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 saltemail(propcode, obsdate,readme,server='mail.saao.ac.za',username='', password='',
bcc='',sdbhost='sdb.saao',sdbname='sdb',sdbuser='******',
logfile='salt.log',verbose=True):
"""For a given date, look into the database for observations made on that
date. If propcode='all' send an email to all of the PIs that had data taken on that date.
If propcode gives a specific proposal, only send emails to that PI.
"""
# set up
sender = '*****@*****.**'
bcclist = bcc.split(',')
date_obss = []
propids = []
pis = []
pids = []
email = []
with logging(logfile,debug) as log:
#set up the proposal list
pids = saltio.argunpack('propcode',propcode)
#check to see if the argument is defined
saltio.argdefined('obsdate',obsdate)
# check readme file exists
saltio.fileexists(readme)
#connect to the email server
try:
smtp = smtplib.SMTP()
smtp.connect(server)
smtp.ehlo()
smtp.starttls()
smtp.ehlo()
except Exception, e:
message = 'Cannot connect to %s because %s' % (server, e)
log.error(message)
try:
smtp.login(username,password)
except Exception, e:
message = 'Cannot login to %s as %s because %s' % (server, username, e)
log.error(message)
def saltdataquality(obsdate, sdbhost = "sdb.saao", sdbname = "sdb", sdbuser = "",
password = '', clobber=False, logfile='salt.log',verbose=True):
"""For a given SALT data. Move the data to /salt/data after it has been run by the pipeline"""
#make a dataquality directory
dqdir='dq%s' % obsdate
if os.path.isdir(dqdir) and clobber:
saltio.deletedir(dqdir)
saltio.createdir(dqdir)
saltio.changedir(dqdir)
with logging(logfile,debug) as log:
#check the entries
saltio.argdefined('obsdate',str(obsdate))
#open up the database
sdb=saltmysql.connectdb(sdbhost, sdbname, sdbuser, password)
#run for each instrument
for instrume in ['rss', 'scam']:
log.message('Measuring Data Quality for %s observations' % instrume.upper())
dataquality(str(obsdate), sdb, instrume, clobber, logfile, verbose)
def saltpipe(obsdate,pinames,archive,ftp,email,emserver,emuser,empasswd,bcc, qcpcuser,qcpcpasswd,
ftpserver,ftpuser,ftppasswd,sdbhost, sdbname, sdbuser, sdbpass, elshost, elsname,
elsuser, elspass, median,function,order,rej_lo,rej_hi,niter,interp,
clobber, runstatus, logfile,verbose):
# set up
basedir=os.getcwd()
propcode=pinames
sender = emuser + '@salt.ac.za'
recipient = sender
emessage = ''
emailfile = '../piemaillist/email.lis'
# check the observation date is sensible
if ('/' in obsdate or '20' not in obsdate or len(obsdate) != 8):
emessage = 'Observation date does not look sensible - YYYYMMDD\n'
raise SaltError(emessage)
# stop if the obsdate temporary directory already exists
obsdir='%s' % obsdate
if os.path.exists(obsdir):
emessage += 'The temporary working directory ' + os.getcwd() + '/'
emessage += obsdate + ' already exists. '
raise SaltError(emessage)
# create a temporary working directory and move to it
saltio.createdir(obsdir)
saltio.changedir(obsdir)
workpath = saltio.abspath('.')
