def saltprepare(images,outimages,outpref,createvar=False, badpixelimage=None, clobber=True,logfile='salt.log',verbose=True):
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create list of output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
#verify that the input and output lists are the same length
saltio.comparelists(infiles,outfiles,'Input','output')
# open the badpixel image
if saltio.checkfornone(badpixelimage) is None:
badpixelstruct=None
else:
try:
badpixelstruct = saltio.openfits(badpixelimage)
except saltio.SaltIOError,e:
msg='badpixel image must be specificied\n %s' % e
raise SaltError(msg)
# open each raw image file
for img, oimg, in zip(infiles, outfiles):
#open the fits file
struct=saltio.openfits(img)
#if createvar, throw a warning if it is using slotmode
if saltkey.fastmode(saltkey.get('DETMODE', struct[0])) and createvar:
msg='Creating variance frames for slotmode data in %s' % img
log.warning(msg)
# identify instrument
instrume,keyprep,keygain,keybias,keyxtalk,keyslot = saltkey.instrumid(struct)
# has file been prepared already?
try:
key = struct[0].header[keyprep]
message = 'ERROR -- SALTPREPARE: File ' + infile
message += ' has already been prepared'
raise SaltError(message)
except:
pass
# prepare file
struct=prepare(struct,createvar=createvar, badpixelstruct=badpixelstruct)
# housekeeping keywords
fname, hist=history(level=1, wrap=False, exclude=['images', 'outimages', 'outpref'])
saltkey.housekeeping(struct[0],keyprep, 'File prepared for IRAF', hist)
# write FITS file
saltio.writefits(struct,oimg, clobber=clobber)
saltio.closefits(struct)
message = 'SALTPREPARE -- %s => %s' % (img, oimg)
log.message(message, with_header=False)
def specselfid(images, outimages, outpref, refimage=None, ystart='middlerow',
rstep=3, clobber=False, logfile='salt.log', verbose=True):
with logging(logfile, debug) as log:
# set up the variables
infiles = []
outfiles = []
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse(
'Outimages',
outimages,
outpref,
infiles,
'')
# set up defaults
if saltio.checkfornone(refimage) is not None:
rhdu = saltio.openfits(refimage)
else:
refimage = None
# read in rectify each image
for img, oimg, in zip(infiles, outfiles):
hdu = saltio.openfits(img)
log.message(
'Performing self-identification and rectification on %s' %
img)
for i in range(1, len(hdu)):
if hdu[i].name == 'SCI':
if refimage is None:
sdata = hdu[i].data
else:
sdata = rhdu[i].data
hdu[i].data = selfid(
hdu[i].data,
sdata,
ystart=ystart,
rstep=rstep)
if saltkey.found('VAREXT', hdu[i]):
varext = saltkey.get('VAREXT', hdu[i])
hdu[varext].data = selfid(
hdu[varext].data,
sdata,
ystart=ystart,
rstep=rstep)
if saltkey.found('BPMEXT', hdu[i]):
bpmext = saltkey.get('BPMEXT', hdu[i])
hdu[bpmext].data = selfid(
hdu[bpmext].data,
sdata,
ystart=ystart,
rstep=rstep)
# write out the oimg
saltio.writefits(hdu, oimg, clobber=clobber)
def saltprepare(images,outimages,outpref,createvar=False, badpixelimage=None, clobber=True,logfile='salt.log',verbose=True):
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create list of output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
#verify that the input and output lists are the same length
saltio.comparelists(infiles,outfiles,'Input','output')
# open the badpixel image
if saltio.checkfornone(badpixelimage) is None:
badpixelstruct=None
else:
try:
badpixelstruct = saltio.openfits(badpixelimage)
except saltio.SaltIOError,e:
msg='badpixel image must be specificied\n %s' % e
raise SaltError(msg)
# open each raw image file
for img, oimg, in zip(infiles, outfiles):
#open the fits file
struct=saltio.openfits(img)
#if createvar, throw a warning if it is using slotmode
if saltkey.fastmode(saltkey.get('DETMODE', struct[0])) and createvar:
msg='Creating variance frames for slotmode data in %s' % img
log.warning(msg)
# identify instrument
instrume,keyprep,keygain,keybias,keyxtalk,keyslot = saltkey.instrumid(struct)
# has file been prepared already?
try:
key = struct[0].header[keyprep]
message = 'ERROR -- SALTPREPARE: File ' + infile
message += ' has already been prepared'
raise SaltError(message)
except:
pass
# prepare file
struct=prepare(struct,createvar=createvar, badpixelstruct=badpixelstruct)
# housekeeping keywords
fname, hist=history(level=1, wrap=False, exclude=['images', 'outimages', 'outpref'])
saltkey.housekeeping(struct[0],keyprep, 'File prepared for IRAF', hist)
# write FITS file
saltio.writefits(struct,oimg, clobber=clobber)
saltio.closefits(struct)
message = 'SALTPREPARE -- %s => %s' % (img, oimg)
log.message(message, with_header=False)
def specselfid(images,
outimages,
outpref,
refimage=None,
ystart='middlerow',
rstep=3,
clobber=False,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# set up the variables
infiles = []
outfiles = []
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outimages', outimages, outpref, infiles,
'')
# set up defaults
if saltio.checkfornone(refimage) is not None:
rhdu = saltio.openfits(refimage)
else:
refimage = None
# read in rectify each image
for img, oimg, in zip(infiles, outfiles):
hdu = saltio.openfits(img)
log.message(
'Performing self-identification and rectification on %s' % img)
for i in range(1, len(hdu)):
if hdu[i].name == 'SCI':
if refimage is None:
sdata = hdu[i].data
else:
sdata = rhdu[i].data
hdu[i].data = selfid(hdu[i].data,
sdata,
ystart=ystart,
rstep=rstep)
if saltkey.found('VAREXT', hdu[i]):
varext = saltkey.get('VAREXT', hdu[i])
hdu[varext].data = selfid(hdu[varext].data,
sdata,
ystart=ystart,
rstep=rstep)
if saltkey.found('BPMEXT', hdu[i]):
bpmext = saltkey.get('BPMEXT', hdu[i])
hdu[bpmext].data = selfid(hdu[bpmext].data,
sdata,
ystart=ystart,
rstep=rstep)
# write out the oimg
saltio.writefits(hdu, oimg, clobber=clobber)
def saltarith(operand1, op, operand2, result, outpref, divzero=0, clobber=False, \
logfile='salt.log',verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', operand1)
# create list of output files
outfiles = saltio.listparse('Outfile', result, outpref, infiles, '')
#verify that the input and output lists are the same length
saltio.comparelists(infiles, outfiles, 'Input', 'output')
#let's keep track of whether operand2 is an image or not
is_image = False
#load in operand2, or, if it's not an image, assume it's a number
try:
operand2struct = float(operand2)
except ValueError:
operand2struct = saltio.openfits(operand2)
is_image = True
#open the input image files
for infile, outfile in zip(infiles, outfiles):
struct = saltio.openfits(infile)
#do some math!
outstruct = arith(struct, op, operand2struct, is_image, divzero)
try:
pass
except Exception, e:
msg = 'Unable to do math %s because %s' % (infile, e)
raise SaltError(msg)
#update header stuff
fname, hist = history(level=1, wrap=False)
saltkey.housekeeping(struct[0], 'SARITH',
'Some arithmatic was performed', hist)
#write it. close it.
saltio.writefits(outstruct, outfile, clobber=clobber)
saltio.closefits(struct)
#output the information
log.message('imarith: %s %s %s %s' %
(infile, op, operand2, outfile),
with_header=False,
with_stdout=verbose)
#close the operand2 image
if is_image: saltio.closefits(operand2struct)
def saltarith(operand1, op, operand2, result, outpref, divzero=0, clobber=False, \
logfile='salt.log',verbose=True):
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',operand1)
# create list of output files
outfiles=saltio.listparse('Outfile', result, outpref, infiles,'')
#verify that the input and output lists are the same length
saltio.comparelists(infiles,outfiles,'Input','output')
#let's keep track of whether operand2 is an image or not
is_image = False
#load in operand2, or, if it's not an image, assume it's a number
try: operand2struct = float(operand2)
except ValueError:
operand2struct = saltio.openfits(operand2)
is_image = True
#open the input image files
for infile, outfile in zip(infiles,outfiles):
struct = saltio.openfits(infile)
#do some math!
outstruct = arith(struct, op, operand2struct, is_image, divzero)
try:
pass
except Exception as e:
msg='Unable to do math %s because %s' % (infile, e)
raise SaltError(msg)
#update header stuff
fname, hist = history(level=1, wrap=False)
saltkey.housekeeping(struct[0],'SARITH', 'Some arithmatic was performed',hist)
#write it. close it.
saltio.writefits(outstruct,outfile,clobber=clobber)
saltio.closefits(struct)
#output the information
log.message('imarith: %s %s %s %s' % (infile, op, operand2, outfile), with_header=False, with_stdout=verbose)
#close the operand2 image
if is_image: saltio.closefits(operand2struct)
def saltgain(images,
outimages,
outpref,
gaindb=None,
usedb=False,
mult=True,
clobber=True,
logfile='salt.log',
verbose=True):
#start logging
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
#verify that the input and output lists are the same length
saltio.comparelists(infiles, outfiles, 'Input', 'output')
# read in the database file if usedb is true
if usedb:
gaindb = gaindb.strip()
dblist = saltio.readgaindb(gaindb)
else:
dblist = []
for img, oimg in zip(infiles, outfiles):
#open the fits file
struct = saltio.openfits(img)
# identify instrument
instrume, keyprep, keygain, keybias, keyxtalk, keyslot = saltkey.instrumid(
struct)
# has file been prepared already?
if saltkey.found(keygain, struct[0]):
message = 'SALTGAIN: %s has already been gain-corrected' % img
raise SaltError(message)
# gain correct the data
struct = gain(struct,
mult=mult,
usedb=usedb,
dblist=dblist,
log=log,
verbose=verbose)
# housekeeping keywords
fname, hist = history(level=1,
wrap=False,
exclude=['images', 'outimages', 'outpref'])
saltkey.housekeeping(struct[0], keygain,
'Images have been gain corrected', hist)
# write FITS file
saltio.writefits(struct, oimg, clobber=clobber)
saltio.closefits(struct)
def hrsprepare(images, outimages, outpref, clobber=True, logfile='salt.log',verbose=True):
"""Convert .fit files to .fits files and place HRS data into
standard SALT FITS format
"""
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create list of output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
#verify that the input and output lists are the same length
saltio.comparelists(infiles,outfiles,'Input','output')
#open the file and write out as a fits files in the output directory
for img,oimg in zip(infiles, outfiles):
hdu=saltio.openfits(img)
hdu=prepare(hdu)
log.message('Preparing HRS %s to %s' % (img, oimg), with_header=False)
saltio.writefits(hdu, oimg, clobber=clobber)
return
def identify(img, oimg, slines, sfluxes, guesstype, guessfile, function, order,
rstep, interact, clobber, verbose):
"""For a given image, find the solution for each row in the file. Use the appropriate first guess and
guess type along with the appropriate function and order for the fit.
