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 saltweather(weathertime, timespan, elshost, elsname, elsuser, elspass, sdbhost, sdbname, sdbuser, password):
print weathertime
# open the database
els = saltmysql.connectdb(elshost, elsname, elsuser, elspass)
sdb = saltmysql.connectdb(sdbhost, sdbname, sdbuser, password)
# determine the obsdate
obsdate = weathertime - datetime.timedelta(seconds=43200)
obsdate = "%i%s%s" % (obsdate.year, string.zfill(obsdate.month, 2), string.zfill(obsdate.day, 2))
nid = saltmysql.getnightinfoid(sdb, obsdate)
print nid
# get the most recent weather data
airpressure, dewout, extrelhum, temp2m, temp30m, windspeed, winddir, rain = getweatherdata(
els, weathertime, timespan
)
dewin, relhum = getinsidedata(els, weathertime, timespan)
tempin = getacdata(els, weathertime, timespan)
# upload that to the sdb
upcmd = "Weather_Time='%s', NightInfo_Id=%i" % (weathertime, nid)
if tempin is not None:
upcmd += ",TemperatureInside=%4.2f" % tempin
if temp2m is not None:
upcmd += ",Temperature2m=%4.2f" % temp2m
if temp30m is not None:
upcmd += ",Temperature30m=%4.2f" % temp30m
if windspeed is not None:
upcmd += ",WindSpeed=%5.2f" % windspeed
if winddir is not None:
upcmd += ",WindDirection=%5.2f" % winddir
if dewin is not None:
upcmd += ",DewPointInside=%3.2f" % dewin
if dewout is not None:
upcmd += ",DewPointOutside=%3.2f" % dewout
if airpressure is not None:
upcmd += ",AirPressure=%4.2f" % airpressure
if relhum is not None:
upcmd += ",RelativeHumidty=%4.2f" % relhum
if extrelhum is not None:
upcmd += ",ExternalRelativeHumidity=%4.2f" % extrelhum
if rain is not None:
upcmd += ",Rain=%i" % rain
saltmysql.insert(sdb, upcmd, "Weather")
print upcmd
return
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 runfast(filename, propcode, obsdate, server, readmefile, sdbhost, sdbname, sdbuser, password):
"""Handle fast data delivery for the proposal. For a given filename
"""
if propcode is None or propcode=='None': return
#first check in the sdb if fast data delivery is needed
sdb=saltmysql.connectdb(sdbhost,sdbname, sdbuser, password)
select_term='Distinct Surname, email, username, ProposalCode_Id'
from_term='''
Block join Pointing using (Block_Id)
join PipelineConfig using (Pointing_Id)
join Proposal using (Proposal_Id)
join ProposalCode using (ProposalCode_Id)
join PipelineDataAccessMethod using (PipelineDataAccessMethod_Id)
join ProposalContact using (Proposal_Id)
join Investigator on (Investigator_Id=Contact_Id)
join PiptUser using (PiptUser_Id)
'''
where_term="Proposal_Code like '%s' and current=1 and DataAccessMethod='Fast'" \
% (propcode)
print 'Select %s from %s where %s' % (select_term, from_term, where_term)
try:
record=saltmysql.select(sdb, select_term, from_term, where_term)
except Exception, e:
print e
return None
def runfast(filename, propcode, obsdate, server, readmefile, sdbhost, sdbname,
sdbuser, password):
"""Handle fast data delivery for the proposal. For a given filename
"""
if propcode is None or propcode == 'None': return
#first check in the sdb if fast data delivery is needed
sdb = saltmysql.connectdb(sdbhost, sdbname, sdbuser, password)
select_term = 'Distinct Surname, email, username, ProposalCode_Id'
from_term = '''
Block join Pointing using (Block_Id)
join PipelineConfig using (Pointing_Id)
join ProposalCode using (ProposalCode_Id)
join PipelineDataAccessMethod using (PipelineDataAccessMethod_Id)
join ProposalContact using (ProposalCode_Id)
join Investigator on (Investigator_Id=Contact_Id)
join PiptUser using (PiptUser_Id)
'''
where_term="Proposal_Code like '%s' and DataAccessMethod='Fast'" \
% (propcode)
#print 'Select %s from %s where %s' % (select_term, from_term, where_term)
try:
record = saltmysql.select(sdb, select_term, from_term, where_term)
except Exception, e:
print e
return None
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 sdbloadobslog(logstr, obsdate, sdbhost, sdbname, sdbuser, password):
"""Load logstr into the SDB"""
print logstr
#connect to the db
sdb = saltmysql.connectdb(sdbhost, sdbname, sdbuser, password)
#get the nightinfoid
#date='YYYY-MM-DD' <- note speechmarks
#data= your table
#Select NightInfo_Id from NightInfo where Date=$date;
#(get nightinfo_Id)
#Insert into ObsLogTable values ($nightinfo_Id, $data);
logic = "Date='%4s-%2s-%2s'" % (obsdate[0:4], obsdate[4:6], obsdate[6:8])
results = saltmysql.select(sdb, 'NightInfo_Id', 'NightInfo', logic)
night_id = results[0][0]
#check to see if it exists
logic = 'NightInfo_Id=%i' % night_id
results = saltmysql.select(sdb, 'NightInfo_Id', 'ObsLogTable', logic)
