def saltcombine(images,outimage, method='average', reject=None, mask=True, \
weight=True, blank=0, scale=None, statsec=None, lthresh=3, \
hthresh=3, clobber=False, logfile='salt.log',verbose=True):
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
#set reject as None
reject=saltio.checkfornone(reject)
if reject is not None: reject=reject.lower()
#set scale
scale=saltio.checkfornone(scale)
if scale is not None: scale=scale.lower()
#set statsec
statsec=saltio.checkfornone(statsec)
statsec=saltio.getSection(statsec, iraf_format=True)
#Fast combine the images
outstruct=imcombine(infiles, method=method, reject=reject, mask=mask, \
weight=weight, blank=blank, scale=scale, \
statsec=statsec, lthresh=lthresh, hthresh=hthresh)
# housekeeping keywords
fname, hist=history(level=1, wrap=False)
saltkey.housekeeping(outstruct[0],'SCOMBINE', 'File Combined by SALTCOMBINE', hist)
# write FITS file
saltio.writefits(outstruct, outimage)
def erroremail(obsdate, server='', username='', password='', sender='', recipient='', bcc='',
sdbhost='sdb.salt', sdbname='sdb', sdbuser='', sdbpass='', logfile='saltlog.log', verbose=True):
"""Update the PipelineStatistics table with the current information
about the pipeline
"""
with logging(logfile,debug) as log:
#connect the database
sdb=saltmysql.connectdb(sdbhost, sdbname, sdbuser, sdbpass)
#get the nightinfo_id
night_id=saltmysql.getnightinfoid(sdb, obsdate)
#create the message
try:
record=saltmysql.select(sdb, 'PipelineStatus, ErrorMessage', 'PipelineStatistics join PipelineStatus using (PipelineStatus_Id)', 'NightInfo_Id=%i' % night_id)
status, error_message=record[0]
except Exception, e:
raise SaltError('Unable to download information: %s' % e)
#set up the subject and message
subject='Pipeline Error on %s' % obsdate
message="Failure is simply the opportunity to begin again, this time more intelligently.--Henry Ford\n\n"
message+="%s" % error_message
log.message(message, with_stdout=verbose)
#send the email
saltio.email(server,username,password,sender,recipient,bcc, subject,message)
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 saltobslog(images,
outfile,
clobber=False,
logfile='salt.log',
verbose=True):
"""Create the observation log from the input files"""
#start the logging
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
#create the header dictionary
headerDict = obslog(infiles, log)
#clobber the output if it exists
if (clobber and os.path.isfile(outfile)):
saltio.delete(outfile)
#create the fits file
struct = createobslogfits(headerDict)
# close table file
saltio.writefits(struct, outfile)
#indicate the log was created
log.message('\nSALTLOG -- created observation log ' + outfile)
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 bvitftp(propcode, obsdate, sdbhost,sdbname,sdbuser, password,
server,username,sender, bcc, emailfile,
notify=False, clobber=True,logfile='salt.log',verbose=True):
# set up
proposers = []
propids = []
pids = []
with logging(logfile,debug) as log:
# are the arguments defined
if propcode.strip().upper()=='ALL':
pids=getbvitproposalcodes(str(obsdate))
else:
pids = saltio.argunpack('propcode',propcode)
if len(pids)==0:
#throw a warning adn exit if not data needs to be filterd
log.warning('No data to distribute\n', with_stdout=verbose)
return
#log into the database
sdb=saltmysql.connectdb(sdbhost,sdbname,sdbuser,password)
# check PI directories exist
ftpdir='/salt/ftparea/'
for datapath in pids:
pid=os.path.basename(datapath)
movebvitdata(pid, datapath, ftpdir, obsdate, sdb, clobber)
if notify:
notifybvituser(sdb, pid, obsdate, server,username,password,sender, bcc, emailfile)
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 masktool(catalog='', image='', logfile='salt.log', verbose=True):
with logging(logfile,debug) as log:
app = QtGui.QApplication([])
myapp = SlitMaskGui(infile=catalog, inimage=image)
myapp.show()
app.exec_()
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 salt2iraf(images,
outimages,
outpref,
ext=1,
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')
for img, oimg in zip(infiles, outfiles):
message = "SALT2IRAF--Converting %s to %s" % (img, oimg)
