def writeenvlog(elogfile,date,caldate,clobber,logfile,verbose,status):
# overwrite old environemnt log html file if it exists
line = ' '
if (status == 0): status = saltio.overwrite(elogfile,clobber,logfile)
# open environment log html file
if (status == 0):
saltprint.log(logfile,'SALTHTML -- creating EnvironmentLog' + date + '.html',verbose)
outfile, status = saltio.openascii(elogfile,'w',logfile)
# write html header
if (status == 0): status = htmlheader(outfile,date,caldate,'EnvironmentLog',0,logfile)
# content pending
outfile.write('Content pending\n')
# write html footer
if (status == 0): status = htmlfooter(outfile,logfile)
# close htmlfile
if (status == 0): status = saltio.closeascii(outfile,logfile)
return status
def symlink(infile,linkfile,clobber,verbose,logfile):
# delete file if one of the same name already exists
status = 0
message = 'SALTIO.SYMLINK -- created symbolic link from ' + infile + ' to ' + linkfile
if (os.path.exists(linkfile) and not clobber):
message = 'ERROR: SALTIO.SYMLINK -- file ' + linkfile + ' exists, use clobber=y'
status = saltprint.err(logfile,message)
if (status == 0 and clobber):
try:
os.remove(linkfile)
except:
status = 0
# create symbolic link
if (status == 0):
try:
os.symlink(infile,linkfile)
except:
message = 'ERROR: SALTIO.SYMLINK -- could not create symbolic link from '
message += infile + ' to ' + linkfile
status = saltprint.err(logfile,message)
if (status == 0): saltprint.log(logfile,message,verbose)
return status
def writediaglog(dlogfile,date,caldate,clobber,logfile,verbose,status):
# overwrite old diagnostic html file if it exists
line = ' '
if (status == 0): status = saltio.overwrite(dlogfile,clobber,logfile)
# open diagnostic log html file
if (status == 0):
saltprint.log(logfile,'SALTHTML -- creating InstrumentDiagnostics' + date + '.html',verbose)
outfile, status = saltio.openascii(dlogfile,'w',logfile)
# write html header
if (status == 0): status = htmlheader(outfile,date,caldate,'InstrumentDiagnostics',0,logfile)
# content pending
outfile.write('Content pending\n')
# write html footer
if (status == 0): status = htmlfooter(outfile,logfile)
# close htmlfile
if (status == 0): status = saltio.closeascii(outfile,logfile)
return status
def symlink(infile,linkfile,clobber,verbose,logfile):
# delete file if one of the same name already exists
status = 0
message = 'SALTIO.SYMLINK -- created symbolic link from ' + infile + ' to ' + linkfile
if (os.path.exists(linkfile) and not clobber):
message = 'ERROR: SALTIO.SYMLINK -- file ' + linkfile + ' exists, use clobber=y'
status = saltprint.err(logfile,message)
if (status == 0 and clobber):
try:
os.remove(linkfile)
except:
status = 0
# create symbolic link
if (status == 0):
try:
os.symlink(infile,linkfile)
except:
message = 'ERROR: SALTIO.SYMLINK -- could not create symbolic link from '
message += infile + ' to ' + linkfile
status = saltprint.err(logfile,message)
if (status == 0): saltprint.log(logfile,message,verbose)
return status
def delete(file,verbose,logfile):
status = 0
message = 'SALTIO.DELETE -- deleted file ' + file
try:
os.remove(file)
saltprint.log(logfile,message,verbose)
except Exception, e:
message = 'ERROR -- SALTIO.DELETE: Could not delete %s because %s' % (file ,e)
status = saltprint.err(logfile,message)
def move(file1,file2,verbose,logfile):
status = 0
message = 'SALTIO.MOVE -- moved ' + file1 + ' to ' + file2
try:
shutil.move(file1,file2)
saltprint.log(logfile,message,verbose)
except:
message = 'ERROR -- SALTIO.MOVE: Could not move ' + file1 + ' to ' + file2
status = saltprint.err(logfile,message)
return status
def copy(file1,file2,verbose,logfile):
status = 0
message = 'SALTIO.COPY -- copied ' + file1 + ' to ' + file2
try:
shutil.copy2(file1,file2)
saltprint.log(logfile,message,verbose)
except:
message = 'ERROR -- SALTIO.COPY: could not copy ' + file1 + ' to ' + file2
status = saltprint.err(logfile,message)
return status
def move(file1,file2,verbose,logfile):
status = 0
message = 'SALTIO.MOVE -- moved ' + file1 + ' to ' + file2
try:
shutil.move(file1,file2)
saltprint.log(logfile,message,verbose)
except:
message = 'ERROR -- SALTIO.MOVE: Could not move ' + file1 + ' to ' + file2
status = saltprint.err(logfile,message)
return status
def copy(file1,file2,verbose,logfile):
status = 0
message = 'SALTIO.COPY -- copied ' + file1 + ' to ' + file2
try:
shutil.copy2(file1,file2)
saltprint.log(logfile,message,verbose)
except:
message = 'ERROR -- SALTIO.COPY: could not copy ' + file1 + ' to ' + file2
status = saltprint.err(logfile,message)
return status
def tmpfile(path,verbose,logfile):
status = 0
message = 'SALTIO.TMPFILE -- Created temporary file name '
try:
tempfile.tempdir = path
file = tempfile.mktemp()
saltprint.log(logfile,message + file,verbose)
except:
file = ''
message = 'ERROR -- SALTPRINT.TMPFILE: Cannot create temporary file name'
status = saltprint.err(logfile,message)
return file, status
def changedir(path,verbose,logfile):
status = 0
path = path.strip()
message = 'SALTIO.CHANGEDIR -- Moved to directory ' + path
try:
os.chdir(path)
saltprint.log(logfile,message,verbose)
except:
message = 'ERROR -- SALTIO.CREATEDIR: Could not move to directory ' + path
status = saltprint.err(logfile,message)
return status
def changedir(path,verbose,logfile):
status = 0
path = path.strip()
message = 'SALTIO.CHANGEDIR -- Moved to directory ' + path
try:
os.chdir(path)
saltprint.log(logfile,message,verbose)
except:
message = 'ERROR -- SALTIO.CREATEDIR: Could not move to directory ' + path
status = saltprint.err(logfile,message)
return status
def tmpfile(path,verbose,logfile):
status = 0
message = 'SALTIO.TMPFILE -- Created temporary file name '
try:
tempfile.tempdir = path
file = tempfile.mktemp()
saltprint.log(logfile,message + file,verbose)
except:
file = ''
message = 'ERROR -- SALTPRINT.TMPFILE: Cannot create temporary file name'
status = saltprint.err(logfile,message)
return file, status
def writecapetownnotes(notefile,readme,date,caldate,clobber,logfile,verbose,status):
# overwrite old observation log html file if it exists
line = ' '
if (status == 0): status = saltio.overwrite(notefile,clobber,logfile)
# open observation log html file
if (status == 0):
saltprint.log(logfile,'SALTHTML -- creating CapeTownNotes' + date + '.html',verbose)
outfile, status = saltio.openascii(notefile,'w',logfile)
# write html header
if (status == 0): status = htmlheader(outfile,date,caldate,'CapeTownNotes',0,logfile)