if results:
update_cmd = "ObsLogTable='%s'" % (logstr)
saltmysql.update(sdb, update_cmd, 'ObsLogTable', logic)
else:
insert_cmd = "NightInfo_Id=%i, ObsLogTable='%s'" % (night_id, logstr)
saltmysql.insert(sdb, insert_cmd, 'ObsLogTable')
print obsdate, night_id
def sdbloadobslog(logstr, obsdate, sdbhost, sdbname, sdbuser, password):
"""Load logstr into the SDB"""
print logstr
#connect to the db
sdb=saltmysql.connectdb(sdbhost, sdbname, sdbuser, password)
#get the nightinfoid
#date='YYYY-MM-DD' <- note speechmarks
#data= your table
#Select NightInfo_Id from NightInfo where Date=$date;
#(get nightinfo_Id)
#Insert into ObsLogTable values ($nightinfo_Id, $data);
logic="Date='%4s-%2s-%2s'" % (obsdate[0:4], obsdate[4:6], obsdate[6:8])
results=saltmysql.select(sdb, 'NightInfo_Id', 'NightInfo', logic)
night_id=results[0][0]
#check to see if it exists
logic='NightInfo_Id=%i' % night_id
results=saltmysql.select(sdb, 'NightInfo_Id', 'ObsLogTable', logic)
if results:
update_cmd="ObsLogTable='%s'" % (logstr)
saltmysql.update(sdb, update_cmd, 'ObsLogTable', logic)
else:
insert_cmd="NightInfo_Id=%i, ObsLogTable='%s'" % (night_id, logstr)
saltmysql.insert(sdb, insert_cmd, 'ObsLogTable')
print obsdate, night_id
def cleandata(self,
filename,
iminfo=None,
prodir='.',
interp='linear',
cleanup=True,
clobber=False,
logfile='saltclean.log',
reduce_image=True,
display_image=False,
verbose=True):
"""Start the process to reduce the data and produce a single mosaicked image"""
#print filename
status = 0
#create the input file name
infile = os.path.basename(filename)
rawpath = os.path.dirname(filename)
outpath = './'
outfile = outpath + 'mbxp' + infile
#print infile, rawpath, outpath
#If it is a bin file, pre-process the data
if filename.count('.bin'):
print "I can't handle this yet"
#ignore bcam files
if infile.startswith('B'):
return iminfo
#check to see if it exists and return if clobber is no
if os.path.isfile(outfile) and not clobber: return iminfo
#handle HRS data
print filename
if infile.startswith('H') or infile.startswith('R'):
outfile = os.path.basename(filename) + 's'
print filename, outfile
if not os.path.isfile(outfile): os.symlink(filename, outfile)
#display the image
if display_image:
print "Displaying %s" % outfile
try:
display(outfile)
except Exception, e:
print e
try:
log = None #open(logfile, 'a')
sdb = saltmysql.connectdb(self.sdbhost, self.sdbname,
self.sdbuser, self.password)
sdbloadfits(outfile, sdb, log, False)
print 'SDBLOADFITS: SUCCESS'
except Exception, e:
print 'SDBLOADFITSERROR:', e
def saltnightstats(obsdate, outfile, 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
obsdate=str(obsdate)
#create the night stats for the
makenightstats(els, sdb, outfile, obsdate, clobber=clobber)
def saltdasload(obsdate, sdbhost, sdbname, sdbuser, password, dashost, dasname, dasuser, daspassword, logfile, verbose):
"""Upload data from the science database to the SALTDAS database
"""
with logging(logfile,debug) as log:
#open the science database
sdb=saltmysql.connectdb(sdbhost,sdbname,sdbuser,password)
#open saltdas
das=saltmysql.connectdb(dashost,dasname,dasuser,daspassword)
select='FileData_Id, FileName, Proposal_Code'
table='FileData join ProposalCode using (ProposalCode_Id)'
logic="FileName like '%"+str(obsdate)+"%'"
record=saltmysql.select(sdb, select, table, logic)
for r in record[:]:
if not isproprietary(r[0], sdb):
print r
loaddata(r[0], r[1], sdb, das)
return
def cleandata(self, filename, iminfo=None, prodir='.', interp='linear', cleanup=True,
clobber=False,
logfile='saltclean.log', reduce_image=True,
display_image=False, verbose=True):
"""Start the process to reduce the data and produce a single mosaicked image"""
#print filename
status=0
#create the input file name
infile=os.path.basename(filename)
rawpath=os.path.dirname(filename)
outpath='./'
outfile=outpath+'mbxp'+infile
#print infile, rawpath, outpath
#If it is a bin file, pre-process the data
if filename.count('.bin'):
print "I can't handle this yet"
#ignore bcam files
if infile.startswith('B'):
return iminfo
#check to see if it exists and return if clobber is no
if os.path.isfile(outfile) and not clobber: return iminfo
#handle HRS data
print filename
if infile.startswith('H') or infile.startswith('R'):
outfile = os.path.basename(filename) +'s'
print filename, outfile
if not os.path.isfile(outfile): os.symlink(filename, outfile)
#display the image
if display_image:
print "Displaying %s" % outfile
try:
display(outfile)
except Exception, e:
print e
try:
log=None #open(logfile, 'a')
