write('\n')
_ftrl.close()
print(
'ERROR: Could not complete astrodrizzle processing of %s.'
% _infile)
raise Exception(str(errorobj))
# Now, append comments created by PyDrizzle to CALXXX trailer file
print('Updating trailer file %s with astrodrizzle comments.' %
_trlfile)
_appendTrlFile(_trlfile, _drizlog)
# Save this for when astropy.io.fits can modify a file 'in-place'
# Update calibration switch
_fimg = fits.open(_cal_prodname, mode='update')
_fimg['PRIMARY'].header[dkey] = 'COMPLETE'
_fimg.close()
del _fimg
# Enforce pipeline convention of all lower-case product
# names
_prodlist = glob.glob('*drz.fits')
for _prodname in _prodlist:
_plower = _prodname.lower()
if _prodname != _plower: os.rename(_prodname, _plower)
else:
# Create default trailer file messages when astrodrizzle is not
# run on a file. This will typically apply only to BIAS,DARK
# and other reference images.
# Start by building up the message...
_trlmsg = _timestamp('astrodrizzle skipped ')
_trlmsg = _trlmsg + __trlmarker__
_trlmsg = _trlmsg + '%s: astrodrizzle processing not requested for %s.\n' % (
time_str, inFilename)
_trlmsg = _trlmsg + ' astrodrizzle will not be run at this time.\n'
print(_trlmsg)
# Write message out to temp file and append it to full trailer file
ftmp = open(_tmptrl, 'w')
ftmp.writelines(_trlmsg)
ftmp.close()
_appendTrlFile(_trlfile, _tmptrl)
_fmsg = None
# Append final timestamp to trailer file...
_final_msg = '%s: Finished processing %s \n' % (time_str, inFilename)
_final_msg += _timestamp('astrodrizzle completed ')
_trlmsg += _final_msg
ftmp = open(_tmptrl, 'w')
ftmp.writelines(_trlmsg)
ftmp.close()
_appendTrlFile(_trlfile, _tmptrl)
# If we created a new ASN table, we need to remove it
if _new_asn != None:
for _name in _new_asn:
fileutil.removeFile(_name)
# Clean up any generated OrIg_files directory
if os.path.exists("OrIg_files"):
# check to see whether this directory is empty
flist = glob.glob('OrIg_files/*.fits')
if len(flist) == 0:
os.rmdir("OrIg_files")
else:
print(
'OrIg_files directory NOT removed as it still contained images...'
)
if headerlets:
# Generate headerlets for each updated FLT image
hlet_msg = _timestamp("Writing Headerlets started")
for fname in _calfiles:
frootname = fileutil.buildNewRootname(fname)
hname = "%s_flt_hlet.fits" % frootname
hlet_msg += "Created Headerlet file %s \n" % hname
try:
headerlet.write_headerlet(
fname,
'OPUS',
output='flt',
wcskey='PRIMARY',
author="OPUS",
descrip="Default WCS from Pipeline Calibration",
attach=False,
clobber=True,
logging=False)
except ValueError:
hlet_msg += _timestamp(
"SKIPPED: Headerlet not created for %s \n" % fname)
# update trailer file to log creation of headerlet files
hlet_msg += _timestamp("Writing Headerlets completed")
ftrl = open(_trlfile, 'a')
ftrl.write(hlet_msg)
ftrl.close()
# If processing was done in a temp working dir, restore results to original
# processing directory, return to original working dir and remove temp dir
if newpath:
_restoreResults(new_processing_dir, orig_processing_dir)
os.chdir(orig_processing_dir)
_removeWorkingDir(new_processing_dir)
# Provide feedback to user
print(_final_msg)
def processFilenames(input=None, output=None, infilesOnly=False):
"""Process the input string which contains the input file information and
return a filelist,output
"""
ivmlist = None
oldasndict = None
if input is None:
print("No input files provided to processInput")
raise ValueError
if not isinstance(input, list) and ('_asn' in input or '_asc' in input):
# Input is an association table
# Get the input files, and run makewcs on them
oldasndict = asnutil.readASNTable(input, prodonly=infilesOnly)
if not infilesOnly:
if output in ["", None, "None"]:
output = oldasndict['output'].lower(
) # insure output name is lower case
asnhdr = fits.getheader(input, memmap=False)
# Only perform duplication check if not already completed...
dupcheck = asnhdr.get('DUPCHECK', default="PERFORM") == "PERFORM"
#filelist = [fileutil.buildRootname(fname) for fname in oldasndict['order']]
filelist = buildASNList(oldasndict['order'],
input,
check_for_duplicates=dupcheck)
elif (not isinstance(input, list)) and \
(input[0] == '@') :
# input is an @ file
f = open(input[1:])
# Read the first line in order to determine whether
# IVM files have been specified in a second column...
line = f.readline()
f.close()
# Parse the @-file with irafglob to extract the input filename
filelist = irafglob.irafglob(input, atfile=util.atfile_sci)
# If there is a second column...
if len(line.split()) == 2:
# ...parse out the names of the IVM files as well
ivmlist = irafglob.irafglob(input, atfile=util.atfile_ivm)
if output in ['', None, "None"]:
if len(filelist) == 1:
output = fileutil.buildNewRootname(filelist[0])
else:
output = 'final'
else:
#input is a string or a python list
try:
filelist, output = parseinput.parseinput(input, outputname=output)
if output in ['', None, "None"]:
if len(filelist) == 1:
output = fileutil.buildNewRootname(filelist[0])
else:
output = 'final'
if not isinstance(input, list):
filelist.sort()
except IOError:
raise
# sort the list of input files
# this ensures the list of input files has the same order on all platforms
# it can have ifferent order because listdir() uses inode order, not unix type order
#filelist.sort()
return filelist, output, ivmlist, oldasndict
def buildEmptyDRZ(input, output):
"""
Create an empty DRZ file.
This module creates an empty DRZ file in a valid FITS format so that the HST
pipeline can handle the Multidrizzle zero expossure time exception
where all data has been excluded from processing.
Parameters
----------
input : str
filename of the initial input to process_input
output : str
filename of the default empty _drz.fits file to be generated
"""
# Identify the first input image
inputfile = parseinput.parseinput(input)[0]
if not inputfile:
print('\n******* ERROR *******', file=sys.stderr)
print(
'No input file found! Check specification of parameter '
'"input". ',
file=sys.stderr)
print('Quitting...', file=sys.stderr)
print('******* ***** *******\n', file=sys.stderr)
return # raise IOError, "No input file found!"