# readme file exists?
if (status == 0):
if (not os.path.isfile(readme)):
status=1
message = 'ERRROR: SALTHTML -- readme file does not exist'
else:
# open nightlog file
if (status == 0): infile, status = saltio.openascii(readme,'r',logfile)
# append night log to html file
if (status == 0):
while line:
line = infile.readline()
outfile.write(line)
# append readme to html file
if (status == 0):
while line:
line = infile.readline()
outfile.write(line)
# write html footer
if (status == 0): status = htmlfooter(outfile,logfile)
return status
def createdir(path,verbose,logfile):
status = 0
path = path.strip()
message = 'SALTIO.CREATEDIR -- Created directory ' + path
if (path[-1] != '/'): path += '/'
if (not os.path.exists(path)):
try:
os.mkdir(path)
saltprint.log(logfile,message,verbose)
except:
message = 'ERROR -- SALTIO.CREATEDIR: Could not create directory ' + path
status = saltprint.err(logfile,message)
else:
message = 'SALTIO.CREATEDIR -- ' + path + ' directory exists'
saltprint.log(logfile,message,verbose)
return status
def createdir(path,verbose,logfile):
status = 0
path = path.strip()
message = 'SALTIO.CREATEDIR -- Created directory ' + path
if (path[-1] != '/'): path += '/'
if (not os.path.exists(path)):
try:
os.mkdir(path)
saltprint.log(logfile,message,verbose)
except:
message = 'ERROR -- SALTIO.CREATEDIR: Could not create directory ' + path
status = saltprint.err(logfile,message)
else:
message = 'SALTIO.CREATEDIR -- ' + path + ' directory exists'
saltprint.log(logfile,message,verbose)
return status
def writepipelog(plogfile,date,caldate,clobber,logfile,verbose,status):
# overwrite old pipeline log html file if it exists
line = ' '
if (status == 0): status = saltio.overwrite(plogfile,clobber,logfile)
# open pipeline log html file
if (status == 0):
saltprint.log(logfile,'SALTHTML -- creating PipelineLog' + date + '.html',verbose)
outfile, status = saltio.openascii(plogfile,'w',logfile)
# write html header
if (status == 0): status = htmlheader(outfile,date,caldate,'PipelineLog',0,logfile)
# nightlog file exists?
if (status == 0):
if (not os.path.isfile(logfile)):
message = 'WARNING: SALTHTML -- pipeline log does not exist'
else:
# open nightlog file
if (status == 0): infile, status = saltio.openascii(logfile,'r',logfile)
# append night log to html file
if (status == 0):
while line:
line = infile.readline()
outfile.write(line)
# write html footer
if (status == 0): status = htmlfooter(outfile,logfile)
# close htmlfile
if (status == 0): status = saltio.closeascii(outfile,logfile)
return status
def mkheader(file,keyword,value,comment,verbose,logfile):
"""create keyword with mkheader IRAF tool i.e. without opening the whole file"""
status = 0
message = 'SALTKEY.MKHEADER: Created keyword ' + keyword + ' in ' + file
try:
tmpfile, status = saltio.tmpfile('.',False,logfile)
tmp, status = saltio.openascii(tmpfile,'w',logfile)
tmp.write('%-8s= \'%-18s\' / %-s\n' % (keyword,value,comment))
status = saltio.closeascii(tmp,logfile)
iraf.noao.artdata.mkheader(file,tmpfile,append='y',verbose='n')
saltio.delete(tmpfile,False,logfile)
saltprint.log(logfile,message,verbose)
except:
message = 'ERROR -- SALTKEY.MKHEADER: Cannot edit keyword ' + keyword
message += ' in ' + file
status = saltprint.err(logfile,message)
return status
def salthtml(propcode,scamobslog,rssobslog, hrsobslog, htmlpath,nightlog,readme,clobber,logfile,verbose):
# set up
filenames = []
proposers = []
propids = []
instrumes = []
objects = []
ras = []
decs = []
detmodes = []
ccdtypes = []
ccdsums = []
gainsets = []
rospeeds = []
filters = []
gratings = []
gr_angles = []
ar_angles = []
time_obss = []
date_obss = []
exptimes = []
hours = []
filename = {}
proposer = {}
propid = {}
instrume = {}
object = {}
ra = {}
dec = {}
detmode = {}
ccdsum = {}
ccdtype = {}
gainset = {}
rospeed = {}
filter = {}
grating = {}
gr_angle = {}
ar_angle = {}
time_obs = {}
exptime = {}
status=0
# test the logfile
logfile = saltio.logname(logfile)
# log the call
saltprint.line(logfile,verbose)
history = 'SALTHTML -- '
history += 'scamobslog='+scamobslog+' '
history += 'rssobslog='+rssobslog+' '
history += 'htmlpath='+htmlpath+' '
history += 'nightlog='+nightlog+' '
history += 'readme='+readme+' '
yn = 'n'
if (clobber): yn = 'y'
history += 'clobber='+yn+' '
history += 'logfile='+logfile+' '
yn = 'n'
if (verbose): yn = 'y'
history += 'verbose='+yn
saltprint.log(logfile,history,verbose)
# start time
saltprint.time('\nSALTHTML -- started at',logfile,verbose)
saltprint.log(logfile,' ',verbose)
# are the arguments defined
if (status == 0): pids,status = saltio.argunpack('propcode',propcode ,logfile)