# test the logfile
logfile = workpath+logfile
logfile = saltio.logname(logfile)
#note the starttime
starttime = time.time()
#start logging
with logging(logfile,debug) as log:
#connect to the database
sdb=saltmysql.connectdb(sdbhost, sdbname, sdbuser, sdbpass)
#get the nightinfo id
nightinfoid=saltmysql.getnightinfoid(sdb, obsdate)
#Get the list of proposal codes
state_select='Proposal_Code'
state_tables='Proposal join ProposalCode using (ProposalCode_Id)'
state_logic="current=1"
records=saltmysql.select(sdb, state_select, state_tables, state_logic)
propids=[k[0] for k in records]
# Calculate the current date
currentdate=salttime.currentobsdate()
# are the arguments defined
saltio.argdefined('obsdate',obsdate)
# check email and ftp arguments are consistent
if email and not ftp:
message = 'ERROR: SALTPIPE -- cannot send email to PI(s) unless data is transferred '
message += 'to the FTP server; use ftp=\'yes\' email=\'yes\''
raise SaltError(message)
# identify a potential list of keyword edits
keyfile = '../newheadfiles/list_newhead_' + obsdate
if not os.path.isfile(keyfile):
message = '\nSALTPIPE -- keyword edits ' + keyfile + ' not found locally'
log.message(message)
# check directories for the raw RSS data
rssrawpath = makerawdir(obsdate, 'rss')
# check directories for the raw SALTICAM data
scmrawpath = makerawdir(obsdate, 'scam')
# check raw directories for the disk.file record and find last file number
#check rss data
lastrssnum = checkfordata(rssrawpath, 'P', obsdate, log)
#check scame data
lastscmnum = checkfordata(scmrawpath, 'S', obsdate, log)
#check for HRS Data--not filedata yet, so cannot check
if lastrssnum == 1 and lastscmnum == 1:
message = 'SALTPIPE -- no SALTICAM or RSS data obtained on ' + obsdate
emessage += '\n' + message + '\n'
log.message(message)
#copy the data to the working directory
if lastrssnum > 1:
message = 'Copy ' + rssrawpath + ' --> ' + workpath + 'raw/'
log.message(message)
saltio.copydir(rssrawpath,'rss/raw')
if lastscmnum > 1:
message = 'Copy ' + scmrawpath + ' --> ' + workpath + 'raw/'
log.message(message)
saltio.copydir(scmrawpath,'scam/raw')
#copy and pre-process the HRS data
try:
hrsbrawpath = makerawdir(obsdate, 'hbdet')
saltio.createdir('hrs')
saltio.createdir('hrs/raw')
message = 'Copy ' + hrsbrawpath + ' --> ' + workpath + 'raw/'
log.message(message)
salthrspreprocess(hrsbrawpath, 'hrs/raw/', clobber=True, log=log, verbose=verbose)
lasthrbnum=len(glob.glob('hrs/raw/*fits'))
except Exception,e:
log.message('Could not copy HRS data because %s' % e)
lasthrbnum=0
try:
hrsrrawpath = makerawdir(obsdate, 'hrdet')
message = 'Copy ' + hrsrrawpath + ' --> ' + workpath + 'raw/'
log.message(message)
salthrspreprocess(hrsrrawpath, 'hrs/raw/', clobber=True, log=log, verbose=verbose)
lasthrsnum=max(lasthrbnum, len(glob.glob('hrs/raw/*fits')))
except Exception,e:
log.message('Could not copy HRS data because %s' % e)
lasthrsnum=lasthrbnum
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 salteditkey(images,outimages,outpref, keyfile, recfile=None,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')
#is key file defined
saltio.argdefined('keyfile',keyfile)
keyfile = keyfile.strip()
saltio.fileexists(keyfile)
# if the data are the same, set up to use update instead of write
openmode='copyonwrite'
if (infiles!=outfiles): openmode='copyonwrite'
# determine the date of the observations
obsdate=saltstring.makeobsdatestr(infiles, 1,9)
if len(obsdate)!=8:
message = 'Either FITS files from multiple dates exist, '
message += 'or raw FITS files exist with non-standard names.'