Write out the new image with the solution in the headers and/or as a table in the multi-extension
fits file
returns the status
"""
status=0
ImageSolution={}
#Open up the image
hdu=saltsafeio.openfits(img)
#Read in important keywords
#determine the central row and read it in
try:
data=hdu[1].data
midline=int(0.5*len(data))
xarr=np.arange(len(data[midline]))
specarr=st.flatspectrum(xarr, data[midline, :], mode='poly', order=2)
except Exception, e:
message = 'Unable to read in data array in %s because %s' % (img, e)
raise SALTSpecError(message)
def saltillum(images, outimages, outpref, mbox=11, clobber=False, logfile="salt.log", verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack("Input", images)
# create list of output files
outfiles = saltio.listparse("Outfile", outimages, outpref, infiles, "")
# verify that the input and output lists are the same length
saltio.comparelists(infiles, outfiles, "Input", "output")
# open each raw image file
for infile, outfile in zip(infiles, outfiles):
struct = saltio.openfits(infile)
struct = illum_cor(struct, mbox)
# add any header keywords like history
fname, hist = history(level=1, wrap=False)
saltkey.housekeeping(struct[0], "SILLUM", "File Illumination corrected", hist)
# write it out and close it
saltio.writefits(struct, outfile, clobber=clobber)
saltio.closefits(struct)
# output the information
log.message("Illumination corrected image %s " % (infile), with_header=False, with_stdout=verbose)
def saltsurface(images,outimages,outpref, mask=True, order=3, minlevel=0,
clobber=False, logfile='salt.log',verbose=True):
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create list of output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
#verify that the input and output lists are the same length
saltio.comparelists(infiles,outfiles,'Input','output')
# open each raw image file
for infile, outfile in zip(infiles,outfiles):
struct = saltio.openfits(infile)
struct = surface_fit(struct, order=order, mask=mask, minlevel=minlevel)
#add any header keywords like history
fname, hist=history(level=1, wrap=False)
saltkey.housekeeping(struct[0],'SURFIT', 'File fit by a surface', hist)
#write it out and close it
saltio.writefits(struct,outfile,clobber=clobber)
saltio.closefits(struct)
#output the information
log.message('Surface fitted image %s ' % (infile), with_header=False, with_stdout=verbose)
def specsky(images,outimages,outpref, method='normal', section=None,
function='polynomial', order=2,
clobber=True,logfile='salt.log',verbose=True):
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create list of output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
if method not in ['normal', 'fit']:
msg='%s mode is not supported yet' % method
raise SALTSpecError(msg)
if section is None:
section=saltio.getSection(section)
msg='This mode is not supported yet'
raise SALTSpecError(msg)
else:
section=saltio.getSection(section)
# Identify the lines in each file
for img, ofile in zip(infiles, outfiles):
log.message('Subtracting sky spectrum in image %s into %s' % (img, ofile))
#open the images
hdu=saltio.openfits(img)
#sky subtract the array
hdu=skysubtract(hdu, method=method, section=section, funct=function, order=order)
#write out the image
if clobber and os.path.isfile(ofile): saltio.delete(ofile)
hdu.writeto(ofile)
def saltillum(images,outimages,outpref, mbox=11, clobber=False, \
logfile='salt.log',verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
#verify that the input and output lists are the same length
saltio.comparelists(infiles, outfiles, 'Input', 'output')
# open each raw image file
for infile, outfile in zip(infiles, outfiles):
struct = saltio.openfits(infile)
struct = illum_cor(struct, mbox)
#add any header keywords like history
fname, hist = history(level=1, wrap=False)
saltkey.housekeeping(struct[0], 'SILLUM',
'File Illumination corrected', hist)
#write it out and close it
saltio.writefits(struct, outfile, clobber=clobber)
saltio.closefits(struct)
#output the information
log.message('Illumination corrected image %s ' % (infile),
with_header=False,
with_stdout=verbose)
def hrsstack(images, outimages, outpref, clobber=True, logfile='salt.log',verbose=True):
"""Convert MEF HRS data into a single image. If variance frames and BPMs, then
convert them to the same format as well. Returns an MEF image but that is
combined into a single frame
"""
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create list of output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
#verify that the input and output lists are the same length
saltio.comparelists(infiles,outfiles,'Input','output')
#open the file and write out as a fits files in the output directory
for img,oimg in zip(infiles, outfiles):
hdu=saltio.openfits(img)
hdu=stack(hdu)
log.message('Stacking HRS %s to %s' % (img, oimg), with_header=False)
saltio.writefits(hdu, oimg, clobber=clobber)
return
def hrsstack(images,
outimages,
outpref,
clobber=True,
logfile='salt.log',
verbose=True):
"""Convert MEF HRS data into a single image. If variance frames and BPMs, then
convert them to the same format as well. Returns an MEF image but that is
combined into a single frame
"""
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
#verify that the input and output lists are the same length
saltio.comparelists(infiles, outfiles, 'Input', 'output')
#open the file and write out as a fits files in the output directory
for img, oimg in zip(infiles, outfiles):
hdu = saltio.openfits(img)
hdu = stack(hdu)
log.message('Stacking HRS %s to %s' % (img, oimg),
with_header=False)
saltio.writefits(hdu, oimg, clobber=clobber)
return
def obslog(infiles, log=None):
"""For a set of input files, create a dictionary contain all the header
information from the files. Will print things to a saltlog if log is
not None
returns Dictionary
"""
#create the header dictionary
headerDict = {}
for k in headerList:
headerDict[k] = []
for k in scamheaderList:
headerDict[k] = []
for k in rssheaderList:
headerDict[k] = []
# interate over and open image files
infiles.sort()
for infile in infiles:
#open the file
struct = saltio.openfits(infile)
# instrument
scam = False
rss = False
instrume = saltkey.get('INSTRUME', struct[0])
if (instrume == 'RSS'): rss = True
if (instrume == 'SALTICAM'): scam = True
#add in the image name
headerDict['FILENAME'].append(os.path.basename(infile))
# ingest primary keywords from files in the image list
for k, f in zip(headerList[1:], formatList[1:]):
default = finddefault(f)
headerDict[k].append(
getkey(struct[0], k, default=default, log=log, warn=True))
# ingest scam specific primary keywords from files in the image list
for k, f in zip(scamheaderList[1:], scamformatList[1:]):
default = finddefault(f)
headerDict[k].append(
getkey(struct[0], k, default=default, log=log, warn=scam))
# ingest rss specific primary keywords from files in the image list
for k, f in zip(rssheaderList[1:], rssformatList[1:]):
default = finddefault(f)
headerDict[k].append(
getkey(struct[0], k, default=default, log=log, warn=rss))
# close image files
saltio.closefits(struct)
if log:
log.message('SALTOBSLOG -- read %s' % infile, with_header=False)
return headerDict
def saltfpskyring(
images,
outimages,
outpref,
axc,
ayc,
arad,
rxc,
ryc,
pmin,
pmax,
swindow=5,
clobber=False,
logfile="salt.log",
verbose=True,
):
"""Sky subtracts Fabry-Perot images"""
# start log now that all parameter are set up
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack("Input", images)
# create list of output files
outfiles = saltio.listparse("Outfile", outimages, outpref, infiles, "")
# verify that the input and output lists are the same length
saltio.comparelists(infiles, outfiles, "Input", "output")
for img, oimg in zip(infiles, outfiles):
# open up the file
hdu = saltio.openfits(img)
# determine the azimuthally averaged profile
rpro, radial_profile = median_radial_profile(
hdu[0].data, xc=axc, yc=ayc, rmax=arad, nbins=100, pmin=pmin, pmax=pmax
)
if swindow > 1:
radial_profile = np.convolve(radial_profile, np.ones(swindow), mode="same") / swindow
# calculate the indices from the image
y, x = np.indices(hdu[0].data.shape)
radius = np.hypot(x - axc, y - ayc)
# subtract off the sky data
mdata = hdu[0].data - np.interp(radius, rpro, radial_profile)
hdu[0].data = mdata
# write FITS file
saltio.writefits(hdu, oimg, clobber=clobber)
saltio.closefits(hdu)
message = "SALTFPSKYRING -- Subtracted sky from %s" % (img)
log.message(message, with_header=False)
def specextract(images,
outfile,
method='normal',
section=None,
thresh=3.0,
minsize=3.0,
outformat='ascii',
ext=1,
convert=True,
clobber=True,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.argunpack('outfile', outfile)
if method is 'weighted':
msg = 'This mode is not supported yet'
raise SALTSpecError(msg)
section = saltio.checkfornone(section)
if section is not None:
sections = saltio.getSection(section, iraf_format=False)
section = []
for i in range(0, len(sections), 2):
section.append((sections[i], sections[i + 1]))
# Identify the lines in each file
for img, ofile in zip(infiles, outfiles):
log.message('\nExtracting spectrum in image %s to %s' %
(img, ofile),
with_header=False,
with_stdout=verbose)
# open the images
hdu = saltio.openfits(img)
ap_list = extract(hdu,
ext=ext,
method=method,
section=section,
minsize=minsize,
thresh=thresh,
convert=convert)
# write the spectra out
if ap_list:
write_extract(ofile.strip(),
ap_list,
outformat=outformat,
clobber=clobber)
log.message('', with_header=False, with_stdout=verbose)
def saltcrclean(images,outimages,outpref,crtype='fast',thresh=5,mbox=3, \
bthresh=3, flux_ratio=0.2, bbox=11, gain=1, rdnoise=5, fthresh=5,\
bfactor=2, gbox=3, maxiter=5, multithread=False, update=True,
clobber=True, logfile='salt.log', verbose=True):
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create list of output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
#verify that the input and output lists are the same length
saltio.comparelists(infiles,outfiles,'Input','output')
#check to see if multithreading is available
if mp:
pass
else:
multithread=False
log.warning('multiprocessing module is not available. Setting multiththread=False')
# Begin processes each file
for infile,outfile in zip(infiles,outfiles):
#open the infile
struct=saltio.openfits(infile)
#clean the cosmic rays
if multithread and len(struct)>1:
struct=multicrclean(struct, crtype, thresh, mbox, bbox, bthresh, flux_ratio, \
gain, rdnoise, bfactor, fthresh, gbox, maxiter, log, verbose=verbose)
else:
struct=crclean(struct, crtype, thresh, mbox, bbox, bthresh, flux_ratio, \
gain, rdnoise, bfactor, fthresh, gbox, maxiter, update, log, verbose=verbose)
#log the call
#log.message('Cleaned %i cosmic rays from %s using %s method' % (totcr, infile, crtype), with_header=False)
log.message('', with_header=False, with_stdout=verbose)
#add house keeping keywords
saltkey.put('SAL-TLM',time.asctime(time.localtime()), struct[0])
#add the history keyword
fname, hist=history(level=1, wrap=False)
saltkey.history(struct[0],hist)
#write out the file
saltio.writefits(struct, outfile, clobber=clobber)
#close the image
saltio.closefits(struct)
def saltxtalk(images,outimages,outpref,xtalkfile=None, usedb=False,
clobber=True, logfile='salt.log',verbose=True):
#start logging
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create list of output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