log.message(message, with_header=False)
try:
convertsalt(img, oimg, ext=ext, clobber=clobber)
except SaltError, e:
log.message('%s' % e)
def specidentify(images, linelist, outfile, guesstype, guessfile, function,
order, rstep, interact, clobber, logfile, verbose, status):
with logging(logfile, debug) as log:
# set up the variables
infiles = []
outfiles = []
# Check the input images
infiles = saltsafeio.argunpack('Input', images)
print(infiles)
# create list of output files
outfiles = saltsafeio.argunpack('Input', outfile)
# if outfiles is a single image, turn it into a list
# of the same length as infiles
if len(outfiles) != len(infiles):
if len(outfiles) == 1:
outfiles = outfiles * len(infiles)
elif len(outfiles) == 0:
outfiles = [None] * len(infiles)
else:
msg = 'Please enter an appropriate number of outfiles'
raise SALTSpecError(msg)
# open the line lists
slines, sfluxes = st.readlinelist(linelist)
# Identify the lines in each file
for img, oimg in zip(infiles, outfiles):
log.message('Proccessing image %s' % img)
identify(img, oimg, slines, sfluxes, guesstype, guessfile,
function, order, rstep, interact, clobber, log, 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 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 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 saltfirst(obsdate, imdir, prodir, server='smtp.saao.ac.za', readme='readme.fast.template', sdbhost='sdb.salt', sdbname='sdb', sdbuser='', password='',imreduce=True, sexfile='/home/ccd/tools/qred.sex', update=True, clobber=False,logfile='salt.log',verbose=True):
#Move into the working directory
if os.path.isdir(prodir):
if clobber:
shutil.rmtree(prodir)
os.mkdir(prodir)
else:
os.mkdir(prodir)
os.chdir(prodir)
with logging(logfile,debug) as log:
#create GUI
App = QtGui.QApplication([])
#Add information to gui
aw=FirstWindow(obsdate, imdir, prodir, server=server, readme=readme, sdbhost=sdbhost, sdbname=sdbname, sdbuser=sdbuser, password=password, imreduce=imreduce, sexfile=sexfile, update=update, clobber=clobber, log=log, verbose=verbose)
aw.setMinimumHeight(800)
aw.setMinimumWidth(500)
aw.show()
# Start application event loop
exit=App.exec_()
# Check if GUI was executed succesfully
if exit!=0:
raise SaltError('SALTFIRST GUI has unexpected exit status '+str(exit))
def saltobslog(images,outfile,clobber=False,logfile='salt.log',verbose=True):
"""Create the observation log from the input files"""
#start the logging
with logging(logfile,debug) as log:
# Check the input images
infiles = saltio.argunpack ('Input',images)
#create the header dictionary
headerDict=obslog(infiles, log)
#clobber the output if it exists
if (clobber and os.path.isfile(outfile)):
saltio.delete(outfile)
#create the fits file
struct=createobslogfits(headerDict)
# close table file
saltio.writefits(struct, outfile)
#indicate the log was created
log.message('\nSALTLOG -- created observation log ' + outfile)
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 saltarchive(obsdate,archpath, clobber,logfile,verbose):
"""Archive the SALT data. Move the data to /salt/data after it has been run by the pipeline"""
with logging(logfile,debug) as log:
#check the entries
saltio.argdefined('obsdate',obsdate)
saltio.argdefined('archpath',archpath)
# create the directory if it does not already exist
if (not os.path.exists(archpath+obsdate[:4])):
saltio.createdir(archpath+obsdate[:4])
#cleen up the directory if it already exists
archdir=archpath+obsdate[:4]+'/'+obsdate[4:]
if (os.path.exists(archdir) and clobber):
for root, dirs, files in os.walk(archpath+obsdate[:4]+'/'+obsdate[4:],topdown=False):
for file in files:
os.remove(os.path.join(root,file))
for dir in dirs:
os.rmdir(os.path.join(root,dir))
os.rmdir(archpath+obsdate[:4]+'/'+obsdate[4:])
elif (os.path.exists(archdir) and not clobber):
message = 'Cannot overwrite '+archpath+obsdate[:4]+'/'+obsdate[4:]
raise SaltError(message)
elif (not os.path.exists(archdir)):
pass
saltio.move(obsdate,archdir)
def saltcombine(images,outimage, method='average', reject=None, mask=True, \
weight=True, blank=0, scale=None, statsec=None, lthresh=3, \
hthresh=3, clobber=False, logfile='salt.log',verbose=True):