# Set up output file here...
if output is None:
if len(input) == 1:
oname = fileutil.buildNewRootname(input[0])
else:
oname = 'final'
output = fileutil.buildNewRootname(oname, extn='_drz.fits')
else:
if '_drz' not in output:
output = fileutil.buildNewRootname(output, extn='_drz.fits')
print('Building emtpy DRZ file with output name: %s' % output)
# Open the first image (of the excludedFileList?) to use as a template to build
# the DRZ file.
try:
log.info('Building empty DRZ file from %s' % inputfile[0])
img = fits.open(inputfile[0], memmap=False)
except:
raise IOError('Unable to open file %s \n' % inputfile)
# Create the fitsobject
fitsobj = fits.HDUList()
# Copy the primary header
hdu = img[0].copy()
fitsobj.append(hdu)
# Modify the 'NEXTEND' keyword of the primary header to 3 for the
#'sci, wht, and ctx' extensions of the newly created file.
fitsobj[0].header['NEXTEND'] = 3
# Create the 'SCI' extension
hdu = fits.ImageHDU(header=img['sci', 1].header.copy())
hdu.header['EXTNAME'] = 'SCI'
fitsobj.append(hdu)
# Create the 'WHT' extension
hdu = fits.ImageHDU(header=img['sci', 1].header.copy())
hdu.header['EXTNAME'] = 'WHT'
fitsobj.append(hdu)
# Create the 'CTX' extension
hdu = fits.ImageHDU(header=img['sci', 1].header.copy())
hdu.header['EXTNAME'] = 'CTX'
fitsobj.append(hdu)
# Add HISTORY comments explaining the creation of this file.
fitsobj[0].header.add_history("** AstroDrizzle has created this empty "
"DRZ product because**")
fitsobj[0].header.add_history("** all input images were excluded from "
"processing.**")
# Change the filename in the primary header to reflect the name of the output
# filename.
fitsobj[0].header['FILENAME'] = str(output) # +"_drz.fits"
# Change the ROOTNAME keyword to the ROOTNAME of the output PRODUCT
fitsobj[0].header['ROOTNAME'] = str(output.split('_drz.fits')[0])
# Modify the ASN_MTYP keyword to contain "PROD-DTH" so it can be properly
# ingested into the archive catalog.
# stis has this keyword in the [1] header, so I am directing the code
#t o first look in the primary, then the 1
try:
fitsobj[0].header['ASN_MTYP'] = 'PROD-DTH'
except:
fitsobj[1].header['ASN_MTYP'] = 'PROD-DTH'
# If the file is already on disk delete it and replace it with the
# new file
dirfiles = os.listdir(os.curdir)
if dirfiles.count(output) > 0:
os.remove(output)
log.info(" Replacing %s..." % output)
# Write out the empty DRZ file
fitsobj.writeto(output)
print(textutil.textbox(
'ERROR:\nAstroDrizzle has created an empty DRZ product because all '
'input images were excluded from processing or a user requested the '
'program to stop.') + '\n',
file=sys.stderr)
return
def buildEmptyDRZ(input, output):
"""
METHOD : _buildEmptyDRZ
PURPOSE : Create an empty DRZ file in a valid FITS format so that the HST
pipeline can handle the Multidrizzle zero expossure time exception
where all data has been excluded from processing.
INPUT : None
OUTPUT : DRZ file on disk
"""
if output == None:
if len(input) == 1:
oname = fu.buildNewRootname(input[0])
else:
oname = 'final'
_drzextn = '_drz.fits'
if '_flc.fits' in input[0]:
_drzextn = '_drc.fits'
output = fileutil.buildNewRootname(oname,extn=_drzextn)
else:
if 'drz' not in output:
output = fileutil.buildNewRootname(output,extn='_drz.fits')
print('Setting up output name: ',output)
# Open the first image of the excludedFileList to use as a template to build
# the DRZ file.
inputfile = parseinput.parseinput(input)[0]
try :
img = pyfits.open(inputfile[0])
except:
raise IOError('Unable to open file %s \n' %inputfile)
# Create the fitsobject
fitsobj = pyfits.HDUList()
# Copy the primary header
hdu = img[0].copy()
fitsobj.append(hdu)
# Modify the 'NEXTEND' keyword of the primary header to 3 for the
#'sci, wht, and ctx' extensions of the newly created file.
fitsobj[0].header['NEXTEND'] = 3
# Create the 'SCI' extension
hdu = pyfits.ImageHDU(header=img['sci',1].header.copy(),data=None)
hdu.header['EXTNAME'] = 'SCI'
fitsobj.append(hdu)
# Create the 'WHT' extension
hdu = pyfits.ImageHDU(header=img['sci',1].header.copy(),data=None)
hdu.header['EXTNAME'] = 'WHT'
fitsobj.append(hdu)
# Create the 'CTX' extension
hdu = pyfits.ImageHDU(header=img['sci',1].header.copy(),data=None)
hdu.header['EXTNAME'] = 'CTX'
fitsobj.append(hdu)
# Add HISTORY comments explaining the creation of this file.
fitsobj[0].header.add_history("** Multidrizzle has created this empty DRZ **")
fitsobj[0].header.add_history("** product because all input images were **")
fitsobj[0].header.add_history("** excluded from processing because their **")
fitsobj[0].header.add_history("** header EXPTIME values were 0.0. If you **")
fitsobj[0].header.add_history("** still wish to use this data make the **")
fitsobj[0].header.add_history("** EXPTIME values in the header non-zero. **")
# Change the filename in the primary header to reflect the name of the output
# filename.
fitsobj[0].header['FILENAME'] = str(output) #+"_drz.fits"
# Change the ROOTNAME keyword to the ROOTNAME of the output PRODUCT
_drzsuffix = 'drz'
if 'drc' in output:
_drzsuffix = 'drc'
fitsobj[0].header['ROOTNAME'] = str(output.split('_%s.fits'%_drzsuffix)[0])
print('self.output', output)
# Modify the ASN_MTYP keyword to contain "PROD-DTH" so it can be properly
# ingested into the archive catalog.
fitsobj[0].header['ASN_MTYP'] = 'PROD-DTH'
errstr = "#############################################\n"
errstr += "# #\n"
errstr += "# ERROR: #\n"
errstr += "# Multidrizzle has created this empty DRZ #\n"
errstr += "# product because all input images were #\n"
errstr += "# excluded from processing because their #\n"
errstr += "# header EXPTIME values were 0.0. If you #\n"
errstr += "# still wish to use this data make the #\n"
errstr += "# EXPTIME values in the header non-zero. #\n"
errstr += "# #\n"
errstr += "#############################################\n\n"
print(errstr)
# If the file is already on disk delete it and replace it with the
# new file
dirfiles = os.listdir(os.curdir)
if (dirfiles.count(output) > 0):
os.remove(output)
print(" Replacing "+output+"...")
# Write out the empty DRZ file
fitsobj.writeto(output)
return
def run(scifile,dgeofile=None,output=False,match_sci=False,update=True,vmin=None,vmax=None,plot_offset=0,plot_samp=32):
"""
This routine compares how well the sub-sampled DGEOFILE (generated
using the 'makesmall' module) corrects the input science image as
opposed to the full-size DGEOFILE.
SYNTAX:
import test_small_dgeo
test_small_dgeo.run(scifile,dgeofile=None,output=False)
where:
scifile - name of science image
dgeofile - name of full-sized DGEOFILE if not in DGEOFILE keyword
output - if True, write out differences to FITS file(s)
The user can either specify the full-size DGEOFILE reference filename
as the 'dgeofile' parameter or the code will look for the 'DGEOFILE'
keyword in the primary header for the name of the full-sized reference
file.