sdb=saltmysql.connectdb(self.sdbhost, self.sdbname, self.sdbuser, self.password)
sdbloadfits(outfile, sdb, log, False)
print 'SDBLOADFITS: SUCCESS'
except Exception, e:
print 'SDBLOADFITSERROR:', e
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 pipelinestatus(obsdate, status, message=None, rawsize=None, reducedsize=None,
runtime=None, emailsent=None, sdbhost='sdb.saao', sdbname='sdb', sdbuser='', password='',
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, password)
#get the nightinfo_id
night_id=saltmysql.getnightinfoid(sdb, obsdate)
#get the status_id for the given status
status_id=getstatusid(sdb, status)
#create the insert command
obsdate=str(obsdate)
inst_cmd="NightInfo_Id=%s, PipelineStatus_Id=%i" % (night_id, status_id)
if status_id>10:
inst_cmd+=',ErrorMessage="%s"' % message
if rawsize is not None:
inst_cmd+=",RawSize=%f" % rawsize
if reducedsize is not None:
inst_cmd+=",ReducedSize=%f" % rawsize
if runtime is not None:
inst_cmd+=",PipelineRunTime=%i" % runtime
if emailsent is not None:
inst_cmd+=",EmailSent=%i" % emailsent
print inst_cmd
#insert or update the pipeline
if checktable(sdb, night_id):
saltmysql.update(sdb, inst_cmd, 'PipelineStatistics', 'NightInfo_Id=%i' % night_id)
msg="Updating information for Night_Id=%i\n" % night_id
else:
saltmysql.insert(sdb, inst_cmd, 'PipelineStatistics')
msg="Inserting information for Night_Id=%i\n" % night_id
#log the call
log.message(msg+inst_cmd, with_stdout=verbose)
def updatenightinfo(obsdate, sdbhost='sdb.saao', sdbname='sdb', \
sdbuser='', password='', logfile='saltlog.log', verbose=True):
"""Update the nightinfo table with current information about the
night
"""
with logging(logfile,debug) as log:
#connect the database
sdb=saltmysql.connectdb(sdbhost, sdbname, sdbuser, password)
#get the nightinfo_id
try:
night_id=saltmysql.getnightinfoid(sdb, obsdate)
except SaltError:
night_id=None
#get the information for the night
time_list=get_nightdetails(obsdate)
#create the insert command
obsdate=str(obsdate)
inst_cmd="Date='%s-%s-%s'," % (obsdate[0:4], obsdate[4:6], obsdate[6:8])
inst_cmd+="SunSet='%s', SunRise='%s', MoonSet='%s', MoonRise='%s', EveningTwilightEnd='%s', MorningTwilightStart='%s'" % \
(time_list[0], time_list[1], time_list[2], time_list[3], time_list[4], time_list[5])
inst_cmd+=",MoonPhase_Percent=%i" % (round(float(time_list[6])))
if night_id:
saltmysql.update(sdb, inst_cmd, 'NightInfo', 'NightInfo_Id=%i' % night_id)
msg="Updating information for Night_Id=%i\n" % night_id
else:
saltmysql.insert(sdb, inst_cmd, 'NightInfo')
msg="Inserting information for Night_Id=%i\n" % night_id
#log the call
log.message(msg+inst_cmd, with_stdout=verbose)
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 saltelsdata(propcode, obsdate, elshost, elsname, elsuser, elspass,
sdbhost,sdbname,sdbuser, password, clobber,logfile,verbose):
# set up
proposers = []
propids = []
pids = []
with logging(logfile,debug) as log:
# are the arguments defined
if propcode.strip().upper()=='ALL':
pids=saltmysql.getproposalcodes(str(obsdate), sdbhost,sdbname,sdbuser, password)
else:
pids = saltio.argunpack('propcode',propcode)
#open the database
els=saltmysql.connectelsview(elshost, elsname, elsuser, elspass)
sdb=saltmysql.connectdb(sdbhost,sdbname,sdbuser, password)
#create the values for the entire night
#loop through the proposals
for pid in pids:
outfile='%s_%s_elsdata.fits' % (pid, obsdate)
if clobber and os.path.isfile(outfile):
saltio.delete(outfile)
mintime, maxtime=determinetime(sdb, pid, obsdate)
message='Extracting ELS data for %s from %s to %s' % (pid, mintime, maxtime)
log.message(message, with_stdout=verbose)
getelsdata(els, sdb, outfile, mintime, maxtime)
def saltcharge(
obsdate,
outfile,
sdbhost="sdb.saao",
sdbname="sdb",
sdbuser="",
password="",
clobber=False,
logfile="saltlog.log",
verbose=True,
):
"""Calculate the charged time for proposals observed during a night
"""
with logging(logfile, debug) as log:
# check the outfiles
if not saltio.checkfornone(outfile):
outfile = None
# check that the output file can be deleted
if outfile:
saltio.overwrite(outfile, clobber)
# connect the database
sdb = saltmysql.connectdb(sdbhost, sdbname, sdbuser, password)
# get all the proposals observed during the night
select_state = "distinct Proposal_Code"
table_state = "FileData Join ProposalCode using (ProposalCode_Id)"
logic_state = "FileName like '%" + obsdate + "%'"
records = saltmysql.select(sdb, select_state, table_state, logic_state)
pids = []
pid_time = {}
for r in records:
pids.append(r[0])
pid_time[r[0]] = 0