if (status == 0): status = saltio.argdefined('scamobslog',scamobslog,logfile)
if (status == 0): status = saltio.argdefined('rssobslog',rssobslog,logfile)
if (status == 0): status = saltio.argdefined('htmlpath',htmlpath,logfile)
# check htmlpath exists, ends with a "/" and convert to absolute path
if (status == 0): htmlpath, status = saltio.abspath(htmlpath,logfile)
# check observation log files exist
if (status == 0 and scamobslog.upper() != 'NONE'): status = saltio.fileexists(scamobslog,logfile)
if (status == 0 and rssobslog.upper() != 'NONE'): status = saltio.fileexists(rssobslog,logfile)
# read observation logs
for obslog in [scamobslog, rssobslog, hrsobslog]:
if (status == 0 and obslog.upper() != 'NONE'): struct,status = saltio.openfits(obslog,logfile)
if (status == 0 and obslog.upper() != 'NONE'): obstab,status = saltio.readtab(struct[1],obslog,logfile)
if (status == 0 and obslog.upper() != 'NONE'): status = saltio.closefits(struct,logfile)
if (status == 0 and obslog.upper() != 'NONE'):
filenames.extend(obstab.field('filename'))
objects.extend(obstab.field('object'))
ras.extend(obstab.field('ra'))
decs.extend(obstab.field('dec'))
instrumes.extend(obstab.field('instrume'))
proposers.extend(obstab.field('proposer'))
propids.extend(obstab.field('propid'))
ccdtypes.extend(obstab.field('ccdtype'))
ccdsums.extend(obstab.field('ccdsum'))
gainsets.extend(obstab.field('gainset'))
rospeeds.extend(obstab.field('rospeed'))
detmodes.extend(obstab.field('detmode'))
filters.extend(obstab.field('filter'))
time_obss.extend(obstab.field('time-obs'))
date_obss.extend(obstab.field('date-obs'))
exptimes.extend(obstab.field('exptime'))
if (obslog == rssobslog):
gratings.extend(obstab.field('grating'))
gr_angles.extend(obstab.field('gr-angle'))
ar_angles.extend(obstab.field('ar-angle'))
else:
for i in range(len(filenames)):
gratings.append(' ')
gr_angles.append(0.)
ar_angles.append(0.)
# Create the list of proposals
if (status == 0): pids,status=saltio.cleanpropcode(pids, propids, logfile)
# date of observations
date, caldate = salttime.date_obs2yyyymmdd(date_obss[0])
# sort into chronological order
for i in range(len(filenames)):
hours.append(salttime.time_obs2hr(time_obss[i]))
if (hours[i] < 12.): hours[i] += 24
filename[str(hours[i])] = filenames[i]
object[str(hours[i])] = objects[i]
ra[str(hours[i])] = ras[i]
dec[str(hours[i])] = decs[i]
instrume[str(hours[i])] = instrumes[i]
proposer[str(hours[i])] = proposers[i]
propid[str(hours[i])] = propids[i]
ccdsum[str(hours[i])] = ccdsums[i].replace(' ','x')
ccdtype[str(hours[i])] = ccdtypes[i]
gainset[str(hours[i])] = gainsets[i]
rospeed[str(hours[i])] = rospeeds[i]
detmode[str(hours[i])] = detmodes[i]
filter[str(hours[i])] = filters[i]
time_obs[str(hours[i])] = time_obss[i]
grating[str(hours[i])] = gratings[i]
gr_angle[str(hours[i])] = gr_angles[i]
ar_angle[str(hours[i])] = ar_angles[i]
exptime[str(hours[i])] = exptimes[i]
if (instrume[str(hours[i])] == 'SALTICAM'): instrume[str(hours[i])] = 'SCM'
if ('Video Mode' in detmode[str(hours[i])]): detmode[str(hours[i])] = 'VI'
if ('Slot Mode' in detmode[str(hours[i])]): detmode[str(hours[i])] = 'SL'
if ('Frame Transfer' in detmode[str(hours[i])]): detmode[str(hours[i])] = 'FT'
if ('Normal' in detmode[str(hours[i])]): detmode[str(hours[i])] = 'IM'
if ('Bright' in gainset[str(hours[i])]): gainset[str(hours[i])] = 'BR'
if ('Faint' in gainset[str(hours[i])]): gainset[str(hours[i])] = 'FA'
if ('Fast' in rospeed[str(hours[i])]): rospeed[str(hours[i])] = 'FA'
if ('Slow' in rospeed[str(hours[i])]): rospeed[str(hours[i])] = 'SL'
if ('OBJECT' not in ccdtype[str(hours[i])].upper() and
'UNKNOWN' in proposer[str(hours[i])].upper()):
proposer[str(hours[i])] = ''
hours.sort()
# create HTML directory in datapath and define html files
docpath = htmlpath + 'doc/'
if (status == 0 and not os.path.exists(docpath)): status = saltio.createdir(docpath,False,logfile)
htmlfile = docpath + 'ObservationSequence' + date +'.html'
notefile = docpath + 'CapeTownNotes' + date + '.html'
nlogfile = docpath + 'AstronomersLog' + date + '.html'
plogfile = docpath + 'PipelineLog' + date + '.html'
elogfile = docpath + 'EnvironmentLog' + date + '.html'
dlogfile = docpath + 'InstrumentDiagnostics' + date + '.html'
# Copy css and banner images to the doc directory
if (status == 0):
status=saltio.copy(iraf.osfn('pipetools$html/style.css'),docpath,False,logfile)
status=saltio.copy(iraf.osfn('pipetools$html/style_home.css'),docpath,False,logfile)
status=saltio.copy(iraf.osfn('pipetools$html/header_salt.jpg'),docpath,False,logfile)
# write observation log html file
if (status == 0):
status = writeobslog(htmlfile,filename,object,ra,dec,instrume,detmode,filter,ccdsum,