# are input and output lists the same length?
saltio.comparelists(infiles,outfiles,'Input','output')
# does crosstalk coefficient data exist
if usedb:
xtalkfile = xtalkfile.strip()
xdict = saltio.readxtalkcoeff(xtalkfile)
else:
xdict=None
for img, oimg in zip(infiles, outfiles):
#open the fits file
struct=saltio.openfits(img)
#find the best xcoeff for the image if using the db
if usedb:
obsdate=saltkey.get('DATE-OBS', struct[0])
obsdate=int('%s%s%s' % (obsdate[0:4],obsdate[5:7], obsdate[8:]))
xkey=np.array(xdict.keys())
date=xkey[abs(xkey-obsdate).argmin()]
xcoeff=xdict[date]
else:
xcoeff=[]
# identify instrument
instrume,keyprep,keygain,keybias,keyxtalk,keyslot = saltkey.instrumid(struct)
# has file been prepared already?
if saltkey.found(keyxtalk, struct[0]):
message='%s has already been xtalk corrected' % img
raise SaltError(message)
#apply the cross-talk correction
struct = xtalk(struct, xcoeff, log=log, verbose=verbose)
# housekeeping keywords
fname, hist=history(level=1, wrap=False, exclude=['images', 'outimages', 'outpref'])
saltkey.housekeeping(struct[0], 'SXTALK', 'Images have been xtalk corrected', hist)
# write FITS file
saltio.writefits(struct,oimg, clobber=clobber)
saltio.closefits(struct)
def specwavemap(
images,
outimages,
outpref,
solfile=None,
caltype="line",
function="polynomial",
order=3,
blank=0,
nearest=False,
clobber=True,
logfile="salt.log",
verbose=True,
):
with logging(logfile, debug) as log:
# set up the variables
infiles = []
outfiles = []
# Check the input images
infiles = saltsafeio.argunpack("Input", images)
# create list of output files
outfiles = saltsafeio.listparse("Outimages", outimages, outpref, infiles, "")
# read in the wavelength solutions and enter them into
# there own format
if caltype == "line":
soldict = sr.entersolution(solfile)
else:
soldict = None
# read in rectify each image
for img, oimg in zip(infiles, outfiles):
if caltype == "line":
msg = "Creating wave map image %s from image %s using files %s" % (oimg, img, solfile)
else:
msg = "Creating wave map image %s from image %s using RSS Model" % (oimg, img)
log.message(msg)
hdu = saltsafeio.openfits(img)
hdu = wavemap(
hdu,
soldict,
caltype=caltype,
function=function,
order=order,
blank=blank,
nearest=nearest,
clobber=clobber,
log=log,
verbose=verbose,
)
saltsafeio.writefits(hdu, oimg, clobber=clobber)
def saltcrclean(images,outimages,outpref,crtype='fast',thresh=5,mbox=3, \
bthresh=3, flux_ratio=0.2, bbox=11, gain=1, rdnoise=5, fthresh=5,\
bfactor=2, gbox=3, maxiter=5, multithread=False, update=True,
clobber=True, logfile='salt.log', verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
#verify that the input and output lists are the same length
saltio.comparelists(infiles, outfiles, 'Input', 'output')
#check to see if multithreading is available
if mp:
pass
else:
multithread = False
log.warning(
'multiprocessing module is not available. Setting multiththread=False'
)
# Begin processes each file
for infile, outfile in zip(infiles, outfiles):
#open the infile
struct = saltio.openfits(infile)
#clean the cosmic rays
if multithread and len(struct) > 1:
struct=multicrclean(struct, crtype, thresh, mbox, bbox, bthresh, flux_ratio, \
gain, rdnoise, bfactor, fthresh, gbox, maxiter, log, verbose=verbose)
else:
struct=crclean(struct, crtype, thresh, mbox, bbox, bthresh, flux_ratio, \
gain, rdnoise, bfactor, fthresh, gbox, maxiter, update, log, verbose=verbose)
#log the call
#log.message('Cleaned %i cosmic rays from %s using %s method' % (totcr, infile, crtype), with_header=False)
log.message('', with_header=False, with_stdout=verbose)
#add house keeping keywords
saltkey.put('SAL-TLM', time.asctime(time.localtime()), struct[0])
#add the history keyword
fname, hist = history(level=1, wrap=False)
saltkey.history(struct[0], hist)
#write out the file
saltio.writefits(struct, outfile, clobber=clobber)
#close the image
saltio.closefits(struct)
def specwavemap(images,
outimages,
outpref,
solfile=None,
caltype='line',
function='polynomial',
order=3,
blank=0,
nearest=False,
clobber=True,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# set up the variables
infiles = []
outfiles = []
# Check the input images
infiles = saltsafeio.argunpack('Input', images)
# create list of output files
outfiles = saltsafeio.listparse('Outimages', outimages, outpref,
infiles, '')
# read in the wavelength solutions and enter them into
# there own format
if caltype == 'line':
soldict = sr.entersolution(solfile)
else:
soldict = None
# read in rectify each image
for img, oimg, in zip(infiles, outfiles):
if caltype == 'line':
msg = 'Creating wave map image %s from image %s using files %s' % (
oimg, img, solfile)
else:
msg = 'Creating wave map image %s from image %s using RSS Model' % (
oimg, img)
log.message(msg)
hdu = saltsafeio.openfits(img)
hdu = wavemap(hdu,
soldict,
caltype=caltype,
function=function,
order=order,
blank=blank,
nearest=nearest,
clobber=clobber,
log=log,
verbose=verbose)
saltsafeio.writefits(hdu, oimg, clobber=clobber)
def saltslot(images,
outimages,
outpref,
gaindb='',
xtalkfile='',
usedb=False,
clobber=False,
logfile='salt.log',
verbose=True):
#start logging
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
# are input and output lists the same length?
saltio.comparelists(infiles, outfiles, 'Input', 'output')
# does crosstalk coefficient data exist
if usedb:
dblist = saltio.readgaindb(gaindb)
xtalkfile = xtalkfile.strip()
xdict = saltio.readxtalkcoeff(xtalkfile)
else:
dblist = []
xdict = None
for img, oimg in zip(infiles, outfiles):
#open the fits file
struct = saltio.openfits(img)
# identify instrument
instrume, keyprep, keygain, keybias, keyxtalk, keyslot = saltkey.instrumid(
struct)