if len(pids) == 0:
message = "There are no proposal to charge time for %s" % obsdate
log.message(message)
return
# get the nightinfo_id
night_id = saltmysql.getnightinfoid(sdb, obsdate)
print night_id
# get a list of all the images taken during the night
select_state = "FileName, Proposal_Code, Target_Name, ExposureTime, UTSTART, INSTRUME, OBSMODE, DETMODE, CCDTYPE, NExposures"
table_state = "FileData Join ProposalCode using (ProposalCode_Id) join FitsHeaderImage using (FileData_Id)"
logic_state = "FileName like '%" + obsdate + "%'"
img_list = saltmysql.select(sdb, select_state, table_state, logic_state)
# get all the blocks visited
select_state = "Block_Id, Accepted, Proposal_Code"
table_state = "Block join BlockVisit using (Block_Id) join Proposal using (Proposal_Id) join ProposalCode using (ProposalCode_Id)"
logic_state = "NightInfo_Id=%i" % night_id
block_list = saltmysql.select(sdb, select_state, table_state, logic_state)
print block_list
# get the start and end of twilight
nightstart = saltmysql.select(sdb, "EveningTwilightEnd", "NightInfo", "NightInfo_Id=%i" % night_id)[0][0]
nightend = saltmysql.select(sdb, "MorningTwilightStart", "NightInfo", "NightInfo_Id=%i" % night_id)[0][0]
print nightstart, nightend, (nightend - nightstart).seconds
print
# download the SOMMI log from the night
try:
sommi_log = saltmysql.select(sdb, "SONightLog", "NightLogs", "NightInfo_Id=%i" % night_id)[0][0]
except Exception, e:
msg = "Unable to read in SOMMI log for %s" % obsdate
raise SaltError(msg)
# add to account for error in SOMMI log
if int(obsdate) < 20111027:
sommi_log = sommi_log.replace("Object name", "\nObject name")
# parse the sommi log
point_list = parseforpointings(sommi_log)
# now find all blocks observed during a night
for point in point_list:
# proposal for that block
pid = point[0].strip()
# start time for that block
starttime = point[1]
# find the end time for that block
endtime = findnexttime(point[1], point_list, nightend)
# find the start time of the first object to be observed
# for this block
startimage = findfirstimage(pid, starttime, img_list)
lastimage = findlastimage(pid, endtime, img_list)
# check to see if the end time for the last file observed for
# this block
if startimage is not None:
if startimage > endtime:
startimage = None
# determine the acquisition time for the block
if startimage is not None:
acqdelta = (startimage - starttime).seconds
else:
acqdelta = -1
# find the shutter open time
shuttertime = calculate_shutteropen(img_list, starttime, endtime)
# if the shutter and time of the last image is substantially different from the
# end of the block, then take the last image as the end of the block
# *TODO* Change to use expected block time
st = starttime + datetime.timedelta(0, shuttertime + acqdelta)
if (endtime - st).seconds > 900:
if lastimage is None:
endtime = st
elif (lastimage - st).seconds > 3600:
endtime = st
else:
endtime = lastimage
# account for the time for that block
tblock = (endtime - starttime).seconds
if acqdelta > -1:
# find the associated block
block_id, blockvisit_id, accepted = getblockid(sdb, night_id, pid, img_list, starttime, endtime)
if accepted and pid.count("-3-"):
# charged time for that block
try:
pid_time[pid] += tblock
except KeyError:
pid_time[pid] = tblock
print block_id, blockvisit_id, pid, starttime, tblock, acqdelta, shuttertime, shuttertime / tblock, block_id, accepted
# update the charge time
slewdelta = 0
scidelta = tblock - acqdelta
update_cmd = "TotalSlewTime=%i, TotalAcquisitionTime=%i, TotalScienceTime=%i" % (
slewdelta,
acqdelta,
scidelta,
)
table_cmd = "BlockVisit"
logic_cmd = "BlockVisit_Id=%i" % blockvisit_id
saltmysql.update(sdb, update_cmd, table_cmd, logic_cmd)
return
# update the charged time information
# TODO: Check to see if the block was approved
ptime_tot = 0
stime_tot = 0
for k in pid_time:
ptime = pid_time[k]
if ptime > 0:
obsratio = stime / ptime
else:
obsratio = 0
print "%25s %5i %5i %3.2f" % (k, ptime, stime, obsratio)
if k.count("-3-"):
ptime_tot += ptime
stime_tot += stime
# print out the total night statistics
tdelta = nightend - nightstart
print tdelta.seconds, ptime_tot, stime_tot
#if detmode=='FT' or detmode=='FRAME TRANSFER': return iminfo
#reduce the data
if reduce_image:
try:
quickclean(filename, interp, cleanup, clobber, logfile, verbose)
except Exception, e:
print e
return iminfo
#load the data into the SDB
if self.sdbhost and self.update:
try:
log=None #open(logfile, 'a')
sdb=saltmysql.connectdb(self.sdbhost, self.sdbname, self.sdbuser, self.password)