log.warning(message)
# FITS file columns to record keyword changes
fitcol = []
keycol = []
oldcol = []
newcol = []
# Set up the rules to change the files
keyedits=readkeyfile(keyfile, log=log, verbose=verbose)
#now step through the images
for img, oimg in zip(infiles, outfiles):
#determine the appropriate keyword edits for the image
klist=[]
for frange in keyedits:
if checkfitsfile(img, frange, keyedits[frange]):
klist.append(keyedits[frange][3])
if klist:
#open up the new files
struct = saltio.openfits(img,mode=openmode)
struct.verify('fix')
for kdict in klist:
for keyword in kdict:
#record the changes
value=kdict[keyword]
fitcol.append(img)
keycol.append(keyword)
newcol.append(value)
try:
oldcol.append(struct[0].header[keyword].lstrip())
except:
oldcol.append('None')
#update the keyword
if saltkey.found(keyword, struct[0]):
try:
saltkey.put(keyword,value,struct[0])
message='\tUpdating %s in %s to %s' % (keyword, os.path.basename(img), value)
log.message(message, with_header=False, with_stdout=verbose)
except Exception, e:
message = 'Could not update %s in %s because %s' % (keyword, img, str(e))
raise SaltError(message)
else:
try:
saltkey.new(keyword.strip(),value,'Added Comment',struct[0])
message='\tAdding %s in %s to %s' % (keyword, os.path.basename(img), value)
log.message(message, with_header=False, with_stdout=verbose)
except Exception,e :
message = 'Could not update %s in %s because %s' % (keyword, img, str(e))
raise SaltError(message)
#updat the history keywords
#fname, hist=history(level=1, wrap=False, exclude=['images', 'outimages', 'outpref'])
#saltkey.housekeeping(struct[0],'SAL-EDT', 'Keywords updated by SALTEDITKEY', hist)
#write the file out
if openmode=='update':
saltio.updatefits(struct)
message = 'Updated file ' + os.path.basename(oimg)
else:
saltio.writefits(struct, oimg, clobber)
message = 'Created file ' + os.path.basename(oimg)
log.message(message, with_header=False, with_stdout=True)
struct.close()
def saltpipe(obsdate,pinames,archive,ftp,email,emserver,emuser,empasswd,bcc, qcpcuser,qcpcpasswd,
ftpserver,ftpuser,ftppasswd,sdbhost, sdbname, sdbuser, sdbpass, elshost, elsname,
elsuser, elspass, median,function,order,rej_lo,rej_hi,niter,interp,
clobber, runstatus, logfile,verbose):
# set up
basedir=os.getcwd()
propcode=pinames
sender = emuser + '@salt.ac.za'
recipient = sender
emessage = ''
emailfile = '../piemaillist/email.lis'
# check the observation date is sensible
if ('/' in obsdate or '20' not in obsdate or len(obsdate) != 8):
emessage = 'Observation date does not look sensible - YYYYMMDD\n'
raise SaltError(emessage)
# stop if the obsdate temporary directory already exists
obsdir='%s' % obsdate
if os.path.exists(obsdir):
emessage += 'The temporary working directory ' + os.getcwd() + '/'
emessage += obsdate + ' already exists. '
raise SaltError(emessage)
# create a temporary working directory and move to it
saltio.createdir(obsdir)
saltio.changedir(obsdir)
workpath = saltio.abspath('.')
# test the logfile
logfile = workpath+logfile
logfile = saltio.logname(logfile)
#note the starttime
starttime = time.time()
#start logging
with logging(logfile,debug) as log:
#connect to the database
sdb=saltmysql.connectdb(sdbhost, sdbname, sdbuser, sdbpass)
#get the nightinfo id
nightinfoid=saltmysql.getnightinfoid(sdb, obsdate)
#Get the list of proposal codes
state_select='Proposal_Code'
state_tables='Proposal join ProposalCode using (ProposalCode_Id)'
state_logic="current=1"
records=saltmysql.select(sdb, state_select, state_tables, state_logic)
propids=[k[0] for k in records]
# Calculate the current date
currentdate=salttime.currentobsdate()