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
#set reject as None
reject = saltio.checkfornone(reject)
if reject is not None: reject = reject.lower()
#set scale
scale = saltio.checkfornone(scale)
if scale is not None: scale = scale.lower()
#set statsec
statsec = saltio.checkfornone(statsec)
statsec = saltio.getSection(statsec, iraf_format=True)
#Fast combine the images
outstruct=imcombine(infiles, method=method, reject=reject, mask=mask, \
weight=weight, blank=blank, scale=scale, \
statsec=statsec, lthresh=lthresh, hthresh=hthresh)
# housekeeping keywords
fname, hist = history(level=1, wrap=False)
saltkey.housekeeping(outstruct[0], 'SCOMBINE',
'File Combined by SALTCOMBINE', hist)
# write FITS file
saltio.writefits(outstruct, outimage)
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 masktool(catalog='', image='', logfile='salt.log', verbose=True):
with logging(logfile, debug) as log:
app = QtGui.QApplication([])
myapp = SlitMaskGui(infile=catalog, inimage=image)
myapp.show()
app.exec_()
def specidentify(images,linelist, outfile, guesstype, guessfile, function, \
order, rstep, interact, clobber,logfile,verbose,status):
with logging(logfile,debug) as log:
#set up the variables
infiles = []
outfiles = []
status = 0
# Check the input images
infiles = saltsafeio.argunpack ('Input',images)
# create list of output files
outfiles = saltsafeio.argunpack ('Input',outfile)
#if outfiles is a single image, turn it into a list
#of the same length as infiles
if len(outfiles)!=len(infiles):
if len(outfiles)==1:
outfiles=outfiles*len(infiles)
elif len(outfiles)==0:
outfiles=[None]*len(infiles)
else:
msg='Please enter an appropriate number of outfiles'
raise SALTSpecError(msg)
# open the line lists
slines, sfluxes = readlinelist(linelist)
# Identify the lines in each file
for img, oimg in zip(infiles, outfiles):
identify(img, oimg, slines, sfluxes, guesstype, guessfile, function,
order, rstep, interact, clobber, verbose)
def saltfirst(obsdate, imdir, prodir, server='smtp.saao.ac.za', readme='readme.fast.template', sdbhost='sdb.salt', sdbname='sdb', sdbuser='', password='',imreduce=True, sexfile='/home/ccd/tools/qred.sex', update=True, clobber=False,logfile='salt.log',verbose=True):
#Move into the working directory
if os.path.isdir(prodir):
if clobber:
shutil.rmtree(prodir)
os.mkdir(prodir)
else:
os.mkdir(prodir)
os.chdir(prodir)
with logging(logfile,debug) as log:
#create GUI
App = QtGui.QApplication([])
#Add information to gui
aw=FirstWindow(obsdate, imdir, prodir, server=server, readme=readme, sdbhost=sdbhost, sdbname=sdbname, sdbuser=sdbuser, password=password, imreduce=imreduce, sexfile=sexfile, update=update, clobber=clobber, log=log, verbose=verbose)
aw.setMinimumHeight(800)
aw.setMinimumWidth(500)
aw.show()
# Start application event loop
exit=App.exec_()
# Check if GUI was executed succesfully
if exit!=0:
raise SaltError('SALTFIRST GUI has unexpected exit status '+str(exit))
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 saltelserror(obsdate, elshost, elsname, elsuser, elspass,
sdbhost,sdbname,sdbuser, password, clobber,logfile,verbose):
# set up
proposers = []
propids = []
pids = []
with logging(logfile,debug) as log:
#open the database
els=saltmysql.connectdb(elshost, elsname, elsuser, elspass)
sdb=saltmysql.connectdb(sdbhost,sdbname,sdbuser, password)
#create the values for the entire night
nid=saltmysql.getnightinfoid(sdb, obsdate)
stime, etime=saltmysql.select(sdb, 'EveningTwilightEnd,MorningTwilightStart', 'NightInfo', 'NightInfo_Id=%i' % nid)[0]
print stime, etime
errors=gettcserrors(els, stime, etime)
if not errors: return None
for e in errors:
i=e.index('T')
print i, error_list[i], e[-1]
print len(errors)
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 saltfpevelocity(infile, existfit, xc, yc, rmax, logfile, verbose):
"""XXX"""
# getting paths for filenames
pathin = os.path.dirname(infile)
basein = os.path.basename(infile)
pathlog = os.path.dirname(logfile)
baselog = os.path.basename(logfile)
print pathin, basein
# start log now that all parameters are set up
with logging(logfile, debug) as log:
# Some basic checks, some tests are done in the FORTRAN code itself
# is the input file specified?
saltsafeio.filedefined('Input', infile)
# if the input file is a file, does it exist?
if basein[0] != '@':
saltsafeio.fileexists(infile)
# if a list is input throw an error
if basein[0] == '@':
raise SaltIOError(basein + ' list input instead of a file')
# The file contains a list of images, check they exist
# format is 4x dummy lines, then a line/lines containing: x,y,wave0,sn,norm,dnorm,filename
testfile = open(infile)
print testfile
for i in range(1, 5):
line = testfile.readline()
line = 'dummy'
infiles = []
while (len(line.strip()) != 0):
line = testfile.readline()
if (len(line.strip()) > 0):
linearray = line.split()
infiles.append(linearray[6])
# check input files exist
saltsafeio.filesexist(infiles, '', 'r')
# convert existfile to a one letter string
if existfit == 'yes':
existfit == 'y'
else:
existfit == 'n'
# If all looks OK, run the FORTRAN code
print infile, 'input filename'
print existfit, xc, yc, rmax
evelocity_wrapper2.evelocity2(infile, existfit, xc, yc, rmax)
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 saltfpeprofile(plottype, infile, logfile, verbose):
"""Line profile fitting and display"""
plottype = str(plottype)
plottype = plottype.strip()
if plottype == 'xwindow':
plottype = '/xw'
else:
plottype = '/ps'
# getting paths for filenames
pathin = os.path.dirname(infile)
basein = os.path.basename(infile)
pathlog = os.path.dirname(logfile)
baselog = os.path.basename(logfile)
print pathin, basein
# start log now that all parameters are set up
with logging(logfile, debug) as log:
# Some basic checks, some tests are done in the FORTRAN code itself
# is the input file specified?
saltsafeio.filedefined('Input', infile)
# if the input file is a file, does it exist?
if basein[0] != '@':
saltsafeio.fileexists(infile)
# if a list is input throw an error
if basein[0] == '@':
raise SaltIOError(basein + ' list input instead of a file')
# The file contains a list of images, check they exist
# format is 4x dummy lines, then a line/lines containing: x,y,wave0,sn,norm,dnorm,filename
testfile = open(infile)
print testfile
for i in range(1, 5):
line = testfile.readline()
line = 'dummy'
infiles = []
while (len(line.strip()) != 0):
line = testfile.readline()
if (len(line.strip()) > 0):
linearray = line.split()
infiles.append(linearray[6])
# check input files exist
saltsafeio.filesexist(infiles, '', 'r')
# If all looks OK, run the FORTRAN code
print 'input filename = ', infile
eprofile_wrapper.eprofile(plottype, infile)
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 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 saltfpcalibrate(plottype, infile, outfile, calibratelogfile, logfile,
verbose):
"""Determines the wavelength calibration of the Fabry-Perot
interactively, using the ring measurements from the CALRING program."""