sdbloadfits(filename, sdb, log, False)
print 'SDBLOADFITS: SUCCESS'
except Exception, e:
print 'SDBLOADFITSERROR:', e
#display the image
if display_image:
print "Displaying %s" % outfile
try:
display(outfile)
except Exception, e:
print e
#if the images are imaging data, run sextractor on them
name=iminfo[0]
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)
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)
# log into the mysql data base and download a list of proposal codes
sdb=saltmysql.connectdb(sdbhost, sdbname, sdbuser, password)
select='distinct Proposal_Code'
table='FileData join ProposalCode using (ProposalCode_Id)'
logic="FileName like '%" + obsdate + "%'"
records=saltmysql.select(sdb, select, table, logic)
if len(records)<1:
msg="No observations available for %s" % obsdate
log.warning(msg)
return
else:
for p in records:
propids.append(p[0])
#clean the proposal list
print pids, propids
def saltslewstats(startdate, enddate, 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)
#loop through each night and determine the statistics for the slew times
#for each night
obsdate=int(startdate)
slew_list=[]
while obsdate < int(enddate):
night_id=saltmysql.getnightinfoid(sdb, obsdate)
start,end=saltmysql.select(sdb,'EveningTwilightEnd,MorningTwilightStart','NightInfo', 'NightInfo_Id=%i' % night_id)[0]
tslew, nslew=slewtime(els, start, end)
if nslew>0:
print obsdate, night_id, start, end, nslew, tslew/nslew
slew_list.append([start, nslew, tslew])
obsdate=int(getnextdate(obsdate))
slew_arr=np.array(slew_list)
days=np.zeros(len(slew_arr))
for i in range(len(slew_arr)):
days[i]=(slew_arr[i,0]-slew_arr[0,0]).days
coef=np.polyfit(days, slew_arr[:,2]/slew_arr[:,1], 2)
ave_date=[]
ave_values=[]
ave_nslews=[]
nstep=10
for i in np.arange(15,len(slew_arr), 2*nstep):
ave_date.append(slew_arr[i,0])
i1=i-nstep
i2=min(i+nstep, len(slew_arr))
#ave_values.append(np.median(slew_arr[i1:i2,2]/slew_arr[i1:i2,1]))
ave_nslews.append(np.median(slew_arr[i1:i2,1]))
ave_values.append(np.median(slew_arr[i1:i2,2]))
print ave_date[-1], ave_values[-1], ave_nslews[-1]
ave_values=np.array(ave_values)
ave_nslews=np.array(ave_nslews)
mean_slew=ave_nslews.mean()
mean_slew=11
for i in range(len(ave_date)):
#value is an attempt to correct for the average number of slews
value=(ave_values[i]+30*(mean_slew-ave_nslews[i]))/mean_slew
print ave_date[i], '%i %i %i' % (ave_values[i]/ave_nslews[i], ave_nslews[i], value)
plt.figure()
plt.plot(slew_arr[:,0], slew_arr[:,2]/slew_arr[:,1], ls='', marker='o')
#plt.plot(slew_arr[:,0], slew_arr[:,1], ls='', marker='o')
#plt.plot(slew_arr[:,0], slew_arr[:,2], ls='', marker='o')
plt.plot(ave_date, ave_values/ave_nslews)
#plt.plot(days, np.polyval(coef, days))
plt.ylabel('Slew Time(s)')
plt.xlabel('Date')
plt.show()
def findcal(obsdate, sdbhost, sdbname, sdbuser, password):
"""Find all of the unique configuration settings used on a night
and insert it into the database
obsdate--Observation date in YYYYMMDD
sdbhost--host name for sdb
sdbname--name of the sdb
sdbuser--user for the sdb
password--sdb password
"""
#connect to the db
sdb=saltmysql.connectdb(sdbhost, sdbname, sdbuser, password)
#get the nightinfo id
logic="Date='%4s-%2s-%2s'" % (obsdate[0:4], obsdate[4:6], obsdate[6:8])
results=saltmysql.select(sdb, 'NightInfo_Id', 'NightInfo', logic)
night_id=results[0][0]
#select all the scam data from this obsdate
cmd_select='d.FileName, d.FileData_Id, f.CCDTYPE, d.DETMODE, CCDSUM, GAINSET, ROSPEED, FILTER'
cmd_table=''' FileData as d
left join FitsHeaderImage as f using (FileData_Id)
left join FitsHeaderSalticam using (FileData_Id)
'''
cmd_logic="d.FileName like 'S" + obsdate+"%' and f.CCDTYPE='OBJECT'"
results=saltmysql.select(sdb, cmd_select, cmd_table, cmd_logic)
#loop through all the results and return only the Set of identical results
caldict=create_caldict(results)
#insert the results into the database
for k in caldict:
#first check to see if it has already been entered
record=saltmysql.select(sdb, 'FileData_Id', 'SalticamNightlyCalibration', 'FileData_Id=%i' % k)
if len(record)<1:
#check for block_id
blockid=saltmysql.select(sdb, 'Block_Id', 'FileData', 'FileData_Id=%i' % k)[0][0]
#get the calibration types requested
if blockid:
request=saltmysql.select(sdb, 'SalticamCalibrationType_Id', 'SalitcamCalibration', 'Block_Id=%i' % blockid)
for cid in request:
cid=cid[0]
cmd_insert='NightInfo_Id=%i, FileData_Id=%i, SatlicamCalibrationType_Id=%i' % (night_id, k, cid)
#saltmysql.insert(sdb, cmd_insert, 'SalitcamNightlyCalibration')
print(k, " ".join([str(k) for k in caldict[k]]))