# are the arguments defined
saltio.argdefined('obsdate',obsdate)
# check email and ftp arguments are consistent
if email and not ftp:
message = 'ERROR: SALTPIPE -- cannot send email to PI(s) unless data is transferred '
message += 'to the FTP server; use ftp=\'yes\' email=\'yes\''
raise SaltError(message)
# identify a potential list of keyword edits
keyfile = '../newheadfiles/list_newhead_' + obsdate
if not os.path.isfile(keyfile):
message = '\nSALTPIPE -- keyword edits ' + keyfile + ' not found locally'
log.message(message)
# check directories for the raw RSS data
rssrawpath = makerawdir(obsdate, 'rss')
# check directories for the raw SALTICAM data
scmrawpath = makerawdir(obsdate, 'scam')
# check raw directories for the disk.file record and find last file number
#check rss data
lastrssnum = checkfordata(rssrawpath, 'P', obsdate, log)
#check scame data
lastscmnum = checkfordata(scmrawpath, 'S', obsdate, log)
#check for HRS Data--not filedata yet, so cannot check
if lastrssnum == 1 and lastscmnum == 1:
message = 'SALTPIPE -- no SALTICAM or RSS data obtained on ' + obsdate
emessage += '\n' + message + '\n'
log.message(message)
#copy the data to the working directory
if lastrssnum > 1:
message = 'Copy ' + rssrawpath + ' --> ' + workpath + 'raw/'
log.message(message)
saltio.copydir(rssrawpath,'rss/raw')
if lastscmnum > 1:
message = 'Copy ' + scmrawpath + ' --> ' + workpath + 'raw/'
log.message(message)
saltio.copydir(scmrawpath,'scam/raw')
#copy and pre-process the HRS data
try:
hrsbrawpath = makerawdir(obsdate, 'hbdet')
saltio.createdir('hrs')
saltio.createdir('hrs/raw')
message = 'Copy ' + hrsbrawpath + ' --> ' + workpath + 'raw/'
log.message(message)
salthrspreprocess(hrsbrawpath, 'hrs/raw/', clobber=True, log=log, verbose=verbose)
hrsrrawpath = makerawdir(obsdate, 'hrdet')
message = 'Copy ' + hrsrrawpath + ' --> ' + workpath + 'raw/'
log.message(message)
salthrspreprocess(hrsrrawpath, 'hrs/raw/', clobber=True, log=log, verbose=verbose)
lasthrsnum=len(glob.glob('hrs/raw/*fits'))
except Exception,e:
log.message('Could not copy HRS data because %s' % e)
lasthrsnum=0
if lastrssnum>1 or lastscmnum>1:
message = 'Copy of data is complete'
log.message(message)
else:
message = 'No data was taken on %s' % obsdate
log.message(message)
#process the data RSS data
if lastrssnum>1:
preprocessdata('rss', 'P', obsdate, keyfile, log, logfile, verbose)
#process the SCAM data
if lastscmnum>1:
preprocessdata('scam', 'S', obsdate, keyfile, log, logfile, verbose)
#process the HRS data
if lasthrsnum>1:
preprocessdata('hrs', 'H', obsdate, keyfile, log, logfile, verbose)
preprocessdata('hrs', 'R', obsdate, keyfile, log, logfile, verbose)
#check that all data was given a proper proposal id
#only do it for semesters after the start of science operations
if int(obsdate)>=20110901:
# Check to see that the PROPID keyword exists and if not add it
message = '\nSALTPIPE -- Checking for PROPID keyword'
log.message(message)
#check rss data
rssstatus=runcheckforpropid(glob.glob('rss/raw/P*.fits'), propids, log)
#check scam data
scmstatus=runcheckforpropid(glob.glob('scam/raw/S*.fits'), propids, log)
#check hrsB data
hrsbstatus=runcheckforpropid(glob.glob('hrs/raw/H*.fits'), propids, log)
#check hrsB data
hrsrstatus=runcheckforpropid(glob.glob('hrs/raw/R*.fits'), propids, log)
if not rssstatus or not scmstatus or not hrsbstatus or not hrsrstatus:
msg='The PROPIDs for these files needs to be updated and re-start the pipeline'
raise SaltError("Invalid PROPID in images:"+msg)
#process the RSS data
rssrawsize, rssrawnum, rssprodsize, rssprodnum=processdata('rss', obsdate, propcode, median, function, order, rej_lo, rej_hi, niter, interp,logfile, verbose)