plottype = str(plottype)
plottype = plottype.strip()
if plottype == 'xwindow':
plottype = '/xw'
else:
plottype = '/ps'
# start log now that all parameter are set up
with logging(logfile, debug) as log:
# Some basic checks, many tests are done in the FORTRAN code itself
# is the input file specified?
saltsafeio.filedefined('Input', infile)
# The input file in this case is a file, does it exist?
if infile[0] != '@':
saltsafeio.fileexists(infile)
# is the proposed output file specified?
saltsafeio.filedefined('Output', outfile)
# check whether the proposed output file exists
path = os.path.dirname(infile)
if len(path) > 0:
dir = path + '/'
else:
dir = './'
print dir, ' directory with data'
outfile = outfile.strip()
if os.path.isfile(outfile):
print 'output file exists, appending'
# saltsafeio.delete(outfile)
# check whether the calibrate logfile is defined
saltsafeio.filedefined('Log', calibratelogfile)
# Get current working directory as the Fortran code changes dir
startdir = os.getcwd()
# If all looks OK, run the FORTRAN code
calibrate_wrapper.calibrate(plottype, infile, outfile,
calibratelogfile)
# go back to starting directory
os.chdir(startdir)
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 saltfpcalibrate(plottype,infile,outfile,calibratelogfile,logfile,verbose):
"""Determines the wavelength calibration of the Fabry-Perot
interactively, using the ring measurements from the CALRING program."""
plottype = str(plottype)
plottype = plottype.strip()
if plottype == 'xwindow':
plottype = '/xw'
else:
plottype = '/ps'
# start log now that all parameter are set up
with logging(logfile, debug) as log:
# Some basic checks, many tests are done in the FORTRAN code itself
# is the input file specified?
saltsafeio.filedefined('Input',infile)
# The input file in this case is a file, does it exist?
if infile[0] != '@':
saltsafeio.fileexists(infile)
# is the proposed output file specified?
saltsafeio.filedefined('Output',outfile)
# check whether the proposed output file exists
path = os.path.dirname(infile)
if len(path) > 0:
dir = path + '/'
else:
dir = './'
print dir, ' directory with data'
outfile = outfile.strip()
if os.path.isfile(outfile):
print 'output file exists, appending'
# saltsafeio.delete(outfile)
# check whether the calibrate logfile is defined
saltsafeio.filedefined('Log',calibratelogfile)
# Get current working directory as the Fortran code changes dir
startdir = os.getcwd()
# If all looks OK, run the FORTRAN code
calibrate_wrapper.calibrate(plottype,infile, outfile, calibratelogfile)
# go back to starting directory
os.chdir(startdir)
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 specsens(specfile, outfile, stdfile, extfile, airmass=None, exptime=None,
stdzp=3.68e-20, function='polynomial', order=3, thresh=3, niter=5,
clobber=True, logfile='salt.log',verbose=True):
with logging(logfile,debug) as log:
#read in the specfile and create a spectrum object
obs_spectra=st.readspectrum(specfile, error=True, ftype='ascii')
#read in the std file and convert from magnitudes to fnu
#then convert it to fwave (ergs/s/cm2/A)
std_spectra=st.readspectrum(stdfile, error=False, ftype='ascii')
std_spectra.flux=Spectrum.magtoflux(std_spectra.flux, stdzp)
std_spectra.flux=Spectrum.fnutofwave(std_spectra.wavelength, std_spectra.flux)
#read in the extinction file (leave in magnitudes)
ext_spectra=st.readspectrum(extfile, error=False, ftype='ascii')
#determine the airmass if not specified
if saltio.checkfornone(airmass) is None:
message='Airmass was not supplied'
raise SALTSpecError(message)
#determine the exptime if not specified
if saltio.checkfornone(airmass) is None:
message='Exposure Time was not supplied'
raise SALTSpecError(message)
#calculate the calibrated spectra
log.message('Calculating the calibration curve for %s' % specfile)
cal_spectra=sensfunc(obs_spectra, std_spectra, ext_spectra, airmass, exptime)
#fit the spectra--first take a first cut of the spectra
#using the median absolute deviation to throw away bad points
cmed=np.median(cal_spectra.flux)
cmad=saltstat.mad(cal_spectra.flux)
mask=(abs(cal_spectra.flux-cmed)<thresh*cmad)
mask=(cal_spectra.flux>0)
#now fit the data
fit=interfit(cal_spectra.wavelength[mask], cal_spectra.flux[mask], function=function, order=order, thresh=thresh, niter=niter)
fit.interfit()
#print 'plotting...'