#list of rss calibration types
#+-----------------------+----------------------------------+
#| RssCalibrationType_Id | CalibrationType |
#+-----------------------+----------------------------------+
#| 2 | Arc |
#| 1 | Bias |
#| 14 | Imaging flat - Lamp |
#| 15 | Imaging flat - Twilight |
#| 3 | Spectroscopic flat - Lamp |
#| 4 | Spectroscopic flat - Twilight |
#| 12 | Standard - Circular polarimetric |
#| 13 | Standard - Lick |
#| 9 | Standard - Linear polarimetric |
#| 5 | Standard - Photometric |
#| 8 | Standard - RV |
#| 11 | Standard - Smooth spectrum |
#| 7 | Standard - Spectrophotometric |
#| 6 | Standard - Spectroscopic |
#| 10 | Standard - Unpolarised |
#+-----------------------+----------------------------------+
#select all the RSS data from this obsdate
rssheaderlist='f.CCDTYPE, d.DETMODE, d.OBSMODE, CCDSUM, GAINSET, ROSPEED, FILTER, GRATING, GR_STA, AR_STA, MASKID'
cmd_select='d.FileName,d.FileData_Id, %s' % rssheaderlist
# CCDTYPE, DETMODE, OBSMODE, CCDSUM, GAINSET, ROSPEED, FILTER, GRATING, GR_STA, AR_STA, MASKID'
cmd_table=''' FileData as d
left join FitsHeaderImage as f using (FileData_Id)
left join FitsHeaderRss using (FileData_Id)
join ProposalCode using (ProposalCode_Id)
'''
cmd_logic="d.FileName like 'P" + obsdate+"%' and CCDTYPE='OBJECT' and Proposal_Code not like 'CAL_SPST'"
results=saltmysql.select(sdb, cmd_select, cmd_table, cmd_logic)
#loop through all the results and return only the Set of identical results
caldict=create_caldict(results)
#insert the rss results into the database
for k in caldict:
#first check to see if it has already been entered
record=saltmysql.select(sdb, 'FileData_Id', 'RssNightlyCalibration', 'FileData_Id=%i' % k)
if len(record)<1:
#period for checking for SPST. If the uses requests this, it gets set to
# 7 days, but the default is taken within the last month for non-requests
period=30
#check for block_id
blockid=saltmysql.select(sdb, 'Block_Id', 'FileData', 'FileData_Id=%i' % k)[0][0]
#get the calibration types requested
if blockid:
request=saltmysql.select(sdb, 'RssCalibrationType_Id', 'RssCalibration', 'Block_Id=%i' % blockid)
for cid in request:
cid=cid[0]
#check to see if the request is already in the database or if a similar request has
#been taken recently
if cid==1: #bias
if not checkforbias(sdb, k):
cmd_insert='NightInfo_Id=%i, FileData_Id=%i, RssCalibrationType_Id=%i' % (night_id, k, cid)
saltmysql.insert(sdb, cmd_insert, 'RssNightlyCalibration')
elif cid in [3,4]: #flats
if not checkforflats(sdb, k, cid, rssheaderlist, instr='rss', keylist=caldict[k], period=90):
cmd_insert='NightInfo_Id=%i, FileData_Id=%i, RssCalibrationType_Id=%i' % (night_id, k, cid)
saltmysql.insert(sdb, cmd_insert, 'RssNightlyCalibration')
elif cid==7: #specstand
period=7
#print period, k, caldict[k]
if not checkforspst(sdb, k, caldict[k], rssheaderlist, period=period):
cmd_insert='NightInfo_Id=%i, FileData_Id=%i, RssCalibrationType_Id=7' % (night_id, k)
saltmysql.insert(sdb, cmd_insert, 'RssNightlyCalibration')
else:
cmd_insert='NightInfo_Id=%i, FileData_Id=%i, RssCalibrationType_Id=%i' % (night_id, k, cid)
saltmysql.insert(sdb, cmd_insert, 'RssNightlyCalibration')
print(k, cid," ".join([str(w) for w in caldict[k]]))
return
def runfast(filename, propcode, obsdate, server, readmefile, sdbhost, sdbname, sdbuser, password):
"""Handle fast data delivery for the proposal. For a given filename
"""
if propcode is None or propcode=='None': return
#first check in the sdb if fast data delivery is needed
sdb=saltmysql.connectdb(sdbhost,sdbname, sdbuser, password)
select_term='Distinct Surname, email, username, ProposalCode_Id'
from_term='''
Block join Pointing using (Block_Id)
join PipelineConfig using (Pointing_Id)
join Proposal using (Proposal_Id)
join ProposalCode using (ProposalCode_Id)
join PipelineDataAccessMethod using (PipelineDataAccessMethod_Id)
join ProposalContact using (Proposal_Id)
join Investigator on (Investigator_Id=Contact_Id)
join PiptUser using (PiptUser_Id)
'''
where_term="Proposal_Code like '%s' and current=1 and DataAccessMethod='Fast'" \
% (propcode)
#print 'Select %s from %s where %s' % (select_term, from_term, where_term)
try:
record=saltmysql.select(sdb, select_term, from_term, where_term)
except Exception as e:
print(e)
return None
#print "Checking for fast data"
#print record
if record:
surname, email, username, propid= record[0]
#print surname, email, username, propid
else:
return
#second if so, then copy the data to the contact PI directory
#on saltpipe under the fast directory.