The primary output will be a series of plots showing the difference images
with the mean and stddev of the differences in the label of the image display.
If the 'output' parameter is set to True, these differences
will then be written out to FITS files based on the input science image
rootname. Both the DX and DY differences for a single chip will be written
out to the same file, with a separate file for each chip.
"""
from stsci.tools import fileutil
from stwcs import updatewcs
if update:
# update input SCI file to be consistent with reference files in header
print('Updating input file ',scifile,' to be consistent with reference files listed in header...')
updatewcs.updatewcs(scifile)
# Now, get the original NPOLFILE and overwrite the data in the scifile
# WCSDVARR extensions to remove the scaling by the linear terms imposed by
# the SIP convention
npolfile = fileutil.osfn(pyfits.getval(scifile,'NPOLFILE'))
npolroot = os.path.split(npolfile)[1]
dxextns = []
for extn in pyfits.open(npolfile):
if 'extname' in extn.header and extn.header['extname'] in ['DX','DY']:
dxextns.append([extn.header['extname'],extn.header['extver']])
#dxextns = [['dx',1],['dy',1],['dx',2],['dy',2]]
ndxextns = len(dxextns)
# Update input file with NPOLFILE arrays now
print('Updating input file ',scifile,' with original ')
print(' NPOLFILE arrays from ',npolfile)
fsci =pyfits.open(scifile,mode='update')
try:
next = fsci.index_of(('wcsdvarr',1))
except KeyError:
fsci.close()
print('=====')
print('ERROR: No WCSDVARR extensions found!')
print(' Please make sure NPOLFILE is specified and run this task with "update=True".')
print('=====')
return
# Replace WCSDVARR arrays here...
for dxe,wextn in zip(dxextns,list(range(1,ndxextns+1))):
fsci['wcsdvarr',wextn].data = pyfits.getdata(npolfile,dxe[0],dxe[1])
# Now replace the NPOLEXT keyword value with a new one so that it will automatically
# update with the correct file next time updatewcs is run.
fsci['sci',1].header['npolext'] = npolroot
print('Updated NPOLEXT with ',npolroot)
fsci.close()
print('\n=====')
print('WARNING: Updated file ',scifile,' NO LONGER conforms to SIP convention!')
print(' This file will need to be updated with updatewcs before using with MultiDrizzle.')
print('=====\n')
# Get info on full-size DGEOFILE
if dgeofile is None:
# read in full dgeofile from header
fulldgeofile = pyfits.getval(scifile,'DGEOFILE')
else:
fulldgeofile = dgeofile
print('Opening full-size DGEOFILE ',fulldgeofile,' for comparison.')
fulldgeofile = fileutil.osfn(fulldgeofile)
full_shape = [pyfits.getval(fulldgeofile,'NAXIS2','DX',1),pyfits.getval(fulldgeofile,'NAXIS1','DX',1)]
filter_names = fileutil.getFilterNames(pyfits.getheader(scifile))
detector = pyfits.getval(fulldgeofile,'DETECTOR')
# count the number of chips in DGEOFILE
xyfile = pyfits.open(scifile)
numchips = 0
ccdchip = []
extname = xyfile[1].header['EXTNAME']
for extn in xyfile:
if 'extname' in extn.header and extn.header['extname'] == extname:
numchips += 1
if 'ccdchip' in extn.header:
ccdchip.append(extn.header['ccdchip'])
else:
ccdchip.append(1)
if not match_sci:
ltv1 = 0
ltv2 = 0
nx = full_shape[1]
ny = full_shape[0]
else:
nx = xyfile['sci',1].header['NAXIS1']
ny = xyfile['sci',1].header['NAXIS2']
ltv1 = xyfile['sci',1].header['ltv1']
ltv2 = xyfile['sci',1].header['ltv2']
grid = [nx,ny,1]
print('grid of : ',nx,ny)
xyfile.close()
xarr,yarr = build_grid_arrays(nx,ny,1)
xgarr = xarr.reshape(grid[1],grid[0])
ygarr = yarr.reshape(grid[1],grid[0])
# initialize plot here
if has_matplotlib:
pl.clf()
pl.gray()
for chip,det in zip(list(range(1,numchips+1)),ccdchip):
xout,yout = transform_d2im_dgeo(scifile,chip,xarr,yarr)
dgeochip = 1
dgeo = pyfits.open(fulldgeofile)
for e in dgeo:
if 'ccdchip' not in e.header:
continue
else:
if e.header['ccdchip'] == det:
dgeochip = e.header['extver']
break
dgeo.close()
print('Matching sci,', chip, ' with DX,', dgeochip)
dx= (xout-xarr).reshape(grid[1],grid[0])
fulldatax = pyfits.getdata(fulldgeofile,'DX',dgeochip)
diffx=(dx-fulldatax[-ltv2:-ltv2+ny,-ltv1:-ltv1+nx]).astype(np.float32)
if has_matplotlib:
pl.imshow(diffx, vmin=vmin, vmax=vmax)
pl.title('dx-full_x: %s %s(DX,%d) with %g +/- %g' %
(filter_names, detector, dgeochip, diffx.mean(),
diffx.std()))
pl.colorbar()
if sys.version_info[0] < 3:
raw_input("Press 'ENTER' to close figure and plot DY...")
else:
input("Press 'ENTER' to close figure and plot DY...")
pl.close()
dy= (yout-yarr).reshape(grid[1],grid[0])
fulldatay = pyfits.getdata(fulldgeofile,'DY',dgeochip)
diffy=(dy-fulldatay[-ltv2:-ltv2+ny,-ltv1:-ltv1+nx]).astype(np.float32)
if has_matplotlib:
pl.imshow(diffy,vmin=vmin,vmax=vmax)
pl.title('dy-full_y: %s %s(DY,%d) with %g +/- %g ' %
(filter_names, detector, dgeochip, diffy.mean(),
diffy.std()))
pl.colorbar()
if sys.version_info[0] < 3:
raw_input("Press 'ENTER' to close figure and show next chip...")
else:
input("Press 'ENTER' to close figure and show next chip...")