gainset,rospeed,grating,gr_angle,ar_angle,exptime,time_obs,proposer,
propid,hours,date,caldate,clobber,logfile,verbose,status)
# write readme html file
if (status == 0):
status = writecapetownnotes(notefile,readme,date,caldate,clobber,logfile,verbose,status)
# write nightlog html file
if (status == 0):
status = writenightlog(nlogfile,nightlog,date,caldate,clobber,logfile,verbose,status)
# write pipeline log html file
if (status == 0):
status = writepipelog(plogfile,date,caldate,clobber,logfile,verbose,status)
# write environment log html file
if (status == 0):
status = writeenvlog(elogfile,date,caldate,clobber,logfile,verbose,status)
# write instrument diagnostics html file
if (status == 0):
status = writediaglog(dlogfile,date,caldate,clobber,logfile,verbose,status)
# copy html files to PI directories
if (status == 0):
saltprint.log(logfile,' ',verbose)
for pids in set(propids):
for pid in pids.split(','):
pid = pid.strip().upper()
pidpath = htmlpath + pid
if (os.path.exists(pidpath)):
if (os.path.exists(pidpath+'/doc')):
for file in glob.glob(pidpath+'/doc/*'):
status = saltio.delete(file,False,logfile)
status = saltio.deletedir(pidpath+'/doc',logfile)
status = saltio.copydir(docpath,pidpath+'/doc',verbose,logfile)
if (status == 0):
infile, status = saltio.openascii(pidpath+'/doc/CapeTownNotes'+date+'.html','r',logfile)
if (status == 0): saltio.delete(pidpath+'/doc/CapeTownNotes'+date+'.html',False,logfile)
if (status == 0):
outfile, status = saltio.openascii(pidpath+'/doc/CapeTownNotes'+date+'.html','w',logfile)
if (status == 0):
for line in infile:
#line = line.replace('SALT user','Dr ' + string.capwords(pi.lower()))
#line = line.replace('yourname',pi)
line = line.replace('yyyymmdd',date)
outfile.write(line)
status = saltio.closeascii(outfile,logfile)
# end time
if (status == 0):
saltprint.time('\nSALTHTML -- completed at',logfile,verbose)
else:
saltprint.time('\nSALTHTML -- aborted at',logfile,verbose)
def deleteframe(self, e):
self.newphot=1
self.goodframes[self.id] = 0
message='SALTPHOT: Extension %i was deleted' % self.pid[self.id]
saltprint.log(self.logfile, message, self.verbose)
def writeobslog(htmlfile,filename,object,ra,dec,instrume,detmode,filter,
ccdsum,gainset,rospeed,grating,gr_angle,ar_angle,exptime,
time_obs,proposer,propid,hours,date,caldate,clobber,logfile,verbose,status):
# overwrite observation log html file
if (status == 0 and os.path.isfile(htmlfile) and clobber):
status = saltio.delete(htmlfile,False,logfile)
elif (status == 0 and os.path.isfile(htmlfile) and not clobber):
message = 'ERROR: SALTHTML -- file ' + htmlfile + ' exists. Use clobber=y'
status = saltprint.err(logfile,message)
# open observation log html file
if (status == 0):
line = ' '
saltprint.log(logfile,'SALTHTML -- creating ObservationSequence' + date + '.html',verbose)
outfile, status = saltio.openascii(htmlfile,'w',logfile)
# write html header
if (status == 0): status = htmlheader(outfile,date,caldate,'ObservationLog',-1,logfile)
# write table headings
if (status == 0):
outfile.write("%14s %12s %10s %9s %3s %2s %7s %3s %2s %2s %6s %5s %6s %6s %8s %15s %16s \n" %
('file'.ljust(14),
'object'.ljust(12),
'ra2000'.rjust(10),
'dec2000'.rjust(9),
'ins'.ljust(3),
'md'.ljust(2),
'filter'.rjust(7),
'bin'.rjust(3),
'gn'.rjust(2),
'sp'.rjust(2),
'grat'.rjust(6),
'gr-ang'.ljust(6),
'ar-ang'.ljust(6),
'exp'.rjust(6),
'UT'.rjust(8),
'Code'.ljust(15),
'PI'.ljust(16)))
for i in range(140):
outfile.write('-')
outfile.write('\n')
# write table
for i in hours:
outfile.write("%15s %12s %10s %9s %3s %2s %7s %3s %2s %2s %6s %5.2f %6.2f %6.1f %8s %15s %16s\n" %
(filename[str(i)].replace('.fits','')[:13].ljust(13),
object[str(i)][:12].ljust(12),
ra[str(i)][:10].ljust(10),
dec[str(i)][:9].ljust(9),
instrume[str(i)][:3].ljust(3),
detmode[str(i)][:2].ljust(2),
filter[str(i)][:7].rjust(7),
ccdsum[str(i)][:3].rjust(3),
gainset[str(i)][:2].rjust(2),
rospeed[str(i)][:2].rjust(2),
grating[str(i)][:6].ljust(6),
gr_angle[str(i)],
ar_angle[str(i)],
exptime[str(i)],
time_obs[str(i)][:8].ljust(8),
propid[str(i)][:15].ljust(15),
proposer[str(i)][:16].ljust(16)))
# write html foolter
if (status == 0): status = htmlfooter(outfile,logfile)
return status
def slot(struct, infile, dbspeed, dbrate, dbgain, dbnoise, dbbias, dbamp,
xcoeff, gaindb, xtalkfile, logfile, verbose):
import saltprint, saltkey, saltio, saltstat, time
# identify instrument
instrume, keyprep, keygain, keybias, keyxtalk, keyslot, status = saltkey.instrumid(
struct, infile, logfile)
# number of image HDU
nextend = 0
while (status == 0):
try:
struct[nextend + 1].header['XTENSION']
nextend += 1