# has file been prepared already?
if saltkey.found(keygain, struct[0]):
message = '%s has already been reduced' % img
raise SaltError(message)
# housekeeping keywords
fname, hist = history(level=1,
wrap=False,
exclude=['images', 'outimages', 'outpref'])
saltkey.housekeeping(struct[0], keyslot,
'Images have been slotmode reduced', hist)
# write FITS file
saltio.writefits(struct, oimg, clobber=clobber)
saltio.closefits(struct)
def specprepare(images,outimages,outpref,badpixelimage='', \
clobber=True,logfile='salt.log',verbose=True):
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create list of output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
#verify that the input and output lists are the same length
saltio.comparelists(infiles,outfiles,'Input','output')
# open the badpixel image
if saltio.checkfornone(badpixelimage) is None:
badpixelstruct=None
else:
try:
badpixelstruct = saltio.openfits(badpixelimage)
except saltio.SaltIOError,e:
msg='badpixel image must be specificied\n %s' % e
raise SALTSpecError(msg)
# open each raw image file
for img, oimg, in zip(infiles, outfiles):
#open the fits file
struct=saltio.openfits(img)
# prepare file
struct=prepare(struct,badpixelstruct)
# write FITS file
saltio.writefits(struct,oimg, clobber=clobber)
saltio.closefits(struct)
message = 'SPECPREPARE -- %s => %s' % (img, oimg)
log.message(message)
def specprepare(images, outimages, outpref, badpixelimage='',
clobber=True, logfile='salt.log', verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
# verify that the input and output lists are the same length
saltio.comparelists(infiles, outfiles, 'Input', 'output')
# open the badpixel image
if saltio.checkfornone(badpixelimage) is None:
badpixelstruct = None
else:
try:
badpixelstruct = saltio.openfits(badpixelimage)
except saltio.SaltIOError as e:
msg = 'badpixel image must be specificied\n %s' % e
raise SALTSpecError(msg)
# open each raw image file
for img, oimg, in zip(infiles, outfiles):
# open the fits file
struct = saltio.openfits(img)
# prepare file
struct = prepare(struct, badpixelstruct)
# write FITS file
saltio.writefits(struct, oimg, clobber=clobber)
saltio.closefits(struct)
message = 'SPECPREPARE -- %s => %s' % (img, oimg)
log.message(message)
def slotreadtimefix(images,
outimages,
outpref,
clobber=False,
logfile='slot.log',
verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
#verify that the input and output lists are the same length
saltio.comparelists(infiles, outfiles, 'Input', 'output')
for img, oimg in zip(infiles, outfiles):
#check to see if the out image already exists
if not clobber and os.path.isfile(oimg):
raise SaltIOError('%s alraedy exists' % oimg)
#open the file
struct = saltio.openfits(img)
#log the message
log.message('Updateing times in %s' % img,
with_header=False,
with_stdout=verbose)
#now for each science frame, corrent the readtime
#Assumes SALT format and that the first extension
#is empty
for i in range(1, len(struct)):
try:
struct[i] = readtimefix(struct[i])
except SaltIOError, e:
raise SaltError('%s %s' % (img, e))
#Add history keywords
# housekeeping keywords
fname, hist = history(level=1,
wrap=False,
exclude=['images', 'outimages', 'outpref'])
saltkey.housekeeping(struct[0], "SLOTREAD", 'READTIME added', hist)
#write to the output
saltio.writefits(struct, oimg, clobber)
return
def obslog(infiles, log=None):
"""For a set of input files, create a dictionary contain all the header
information from the files. Will print things to a saltlog if log is
not None
returns Dictionary
"""
#create the header dictionary
headerDict={}
for k in headerList: headerDict[k]=[]
for k in scamheaderList: headerDict[k]=[]
for k in rssheaderList: headerDict[k]=[]
# interate over and open image files
infiles.sort()
for infile in infiles:
#open the file
struct = saltio.openfits(infile)
# instrument
scam = False
rss = False
instrume = saltkey.get('INSTRUME', struct[0])
if (instrume=='RSS'): rss = True
if (instrume=='SALTICAM'): scam=True
#add in the image name
headerDict['FILENAME'].append(os.path.basename(infile))
# ingest primary keywords from files in the image list
for k,f in zip(headerList[1:], formatList[1:]):
default=finddefault(f)
headerDict[k].append(getkey(struct[0], k, default=default, log=log, warn=True))
# ingest scam specific primary keywords from files in the image list
for k,f in zip(scamheaderList[1:], scamformatList[1:]):
default=finddefault(f)
headerDict[k].append(getkey(struct[0], k, default=default, log=log, warn=scam))
# ingest rss specific primary keywords from files in the image list
for k,f in zip(rssheaderList[1:], rssformatList[1:]):
default=finddefault(f)
headerDict[k].append(getkey(struct[0], k, default=default, log=log, warn=rss))
# close image files
saltio.closefits(struct)
if log: log.message('SALTOBSLOG -- read %s' % infile, with_header=False)
return headerDict
def specextract(
images,
outfile,
method="normal",
section=None,
thresh=3.0,
minsize=3.0,
outformat="ascii",
ext=1,
convert=True,
clobber=True,
logfile="salt.log",
verbose=True,
):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack("Input", images)
# create list of output files
outfiles = saltio.argunpack("outfile", outfile)
if method is "weighted":
msg = "This mode is not supported yet"
raise SALTSpecError(msg)
section = saltio.checkfornone(section)
if section is not None:
sections = saltio.getSection(section, iraf_format=False)
section = []
for i in range(0, len(sections), 2):
section.append((sections[i], sections[i + 1]))
# Identify the lines in each file
for img, ofile in zip(infiles, outfiles):
log.message(
"\nExtracting spectrum in image %s to %s" % (img, ofile), with_header=False, with_stdout=verbose
)
# open the images
hdu = saltio.openfits(img)
ap_list = extract(
hdu, ext=ext, method=method, section=section, minsize=minsize, thresh=thresh, convert=convert
)
# write the spectra out
if ap_list:
write_extract(ofile.strip(), ap_list, outformat=outformat, clobber=clobber)
log.message("", with_header=False, with_stdout=verbose)
def addtoobsdict(self, infile):
try:
self.hdu=saltio.openfits(infile)
self.hdu.verify('exception')
name=getbasename(self.hdu)
imlist=getimagedetails(self.hdu)
self.hdu.close()
except IndexError:
time.sleep(5)
name=self.addtoobsdict(infile)
return name
except Exception, e:
print e
return None
def specsky(images,
outimages,
outpref,
method='normal',
section=None,
function='polynomial',
order=2,
clobber=True,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
if method not in ['normal', 'fit']:
msg = '%s mode is not supported yet' % method
raise SALTSpecError(msg)
if section is None:
section = saltio.getSection(section)
msg = 'This mode is not supported yet'
raise SALTSpecError(msg)
else:
section = saltio.getSection(section)
# Identify the lines in each file
for img, ofile in zip(infiles, outfiles):
log.message('Subtracting sky spectrum in image %s into %s' %
(img, ofile))
# open the images
hdu = saltio.openfits(img)
# sky subtract the array
hdu = skysubtract(hdu,
method=method,
section=section,
funct=function,
order=order)
# write out the image
if clobber and os.path.isfile(ofile):
saltio.delete(ofile)
hdu.writeto(ofile)
def addtoobsdict(self, infile):
try:
warnings.warn('error')
self.hdu=saltio.openfits(infile)
self.hdu.verify('exception')
warnings.warn('default')
name=getbasename(self.hdu)
imlist=getimagedetails(self.hdu)
self.hdu.close()
except IndexError:
time.sleep(10)
name=self.addtoobsdict(infile)
return name
except Exception, e:
print 'Returning none due to: %s' % (str(e))
return None
def addtoobsdict(self, infile):
try:
warnings.warn('error')
self.hdu=saltio.openfits(infile)
self.hdu.verify('exception')
warnings.warn('default')
name=getbasename(self.hdu)
imlist=getimagedetails(self.hdu)
self.hdu.close()
except IndexError:
time.sleep(10)
name=self.addtoobsdict(infile)
return name
except Exception, e:
print 'Returning none due to: %s' % (str(e))
return None
def saltfpcalring(images,outfile, waves, method=None, thresh=5, minsize=10, niter=3, conv=0.05,
axc=None, ayc=None,
clobber=False,logfile='salt.log',verbose=True):
"""Fits rings in Fabry-Perot ring images"""
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# if the outfile exists and not clobber, fail
saltio.overwrite(outfile,clobber)
#open the output file
fout = saltio.openascii(outfile, 'w')
#make sure that the list of waves is convertable to a numpy array
#convert to floats in case the wave is given as a string
if isinstance(waves, str):
waves=[float(x) for x in waves.split(',')]
try:
waves=np.array(waves)
except:
raise SaltError('%s is not convertable to a numpy array' % waves)
#check the value of method
method=saltio.checkfornone(method)
#setup the output file
fout.write('#Comment\n')
fout.write('# radius err xc yc z ut wave dn file\n')
# open each image and detect the ring
for img,w in zip(infiles, waves):
#open the image
hdu=saltio.openfits(img)
#measure the ring in each file
xc, yc, radius, err, z, ut=make_calring(hdu, method=method, thresh=thresh, niter=niter, conv=conv, minsize=minsize, axc=axc, ayc=ayc)
#output the results
outstr=' %7.2f %6.2f %7.2f %7.2f %6.2f %7.4f %8.3f 0 %s\n' % (radius, err, xc, yc, z, ut, w, img)
fout.write(outstr)
log.message(outstr.strip(), with_stdout=verbose, with_header=False)
fout.close()
def saltmosaic(images,outimages,outpref,geomfile,interp='linear',geotran=True, cleanup=True,clobber=False,logfile=None,verbose=True):
#Start the logging
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create list of output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
#verify that the input and output lists are the same length
saltio.comparelists(infiles,outfiles,'Input','output')
# does CCD geometry definition file exist
geomfilefile = geomfile.strip()
saltio.fileexists(geomfile)
gap = 0
xshift = [0, 0]
yshift = [0, 0]
rotation = [0, 0]
gap, xshift, yshift, rotation=saltio.readccdgeom(geomfile)
# open each raw image file and apply the transformation to it
for img, oimg in zip(infiles, outfiles):
#open the structure
struct = saltio.openfits(img)
#create the mosaic
ostruct=make_mosaic(struct, gap, xshift, yshift, rotation, interp_type=interp, geotran=geotran, cleanup=cleanup, log=log, verbose=verbose)
#update the header information
# housekeeping keywords
fname, hist=history(level=1, wrap=False, exclude=['images', 'outimages', 'outpref'])
saltkey.housekeeping(ostruct[0], 'SMOSAIC', 'Images have been mosaicked ', hist)
#write the image out
saltio.writefits(ostruct,oimg, clobber=clobber)
#close the files
saltio.closefits(struct)
saltio.closefits(ostruct)
def saltgain(images,outimages, outpref, gaindb=None,usedb=False, mult=True,
clobber=True, logfile='salt.log',verbose=True):
#start logging
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create list of output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
#verify that the input and output lists are the same length
saltio.comparelists(infiles,outfiles,'Input','output')
# read in the database file if usedb is true
if usedb:
gaindb = gaindb.strip()
dblist= saltio.readgaindb(gaindb)
else:
dblist=[]
for img, oimg in zip(infiles, outfiles):
#open the fits file
struct=saltio.openfits(img)
# identify instrument
instrume,keyprep,keygain,keybias,keyxtalk,keyslot = saltkey.instrumid(struct)
# has file been prepared already?
if saltkey.found(keygain, struct[0]):
message='SALTGAIN: %s has already been gain-corrected' % img
raise SaltError(message)
# gain correct the data
struct = gain(struct,mult=mult, usedb=usedb, dblist=dblist, log=log, verbose=verbose)
# housekeeping keywords
fname, hist=history(level=1, wrap=False, exclude=['images', 'outimages', 'outpref'])
saltkey.housekeeping(struct[0],keygain, 'Images have been gain corrected', hist)
# write FITS file
saltio.writefits(struct,oimg, clobber=clobber)
saltio.closefits(struct)
def saltslot(images,outimages,outpref,gaindb='',xtalkfile='',usedb=False, clobber=False,logfile='salt.log',verbose=True):
#start logging
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create list of output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
# are input and output lists the same length?
saltio.comparelists(infiles,outfiles,'Input','output')
# does crosstalk coefficient data exist
if usedb:
dblist= saltio.readgaindb(gaindb)
xtalkfile = xtalkfile.strip()
xdict = saltio.readxtalkcoeff(xtalkfile)
else:
dblist=[]
xdict=None
for img, oimg in zip(infiles, outfiles):
#open the fits file
struct=saltio.openfits(img)
# identify instrument
instrume,keyprep,keygain,keybias,keyxtalk,keyslot = saltkey.instrumid(struct)