pl.close()
if output:
# parse out rootname from input file if user wants results written to file
outroot = fileutil.buildNewRootname(scifile)
#
# setup DGEOFILE ref file as template for each chip's output results
# we only need dx,1 and dy,1 since each chip will be written out
# to a separate file and since we will use this template for
# writing out 2 different results files
#
fhdulist = pyfits.open(fulldgeofile)
hdulist = pyfits.HDUList()
hdulist.append(fhdulist[0])
hdulist.append(fhdulist['dx',1])
hdulist.append(fhdulist['dy',1])
fhdulist.close()
outname = outroot+'_sci'+str(chip)+'_dgeo_diffxy.match'
if os.path.exists(outname): os.remove(outname)
dxgarr = xgarr+diffx
dygarr = ygarr+diffy
wtraxyutils.write_xy_file(outname,[xgarr[plot_offset::plot_samp,plot_offset::plot_samp].flatten(),
ygarr[plot_offset::plot_samp,plot_offset::plot_samp].flatten(),
dxgarr[plot_offset::plot_samp,plot_offset::plot_samp].flatten(),
dygarr[plot_offset::plot_samp,plot_offset::plot_samp].flatten()],format="%20.8f",append=True)
outname = outroot+'_sci'+str(chip)+'_newfull_dxy.fits'
if os.path.exists(outname): os.remove(outname)
hdulist['dx',1].data = dx
hdulist['dy',1].data = dy
hdulist.writeto(outname)
outname = outroot+'_sci'+str(chip)+'_diff_dxy.fits'
if os.path.exists(outname): os.remove(outname)
hdulist['dx',1].data = diffx
hdulist['dy',1].data = diffy
hdulist.writeto(outname)
print('Created output file with differences named: ',outname)
del dx,dy,diffx,diffy
if output:
hdulist.close()
def splitStis(stisfile, sci_count):
"""
:Purpose: Split a STIS association file into multiple imset MEF files.
Split the corresponding spt file if present into single spt files.
If an spt file can't be split or is missing a Warning is printed.
Returns
-------
names: list
a list with the names of the new flt files.
"""
newfiles = []
f = fits.open(stisfile)
hdu0 = f[0].copy()
for count in range(1,sci_count+1):
fitsobj = fits.HDUList()
fitsobj.append(hdu0)
hdu = f[('sci',count)].copy()
fitsobj.append(hdu)
rootname = hdu.header['EXPNAME']
newfilename = fileutil.buildNewRootname(rootname, extn='_flt.fits')
try:
# Verify error array exists
if f[('err', count)].data is None:
raise ValueError
# Verify dq array exists
if f[('dq', count)].data is None:
raise ValueError
# Copy the err extension
hdu = f[('err',count)].copy()
fitsobj.append(hdu)
# Copy the dq extension
hdu = f[('dq',count)].copy()
fitsobj.append(hdu)
fitsobj[1].header['EXTVER'] = 1
fitsobj[2].header['EXTVER'] = 1
fitsobj[3].header['EXTVER'] = 1
except ValueError:
print('\nWarning:')
print('Extension version %d of the input file %s does not' %(count, stisfile))
print('contain all required image extensions. Each must contain')
print('populates SCI, ERR and DQ arrays.')
continue
# Determine if the file you wish to create already exists on the disk.
# If the file does exist, replace it.
if (os.path.exists(newfilename)):
os.remove(newfilename)
print(" Replacing "+newfilename+"...")
# Write out the new file
fitsobj.writeto(newfilename)
newfiles.append(newfilename)
f.close()
sptfilename = fileutil.buildNewRootname(stisfile, extn='_spt.fits')
try:
sptfile = fits.open(sptfilename)
except IOError:
print('SPT file not found %s \n' % sptfilename)
return newfiles
if sptfile:
hdu0 = sptfile[0].copy()
try:
for count in range(1,sci_count+1):
fitsobj = fits.HDUList()
fitsobj.append(hdu0)
hdu = sptfile[count].copy()
fitsobj.append(hdu)
rootname = hdu.header['EXPNAME']
newfilename = fileutil.buildNewRootname(rootname, extn='_spt.fits')
fitsobj[1].header['EXTVER'] = 1
if (os.path.exists(newfilename)):
os.remove(newfilename)
print(" Replacing "+newfilename+"...")
# Write out the new file
fitsobj.writeto(newfilename)
except:
print("Warning: Unable to split spt file %s " % sptfilename)
sptfile.close()
return newfiles
def find_gsc_offset(obsname, refframe="ICRS"):
"""Find the GSC to GAIA offset based on guide star coordinates
Parameters
----------
obsname : str
Full filename or (preferably)`astropy.io.fits.HDUList` object of
image to be processed.
refframe : str
Reference frame for the guide star coordinates.
Supported options: GSC1, ICRS(default)
NOTES
------
The default transform is GSC2-GAIA. The options were primarily for transforming
individual objects from the catalogs and that is not specified in the limited
documentation. The ipppssoot input is a special case where it pulls the gsids,
epoch and refframe from the dms databases and overrides the transform using this logic::
REFFRAME=GSC1 sets GSC1-GAIA
REFFRAME=ICRS and EPOCH < 2017.75 sets GSC2-GAIA
REFFRAME=ICRS and EPOCH > 2017.75 sets no-offset since it's already in GAIA frame
Returns
-------
deltas : dict
Dict of offset, roll and scale in decimal degrees and pixels for image
based on correction to guide star coordinates relative to GAIA.
Keys: delta_x, delta_y, delta_ra, delta_dec, roll, scale, expwcs, catalog
"""
# check to see whether any URL has been specified as an
# environmental variable.
if gsss_url_envvar in os.environ:
gsss_serviceLocation = os.environ[gsss_url_envvar]
else:
gsss_serviceLocation = gsss_url
# Initialize variables for cases where no offsets are available.
delta_ra = delta_dec = 0.0
delta_roll = 0.0
delta_scale = 1.0
dGSinputRA = dGSoutputRA = 0.0
dGSinputDEC = dGSoutputDEC = 0.0
outputCatalog = None
# Insure input is a fits.HDUList object, if originally provided as a filename(str)
close_obj = False
if isinstance(obsname, str):
obsname = fits.open(obsname)
close_obj = True
if 'rootname' in obsname[0].header:
ippssoot = obsname[0].header['rootname'].upper()
else:
ippssoot = fileutil.buildNewRootname(obsname).upper()
# Define what service needs to be used to get the offsets
serviceType = "GSCConvert/GSCconvert.aspx"
spec_str = "REFFRAME={}&IPPPSSOOT={}"
spec = spec_str.format(refframe, ippssoot)
serviceUrl = "{}/{}?{}".format(gsss_serviceLocation, serviceType, spec)
rawcat = requests.get(serviceUrl)
if not rawcat.ok:
logger.warning(
"Problem accessing service with:\n{}".format(serviceUrl))
logger.warning(" No offset found! ")
if rawcat.status_code == requests.codes.ok:
logger.info("gsReference service retrieved {}".format(ippssoot))
refXMLtree = etree.fromstring(rawcat.content)
delta_ra = float(refXMLtree.findtext('deltaRA'))
delta_dec = float(refXMLtree.findtext('deltaDEC'))
delta_roll = float(refXMLtree.findtext('deltaROLL'))
delta_scale = float(refXMLtree.findtext('deltaSCALE'))
dGSinputRA = float(refXMLtree.findtext('dGSinputRA'))
dGSinputDEC = float(refXMLtree.findtext('dGSinputDEC'))
dGSoutputRA = float(refXMLtree.findtext('dGSoutputRA'))
dGSoutputDEC = float(refXMLtree.findtext('dGSoutputDEC'))
outputCatalog = refXMLtree.findtext('outputCatalog')
# Use GS coordinate as reference point
old_gs = (dGSinputRA, dGSinputDEC)
new_gs = (dGSoutputRA, dGSoutputDEC)
expwcs = build_reference_wcs(obsname)
if delta_ra != 0.0 and delta_dec != 0.0:
# Compute tangent plane for this observation
wcsframe = expwcs.wcs.radesys.lower()
# Use WCS to compute offset in pixels of shift applied to WCS Reference pixel
# RA,Dec of ref pixel in decimal degrees
crval = SkyCoord(expwcs.wcs.crval[0],
expwcs.wcs.crval[1],
unit='deg',
frame=wcsframe)
# Define SkyCoord for Guide Star using old/original coordinates used to
# originally compute WCS for exposure
old_gs_coord = SkyCoord(old_gs[0],
old_gs[1],
unit='deg',
frame=wcsframe)
sof_old = old_gs_coord.skyoffset_frame()
# Define new SkyOffsetFrame based on new GS coords
new_gs_coord = SkyCoord(new_gs[0],
new_gs[1],
unit='deg',
frame=wcsframe)
# Determine offset from old GS position to the new GS position
sof_new = new_gs_coord.transform_to(sof_old)
# Compute new CRVAL position as old CRVAL+GS offset (sof_new)
new_crval_coord = SkyCoord(sof_new.lon.arcsec,
sof_new.lat.arcsec,
unit='arcsecond',
frame=crval.skyoffset_frame())
# Return RA/Dec for new/updated CRVAL position
new_crval = new_crval_coord.icrs
# Compute offset in pixels for new CRVAL
newpix = expwcs.all_world2pix(new_crval.ra.value, new_crval.dec.value,
1)
deltaxy = expwcs.wcs.crpix - newpix # offset from ref pixel position
else:
deltaxy = (0., 0.)