except:
break
nccds, status = saltkey.get('NCCDS', struct[0], infile, logfile)
amplifiers = nccds * 2
if (nextend % (amplifiers) != 0):
message = '\nERROR -- SALTSLOT: Number of image extensions and'
message += 'number of amplifiers are not consistent'
status = saltprint.err(saltlog, message)
status = saltkey.new('NSCIEXT', nextend, 'Number of science extensions',
struct[0], infile, logfile)
status = saltkey.new('NEXTEND', nextend, 'Number of data extensions',
struct[0], infile, logfile)
# check image file and gain database are compatible
if (status == 0):
ngains = len(dbgain)
if (int(max(dbamp)) != amplifiers):
message = '\nERROR -- SALTGSLOT: ' + infile + ' contains ' + str(
amplifiers) + ' amplifiers'
message += ', the gaindb file ' + gaindb + ' contains ' + str(
max(dbamp)) + ' amplifiers'
status = saltprint.err(logfile, message)
# check image file and cross talk database are compatible
if (status == 0):
if (len(xcoeff) - 1 != amplifiers):
message = '\nERROR -- SALTSLOT: ' + infile + ' contains ' + str(
amplifiers) + ' amplifiers'
message += ', the cross talk file ' + xtalkfile + ' contains ' + str(
len(xcoeff) - 1) + ' amplifiers'
status = saltprint.err(logfile, message)
# housekeeping keywords
if (status == 0):
status = saltkey.put('SAL-TLM', time.asctime(time.localtime()),
struct[0], infile, logfile)
status = saltkey.new(keyslot, time.asctime(time.localtime()),
'Data have been cleaned by SALTSLOT', struct[0],
infile, logfile)
# keywords for image extensions
for i in range(nextend):
hdu = i + 1
status = saltkey.new('EXTNAME', 'SCI', 'Extension name', struct[hdu],
infile, logfile)
status = saltkey.new('EXTVER', hdu, 'Extension number', struct[hdu],
infile, logfile)
# log coefficent table
if (status == 0):
message = '%30s %5s %4s %8s' % ('HDU', 'Gain', 'Bias', 'Xtalk')
saltprint.log(logfile,
'\n ---------------------------------------------',
verbose)
saltprint.log(logfile, message, verbose)
saltprint.log(logfile,
' ---------------------------------------------',
verbose)
# loop over image extensions
if (status == 0):
for i in range(nextend / 2):
hdu = i * 2 + 1
amplifier = hdu % amplifiers
if (amplifier == 0): amplifier = amplifiers
if (status == 0):
value, status = saltkey.get('NAXIS1', struct[hdu], infile,
logfile)
naxis1 = int(value)
if (status == 0):
value, status = saltkey.get('NAXIS1', struct[hdu + 1], infile,
logfile)
naxis2 = int(value)
if (status == 0 and hdu == 1):
biassec, status = saltkey.get('BIASSEC', struct[hdu], infile,
logfile)
if (status == 0 and hdu == 1):
ranges = biassec.lstrip('[').rstrip(']').split(',')
x1_1 = int(ranges[0].split(':')[0]) - 1
x2_1 = int(ranges[0].split(':')[1]) - 1
y1_1 = int(ranges[1].split(':')[0]) - 1
y2_1 = int(ranges[1].split(':')[1]) - 1
if (status == 0 and hdu == 1):
biassec, status = saltkey.get('BIASSEC', struct[hdu + 1],
infile, logfile)
if (status == 0 and hdu == 1):
ranges = biassec.lstrip('[').rstrip(']').split(',')
x1_2 = int(ranges[0].split(':')[0]) - 1
x2_2 = int(ranges[0].split(':')[1]) - 1
y1_2 = int(ranges[1].split(':')[0]) - 1
y2_2 = int(ranges[1].split(':')[1]) - 1
if (status == 0 and hdu == 1):
datasec, status = saltkey.get('DATASEC', struct[hdu], infile,
logfile)
if (status == 0 and hdu == 1):
ranges = datasec.lstrip('[').rstrip(']').split(',')
dx1_1 = int(ranges[0].split(':')[0]) - 1
dx2_1 = int(ranges[0].split(':')[1])
dy1_1 = int(ranges[1].split(':')[0]) - 1
dy2_1 = int(ranges[1].split(':')[1])
if (status == 0 and hdu == 1):
datasec, status = saltkey.get('DATASEC', struct[hdu + 1],
infile, logfile)
if (status == 0 and hdu == 1):
ranges = datasec.lstrip('[').rstrip(']').split(',')
dx1_2 = int(ranges[0].split(':')[0]) - 1
dx2_2 = int(ranges[0].split(':')[1])
dy1_2 = int(ranges[1].split(':')[0]) - 1
dy2_2 = int(ranges[1].split(':')[1])
if (status == 0 and dx2_1 - dx1_1 != dx2_2 - dx1_2):
message = 'ERROR -- SALTSLOT: HDUs ' + infile
message += '[' + str(hdu) + '] and ' + infile + '[' + str(
hdu + 1) + ']'
message += ' have different dimensions'
status = saltprint.err(logfile, message)
# read speed and gain of each exposure
if (status == 0 and hdu == 1):
gainset, status = saltkey.get('GAINSET', struct[0], infile,
logfile)
rospeed, status = saltkey.get('ROSPEED', struct[0], infile,
logfile)
if (rospeed == 'NONE'):
saltprint.log(logfile, " ", verbose)
message = "ERROR -- SALTSLOT: Readout speed is 'NONE' in "
message += "primary keywords of " + infile
status = saltprint.err(logfile, message)
# read raw images
if (status == 0):
imagedata1, status = saltio.readimage(struct, hdu, logfile)
imagedata2, status = saltio.readimage(struct, hdu + 1, logfile)
# gain correction
if (status == 0):