# has file been prepared already?
if saltkey.found(keygain, struct[0]):
message='%s has already been reduced' % img
raise SaltError(message)
# housekeeping keywords
fname, hist=history(level=1, wrap=False, exclude=['images', 'outimages', 'outpref'])
saltkey.housekeeping(struct[0],keyslot, 'Images have been slotmode reduced', hist)
# write FITS file
saltio.writefits(struct,oimg, clobber=clobber)
saltio.closefits(struct)
def specrectify(images, outimages, outpref, solfile=None, caltype='line',
function='polynomial', order=3, inttype='linear', w1=None,
w2=None, dw=None, nw=None, blank=0, conserve=False, nearest=False,
clobber=True, logfile='salt.log', verbose=True):
with logging(logfile, debug) as log:
# set up the variables
infiles = []
outfiles = []
# Check the input images
infiles = saltsafeio.argunpack('Input', images)
# create list of output files
outfiles = saltsafeio.listparse(
'Outimages',
outimages,
outpref,
infiles,
'')
# read in the wavelength solutions and enter them into
# there own format
if caltype == 'line':
soldict = entersolution(solfile)
else:
soldict = None
# read in rectify each image
for img, oimg, in zip(infiles, outfiles):
if caltype == 'line':
msg = 'Creating rectified image %s from image %s using files %s' % (
oimg, img, solfile)
else:
msg = 'Creating rectified image %s from image %s using RSS Model' % (
oimg, img)
log.message(msg)
hdu = saltsafeio.openfits(img)
hdu = rectify(hdu, soldict, caltype=caltype, function=function,
order=order, inttype=inttype, w1=w1, w2=w2, dw=dw, nw=nw,
pixscale=0.0, blank=blank, conserve=conserve, nearest=nearest,
clobber=clobber, log=log, verbose=verbose)
# write out the oimg
saltsafeio.writefits(hdu, oimg, clobber=clobber)
def saltfpmask(images, outimages, outpref, axc,ayc, arad, maskmethod='c', maskvalue=0, \
radi=None,rado=None,clobber=False, logfile='saltfp.log', verbose=True):
"""Aperture masks Fabry-Perot images"""
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
#verify that the input and output lists are the same length
saltio.comparelists(infiles, outfiles, 'Input', 'output')
for img, oimg in zip(infiles, outfiles):
#open the image
hdu = saltio.openfits(img)
#test that the data are in the first
try:
data = hdu[0].data
except Exception, e:
message = 'SALTFPMASK--ERROR: Could not access data in Primary exention of %s because %s' % (
img, e)
log.message(message)
#determine the mask value if it is a region
if maskmethod == 'region':
maskvalue = calc_maskvalue(data, axc, ayc, radi, rado)
#mask the image
message = "SALTFPMASK--Masking image %s with a value of %s" % (
img, maskvalue)
log.message(message, with_header=False)
hdu[0].data = maskimage(data, axc, ayc, arad, maskvalue)
try:
pass
except Exception, e:
message = 'SALTFPMASK--ERROR: Could not create mask for %s because %s' % (
img, e)
log.message(message)
#write out the image
saltio.writefits(hdu, oimg, clobber=clobber)
def slotreadtimefix(images,outimages, outpref,
clobber=False, logfile='slot.log',verbose=True):
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create list of output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
#verify that the input and output lists are the same length
saltio.comparelists(infiles,outfiles,'Input','output')
for img, oimg in zip(infiles, outfiles):
#check to see if the out image already exists
if not clobber and os.path.isfile(oimg):
raise SaltIOError('%s alraedy exists' % oimg)
#open the file
struct=saltio.openfits(img)
#log the message
log.message('Updateing times in %s' % img, with_header=False, with_stdout=verbose)
#now for each science frame, corrent the readtime
#Assumes SALT format and that the first extension
#is empty
for i in range(1,len(struct)):
try:
struct[i]=readtimefix(struct[i])
except SaltIOError,e :
raise SaltError('%s %s' % (img,e))
#Add history keywords
# housekeeping keywords
fname, hist=history(level=1, wrap=False, exclude=['images', 'outimages', 'outpref'])
saltkey.housekeeping(struct[0],"SLOTREAD", 'READTIME added', hist)
#write to the output
saltio.writefits(struct, oimg, clobber)
return
def read_slits_from_fits(simg):
"""Read the slit definitions from a FITS fiel where the slit
definitions have been stored in a table in the FITS file under an
extension with the name
"""
# first check if the file exists
saltio.fileexists(simg)
# open the slit image
struct = saltio.openfits(simg)
# get the extension of the slit table
slitext = saltkey.get('SLITEXT', struct[0])
# extract the order of the fit and the positions of each of the slits
order, slit_positions = mt.read_slits_HDUtable(struct[slitext])
return order, slit_positions
def convertsalt(img, oimg, ext=1, clobber=True):
"""Convert a SALT MEF file into a single extension fits file"""
#open the image
hdu=saltio.openfits(img)
#if len one, copy and return
if len(hdu)==1:
hdu.writeto(oimg)
return
#create the new output image
odu = pyfits.PrimaryHDU(data=hdu[ext].data, header=hdu[0].header)
#combine the headers from the primary and first exention
for c in hdu[ext].header.ascardlist(): odu.header.update(c.key, c.value, c.comment)
#write the data out
saltio.writefits(odu, oimg, clobber=clobber)
def read_slits_from_fits(simg):
"""Read the slit definitions from a FITS fiel where the slit
definitions have been stored in a table in the FITS file under an
extension with the name
"""
# first check if the file exists
saltio.fileexists(simg)
# open the slit image
struct = saltio.openfits(simg)
# get the extension of the slit table
slitext = saltkey.get('SLITEXT', struct[0])
# extract the order of the fit and the positions of each of the slits
order, slit_positions = mt.read_slits_HDUtable(struct[slitext])
return order, slit_positions
def saltsurface(images,
outimages,
outpref,
mask=True,
order=3,
minlevel=0,
clobber=False,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
#verify that the input and output lists are the same length
saltio.comparelists(infiles, outfiles, 'Input', 'output')
# open each raw image file
for infile, outfile in zip(infiles, outfiles):
struct = saltio.openfits(infile)
struct = surface_fit(struct,
order=order,
mask=mask,
minlevel=minlevel)
#add any header keywords like history
fname, hist = history(level=1, wrap=False)
saltkey.housekeeping(struct[0], 'SURFIT', 'File fit by a surface',
hist)
#write it out and close it
saltio.writefits(struct, outfile, clobber=clobber)
saltio.closefits(struct)
#output the information
log.message('Surface fitted image %s ' % (infile),
with_header=False,
with_stdout=verbose)
def saltfpmask(images, outimages, outpref, axc,ayc, arad, maskmethod='c', maskvalue=0, \
radi=None,rado=None,clobber=False, logfile='saltfp.log', verbose=True):
"""Aperture masks Fabry-Perot images"""
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create list of output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
#verify that the input and output lists are the same length
saltio.comparelists(infiles,outfiles,'Input','output')
for img, oimg in zip(infiles, outfiles):
#open the image
hdu=saltio.openfits(img)
#test that the data are in the first
try:
data=hdu[0].data
except Exception, e:
message='SALTFPMASK--ERROR: Could not access data in Primary exention of %s because %s' % (img, e)
log.message(message)
#determine the mask value if it is a region
if maskmethod=='region':
maskvalue=calc_maskvalue(data, axc, ayc, radi, rado)
#mask the image
message="SALTFPMASK--Masking image %s with a value of %s" % (img, maskvalue)
log.message(message, with_header=False)
hdu[0].data= maskimage(data, axc, ayc, arad, maskvalue)
try:
pass
except Exception, e:
message='SALTFPMASK--ERROR: Could not create mask for %s because %s' % (img, e)
log.message(message)
#write out the image
saltio.writefits(hdu, oimg, clobber=clobber)
def sdbloadfits(infile, sdb, logfile, verbose):
"""Add a fits file to the science database
"""
#determine the base file name
FileName = findrawfilename(infile)
#determine the reduced file name
if FileName!=infile:
PipelineFileName=infile
else:
PipelineFileName=''
#open the image and extract the header
infits=saltio.openfits(infile)
#Extract the primary header
try:
ext=0
ImageHeader = infits[ext].header
except:
message='SALTSDBLOADFITS -- ERROR: Can not access header for %s' % infile
raise SaltError(message)
#get the FileData_Id if it already exists
FileData_Id = checksdbforfits(FileName, sdb, logfile, verbose)
#create a new entry or update
if FileData_Id == -1:
#add to database and get its new id number
FileData_Id=saltmysql.createnewFileData(sdb,ImageHeader,FileName, PipelineFileName)
else:
#update the FileData information
saltmysql.updateFileData(sdb, ImageHeader, FileData_Id, FileName, PipelineFileName)
#Update all of the fits header tables
saltmysql.updateFitsHeaders(sdb, infits, FileData_Id)
saltio.closefits(infits)
return
def sdbloadfits(infile, sdb, logfile, verbose):
"""Add a fits file to the science database
"""
#determine the base file name
FileName = findrawfilename(infile)
#determine the reduced file name
if FileName != infile:
PipelineFileName = infile
else:
PipelineFileName = ''
#open the image and extract the header
infits = saltio.openfits(infile)
#Extract the primary header
try:
ext = 0
ImageHeader = infits[ext].header
except:
message = 'SALTSDBLOADFITS -- ERROR: Can not access header for %s' % infile
raise SaltError(message)
#get the FileData_Id if it already exists
FileData_Id = checksdbforfits(FileName, sdb, logfile, verbose)
#create a new entry or update
if FileData_Id == -1:
#add to database and get its new id number
FileData_Id = saltmysql.createnewFileData(sdb, ImageHeader, FileName,
PipelineFileName)
else:
#update the FileData information
saltmysql.updateFileData(sdb, ImageHeader, FileData_Id, FileName,
PipelineFileName)
#Update all of the fits header tables
saltmysql.updateFitsHeaders(sdb, infits, FileData_Id)
saltio.closefits(infits)
return
def salthrspreprocess(inpath,outpath,clobber=True, log=None,verbose=True):