offsets = {
'delta_x': deltaxy[0],
'delta_y': deltaxy[1],
'roll': delta_roll,
'scale': delta_scale,
'delta_ra': delta_ra,
'delta_dec': delta_dec,
'expwcs': expwcs,
'catalog': outputCatalog
}
if close_obj:
obsname.close()
return offsets
def process_input(input, output=None, ivmlist=None, updatewcs=True, prodonly=False, shiftfile=None):
ivmlist = None
oldasndict = None
if (isinstance(input, list) == False) and \
('_asn' in input or '_asc' in input) :
# Input is an association table
# Get the input files, and run makewcs on them
oldasndict = asnutil.readASNTable(input, prodonly=prodonly)
if not output:
output = oldasndict['output']
filelist = [fileutil.buildRootname(fname) for fname in oldasndict['order']]
elif (isinstance(input, list) == False) and \
(input[0] == '@') :
# input is an @ file
f = open(input[1:])
# Read the first line in order to determine whether
# IVM files have been specified in a second column...
line = f.readline()
f.close()
# Parse the @-file with irafglob to extract the input filename
filelist = irafglob.irafglob(input, atfile=atfile_sci)
# If there is a second column...
if len(line.split()) == 2:
# ...parse out the names of the IVM files as well
ivmlist = irafglob.irafglob(input, atfile=atfile_ivm)
else:
#input is a string or a python list
try:
filelist, output = parseinput.parseinput(input, outputname=output)
#filelist.sort()
except IOError: raise
# sort the list of input files
# this ensures the list of input files has the same order on all platforms
# it can have ifferent order because listdir() uses inode order, not unix type order
filelist.sort()
newfilelist, ivmlist = checkFiles(filelist, ivmlist)
if not newfilelist:
buildEmptyDRZ(input,output)
return None, None, output
#make an asn table at the end
if updatewcs:
pydr_input = runmakewcs(newfilelist)
else:
pydr_input = newfilelist
# AsnTable will handle the case when output==None
if not oldasndict:
oldasndict = asnutil.ASNTable(pydr_input, output=output)
oldasndict.create()
if shiftfile:
oldasndict.update(shiftfile=shiftfile)
asndict = update_member_names(oldasndict, pydr_input)
# Build output filename
drz_extn = '_drz.fits'
for img in newfilelist:
# special case logic to automatically recognize when _flc.fits files
# are provided as input and produce a _drc.fits file instead
if '_flc.fits' in img:
drz_extn = '_drc.fits'
break
if output in [None,'']:
output = fileutil.buildNewRootname(asndict['output'],
extn=drz_extn)
else:
if '.fits' in output.lower():
pass
elif drz_extn[:4] not in output.lower():
output = fileutil.buildNewRootname(output, extn=drz_extn)
print('Setting up output name: ',output)
return asndict, ivmlist, output
def __init__(self,filename,group=None,inmemory=False):
baseImageObject.__init__(self,filename)
#filutil open returns a fits object
try:
self._image=fileutil.openImage(filename,clobber=False,memmap=0)
except IOError:
raise IOError("Unable to open file: %s" % filename)
#populate the global attributes which are good for all the chips in the file
#self._rootname=self._image['PRIMARY'].header["ROOTNAME"]
self._rootname=fileutil.buildNewRootname(filename)
self.outputNames=self._setOutputNames(self._rootname)
# flag to indicate whether or not to write out intermediate products
# to disk (default) or keep everything in memory
self.inmemory = inmemory
self._initVirtualOutputs()
#self._exptime=self._image["PRIMARY"].header["EXPTIME"]
#exptime should be set in the image subclass code since it's kept in different places
# if(self._exptime == 0):
self._exptime =1. #to avoid divide by zero
# print "Setting exposure time to 1. to avoid div/0!"
#this is the number of science chips to be processed in the file
self._numchips=self._countEXT(extname=self.scienceExt)
self.proc_unit = None
#self._nextend=self._image["PRIMARY"].header["NEXTEND"]
self._nextend = self._countEXT(extname=None)
if (self._numchips == 0):
#the simple fits image contains the data in the primary extension,
#this will help us deal with the rest of the code that looks
#and acts on chips :)
#self._nextend=1
self._numchips=1
self.scienceExt="PRIMARY"
self.maskExt=None
self._image["PRIMARY"].header["EXTNAME"] = "PRIMARY"
self._image["PRIMARY"].header["EXTVER"] = 1
self._image["PRIMARY"].extnum = 0
self._isSimpleFits = False
# Clean out any stray MDRIZSKY keywords from PRIMARY headers
fimg = fileutil.openImage(filename,mode='update')
if 'MDRIZSKY' in fimg['PRIMARY'].header:
del fimg['PRIMARY'].header['MDRIZSKY']
fimg.close()
del fimg
if group not in [None,'']:
# Only use selected chip
if ',' in group:
group_id = group.split(',')
if group_id[0].isalpha(): # user specified a specific extname,extver
self.group = [int(group_id[1])]
else: # user specified a list of extension numbers to process
self.group = []
for grp in group_id:
# find extname/extver which corresponds to this extension number
group_extname = self._image[int(grp)].header['EXTNAME']
group_extver = self._image[int(grp)].header['EXTVER']
self.group.append(group_extver)
else:
# find extname/extver which corresponds to this extension number
group_extver = self._image[int(group)].header['EXTVER']
self.group = [int(group_extver)]
else:
# Use all chips
self.group = None
if not self._isSimpleFits:
#assign chip specific information
for chip in range(1,self._numchips+1,1):
self._assignRootname(chip)
sci_chip = self._image[self.scienceExt,chip]