for j in range(len(dbgain)):
if (gainset == dbrate[j] and rospeed == dbspeed[j]
and amplifier == int(dbamp[j])):
try:
gain1 = float(dbgain[j])
imagedata1 *= gain1
except:
mesage = 'ERROR -- SALTSLOT: Cannot perform gain correction on image '
message += infile + '[' + str(hdu) + ']'
status = saltprint.err(logfile, message)
elif (gainset == dbrate[j] and rospeed == dbspeed[j]
and amplifier + 1 == int(dbamp[j])):
try:
gain2 = float(dbgain[j])
imagedata2 *= gain2
except:
mesage = 'ERROR -- SALTSLOT: Cannot perform gain correction on image '
message += infile + '[' + str(hdu + 1) + ']'
status = saltprint.err(logfile, message)
# crosstalk correction
if (status == 0):
revimage1 = imagedata1 * float(xcoeff[amplifier])
revimage2 = imagedata2 * float(xcoeff[amplifier + 1])
for j in range(dx2_1 - dx1_1 + 1):
imagedata1[:, j] -= revimage2[:, dx2_2 - j - 1]
imagedata2[:, j] -= revimage1[:, dx2_1 - j - 1]
# bias subtraction
if (status == 0):
overx_val_1 = []
overx_val_2 = []
for x in range(x1_1, x2_1 + 1):
list_1 = imagedata1[y1_1:y2_1, x] * 1.0
overx_val_1.append(saltstat.median(list_1, logfile))
overlevel_1 = saltstat.median(overx_val_1, logfile)
for x in range(x1_2, x2_2 + 1):
list_2 = imagedata2[y1_2:y2_2, x] * 1.0
overx_val_2.append(saltstat.median(list_2, logfile))
overlevel_2 = saltstat.median(overx_val_2, logfile)
imagedata1 -= overlevel_1
imagedata2 -= overlevel_2
# trim overscan
if (status == 0):
imagedata1 = imagedata1[dy1_1:dy2_1, dx1_1:dx2_1]
imagedata2 = imagedata2[dy1_2:dy2_2, dx1_2:dx2_2]
datasec = '[1:' + str(dx2_1 - dx1_1) + ',1:' + str(dy2_1 -
dy1_1) + ']'
status = saltkey.put('DATASEC', datasec, struct[hdu], infile,
logfile)
status = saltkey.rem('BIASSEC', struct[hdu], infile, logfile)
datasec = '[1:' + str(dx2_2 - dx1_2) + ',1:' + str(dy2_2 -
dy1_2) + ']'
status = saltkey.put('DATASEC', datasec, struct[hdu + 1],
infile, logfile)
status = saltkey.rem('BIASSEC', struct[hdu + 1], infile,
logfile)
# log coefficient table
if (status == 0):
infilename = infile.split('/')
infilename = infilename[len(infilename) - 1]
message = '%25s[%3d] %5.2f %4d %8.6f' % \
(infilename, hdu, gain1, overlevel_1, float(xcoeff[amplifier+1]))
saltprint.log(logfile, message, verbose)
message = '%25s[%3d] %5.2f %4d %8.6f' % \
(infilename, hdu+1, gain2, overlevel_2,float(xcoeff[amplifier]))
saltprint.log(logfile, message, verbose)
# update image in HDU structure
if (status == 0):
struct, status = saltio.writeimage(struct, hdu, imagedata1,
logfile)
struct, status = saltio.writeimage(struct, hdu + 1, imagedata2,
logfile)
return struct, status
def slot(struct,infile,dbspeed,dbrate,dbgain,dbnoise,dbbias,dbamp,xcoeff,gaindb,xtalkfile,
logfile,verbose):
import saltprint, saltkey, saltio, saltstat, time
# identify instrument
instrume,keyprep,keygain,keybias,keyxtalk,keyslot,status = saltkey.instrumid(struct,infile,logfile)
# number of image HDU
nextend = 0
while (status == 0):
try:
struct[nextend+1].header['XTENSION']
nextend += 1
except:
break
nccds,status = saltkey.get('NCCDS',struct[0],infile,logfile)
amplifiers = nccds * 2
if (nextend%(amplifiers) != 0):
message = '\nERROR -- SALTSLOT: Number of image extensions and'
message += 'number of amplifiers are not consistent'
status = saltprint.err(saltlog,message)
status = saltkey.new('NSCIEXT',nextend,'Number of science extensions',struct[0],infile,logfile)
status = saltkey.new('NEXTEND',nextend,'Number of data extensions',struct[0],infile,logfile)
# check image file and gain database are compatible
if (status == 0):
ngains = len(dbgain)
if (int(max(dbamp)) != amplifiers):
message = '\nERROR -- SALTGSLOT: ' + infile + ' contains ' + str(amplifiers) + ' amplifiers'
message += ', the gaindb file ' + gaindb + ' contains ' + str(max(dbamp)) + ' amplifiers'
status = saltprint.err(logfile,message)
# check image file and cross talk database are compatible
if (status == 0):
if (len(xcoeff)-1 != amplifiers):
message = '\nERROR -- SALTSLOT: ' + infile + ' contains ' + str(amplifiers) + ' amplifiers'
message += ', the cross talk file ' + xtalkfile + ' contains ' + str(len(xcoeff)-1) + ' amplifiers'
status = saltprint.err(logfile,message)
# housekeeping keywords
if (status == 0):
status = saltkey.put('SAL-TLM',time.asctime(time.localtime()),struct[0],infile,logfile)
status = saltkey.new(keyslot,time.asctime(time.localtime()),
'Data have been cleaned by SALTSLOT',struct[0],infile,logfile)
# keywords for image extensions
for i in range(nextend):
hdu = i + 1
status = saltkey.new('EXTNAME','SCI','Extension name',struct[hdu],infile,logfile)
status = saltkey.new('EXTVER',hdu,'Extension number',struct[hdu],infile,logfile)