#figure()
#plot(cal_spectra.wavelength, cal_spectra.flux)
#plot(obs_spectra.wavelength, obs_spectra.flux*cal_spectra.flux.mean()/obs_spectra.flux.mean())
#plot(std_spectra.wavelength, std_spectra.flux*cal_spectra.flux.mean()/std_spectra.flux.mean())
#plot(cal_spectra.wavelength, fit(cal_spectra.wavelength))
#show()
#write the spectra out
cal_spectra.flux=fit(cal_spectra.wavelength)
st.writespectrum(cal_spectra, outfile, ftype='ascii')
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 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 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 saltobsstats(obsdate, statfile, sdbhost='sdb.saao', sdbname='sdb', \
sdbuser='', password='', clobber=False, logfile='salt.log', verbose=True):
"""Measure statistics about SALT observations
obsdate: Night for measuring statistics
statfile: Output file for statistics
"""
with logging(logfile,debug) as log:
#connect to the sdb
sdb=saltmysql.connect(sdbhost, sdbname, sdbuser, password)
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 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 slotpreview(images,outfile,ampperccd=2,ignorexp=6,recenter_radius=5,
tgt_col='b',cmp_col='g', tgt_lw=2,cmp_lw=2,cmap='gray',
scale='zscale',contrast=0.1,clobber=True,logfile='salt.log',
verbose=True):
with logging(logfile,debug) as log:
# is the input file specified?
saltsafeio.filedefined('Input',images)
# if the input file is a list, does it exist?
if images[0] == '@':
saltsafeio.listexists('Input',images)
# parse list of input files
imlist=saltsafeio.listparse('Raw image',images,'','','')
# check input files exist
saltsafeio.filesexist(imlist,'','r')
# is the output file specified?
saltsafeio.filedefined('Output',outfile)
# check output file does not exist, optionally remove it if it does exist
if os.path.exists(outfile) and clobber:
os.remove(outfile)
elif os.path.exists(outfile) and not clobber:
raise SaltIOError('File '+outfile+' already exists, use clobber=y')
# Get the number of ccds to calculate the number of frames to skip
try:
nccds=pyfits.getheader(imlist[0])['NCCDS']
except:
raise SaltIOError('Could not read NCCDS parameter from header of first fits file.')
# Create GUI
App = QtGui.QApplication(sys.argv)
aw = ApplicationWindow(imlist=imlist,
number=ignorexp*ampperccd*nccds+1,
config=outfile, target_line_color=tgt_col,
comparison_line_color=cmp_col, target_line_width=tgt_lw,
comparison_line_width=cmp_lw, distance=recenter_radius,
cmap=cmap, scale=scale, contrast=contrast)
aw.show()
# Start application event loop
exit=App.exec_()
# Check if GUI was executed succesfully
if exit!=0:
log.warning('Slotpreview GUI has unexpected exit status'+str(exit))
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 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 saltsdbloadfits(images, sdbhost, sdbname, sdbuser, password, logfile, verbose):
"""Upload data about images (which is either a fits file, or specificied by @list)
to the science data base, sdb
"""
with logging(logfile,debug) as log:
#open up the infiles
infiles = saltio.argunpack('Input',images)
sdb=saltmysql.connectdb(sdbhost,sdbname,sdbuser,password)
for infile in infiles:
sdbloadfits(infile, sdb, log, verbose)
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 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 speccal(specfile, outfile, calfile, extfile, airmass=None, exptime=None,
clobber=True, logfile='salt.log', verbose=True):
with logging(logfile, debug) as log:
# read in the specfile and create a spectrum object
obs_spectra = st.readspectrum(specfile, error=True, ftype='ascii')
# read in the std file and convert from magnitudes to fnu
# then convert it to fwave (ergs/s/cm2/A)
cal_spectra = st.readspectrum(calfile, error=False, ftype='ascii')