# Set a flag to indicate whether this chip should be included
# or not, based on user input from the 'group' parameter.
if self.group is None or (self.group is not None and chip in self.group):
sci_chip.group_member = True
self._nmembers += 1
else:
sci_chip.group_member = False
sci_chip.signature = None
sci_chip.dqname = None
sci_chip.dqmaskname = None
sci_chip.dqfile,sci_chip.dq_extn = self.find_DQ_extension()
#self.maskExt = sci_chip.dq_extn
if(sci_chip.dqfile != None):
sci_chip.dqname = sci_chip.dqfile +'['+sci_chip.dq_extn+','+str(chip)+']'
# build up HSTWCS object for each chip, which will be necessary for drizzling operations
sci_chip.wcs=wcs_functions.get_hstwcs(self._filename,self._image,sci_chip.extnum)
sci_chip.detnum,sci_chip.binned = util.get_detnum(sci_chip.wcs,self._filename,chip)
sci_chip.wcslin_pscale = 1.0
#assuming all the chips don't have the same dimensions in the file
sci_chip._naxis1=sci_chip.header["NAXIS1"]
sci_chip._naxis2=sci_chip.header["NAXIS2"]
# record the exptime values for this chip so that it can be
# easily used to generate the composite value for the final output image
sci_chip._expstart,sci_chip._expend = util.get_expstart(sci_chip.header,self._image['PRIMARY'].header)
sci_chip.outputNames=self._setChipOutputNames(sci_chip.rootname,chip).copy() #this is a dictionary
# Set the units: both bunit and in_units
self.set_units(chip)
#initialize gain, readnoise, and exptime attributes
# the actual values will be set by each instrument based on
# keyword names specific to that instrument by 'setInstrumentParamters()'
sci_chip._headergain = 1 # gain value read from header
sci_chip._gain = 1.0 # calibrated gain value
sci_chip._rdnoise = 1.0 # calibrated readnoise
sci_chip._exptime = 1.0
sci_chip._effGain = 1.0
sci_chip._conversionFactor = 1.0
sci_chip._wtscl = 1.0
# Keep track of the sky value that should be subtracted from this chip
# Read in value from image header, in case user has already
# determined the sky level
if "MDRIZSKY" in sci_chip.header:
subsky = sci_chip.header['MDRIZSKY']
log.info('Reading in MDRIZSKY of %s' % subsky)
else:
subsky = 0.0
# .computedSky: value to be applied by the
# adrizzle/ablot steps.
# .subtractedSky: value already (or will be by adrizzle/ablot)
# subtracted from the image
sci_chip.subtractedSky = subsky
sci_chip.computedSky = subsky
sci_chip.darkcurrent = 0.0
# The following attributes are used when working with sub-arrays
# and get reference file arrays for auto-generation of IVM masks
try:
sci_chip.ltv1 = sci_chip.header['LTV1'] * -1
sci_chip.ltv2 = sci_chip.header['LTV2'] * -1
except KeyError:
sci_chip.ltv1 = 0
sci_chip.ltv2 = 0
if sci_chip.ltv1 < 0:
sci_chip.ltv1 = 0
if sci_chip.ltv2 < 0:
sci_chip.ltv2 = 0
sci_chip.size1 = sci_chip.header['NAXIS1'] + np.round(sci_chip.ltv1)
sci_chip.size2 = sci_chip.header['NAXIS2'] + np.round(sci_chip.ltv2)
#sci_chip.image_shape = (sci_chip.size2,sci_chip.size1)
sci_chip.image_shape = (sci_chip.header['NAXIS2'],sci_chip.header['NAXIS1'])
# Interpret the array dtype by translating the IRAF BITPIX value
for dtype in IRAF_DTYPES.keys():
if sci_chip.header['BITPIX'] == IRAF_DTYPES[dtype]:
sci_chip.image_dtype = dtype
break
if self.inmemory:
# read image data array into memory
shape = sci_chip.data.shape
def _update(image,idctab,nimsets,apply_tdd=False,
quiet=None,instrument=None,prepend=None,nrchip=None, nrext=None):
tdd_xyref = {1: [2048, 3072], 2:[2048, 1024]}
_prepend = prepend
_dqname = None
# Make a copy of the header for keyword access
# This copy includes both Primary header and
# extension header
hdr = fileutil.getHeader(image)
# Try to get the instrument if we don't have it already
instrument = readKeyword(hdr,'INSTRUME')
binned = 1
# Read in any specified OFFTAB, if present (WFPC2)
offtab = readKeyword(hdr,'OFFTAB')
dateobs = readKeyword(hdr,'DATE-OBS')
if not quiet:
print("OFFTAB, DATE-OBS: ",offtab,dateobs)
print("-Updating image ",image)
if not quiet:
print("-Reading IDCTAB file ",idctab)
# Get telescope orientation from image header
# If PA_V# is not present of header, try to get it from the spt file
pvt = readKeyword(hdr,'PA_V3')
if pvt == None:
sptfile = fileutil.buildNewRootname(image, extn='_spt.fits')
if os.path.exists(sptfile):
spthdr = fileutil.getHeader(sptfile)
pvt = readKeyword(spthdr,'PA_V3')
if pvt != None:
pvt = float(pvt)
else:
print('PA_V3 keyword not found, WCS cannot be updated. Quitting ...')
raise ValueError
# Find out about instrument, detector & filters
detector = readKeyword(hdr,'DETECTOR')
Nrefchip=1
if instrument == 'WFPC2':
filter1 = readKeyword(hdr,'FILTNAM1')
filter2 = readKeyword(hdr,'FILTNAM2')
mode = readKeyword(hdr,'MODE')
if os.path.exists(fileutil.buildNewRootname(image, extn='_c1h.fits')):
_dqname = fileutil.buildNewRootname(image, extn='_c1h.fits')
dqhdr = pyfits.getheader(_dqname,1)
dqext = readKeyword(dqhdr, 'EXTNAME')
if mode == 'AREA':
binned = 2
Nrefchip=nrchip
elif instrument == 'NICMOS':
filter1 = readKeyword(hdr,'FILTER')
filter2 = None
elif instrument == 'WFC3':
filter1 = readKeyword(hdr,'FILTER')
filter2 = None
# use value of 'BINAXIS' keyword to set binning value for WFC3 data
binned = readKeyword(hdr,'BINAXIS1')
else:
filter1 = readKeyword(hdr,'FILTER1')
filter2 = readKeyword(hdr,'FILTER2')
if filter1 == None or filter1.strip() == '': filter1 = 'CLEAR'
else: filter1 = filter1.strip()
if filter2 == None or filter2.strip() == '': filter2 = 'CLEAR'
else: filter2 = filter2.strip()
if filter1.find('CLEAR') == 0: filter1 = 'CLEAR'
if filter2.find('CLEAR') == 0: filter2 = 'CLEAR'
# Set up parity matrix for chip
if instrument == 'WFPC2' or instrument =='STIS' or instrument == 'NICMOS':
parity = PARITY[instrument]
elif detector in PARITY:
parity = PARITY[detector]
else:
raise ValueError('Detector ',detector,
' Not supported at this time. Exiting...')