# log coefficent table
if (status == 0):
message = '%30s %5s %4s %8s' % ('HDU','Gain','Bias','Xtalk')
saltprint.log(logfile,'\n ---------------------------------------------',verbose)
saltprint.log(logfile,message,verbose)
saltprint.log(logfile,' ---------------------------------------------',verbose)
# loop over image extensions
if (status == 0):
for i in range(nextend/2):
hdu = i * 2 + 1
amplifier = hdu%amplifiers
if (amplifier == 0): amplifier = amplifiers
if (status == 0):
value,status = saltkey.get('NAXIS1',struct[hdu],infile,logfile)
naxis1 = int(value)
if (status == 0):
value,status = saltkey.get('NAXIS1',struct[hdu+1],infile,logfile)
naxis2 = int(value)
if (status == 0 and hdu == 1): biassec, status = saltkey.get('BIASSEC',struct[hdu],infile,logfile)
if (status == 0 and hdu == 1):
ranges = biassec.lstrip('[').rstrip(']').split(',')
x1_1 = int(ranges[0].split(':')[0]) - 1
x2_1 = int(ranges[0].split(':')[1]) - 1
y1_1 = int(ranges[1].split(':')[0]) - 1
y2_1 = int(ranges[1].split(':')[1]) - 1
if (status == 0 and hdu == 1): biassec, status = saltkey.get('BIASSEC',struct[hdu+1],infile,logfile)
if (status == 0 and hdu == 1):
ranges = biassec.lstrip('[').rstrip(']').split(',')
x1_2 = int(ranges[0].split(':')[0]) - 1
x2_2 = int(ranges[0].split(':')[1]) - 1
y1_2 = int(ranges[1].split(':')[0]) - 1
y2_2 = int(ranges[1].split(':')[1]) - 1
if (status == 0 and hdu == 1): datasec,status = saltkey.get('DATASEC',struct[hdu],infile,logfile)
if (status == 0 and hdu == 1):
ranges = datasec.lstrip('[').rstrip(']').split(',')
dx1_1 = int(ranges[0].split(':')[0]) - 1
dx2_1 = int(ranges[0].split(':')[1])
dy1_1 = int(ranges[1].split(':')[0]) - 1
dy2_1 = int(ranges[1].split(':')[1])
if (status == 0 and hdu == 1): datasec,status = saltkey.get('DATASEC',struct[hdu+1],infile,logfile)
if (status == 0 and hdu == 1):
ranges = datasec.lstrip('[').rstrip(']').split(',')
dx1_2 = int(ranges[0].split(':')[0]) - 1
dx2_2 = int(ranges[0].split(':')[1])
dy1_2 = int(ranges[1].split(':')[0]) - 1
dy2_2 = int(ranges[1].split(':')[1])
if (status == 0 and dx2_1 - dx1_1 != dx2_2 - dx1_2):
message = 'ERROR -- SALTSLOT: HDUs '+infile
message += '['+str(hdu)+'] and '+infile+'['+str(hdu+1)+']'
message += ' have different dimensions'
status = saltprint.err(logfile,message)
# read speed and gain of each exposure
if (status == 0 and hdu == 1):
gainset,status = saltkey.get('GAINSET',struct[0],infile,logfile)
rospeed,status = saltkey.get('ROSPEED',struct[0],infile,logfile)
if (rospeed == 'NONE'):
saltprint.log(logfile," ",verbose)
message = "ERROR -- SALTSLOT: Readout speed is 'NONE' in "
message += "primary keywords of " + infile
status = saltprint.err(logfile,message)
# read raw images
if (status == 0):
imagedata1,status = saltio.readimage(struct,hdu,logfile)
imagedata2,status = saltio.readimage(struct,hdu+1,logfile)
# gain correction
if (status == 0):
for j in range(len(dbgain)):
if (gainset == dbrate[j] and rospeed == dbspeed[j] and amplifier == int(dbamp[j])):
try:
gain1 = float(dbgain[j])
imagedata1 *= gain1
except:
mesage = 'ERROR -- SALTSLOT: Cannot perform gain correction on image '
message += infile+'['+str(hdu)+']'
status = saltprint.err(logfile,message)
elif (gainset == dbrate[j] and rospeed == dbspeed[j] and amplifier + 1 == int(dbamp[j])):
try:
gain2 = float(dbgain[j])
imagedata2 *= gain2
except:
mesage = 'ERROR -- SALTSLOT: Cannot perform gain correction on image '
message += infile+'['+str(hdu+1)+']'
status = saltprint.err(logfile,message)
# crosstalk correction
if (status == 0):
revimage1 = imagedata1 * float(xcoeff[amplifier])
revimage2 = imagedata2 * float(xcoeff[amplifier+1])
for j in range(dx2_1-dx1_1+1):
imagedata1[:,j] -= revimage2[:,dx2_2-j-1]
imagedata2[:,j] -= revimage1[:,dx2_1-j-1]
# bias subtraction
if (status == 0):
overx_val_1 = []
overx_val_2 = []
for x in range(x1_1,x2_1+1):
list_1 = imagedata1[y1_1:y2_1,x] * 1.0
overx_val_1.append(saltstat.median(list_1,logfile))
overlevel_1 = saltstat.median(overx_val_1,logfile)
for x in range(x1_2,x2_2+1):
list_2 = imagedata2[y1_2:y2_2,x] * 1.0
overx_val_2.append(saltstat.median(list_2,logfile))
overlevel_2 = saltstat.median(overx_val_2,logfile)
imagedata1 -= overlevel_1
imagedata2 -= overlevel_2
# trim overscan
if (status == 0):
imagedata1 = imagedata1[dy1_1:dy2_1,dx1_1:dx2_1]
imagedata2 = imagedata2[dy1_2:dy2_2,dx1_2:dx2_2]
datasec = '[1:'+str(dx2_1-dx1_1)+',1:'+str(dy2_1-dy1_1)+']'
status = saltkey.put('DATASEC',datasec,struct[hdu],infile,logfile)
status = saltkey.rem('BIASSEC',struct[hdu],infile,logfile)
datasec = '[1:'+str(dx2_2-dx1_2)+',1:'+str(dy2_2-dy1_2)+']'
status = saltkey.put('DATASEC',datasec,struct[hdu+1],infile,logfile)