"""Convert .fit files to .fits files and place HRS data into
standard SALT FITS format
"""
#first get a list of images in the directory
infiles=glob.glob(inpath+'*.fit')
if log is not None:
log.message('Processing HRS data in %s' % inpath)
#open the file and write out as a fits files in the output directory
for img in infiles:
oimg=outpath+os.path.basename(img)+'s'
hdu=saltio.openfits(img)
hdu=hrsprepare(hdu)
if log is not None:
log.message('Writing %s to %s' % (img, oimg), with_header=False)
saltio.writefits(hdu, oimg, clobber=clobber)
return
def saltfpzeropoint(images,outimages, outpref, calfile, fpa, fpb, fpc, fpd, fpe, fpf, clobber=False,logfile='salt.log',verbose=True):
"""Adds zeropoint information to each image"""
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create the output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
#verify that the input and output lists are the same length
saltio.comparelists(infiles,outfiles,'Input','output')
#calculate the zeropoint coefficients
fpcoef=np.array([fpa,fpb,fpc,fpd,fpe,fpf])
zpcoef,tstart=calc_zpcoef(calfile, fpcoef)
# open each image and detect the ring
for img, oimg in zip(infiles, outfiles):
hdu=saltio.openfits(img)
#get the image time
t=(get_datetime(hdu)-tstart).seconds
#add the header values to the image
saltkey.new('FPA',fpa+zpcoef[1]+zpcoef[0]*t,'FPA Coef',hdu[0])
saltkey.new('FPB',fpb,'FPB Coef',hdu[0])
saltkey.new('FPC',fpc,'FPC Coef',hdu[0])
saltkey.new('FPD',fpd,'FPD Coef',hdu[0])
saltkey.new('FPE', 0,'FPE Coef',hdu[0])
saltkey.new('FPF',fpf,'FPF Coef',hdu[0])
#write the file out
saltio.writefits(hdu, oimg, clobber)
#log the action
msg='Updating the FP information in %s' % (img)
log.message(msg, with_stdout=verbose, with_header=False)
def calc_zpcoef(calfile, fpcoef):
"""Given the values given in the calibraiton file, calculate the
offset to the FPA value and FPE value that would give an
appropriate calibration values to the frame
The task returns the zeropoint coefficient and the initial
start time
"""
#read in the values for the calfile--assumes the format for the file
#r,r_err,z,t,w,img=np.loadtxt(calfile, usecols=(0,1,4,5,6,8), unpack=True, dtype={8,str})
data=np.loadtxt(calfile, dtype={'names': ('r','r_err', 'x', 'y', 'z', 't', 'w', 'dn', 'image'),'formats':('f4', 'f4', 'f4', 'f4', 'f4', 'f4', 'f4', 'f4','S30')})
#set the start time and convert the time to a date time unit
time_list=[]
time_start=None
if data.size==0:
raise SaltError('%s needs to have at least one entry' % calfile)
elif data.size==1:
img_list=[str(data['image'])]
else:
img_list=data['image']
for img in img_list:
if not os.path.isfile(img):
raise SaltError('%s needs to be available to open' % img)
t=get_datetime(saltio.openfits(img))
if time_start is None: time_start=t
time_list.append((t-time_start).seconds)
time_arr=np.array(time_list)
#calculate the coefficients
wf=fpfunc(data['z'], data['r'], time_arr, coef=fpcoef)
if data.size==1:
coef=np.array([0, data['w']-wf])
else:
coef=np.polyfit(time_arr, data['w']-wf, 1)
return coef, time_start
def saltembed(images,outimages,outpref, clobber=True,logfile='salt.log',verbose=True):
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
# create list of output files
outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')
#verify that the input and output lists are the same length
saltio.comparelists(infiles,outfiles,'Input','output')
# open each raw image file
for img, oimg, in zip(infiles, outfiles):
#open the fits file
struct=saltio.openfits(img)
#get the number of CCDs
nccd=saltkey.get('NCCDS', struct[0])
#set the number of amps per CCD--*TODO* Read from header
namps=2
#get the number of windows--try to read from header
try:
nwindows=saltkey.get('NWINDOWS', struct[0])
except:
nwindows=len(struct)/(nccd*namps)
outstruct=embedimage(struct, nccd, namps, nwindows)
saltio.writefits(outstruct, oimg, clobber=clobber)
message = 'SALTEMBED -- %s => %s' % (img, oimg)
log.message(message, with_header=False)
def specslitnormalize(images,
outimages,
outpref,
response=None,
response_output=None,
order=2,
conv=1e-2,
niter=20,
startext=0,
clobber=False,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
# read in the response function
response = saltio.checkfornone(response)
if response:
log.message('Loading response from %s' % response)
response = readresponse(response)
# Identify the lines in each file
for img, ofile in zip(infiles, outfiles):
# open the image
hdu = saltio.openfits(img)
for i in range(startext, len(hdu)):
if hdu[i].name == 'SCI':
log.message('Normalizing extension %i in %s' % (i, img))
# things that will change for each slit
# set up the data for the source
try:
data = hdu[i].data
except Exception as e:
message = \
'Unable to read in data array in %s because %s' % \
(img, e)
raise SALTSpecError(message)
if response is None:
response = create_response(data,
spatial_axis=1,
order=order,
conv=conv,
niter=niter)
if response_output:
write_response(response, clobber=clobber)
else:
# add a check that the response is the same shape as
# the data
if len(response) != data.shape[0]:
raise SALTSpecError(
'Length of response function does not equal size of image array'
)
# correct the data
data = data / response
# correct the variance frame
if saltkey.found('VAREXT', hdu[i]):
vhdu = saltkey.get('VAREXT', hdu[i])
hdu[vhdu].data = hdu[vhdu].data / response
saltio.writefits(hdu, ofile, clobber=clobber)
def saltxtalk(images,
outimages,
outpref,
xtalkfile=None,
usedb=False,
clobber=True,
logfile='salt.log',
verbose=True):
#start logging
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
# are input and output lists the same length?
saltio.comparelists(infiles, outfiles, 'Input', 'output')
# does crosstalk coefficient data exist
if usedb:
xtalkfile = xtalkfile.strip()
xdict = saltio.readxtalkcoeff(xtalkfile)
else:
xdict = None
for img, oimg in zip(infiles, outfiles):
#open the fits file
struct = saltio.openfits(img)
#find the best xcoeff for the image if using the db
if usedb:
obsdate = saltkey.get('DATE-OBS', struct[0])
obsdate = int('%s%s%s' %
(obsdate[0:4], obsdate[5:7], obsdate[8:]))
xkey = np.array(xdict.keys())
date = xkey[abs(xkey - obsdate).argmin()]
xcoeff = xdict[date]
else:
xcoeff = []
# identify instrument
instrume, keyprep, keygain, keybias, keyxtalk, keyslot = saltkey.instrumid(
struct)
# has file been prepared already?
if saltkey.found(keyxtalk, struct[0]):
message = '%s has already been xtalk corrected' % img
raise SaltError(message)
#apply the cross-talk correction
struct = xtalk(struct, xcoeff, log=log, verbose=verbose)
# housekeeping keywords
fname, hist = history(level=1,
wrap=False,
exclude=['images', 'outimages', 'outpref'])
saltkey.housekeeping(struct[0], 'SXTALK',
'Images have been xtalk corrected', hist)
# write FITS file
saltio.writefits(struct, oimg, clobber=clobber)
saltio.closefits(struct)
def cleandata(filename, iminfo=None, prodir='.', interp='linear', cleanup=True, clobber=False, logfile='saltclean.log', display_image=False, verbose=True):
"""Start the process to reduce the data and produce a single mosaicked image"""
print filename
status=0
#create the input file name
infile=os.path.basename(filename)
rawpath=os.path.dirname(filename)
outpath='./'
outfile=outpath+'mbxp'+infile
print infile, rawpath, outpath
#check to see if the data have detmode
if iminfo is not None:
detmode=iminfo[headerList.index('DETMODE')].strip().upper()
print 'DETMODE:' detmode
#If it is a bin file, pre-process the data
if filename.count('.bin'):
print "I can't handle this yet"
#check to see if it exists and return if clobber is no
if os.path.isfile(outfile) and not clobber: return
#set up the files needed
if infile[0]=='P':
gaindb = '/iraf/extern/pysalt/data/rss/RSSamps.dat'
xtalkfile = '/iraf/extern/pysalt/data/rss/RSSxtalk.dat'
geomfile = '/iraf/extern/pysalt/data/rss/RSSgeom.dat'
usedb=True
elif infile[0]=='S':
gaindb = '/iraf/extern/pysalt/data/scam/SALTICAMamps.dat'
xtalkfile = '/iraf/extern/pysalt/data/scam/SALTICAMxtalk.dat'
geomfile = '/iraf/extern/pysalt/data/scam/SALTICAMgeom.dat'
#verify the file
hdu=saltio.openfits(rawpath+'/'+infile)
hdu.verify('exception')
#reduce the file
saltred.saltprepare(images=infile,rawpath=rawpath,outimages='',outpref=outpath+'p', \
clobber=clobber,logfile=logfile,verbose=verbose,status=status)
pinfile=outpath+'p'+infile
saltred.saltslot(images=pinfile,outimages='',outpref=outpath+'bx',gaindb=gaindb,
xtalkfile=xtalkfile,usedb=True, clobber=clobber,logfile=logfile,verbose=verbose,
status=status)
biasfile=outpath+'bxp'+infile
saltred.saltmosaic(images=biasfile,
outimages='',outpref=outpath+'m',geomfile=geomfile,
interp=interp,cleanup=cleanup,fill=True, clobber=clobber,logfile=logfile,
verbose=verbose, status=status)
profile=outpath+'mbxp'+infile
#remove intermediate steps
if cleanup:
if os.path.isfile(pinfile): os.remove(pinfile)
if os.path.isfile(biasfile): os.remove(biasfile)
i=headerList.index('CCDSUM')
ccdbin=int(iminfo[i].split()[0])
pix_scale=0.14
r_ap=1.5/(pix_scale*ccdbin)
print pix_scale, ccdbin, r_ap
profile=outpath+'mbxp'+infile
outcat=profile.split('.fits')[0]+'.cat'
sexfile='/home/ccd/tools/qred.sex'
backfile = profile.strip().strip('.fits')+'_back.fits'
cmd='sex %s -c %s -PIXEL_SCALE %f -CATALOG_NAME %s -PHOT_APERTURES %f ' % (profile.strip(),sexfile, pix_scale,outcat,r_ap)
print "SALTFIRST--Performing photometry on %s" % profile
if os.path.isfile(sexfile): os.system(cmd)
def specslit(image,
outimage,
outpref,
exttype='auto',
slitfile='',
outputslitfile='',
regprefix='',
sections=3,
width=25,
sigma=2.2,
thres=6,
order=3,
padding=5,
yoffset=0,
inter=False,
clobber=True,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# check all the input and make sure that all the input needed is provided
# by the user
# read the image or image list and check if each in the list exist
infiles = saltio.argunpack('Input', image)
# unpack the outfiles
outfiles = saltio.listparse('Outimages', outimage, outpref, infiles,
'')