# read in the extinction file (leave in magnitudes)
ext_spectra = st.readspectrum(extfile, error=False, ftype='ascii')
# determine the airmass if not specified
if saltio.checkfornone(airmass) is None:
message = 'Airmass was not supplied'
raise SALTSpecError(message)
# determine the exptime if not specified
if saltio.checkfornone(airmass) is None:
message = 'Exposure Time was not supplied'
raise SALTSpecError(message)
# calculate the calibrated spectra
log.message('Calculating the calibration curve for %s' % specfile)
error = False
try:
if obs_spectra.var is not None:
error = True
except:
error = False
flux_spectra = calfunc(
obs_spectra,
cal_spectra,
ext_spectra,
airmass,
exptime,
error)
# write the spectra out
st.writespectrum(flux_spectra, outfile, ftype='ascii', error=error)
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 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 saltfpprep(images, outimages, outpref,
clobber=True, logfile='saltfp.log', verbose=True):
"""Prepares data for Fabry-Perot reductions"""
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):
message="SALTFPPREP--Preparing image %s" % (img)
log.message(message, with_header=False)
try:
convertsalt(img, oimg, clobber=clobber)
except SaltError, e:
log.message('%s' %e)
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 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 saltclean(images,
outpath,
obslogfile=None,
gaindb=None,
xtalkfile=None,
geomfile=None,
subover=True,
trim=True,
masbias=None,
subbias=False,
median=False,
function='polynomial',
order=5,
rej_lo=3,
rej_hi=3,
niter=5,
interp='linear',
clobber=False,
logfile='salt.log',
verbose=True):
"""SALTCLEAN will provide basic CCD reductions for a set of data. It will
sort the data, and first process the biases, flats, and then the science
frames. It will record basic quality control information about each of
the steps.
"""
plotover = False
#start logging
with logging(logfile, debug) as log:
# Check the input images
infiles = saltio.argunpack('Input', images)
# create list of output files
outpath = saltio.abspath(outpath)
#does the gain database file exist
if gaindb:
dblist = saltio.readgaindb(gaindb)
else:
dblist = []
# does crosstalk coefficient data exist
if xtalkfile:
xtalkfile = xtalkfile.strip()
xdict = saltio.readxtalkcoeff(xtalkfile)
else:
xdict = None
#does the mosaic file exist--raise error if no
saltio.fileexists(geomfile)
# Delete the obslog file if it already exists
if os.path.isfile(obslogfile) and clobber: saltio.delete(obslogfile)
#read in the obsveration log or create it
if os.path.isfile(obslogfile):
msg = 'The observing log already exists. Please either delete it or run saltclean with clobber=yes'
raise SaltError(msg)
else:
headerDict = obslog(infiles, log)
obsstruct = createobslogfits(headerDict)
saltio.writefits(obsstruct, obslogfile)
#create the list of bias frames and process them
filename = obsstruct.data.field('FILENAME')
detmode = obsstruct.data.field('DETMODE')
ccdtype = obsstruct.data.field('CCDTYPE')
#set the bias list of objects
biaslist = filename[ccdtype == 'ZERO']
masterbias_dict = {}
for img in infiles:
if os.path.basename(img) in biaslist:
#open the image
struct = fits.open(img)
bimg = outpath + 'bxgp' + os.path.basename(img)
#print the message
if log:
message = 'Processing Zero frame %s' % img
log.message(message, with_stdout=verbose)
#process the image
struct = clean(struct,
createvar=False,
badpixelstruct=None,
mult=True,
dblist=dblist,
xdict=xdict,
subover=subover,
trim=trim,
subbias=False,
bstruct=None,
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], 'SPREPARE',
'Images have been prepared', hist)
saltkey.new('SGAIN', time.asctime(time.localtime()),
'Images have been gain corrected', struct[0])
saltkey.new('SXTALK', time.asctime(time.localtime()),