status = saltkey.rem('BIASSEC',struct[hdu+1],infile,logfile)
# log coefficient table
if (status == 0):
infilename = infile.split('/')
infilename = infilename[len(infilename)-1]
message = '%25s[%3d] %5.2f %4d %8.6f' % \
(infilename, hdu, gain1, overlevel_1, float(xcoeff[amplifier+1]))
saltprint.log(logfile,message,verbose)
message = '%25s[%3d] %5.2f %4d %8.6f' % \
(infilename, hdu+1, gain2, overlevel_2,float(xcoeff[amplifier]))
saltprint.log(logfile,message,verbose)
# update image in HDU structure
if (status == 0):
struct,status = saltio.writeimage(struct,hdu,imagedata1,logfile)
struct,status = saltio.writeimage(struct,hdu+1,imagedata2,logfile)
return struct, status
def saltbin2fit(inpath,outpath,cleanup,fitsconfig,logfile,verbose,status=0):
status = 0
output = {}
headlist18 = []
headlist19 = []
# test the logfile
logfile = saltio.logname(logfile)
# log the call
saltprint.line(logfile,verbose)
message = 'SALTBIN2FIT -- '
message += 'inpath='+inpath+' '
message += 'outpath='+outpath+' '
yn = 'n'
if (cleanup): yn = 'y'
message += 'cleanup='+yn+' '
message += 'fitsconfig='+fitsconfig+' '
message += 'logfile='+logfile+' '
yn = 'n'
if (verbose): yn = 'y'
message += 'verbose='+yn+'\n'
saltprint.log(logfile,message,verbose)
# start time
saltprint.time('SALTBIN2FIT started at ',logfile,verbose)
# check directory inpath exists
if (status == 0): inpath, status = saltio.pathexists(inpath,logfile)
# check directory outpath exists or create it
outpath = outpath.strip()
if (outpath[-1] != '/'): outpath += '/'
if (status == 0 and not os.path.exists(outpath)):
status = saltio.createdir(outpath,'no',logfile)
# are there binary files in directory inpath?
if (status == 0):
binlist = glob.glob(inpath+'*.bin')
if (len(binlist) == 0):
message = 'SALTBIN2FIT: ERROR -- no binary files (*.bin) found in '+inpath
status = saltprint.err(logfile,message)
# determine date of the observations
if (status == 0):
filemax = 4
binpath = binlist[0].split('/')
binfile = binpath[len(binpath)-1]
if (len(binfile) < 19):
date = binfile[-16:-8]
instrument = binfile[-17]
else:
date = binfile[-17:-9]
instrument = binfile[-18]
filemax = 5
# check all files are consistent with one date and have understandable names
if (status == 0):
for file in binlist:
binpath = file.split('/')
file = binpath[len(binpath)-1]
if (len(file) == 17 and file[-16:-8] != date):
status = 10
elif (len(file) == 18 and file[-17:-9] != date):
status = 10
if (status == 10):
message = 'ERROR: SALTBIN2FIT -- Either binary files from multiple dates exist, '
message += 'or binary files exist with non-standard names.'
status = saltprint.err(logfile,message)
if (file[0:1] != instrument):
message = 'ERROR: SALTBIN2FIT -- there may be binary files for more than one instrument '
message += 'because file names do not all start with the same character - '+file
status = saltprint.err(logfile,message)
# create list of header definition files
if (status == 0):
headlist = glob.glob(inpath+'*.head')
headlist.sort()
if (len(headlist) == 0):
message = 'SALTBIN2FIT: ERROR -- no header definition files (*.head) found in '+inpath
status = saltprint.err(logfile,message)
# create list of bin files
if (status == 0):
binlist = glob.glob(inpath+'*.bin')
binlist.sort()
#set the maximum head value that can be used
maxnexthead=findimagenumber(binlist[-1])+10
if (len(binlist) == 0):
message = 'SALTBIN2FIT: ERROR -- no bin files (*.bin) found in '+inpath
status = saltprint.err(logfile,message)
# run vid2fits to convert the data
print maxnexthead
if (status == 0):
#set yo tge counting for the image headers
i=0
inhead=headlist[i]
i+=1
#if only one image header exists
nexthead=maxnexthead
if i<len(headlist):
#if more than one header list
nexthead=findimagenumber(headlist[i])
#loop through the binned images to convert each one
for binimg in binlist:
#name the output file
fitsimg=string.replace(binimg,'.bin','.fits')
#find the right inhead for each frame
if findimagenumber(binimg) >= nexthead:
inhead=headlist[i]
i += 1
if i < len(headlist):
nexthead=findimagenumber(headlist[i])
else:
nexthead=maxnexthead
#convert the images
vid2fits.vid2fits(inhead,binimg,fitsimg,fitsconfig)
try:
message = 'SALTBIN2FIT: Created '+fitsimg+' from '+binimg
message += ' using header file '+inhead
saltprint.log(logfile,message,verbose)
except:
message = 'SALTBIN2FIT ERROR: Unable to create '+fitsimg+' from '+binimg
message += ' using header file '+inhead
saltprint.log(logfile,message,verbose)
# end time
if (status == 0):
saltprint.log(logfile,' ',verbose)
saltprint.time('SALTBIN2FIT completed at',logfile,verbose)
else:
saltprint.time('SALTBIN2FIT aborted at ',logfile,verbose)