#rawfilename=getrawfilename(filename)
y=os.system('scp %s sa@saltpipe:/salt/ftparea/%s/fast%s/' % (filename, username, obsdate))
if y==256:
y=os.system('ssh sa@saltpipe mkdir /salt/ftparea/%s/fast%s' % (username, obsdate))
y=os.system('scp %s sa@saltpipe:/salt/ftparea/%s/fast%s/' % (filename, username, obsdate))
if y!=0:
print("Problem with copying file %s to /salt/ftparea/%s/fast%s/" % (filename, username, obsdate))
#copy the reduced data
y=os.system('scp mbxp%s sa@saltpipe:/salt/ftparea/%s/fast%s/' % (os.path.basename(filename), username, obsdate))
#check the type of data it is and copy over an ancillery data as well
#if it is the first object file, check to see if an email has been
#sent, and if not, send email
#try to copy the spectroscopic data
print(filename, filename.startswith('P'))
if os.path.basename(filename).startswith('P'):
sfilename='smbxp%s.txt' % (os.path.basename(filename).split('.fits')[0])
print(sfilename)
try:
y=os.system('scp %s sa@saltpipe:/salt/ftparea/%s/fast%s/' % (sfilename, username, obsdate))
except Exception as e:
print(e)
if os.path.basename(filename).startswith('S'):
try:
sfilename='mbxp%s.cat' % (os.path.basename(filename).split('.fits')[0])
print(sfilename)
y=os.system('scp %s sa@saltpipe:/salt/ftparea/%s/fast%s/' % (sfilename, username, obsdate))
except Exception as e:
print(e)
#check to see if an email has been sent
select_term='PipelineStatus'
from_term='''
PipelineProposalStatistics
join PipelineStatus using (PipelineStatus_Id)
join NightInfo using (NightInfo_Id)
join ProposalCode using (ProposalCode_Id)
'''
where_term="Proposal_Code like '%s' and Date='%s-%s-%s'" % (propcode, obsdate[0:4], obsdate[4:6], obsdate[6:8])
print(select_term, from_term, where_term)
try:
record=saltmysql.select(sdb, select_term, from_term, where_term)[0][0]
except:
record=None
print(record)
if record=='FastEmail':
return
else:
#insert information into the database
nightinfoid=saltmysql.getnightinfoid(sdb, obsdate)
insert_term="NightInfo_Id=%i, ProposalCode_Id=%i, PipelineStatus_Id=8" % (nightinfoid, propid)
table_term="PipelineProposalStatistics"
saltmysql.insert(sdb, insert_term, "PipelineProposalStatistics")
#send email
sender='*****@*****.**'
recipient=email
bcc='*****@*****.**'
subject='SALT data available for %s' % propcode
message=open(readmefile).read()
message=message.replace('OBSDATE', obsdate)
sendemail(server,'sa',password,sender,recipient,bcc, subject,message)
sdb.close()
return
def saltcalibrations(
propcode,
outfile=None,
sdbhost="sdb.saao",
sdbname="sdb",
sdbuser="",
password="",
clobber=False,
logfile="saltlog.log",
verbose=True,
):
"""Seach the salt database for FITS files
"""
with logging(logfile, debug) as log:
# check the outfiles
if not saltio.checkfornone(outfile):
outfile = None
# check that the output file can be deleted
if outfile:
saltio.overwrite(outfile, clobber)
fout = open(oufile, "w")
# connect to the database
sdb = saltmysql.connectdb(sdbhost, sdbname, sdbuser, password)
# determine the associated
username = saltmysql.getpiptusername(sdb, propcode)
userdir = "/salt/ftparea/%s/spst" % username
if not os.path.exists(userdir):
saltio.createdir(userdir)
log.message("Will copy data to %s" % userdir)
# Find all the data assocated with a proposal
cmd_select = "d.FileName,d.FileData_Id, CCDTYPE, d.DETMODE, d.OBSMODE, CCDSUM, GAINSET, ROSPEED, FILTER, GRATING, GRTILT, CAMANG, MASKID"
cmd_table = """ FileData as d
left join FitsHeaderImage using (FileData_Id)
left join FitsHeaderRss using (FileData_Id)
left join ProposalCode using (ProposalCode_Id)
"""
cmd_logic = 'Proposal_Code="%s" and CCDTYPE="OBJECT" and d.OBSMODE="SPECTROSCOPY"' % (propcode)
record = saltmysql.select(sdb, cmd_select, cmd_table, cmd_logic)
# loop through all the results and return only the Set of identical results
caldict = create_caldict(record)
# prepare for writing out the results
outstr = ""
if outfile:
fout.write(outstr + "\n")
else:
print outstr
# now find all the cal_spst that have the same settings
cmd_select = "d.FileName,d.FileData_Id, CCDTYPE, d.DETMODE, d.OBSMODE, CCDSUM, GAINSET, ROSPEED, FILTER, GRATING, GRTILT, CAMANG, MASKID"
cmd_table = """ FileData as d
left join FitsHeaderImage using (FileData_Id)
left join FitsHeaderRss using (FileData_Id)
left join ProposalCode using (ProposalCode_Id)
"""
for r in caldict:
cmd_logic = "CCDSUM='%s' and GRATING='%s' and GRTILT='%s' and CAMANG='%s' and Proposal_Code='CAL_SPST'" % (
caldict[r][3],
caldict[r][7],
caldict[r][8],
caldict[r][9],
)
# cmd_logic="CCDSUM='%s' and GRATING='%s' and AR_STA='%s' " % (caldict[r][3], caldict[r][7], caldict[r][9])
log.message(cmd_logic, with_header=False)