# from the extraction type, check whether the input file is specified.
# if the slitfile parameter is specified then use the slit files for
# the extraction. if the extraction type is auto then use image for the
# detection and the slit extraction
if exttype == 'rsmt' or exttype == 'fits' or exttype == 'ascii' or exttype == 'ds9':
slitfiles = saltio.argunpack('Slitfile', slitfile)
if len(slitfiles) == 1:
slitfiles = slitfiles * len(infiles)
saltio.comparelists(infiles, slitfiles, 'image', 'slitfile')
elif exttype == 'auto':
slitfiles = infiles
log.message(
'Extraction type is AUTO. Slit detection will be done from image'
)
# read in if an optional ascii file is requested
if len(outputslitfile) > 0:
outslitfiles = saltio.argunpack('Outslitfiles', outputslitfile)
saltio.comparelists(infiles, outslitfiles, 'image',
'outputslitfile')
else:
outslitfiles = [''] * len(infiles)
# check if the width and sigma parameters were specified.
# default is 25 and 2.2
if width < 10.:
msg = 'The width parameter needs be a value larger than 10'
raise SALTSpecError(msg)
if sigma < 0.0:
msg = 'Sigma must be greater than zero'
raise SaltSpecError(msg)
# check the treshold parameter. this needs to be specified by the user
if thres <= 0.0:
msg = 'Threshold must be greater than zero'
raise SaltSpecError(msg)
# check to make sure that the sections are greater than the order
if sections <= order:
msg = 'Number of sections must be greater than the order for the spline fit'
raise SaltSpecError(msg)
# run through each of the images and extract the slits
for img, oimg, sfile, oslit in zip(infiles, outfiles, slitfiles,
outslitfiles):
log.message('Proccessing image %s' % img)
# open the image
struct = saltio.openfits(img)
ylen, xlen = struct[1].data.shape
xbin, ybin = saltkey.ccdbin(struct[0], img)
# setup the VARIANCE and BPM frames
if saltkey.found('VAREXT', struct[1]):
varext = saltkey.get('VAREXT', struct[1])
varlist = []
else:
varext = None
# setup the BPM frames
if saltkey.found('BPMEXT', struct[1]):
bpmext = saltkey.get('BPMEXT', struct[1])
bpmlist = []
else:
bpmext = None
# open the slit definition file or identify the slits in the image
slitmask = None
ycheck = False
if exttype == 'rsmt':
log.message('Using slits from %s' % sfile)
if yoffset is None:
yoffset = 0
ycheck = True
slitmask = mt.read_slitmask_from_xml(sfile)
xpos = -0.3066
ypos = 0.0117
cx = int(xlen / 2.0)
cy = int(ylen / 2.0) + ypos / 0.015 / ybin + yoffset
order, slit_positions = mt.convert_slits_from_mask(
slitmask,
order=1,
xbin=xbin,
ybin=ybin,
pix_scale=0.1267,
cx=cx,
cy=cy)
sections = 1
elif exttype == 'fits':
log.message('Using slits from %s' % sfile)
order, slit_positions = read_slits_from_fits(sfile)
elif exttype == 'ascii':
log.message('Using slits from %s' % sfile)
order, slit_positions = mt.read_slits_from_ascii(sfile)
elif exttype == 'ds9':
log.message('Using slits from %s' % sfile)
order, slit_positions, slitmask = mt.read_slits_from_ds9(
sfile, order=order)
slitmask = None
sections = 1
elif exttype == 'auto':
log.message('Identifying slits in %s' % img)
# identify the slits in the image
order, slit_positions = identify_slits(struct[1].data, order,
sections, width, sigma,
thres)
# write out the slit identifications if ofile has been supplied
if oslit:
log.message('Writing slit positions to %s' % oslit)
mt.write_outputslitfile(slit_positions, oslit, order)
if ycheck:
slit_positions, dy = check_ypos(slit_positions, struct[1].data)
log.message('Using an offset of {}'.format(dy))
# extract the slits
spline_x = mt.divide_image(struct[1].data, sections)
spline_x = 0.5 * (np.array(spline_x[:-1]) + np.array(spline_x[1:]))
extracted_spectra, spline_positions = mt.extract_slits(
slit_positions,
spline_x,
struct[1].data,
order=order,
padding=padding)
if varext:
extracted_var, var_positions = mt.extract_slits(
slit_positions,
spline_x,
struct[varext].data,
order=order,
padding=padding)
if bpmext:
extracted_bpm, bpm_positions = mt.extract_slits(
slit_positions,
spline_x,
struct[bpmext].data,
order=order,
padding=padding)
# write out the data to the new array
# create the new file
hdulist = fits.HDUList([struct[0]])
# log the extracted spectra if needed
log.message('', with_stdout=verbose)
# setup output ds9 file
if regprefix:
regout = open(
regprefix + os.path.basename(img).strip('.fits') + '.reg',
'w')
regout.write('# Region file format: DS9 version 4.1\n')
regout.write('# Filename: %s\n' % img)
regout.write(
'global color=green dashlist=8 3 width=1 font="helvetica 10 normal roman" select=1 highlite=1 dash=0 fixed=0 edit=1 move=1 delete=1 include=1 source=1\nphysical\n'
)
# add each
imglist = []
nslits = len(spline_positions)
for i in range(nslits):
y1 = spline_positions[i][0].min()
y2 = spline_positions[i][1].max()
msg = 'Extracted Spectra %i between %i to %i' % (i + 1, y1, y2)
# log.message(msg, with_header=False, with_stdout=verbose)
sdu = fits.ImageHDU(extracted_spectra[i],
header=struct[1].header)
if varext:
vdu = fits.ImageHDU(extracted_var[i],
header=struct[varext].header)
sdu.header['VAREXT'] = i + nslits + 1
varlist.append(vdu)
if bpmext:
bdu = fits.ImageHDU(extracted_bpm[i],
header=struct[bpmext].header)
sdu.header['BPMEXT'] = i + 2 * nslits + 1
bpmlist.append(bdu)
imglist.append(sdu)
# add in some additional keywords
imglist[i].header['MINY'] = (y1,
'Lower Y value in original image')
imglist[i].header['MAXY'] = (y2,
'Upper Y value in original image')
if regprefix:
xsize = struct[1].data.shape[1]
xsize = int(0.5 * xsize)
rtext = ''
if slitmask:
# rtext='%s, %8.7f, %8.7f, %3.2f' % (slitmask.slitlets.data[i]['name'], slitmask.slitlets.data[i]['targ_ra'], slitmask.slitlets.data[i]['targ_dec'], slitmask.slitlets.data[i]['slit_width'])
pass
regout.write('box(%i,%i, %i, %i) #text={%s}\n' %
(xsize, 0.5 *
(y1 + y2), 2 * xsize, y2 - y1, rtext))
# add slit information
if slitmask:
imglist[i].header['SLITNAME'] = (
slitmask.slitlets.data[i]['name'], 'Slit Name')
imglist[i].header['SLIT_RA'] = (
slitmask.slitlets.data[i]['targ_ra'], 'Slit RA')
imglist[i].header['SLIT_DEC'] = (
slitmask.slitlets.data[i]['targ_dec'], 'Slit DEC')
imglist[i].header['SLIT'] = (
slitmask.slitlets.data[i]['slit_width'], 'Slit Width')
# add to the hdulist
hdulist += imglist
if varext:
hdulist += varlist
if bpmext:
hdulist += bpmlist
# write the slit positions to the header
# create the binary table HDU that contains the split positions
tbhdu = mt.slits_HDUtable(slit_positions, order)
bintable_hdr = tbhdu.header
# add the extname parameter to the extension
tbhdu.header['EXTNAME'] = 'BINTABLE'
# add the extname parameter to the extension
hdulist[0].header['SLITEXT'] = len(hdulist)
hdulist.append(tbhdu)
# add addition header information about the mask
if slitmask:
hdulist[0].header['MASKNAME'] = (slitmask.mask_name,
'SlitMask Name')
hdulist[0].header['MASK_RA'] = (slitmask.center_ra,
'SlitMask RA')
hdulist[0].header['MASK_DEC'] = (slitmask.center_dec,
'SlitMask DEC')
hdulist[0].header['MASK_PA'] = (slitmask.position_angle,
'SlitMask Position Angle')
# write out the image
saltio.writefits(hdulist, oimg, clobber)
def specarcstraighten(images, outfile, function='poly', order=3, rstep=1,
rstart='middlerow', nrows=1,
y1=None, y2=None, sigma=5, sections=3, niter=5,
startext=0, clobber=False, logfile='salt.log', verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.argunpack('Output', outfile)
# Identify the lines in each file
for img, ofile in zip(infiles, outfiles):
# open the image
hdu = saltio.openfits(img)
# get the basic information about the spectrograph
dateobs = saltkey.get('DATE-OBS', hdu[0])
try:
utctime = saltkey.get('UTC-OBS', hdu[0])
except SaltError:
utctime = saltkey.get('TIME-OBS', hdu[0])
instrume = saltkey.get('INSTRUME', hdu[0]).strip()
grating = saltkey.get('GRATING', hdu[0]).strip()
grang = saltkey.get('GR-ANGLE', hdu[0])
grasteps = saltkey.get('GRTILT', hdu[0])
arang = saltkey.get('AR-ANGLE', hdu[0])
arsteps = saltkey.get('CAMANG', hdu[0])
rssfilter = saltkey.get('FILTER', hdu[0])
specmode = saltkey.get('OBSMODE', hdu[0])
masktype = saltkey.get('MASKTYP', hdu[0]).strip().upper()
slitname = saltkey.get('MASKID', hdu[0])
xbin, ybin = saltkey.ccdbin(hdu[0], img)
for i in range(startext, len(hdu)):
if hdu[i].name == 'SCI':
log.message('Proccessing extension %i in %s' % (i, img))
# things that will change for each slit
if masktype == 'LONGSLIT':
slit = st.getslitsize(slitname)
objid = None
#elif masktype == 'MOS':
#slit = 1.5
# slit=saltkey.get('SLIT', hdu[i])
# set up the x and y positions
#miny = hdu[i].header['MINY']
#maxy = hdu[i].header['MAXY']
#ras = hdu[i].header['SLIT_RA']
#des = hdu[i].header['SLIT_DEC']
#objid = hdu[i].header['SLITNAME']
# Check the perfomance of masks at different PA
#rac = hdu[0].header['MASK_RA']
#dec = hdu[0].header['MASK_DEC']
#pac = hdu[0].header['PA']
else:
msg = '%s is not a currently supported masktype' % masktype
raise SALTSpecError(msg)
if instrume not in ['PFIS', 'RSS']:
msg = '%s is not a currently supported instrument' % instrume
raise SALTSpecError(msg)
# set up the data for the source
try:
data = hdu[i].data
except Exception as e:
message = 'Unable to read in data array in %s because %s' % (
img, e)
raise SALTSpecError(message)
# set up the center row
if rstart == 'middlerow':
ystart = int(0.5 * len(data))
else:
ystart = rstart
# set up the xarr array based on the image
xarr = np.arange(len(data[ystart]), dtype='int64')
# calculate the transformation
ImageSolution = arcstraight(data, xarr, ystart, function=function, order=order,
rstep=rstep, y1=y1, y2=y2, sigma=sigma, sections=sections,
niter=niter, log=log, verbose=verbose)
if outfile and len(ImageSolution):
writeIS(ImageSolution, outfile, dateobs=dateobs, utctime=utctime, instrume=instrume,
grating=grating, grang=grang, grasteps=grasteps, arsteps=arsteps,
arang=arang, rfilter=rssfilter, slit=slit, xbin=xbin,
ybin=ybin, objid=objid,
filename=img, log=log, verbose=verbose)
def slotmerge(images, outimages, outpref, geomfile, clobber, logfile, verbose):
with logging(logfile, debug) as log:
# are the arguments defined
saltsafeio.argdefined('images', images)
saltsafeio.argdefined('geomfile', geomfile)
saltsafeio.argdefined('logfile', logfile)