#advance process the data
if rssrawnum > 0:
advanceprocess('rss', obsdate, propcode, median, function, order, rej_lo, rej_hi, niter, interp,sdbhost, sdbname, sdbuser, sdbpass, logfile, verbose)
#process the SCAM data
scmrawsize, scmrawnum, scmprodsize, scmprodnum=processdata('scam', obsdate, propcode, median, function, order, rej_lo, rej_hi, niter, interp,logfile, verbose)
#process the HRS data
hrsrawsize, hrsrawnum, hrsprodsize, hrsprodnum=hrsprocess('hrs', obsdate, propcode, median, function, order, rej_lo, rej_hi, niter, interp, logfile, verbose)
#upload the data to the database
img_list=glob.glob(workpath+'scam/product/*bxgp*.fits')
img_list.extend(glob.glob(workpath+'rss/product/*bxgp*.fits'))
img_list.extend(glob.glob(workpath+'hrs/raw/*.fits'))
if img_list:
img=','.join('%s' % (k) for k in img_list)
saltsdbloadfits(images=img, sdbname=sdbname, sdbhost=sdbhost, sdbuser=sdbuser, \
password=sdbpass, logfile=logfile, verbose=verbose)
#add junk sources to the database
raw_list=glob.glob(workpath+'scam/raw/S*.fits')
raw_list.extend(glob.glob(workpath+'rss/raw/P*.fits'))
if raw_list:
img=''
for img in raw_list:
hdu=pyfits.open(img)
if hdu[0].header['PROPID'].strip()=='JUNK':
saltsdbloadfits(images=img, sdbname=sdbname, sdbhost=sdbhost, sdbuser=sdbuser, \
password=sdbpass, logfile=logfile, verbose=verbose)
hdu.close()
# construct observation and pipeline documentation
if lastrssnum > 1 and rssrawnum>0:
rssobslog = 'rss/product/P' + obsdate + 'OBSLOG.fits'
else:
rssobslog = 'none'
if lastscmnum > 1 and scmrawnum>0:
scmobslog = 'scam/product/S' + obsdate + 'OBSLOG.fits'
else:
scmobslog = 'None'
if lasthrsnum > 1 and hrsrawnum>0:
hrsobslog = 'hrs/product/H' + obsdate + 'OBSLOG.fits'
else:
hrsobslog = 'None'
if rssrawnum==0 and scmrawnum==0 and hrsrawnum==0:
msg='No data processed for %s' % obsdate
email=False
ftp=False
log.message(msg)
htmlpath = '.'
nightlog = '../nightlogfiles/' + obsdate + '.log'
readme = iraf.osfn('pipetools$html/readme.template')
if not os.path.isfile(nightlog):
nightlog = ''
message = 'No night log file ~/nightlogfiles/' + obsdate + '.log found'
log.warning(message)
if (rssrawnum > 0 or scmrawnum > 0 or hrsrawnum>0):
salthtml(propcode=propcode,scamobslog=scmobslog,rssobslog=rssobslog, hrsobslog=hrsobslog, htmlpath=htmlpath,
nightlog=nightlog,readme=readme,clobber=True,logfile=logfile,
verbose=verbose)
#add a pause to allow syncing of the databases
time.sleep(10)
#Add in the environmental information
if (rssrawnum > 0 or scmrawnum > 0 or hrsrawnum>0):
propids=saltmysql.getpropcodes(sdb, obsdate)
for pid in propids:
saltelsdata(pid, obsdate, elshost, elsname, elsuser, elspass,
sdbhost,sdbname,sdbuser, sdbpass, clobber, logfile,verbose)
try:
outfile='%s_%s_elsdata.fits' % (pid, obsdate)
outdir='%s/doc/' % (pid)
shutil.move(outfile, outdir)
except:
os.remove(outfile)
#ftp the data
beachdir='/salt/ftparea/'
if ftp:
try:
saltftp(propcode=propcode,obsdate=obsdate, datapath=workpath,
password=ftppasswd,beachdir=beachdir,sdbhost=sdbhost,
sdbname=sdbname,sdbuser=sdbuser,splitfiles=False,
cleanup=True,clobber=True,logfile=logfile, verbose=verbose)
except Exception,e:
message="Not able to copy data to FTP area:\n%s " % e
raise SaltError(message)
#run with the splitting of files
try:
saltftp(propcode=propcode,obsdate=obsdate, datapath=workpath,
password=ftppasswd,beachdir=beachdir,sdbhost=sdbhost,
sdbname=sdbname,sdbuser=sdbuser,splitfiles=True,
cleanup=True,clobber=True,logfile=logfile, verbose=verbose)
except Exception,e:
message="Not able to copy data to FTP area:\n%s " % e
raise SaltError(message)
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)