'Images have been xtalk corrected', struct[0])
saltkey.new('SBIAS', time.asctime(time.localtime()),
'Images have been de-biased', struct[0])
# write FITS file
saltio.writefits(struct, bimg, clobber=clobber)
saltio.closefits(struct)
#add files to the master bias list
masterbias_dict = compareimages(struct,
bimg,
masterbias_dict,
keylist=biasheader_list)
#create the master bias frame
for i in masterbias_dict.keys():
bkeys = masterbias_dict[i][0]
blist = masterbias_dict[i][1:]
mbiasname = outpath + createmasterbiasname(blist, bkeys)
bfiles = ','.join(blist)
saltcombine(bfiles, mbiasname, method='median', reject='sigclip', mask=False,
weight=False, blank=0, scale=None, statsec=None, lthresh=3, \
hthresh=3, clobber=False, logfile=logfile,verbose=verbose)
#create the list of flatfields and process them
flatlist = filename[ccdtype == 'FLAT']
masterflat_dict = {}
for img in infiles:
if os.path.basename(img) in flatlist:
#open the image
struct = fits.open(img)
fimg = outpath + 'bxgp' + os.path.basename(img)
#print the message
if log:
message = 'Processing Flat frame %s' % img
log.message(message, with_stdout=verbose)
#process the image
struct = clean(struct,
createvar=False,
badpixelstruct=None,
mult=True,
dblist=dblist,
xdict=xdict,
subover=subover,
trim=trim,
subbias=False,
bstruct=None,
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], 'SPREPARE',
'Images have been prepared', hist)
saltkey.new('SGAIN', time.asctime(time.localtime()),
'Images have been gain corrected', struct[0])
saltkey.new('SXTALK', time.asctime(time.localtime()),
'Images have been xtalk corrected', struct[0])
saltkey.new('SBIAS', time.asctime(time.localtime()),
'Images have been de-biased', struct[0])
# write FITS file
saltio.writefits(struct, fimg, clobber=clobber)
saltio.closefits(struct)
#add files to the master bias list
masterflat_dict = compareimages(struct,
fimg,
masterflat_dict,
keylist=flatheader_list)
#create the master flat frame
for i in masterflat_dict.keys():
fkeys = masterflat_dict[i][0]
flist = masterflat_dict[i][1:]
mflatname = outpath + createmasterflatname(flist, fkeys)
ffiles = ','.join(flist)
saltcombine(ffiles, mflatname, method='median', reject='sigclip', mask=False,
weight=False, blank=0, scale=None, statsec=None, lthresh=3, \
hthresh=3, clobber=False, logfile=logfile,verbose=verbose)
#process the science data
for img in infiles:
nimg = os.path.basename(img)
#print nimg, nimg in flatlist, nimg in biaslist
if not (nimg in biaslist):
#open the image
struct = fits.open(img)
simg = outpath + 'bxgp' + os.path.basename(img)
#print the message
if log:
message = 'Processing science frame %s' % img
log.message(message, with_stdout=verbose)
#process the image
struct = clean(struct,
createvar=False,
badpixelstruct=None,
mult=True,
dblist=dblist,
xdict=xdict,
subover=subover,
trim=trim,
subbias=False,
bstruct=None,
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], 'SPREPARE',
'Images have been prepared', hist)
saltkey.new('SGAIN', time.asctime(time.localtime()),
'Images have been gain corrected', struct[0])
saltkey.new('SXTALK', time.asctime(time.localtime()),
'Images have been xtalk corrected', struct[0])
saltkey.new('SBIAS', time.asctime(time.localtime()),
'Images have been de-biased', struct[0])
# write FITS file
saltio.writefits(struct, simg, clobber=clobber)
saltio.closefits(struct)
#mosaic the files--currently not in the proper format--will update when it is
if not saltkey.fastmode(saltkey.get('DETMODE', struct[0])):
mimg = outpath + 'mbxgp' + os.path.basename(img)
saltmosaic(images=simg,
outimages=mimg,
outpref='',
geomfile=geomfile,
interp=interp,
cleanup=True,
clobber=clobber,
logfile=logfile,
verbose=verbose)
#remove the intermediate steps
saltio.delete(simg)
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)