# if the input file is a list, does it exist?
if images[0] == '@':
saltsafeio.listexists('Input', images)
# parse list of input files
infiles = saltsafeio.listparse('Raw image', images, '', '', '')
# check input files exist
saltsafeio.filesexist(infiles, '', 'r')
# load output name list: @list, * and comma separated
outimages = outimages.strip()
outpref = outpref.strip()
if len(outpref) == 0 and len(outimages) == 0:
raise SaltIOError('Output file(s) not specified')
# test output @filelist exists
if len(outimages) > 0 and outimages[0] == '@':
saltsafeio.listexists('Output', outimages)
# parse list of output files
outfiles = saltsafeio.listparse('Output image', outimages, outpref,
infiles, '')
# are input and output lists the same length?
saltsafeio.comparelists(infiles, outfiles, 'Input', 'output')
# do the output files already exist?
if not clobber:
saltsafeio.filesexist(outfiles, '', 'w')
# does CCD geometry definition file exist
geomfilefile = geomfile.strip()
saltsafeio.fileexists(geomfile)
# read geometry definition file
gap = 0
xshift = [0, 0]
yshift = [0, 0]
rotation = [0, 0]
gap, xshift, yshift, rotation = saltsafeio.readccdgeom(geomfile)
for ro in rotation:
if ro != 0:
log.warning('SLOTMERGE currently ignores CCD rotation')
# Begin processes each file
for infile, outfile in zip(infiles, outfiles):
# determine the name for the output file
outpath = outfile.rstrip(os.path.basename(outfile))
if (len(outpath) == 0):
outpath = '.'
# open each raw image
struct = saltsafeio.openfits(infile)
# identify instrument
instrume, keyprep, keygain, keybias, keyxtalk, keyslot = saltsafekey.instrumid(
struct, infile)
# how many amplifiers?
nccds = saltsafekey.get('NCCDS', struct[0], infile)
amplifiers = nccds * 2
#if (nccds != 2):
# raise SaltError('Can not currently handle more than two CCDs')
# CCD geometry coefficients
if instrume == 'RSS' or instrume == 'PFIS':
xsh = [xshift[0], 0., xshift[1]]
ysh = [yshift[0], 0., yshift[1]]
rot = [rotation[0], 0., rotation[1]]
refid = 1
if instrume == 'SALTICAM':
xsh = [xshift[0], 0.]
ysh = [yshift[0], 0.]
rot = [rotation[0], 0]
refid = 1
# how many extensions?
nextend = saltsafekey.get('NEXTEND', struct[0], infile)
# how many exposures
exposures = nextend / amplifiers
# CCD on-chip binning
xbin, ybin = saltsafekey.ccdbin(struct[0], infile)
gp = int(gap / xbin)
# create output hdu structure
outstruct = [None] * int(exposures + 1)
outstruct[0] = struct[0]
# iterate over exposures, stitch them to produce file of CCD images
for i in range(exposures):
# Determine the total size of the image
xsize = 0
ysize = 0
for j in range(amplifiers):
hdu = i * amplifiers + j + 1
try:
xsize += len(struct[hdu].data[0])
if ysize < len(struct[hdu].data):
ysize = len(struct[hdu].data)
except:
msg = 'Unable to access extension %i ' % hdu
raise SaltIOError(msg)
xsize += gp * (nccds - 1)
maxxsh, minxsh = determineshifts(xsh)
maxysh, minysh = determineshifts(ysh)
xsize += (maxxsh - minxsh)
ysize += (maxysh - minysh)
# Determine the x and y origins for each frame
xdist = 0
ydist = 0
shid = 0
x0 = np.zeros(amplifiers)
y0 = np.zeros(amplifiers)
for j in range(amplifiers):
x0[j] = xdist + xsh[shid] - minxsh
y0[j] = ysh[shid] - minysh
hdu = i * amplifiers + j + 1
darr = struct[hdu].data
xdist += len(darr[0])
if j % 2 == 1:
xdist += gp
shid += 1
# make the out image
outarr = np.zeros((ysize, xsize), np.float64)
# Embed each frame into the output array
for j in range(amplifiers):
hdu = i * amplifiers + j + 1
darr = struct[hdu].data
outarr = salttran.embed(darr, x0[j], y0[j], outarr)
# Add the outimage to the output structure
hdu = i * amplifiers + 1
outhdu = i + 1
outstruct[outhdu] = pyfits.ImageHDU(outarr)
outstruct[outhdu].header = struct[hdu].header
# Fix the headers in each extension
datasec = '[1:%4i,1:%4i]' % (xsize, ysize)
saltsafekey.put('DATASEC', datasec, outstruct[outhdu], outfile)
saltsafekey.rem('DETSIZE', outstruct[outhdu], outfile)
saltsafekey.rem('DETSEC', outstruct[outhdu], outfile)
saltsafekey.rem('CCDSEC', outstruct[outhdu], outfile)
saltsafekey.rem('AMPSEC', outstruct[outhdu], outfile)
# add housekeeping key words
outstruct[outhdu] = addhousekeeping(outstruct[outhdu], outhdu,
outfile)
# close input FITS file
saltsafeio.closefits(struct)
# housekeeping keywords
keymosaic = 'SLOTMERG'
fname, hist = history(level=1, wrap=False)
saltsafekey.housekeeping(struct[0], keymosaic,
'Amplifiers have been mosaiced', hist)
#saltsafekey.history(outstruct[0],hist)
# this is added for later use by
saltsafekey.put('NCCDS', 0.5, outstruct[0])
saltsafekey.put('NSCIEXT', exposures, outstruct[0])
saltsafekey.put('NEXTEND', exposures, outstruct[0])
# write FITS file of mosaiced image
outstruct = pyfits.HDUList(outstruct)
saltsafeio.writefits(outstruct, outfile, clobber=clobber)
def saltbias(images,
outimages,
outpref,
subover=True,
trim=True,
subbias=False,
masterbias='bias.fits',
median=False,
function='polynomial',
order=3,
rej_lo=3,
rej_hi=3,
niter=10,
plotover=False,
turbo=False,
clobber=False,
logfile='salt.log',
verbose=True):
status = 0
ifil = 0
ii = 0
mbiasdata = []
bstruct = ''
biasgn = ''
biassp = ''
biasbn = ''
biasin = ''
filetime = {}
biastime = {}
for i in range(1, 7):
filetime[i] = []
biastime[i] = []
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
# are input and output lists the same length?
saltio.comparelists(infiles, outfiles, 'Input', 'output')
# Does master bias frame exist?
# gain, speed, binning and instrument of master bias frame
if subbias:
if os.path.isfile(masterbias):
bstruct = saltio.openfits(masterbias)
else:
message = 'Master bias frame %s does not exist' % masterbias
raise SaltError(message)
else:
bstruct = None
# open each raw image file
for img, oimg in zip(infiles, outfiles):
#open the file
struct = saltio.openfits(img)
#check to see if it has already been bias subtracted
instrume, keyprep, keygain, keybias, keyxtalk, keyslot = saltkey.instrumid(
struct)
# has file been biaseded already?
try:
key = struct[0].header[keybias]
message = 'File %s has already been de-biased ' % infile
raise SaltError(message)
except:
pass
#compare with the master bias to make sure they are the same
if subbias:
pass
#subtract the bias
struct = bias(struct,
subover=subover,
trim=trim,
subbias=subbias,
bstruct=bstruct,
median=median,
function=function,
order=order,
rej_lo=rej_lo,
rej_hi=rej_hi,
niter=niter,
plotover=plotover,
log=log,
verbose=verbose)
#write the file out
# housekeeping keywords
fname, hist = history(level=1,
wrap=False,
exclude=['images', 'outimages', 'outpref'])
saltkey.housekeeping(struct[0], keybias,
'Images have been de-biased', hist)
# write FITS file
saltio.writefits(struct, oimg, clobber=clobber)
saltio.closefits(struct)
def saltmosaic(images,
outimages,
outpref,
geomfile,
interp='linear',
geotran=True,
fill=False,
cleanup=True,
clobber=False,
logfile=None,
verbose=True):
# Start the logging
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outfiles = saltio.listparse('Outfile', outimages, outpref, infiles, '')
# verify that the input and output lists are the same length
saltio.comparelists(infiles, outfiles, 'Input', 'output')
# does CCD geometry definition file exist
geomfilefile = geomfile.strip()
saltio.fileexists(geomfile)
gap = 0
xshift = [0, 0]
yshift = [0, 0]
rotation = [0, 0]
gap, xshift, yshift, rotation = saltio.readccdgeom(geomfile)
# open each raw image file and apply the transformation to it
for img, oimg in zip(infiles, outfiles):
# open the structure
struct = saltio.openfits(img)
# create the mosaic
ostruct = make_mosaic(struct,
gap,
xshift,
yshift,
rotation,
interp_type=interp,
geotran=geotran,
fill=fill,
cleanup=cleanup,
log=log,
verbose=verbose)
# update the header information
# housekeeping keywords
fname, hist = history(level=1,
wrap=False,
exclude=['images', 'outimages', 'outpref'])
saltkey.housekeeping(ostruct[0], 'SMOSAIC',
'Images have been mosaicked', hist)
# write the image out
ostruct.writeto(oimg, clobber=clobber, output_verify='ignore')
# close the files
struct.close()
ostruct.close()