# Get the VAFACTOR keyword if it exists, otherwise set to 1.0
# we also need the reference pointing position of the target
# as this is where
_va_key = readKeyword(hdr,'VAFACTOR')
if _va_key != None:
VA_fac = float(_va_key)
else:
VA_fac=1.0
if not quiet:
print('VA factor: ',VA_fac)
#ra_targ = float(readKeyword(hdr,'RA_TARG'))
#dec_targ = float(readKeyword(hdr,'DEC_TARG'))
# Get the chip number
_c = readKeyword(hdr,'CAMERA')
_s = readKeyword(hdr,'CCDCHIP')
_d = readKeyword(hdr,'DETECTOR')
if _c != None and str(_c).isdigit():
chip = int(_c)
elif _s == None and _d == None:
chip = 1
else:
if _s:
chip = int(_s)
elif str(_d).isdigit():
chip = int(_d)
else:
chip = 1
# For the ACS/WFC case the chip number doesn't match the image
# extension
nr = 1
if (instrument == 'ACS' and detector == 'WFC') or (instrument == 'WFC3' and detector == 'UVIS'):
if nimsets > 1:
Nrefchip = 2
else:
Nrefchip = chip
elif instrument == 'NICMOS':
Nrefchip = readKeyword(hdr,'CAMERA')
elif instrument == 'WFPC2':
nr = nrext
else:
if nimsets > 1:
nr = Nrefchip
if not quiet:
print("-PA_V3 : ",pvt," CHIP #",chip)
# Extract the appropriate information from the IDCTAB
#fx,fy,refpix,order=fileutil.readIDCtab(idctab,chip=chip,direction='forward',
# filter1=filter1,filter2=filter2,offtab=offtab,date=dateobs)
idcmodel = models.IDCModel(idctab,
chip=chip, direction='forward', date=dateobs,
filter1=filter1, filter2=filter2, offtab=offtab, binned=binned,
tddcorr=apply_tdd)
fx = idcmodel.cx
fy = idcmodel.cy
refpix = idcmodel.refpix
order = idcmodel.norder
# Determine whether to perform time-dependent correction
# Construct matrices neded to correct the zero points for TDD
if apply_tdd:
#alpha,beta = mutil.compute_wfc_tdd_coeffs(dateobs,skew_coeffs)
alpha = refpix['TDDALPHA']
beta = refpix['TDDBETA']
tdd = N.array([[beta, alpha], [alpha, -beta]])
mrotp = fileutil.buildRotMatrix(2.234529)/2048.
else:
alpha = 0.0
beta = 0.0
# Get the original image WCS
Old=wcsutil.WCSObject(image,prefix=_prepend)
# Reset the WCS keywords to original archived values.
Old.restore()
#
# Look for any subarray offset
#
ltv1,ltv2 = drutil.getLTVOffsets(image)
#
# If reference point is not centered on distortion model
# shift coefficients to be applied relative to observation
# reference position
#
offsetx = Old.crpix1 - ltv1 - refpix['XREF']
offsety = Old.crpix2 - ltv2 - refpix['YREF']
shiftx = refpix['XREF'] + ltv1
shifty = 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.
if ltv1 != 0. or ltv2 != 0.:
fx,fy = idcmodel.shift(idcmodel.cx,idcmodel.cy,offsetx,offsety)
# Extract the appropriate information for reference chip
ridcmodel = models.IDCModel(idctab,
chip=Nrefchip, direction='forward', date=dateobs,
filter1=filter1, filter2=filter2, offtab=offtab, binned=binned,
tddcorr=apply_tdd)
rfx = ridcmodel.cx
rfy = ridcmodel.cy
rrefpix = ridcmodel.refpix
rorder = ridcmodel.norder
"""
rfx,rfy,rrefpix,rorder=mutil.readIDCtab(idctab,chip=Nrefchip,
direction='forward', filter1=filter1,filter2=filter2,offtab=offtab,
date=dateobs,tddcorr=apply_tdd)
"""
# Create the reference image name
rimage = image.split('[')[0]+"[sci,%d]" % nr
if not quiet:
print("Reference image: ",rimage)
# Create the tangent plane WCS on which the images are defined
# This is close to that of the reference chip
R=wcsutil.WCSObject(rimage)
R.write_archive(rimage)
R.restore()
# Reacd in declination of target (for computing orientation at aperture)
# Note that this is from the reference image
#dec = float(fileutil.getKeyword(rimage,'CRVAL2'))
#crval1 = float(fileutil.getKeyword(rimage,'CRVAL1'))
#crval1 = float(R.crval1)
#crval2 = dec
dec = float(R.crval2)
# Get an approximate reference position on the sky
rref = (rrefpix['XREF']+ltvoffx, rrefpix['YREF']+ltvoffy)
crval1,crval2=R.xy2rd(rref)
if apply_tdd:
# Correct zero points for TDD
tddscale = (R.pscale/fx[1][1])
rxy0 = N.array([[tdd_xyref[Nrefchip][0]-2048.],[ tdd_xyref[Nrefchip][1]-2048.]])
xy0 = N.array([[tdd_xyref[chip][0]-2048.], [tdd_xyref[chip][1]-2048.]])
rv23_corr = N.dot(mrotp,N.dot(tdd,rxy0))*tddscale
v23_corr = N.dot(mrotp,N.dot(tdd,xy0))*tddscale
else:
rv23_corr = N.array([[0],[0]])
v23_corr = N.array([[0],[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
v2ref = rrefpix['V2REF'] + rv23_corr[0][0]*0.05
v3ref = rrefpix['V3REF'] - rv23_corr[1][0]*0.05
v2 = refpix['V2REF'] + v23_corr[0][0]*0.05
v3 = refpix['V3REF'] - v23_corr[1][0] *0.05
pv = wcsutil.troll(pvt,dec,v2ref,v3ref)
# Add the chip rotation angle
if rrefpix['THETA']:
pv += rrefpix['THETA']
# Set values for the rest of the reference WCS
R.crval1=crval1
R.crval2=crval2
R.crpix1=0.0 + offshiftx
R.crpix2=0.0 + offshifty
R_scale=rrefpix['PSCALE']/3600.0
R.cd11=parity[0][0] * cos(pv*pi/180.0)*R_scale
R.cd12=parity[0][0] * -sin(pv*pi/180.0)*R_scale
R.cd21=parity[1][1] * sin(pv*pi/180.0)*R_scale
R.cd22=parity[1][1] * cos(pv*pi/180.0)*R_scale
##print R
R_cdmat = N.array([[R.cd11,R.cd12],[R.cd21,R.cd22]])
if not quiet:
print(" Reference Chip Scale (arcsec/pix): ",rrefpix['PSCALE'])
# Offset and angle in V2/V3 from reference chip to
# new chip(s) - converted to reference image pixels
off = sqrt((v2-v2ref)**2 + (v3-v3ref)**2)/(R_scale*3600.0)
# Here we must include the PARITY
if v3 == v3ref:
theta=0.0
else:
theta = atan2(parity[0][0]*(v2-v2ref),parity[1][1]*(v3-v3ref))
if rrefpix['THETA']: theta += rrefpix['THETA']*pi/180.0
dX=(off*sin(theta)) + offshiftx
dY=(off*cos(theta)) + offshifty
# Check to see whether we are working with GEIS or FITS input
_fname,_iextn = fileutil.parseFilename(image)
if _fname.find('.fits') < 0:
# Input image is NOT a FITS file, so
# build a FITS name for it's copy.
_fitsname = fileutil.buildFITSName(_fname)
else:
_fitsname = None
# Create a new instance of a WCS
if _fitsname == None:
_new_name = image
else:
_new_name = _fitsname+'['+str(_iextn)+']'
#New=wcsutil.WCSObject(_new_name,new=yes)
New = Old.copy()
# Calculate new CRVALs and CRPIXs
New.crval1,New.crval2=R.xy2rd((dX,dY))
New.crpix1=refpix['XREF'] + ltvoffx
New.crpix2=refpix['YREF'] + ltvoffy
# Account for subarray offset
# Angle of chip relative to chip
if refpix['THETA']:
dtheta = refpix['THETA'] - rrefpix['THETA']
else:
dtheta = 0.0
# Create a small vector, in reference image pixel scale
# There is no parity effect here ???
delXX=fx[1,1]/R_scale/3600.
delYX=fy[1,1]/R_scale/3600.
delXY=fx[1,0]/R_scale/3600.
delYY=fy[1,0]/R_scale/3600.
# Convert to radians
rr=dtheta*pi/180.0
# Rotate the vectors
dXX= cos(rr)*delXX - sin(rr)*delYX
dYX= sin(rr)*delXX + cos(rr)*delYX
dXY= cos(rr)*delXY - sin(rr)*delYY
dYY= sin(rr)*delXY + cos(rr)*delYY
# Transform to sky coordinates
a,b=R.xy2rd((dX+dXX,dY+dYX))
c,d=R.xy2rd((dX+dXY,dY+dYY))
# Calculate the new CDs and convert to degrees
New.cd11=diff_angles(a,New.crval1)*cos(New.crval2*pi/180.0)
New.cd12=diff_angles(c,New.crval1)*cos(New.crval2*pi/180.0)
New.cd21=diff_angles(b,New.crval2)
New.cd22=diff_angles(d,New.crval2)
# Apply the velocity aberration effect if applicable
if VA_fac != 1.0:
# First shift the CRVALs apart
# New.crval1 = ra_targ + VA_fac*(New.crval1 - ra_targ)
# New.crval2 = dec_targ + VA_fac*(New.crval2 - dec_targ)
# First shift the CRVALs apart
# This is now relative to the reference chip, not the
# target position.
New.crval1 = R.crval1 + VA_fac*diff_angles(New.crval1, R.crval1)
New.crval2 = R.crval2 + VA_fac*diff_angles(New.crval2, R.crval2)
# and scale the CDs
New.cd11 = New.cd11*VA_fac
New.cd12 = New.cd12*VA_fac
New.cd21 = New.cd21*VA_fac
New.cd22 = New.cd22*VA_fac
New_cdmat = N.array([[New.cd11,New.cd12],[New.cd21,New.cd22]])
# Store new one
# archive=yes specifies to also write out archived WCS keywords
# overwrite=no specifies do not overwrite any pre-existing archived keywords
New.write(fitsname=_new_name,overwrite=no,quiet=quiet,archive=yes)
if _dqname:
_dq_iextn = _iextn.replace('sci', dqext.lower())
_new_dqname = _dqname +'['+_dq_iextn+']'
dqwcs = wcsutil.WCSObject(_new_dqname)
dqwcs.write(fitsname=_new_dqname, wcs=New,overwrite=no,quiet=quiet, archive=yes)
""" Convert distortion coefficients into SIP style
values and write out to image (assumed to be FITS).
"""
#First the CD matrix:
f = refpix['PSCALE']/3600.0
a = fx[1,1]/3600.0
b = fx[1,0]/3600.0
c = fy[1,1]/3600.0
d = fy[1,0]/3600.0
det = (a*d - b*c)*refpix['PSCALE']
# Write to header
fimg = fileutil.openImage(_new_name,mode='update')
_new_root,_nextn = fileutil.parseFilename(_new_name)
_new_extn = fileutil.getExtn(fimg,_nextn)
# Transform the higher-order coefficients
for n in range(order+1):
for m in range(order+1):
if n >= m and n>=2:
# Form SIP-style keyword names
Akey="A_%d_%d" % (m,n-m)
Bkey="B_%d_%d" % (m,n-m)
# Assign them values
Aval= f*(d*fx[n,m]-b*fy[n,m])/det
Bval= f*(a*fy[n,m]-c*fx[n,m])/det
_new_extn.header.update(Akey,Aval)
_new_extn.header.update(Bkey,Bval)
# Update the SIP flag keywords as well
#iraf.hedit(image,"CTYPE1","RA---TAN-SIP",verify=no,show=no)
#iraf.hedit(image,"CTYPE2","DEC--TAN-SIP",verify=no,show=no)
_new_extn.header.update("CTYPE1","RA---TAN-SIP")
_new_extn.header.update("CTYPE2","DEC--TAN-SIP")
# Finally we also need the order
#iraf.hedit(image,"A_ORDER","%d" % order,add=yes,verify=no,show=no)
#iraf.hedit(image,"B_ORDER","%d" % order,add=yes,verify=no,show=no)
_new_extn.header.update("A_ORDER",order)
_new_extn.header.update("B_ORDER",order)
# Update header with additional keywords required for proper
# interpretation of SIP coefficients by PyDrizzle.
_new_extn.header.update("IDCSCALE",refpix['PSCALE'])
_new_extn.header.update("IDCV2REF",refpix['V2REF'])
_new_extn.header.update("IDCV3REF",refpix['V3REF'])
_new_extn.header.update("IDCTHETA",refpix['THETA'])
_new_extn.header.update("OCX10",fx[1][0])
_new_extn.header.update("OCX11",fx[1][1])
_new_extn.header.update("OCY10",fy[1][0])
_new_extn.header.update("OCY11",fy[1][1])
#_new_extn.header.update("TDDXOFF",rv23_corr[0][0] - v23_corr[0][0])
#_new_extn.header.update("TDDYOFF",-(rv23_corr[1][0] - v23_corr[1][0]))
# Report time-dependent coeffs, if computed
if instrument == 'ACS' and detector == 'WFC':
_new_extn.header.update("TDDALPHA",alpha)
_new_extn.header.update("TDDBETA",beta)
# Close image now
fimg.close()
del fimg