record = saltmysql.select(sdb, cmd_select, cmd_table, cmd_logic)
# print record
# write out hte results
for r in record:
outstr = " ".join(["%s" % x for x in r])
if outfile:
fout.write(outstr + "\n")
else:
log.message(outstr, with_header=False)
# copy to the user directory
cfile = makefilename(r[0], state="product")
shutil.copy(cfile, userdir)
cfile = makefilename(r[0], state="raw")
shutil.copy(cfile, userdir)
# close outfile
if outfile:
fout.close()
def hrscalibrations(
obsdate,
sdbhost="sdb.saao",
sdbname="sdb",
sdbuser="",
password="",
clobber=False,
logfile="saltlog.log",
verbose=True,
):
"""Seach the salt database for FITS files
"""
with logging(logfile, debug) as log:
# make obsdate a string if needed
obsdate = str(obsdate)
log.message("Sorting HRS calibration data")
# connect to the database
sdb = saltmysql.connectdb(sdbhost, sdbname, sdbuser, password)
# first select propcodes for all HRS data from that day and check for any CAL data
table = "FileData join ProposalCode using (ProposalCode_Id)"
logic = "FileName like 'H" + obsdate + "%' or FileName like 'R" + obsdate + "%'"
records = saltmysql.select(sdb, "FileName, Proposal_Code", table, logic)
# exit if no data was taken for HRS
if len(records) == 0:
return
# Loop through each of the files and create the directories if needed
image_dict = {}
for filename, propid in records:
if propid.count("CAL"):
# check for directory and create structure
caldir = "/salt/HRS_Cals/%s/" % propid
if not os.path.isdir(caldir):
os.mkdir(caldir)
yeardir = "%s%s/" % (caldir, obsdate[0:4])
if not os.path.isdir(yeardir):
os.mkdir(yeardir)
daydir = "%s%s/%s/" % (caldir, obsdate[0:4], obsdate[4:8])
if not os.path.isdir(daydir):
os.mkdir(daydir)
rawdir = "%s%s/%s/raw/" % (caldir, obsdate[0:4], obsdate[4:8])
if not os.path.isdir(rawdir):
os.mkdir(rawdir)
prodir = "%s%s/%s/product/" % (caldir, obsdate[0:4], obsdate[4:8])
if not os.path.isdir(prodir):
os.mkdir(prodir)
# create the symlinks to the files
infile = "/salt/data/%s/%s/hrs/raw/%s" % (obsdate[0:4], obsdate[4:8], filename)
link = "%s%s" % (rawdir, filename)
saltio.symlink(infile, link, clobber)
infile = "/salt/data/%s/%s/hrs/product/mbgph%s" % (obsdate[0:4], obsdate[4:8], filename)
link = "%smbgph%s" % (prodir, filename)
saltio.symlink(infile, link, clobber)
log.message(
"Copied %s to the HRS_CAL/%s directory" % (filename, propid), with_header=False, with_stdout=verbose
)
# create log of files
image_info = get_image_info(sdb, filename)
try:
image_dict[propid].append([image_info])
except:
image_dict[propid] = [[image_info]]
# create log of each file--currently not enough information
# in database to do this
nightlog = "/salt/logs/sanightlogs/%s.log" % obsdate
for k in image_dict:
nightlink = "/salt/HRS_Cals/%s/%s/%s/%s.log" % (k, obsdate[0:4], obsdate[4:8], obsdate)
saltio.symlink(nightlog, nightlink, clobber)
fout = open("/salt/HRS_Cals/%s/%s/%s/%s.log" % (k, obsdate[0:4], obsdate[4:8], k), "w")
for imlist in image_dict[k]:
for info in imlist:
for f in info:
fout.write("%20s " % str(f))
fout.write("\n")
fout.close()
def cleandata(self, filename, iminfo=None, prodir='.', interp='linear', cleanup=True,
clobber=False,
logfile='saltclean.log', reduce_image=True,
display_image=False, verbose=True):
"""Start the process to reduce the data and produce a single mosaicked image"""
#print filename
status=0
#create the input file name
infile=os.path.basename(filename)
rawpath=os.path.dirname(filename)
outpath='./'
outfile=outpath+'mbxp'+infile
#print infile, rawpath, outpath
#If it is a bin file, pre-process the data
if filename.count('.bin'):
print("I can't handle this yet")
#ignore bcam files
if infile.startswith('B'):
return iminfo
#check to see if it exists and return if clobber is no
if os.path.isfile(outfile) and not clobber: return iminfo
#handle HRS data
print(filename)
if infile.startswith('H') or infile.startswith('R'):
shutil.copy(filename, outfile)
return iminfo
if filename.count('.txt'): return iminfo
#remove frame transfer data
#detmode=iminfo[headerList.index('DETMODE')].strip().upper()
#if detmode=='FT' or detmode=='FRAME TRANSFER': return iminfo
#reduce the data
if reduce_image:
try:
quickclean(filename, interp, cleanup, clobber, logfile, verbose)
except Exception as e:
print(e)
return iminfo
#load the data into the SDB
if self.sdbhost and self.update:
try:
log=None #open(logfile, 'a')
sdb=saltmysql.connectdb(self.sdbhost, self.sdbname, self.sdbuser, self.password)
sdbloadfits(filename, sdb, log, False)
print('SDBLOADFITS: SUCCESS')
except Exception as e:
print('SDBLOADFITSERROR:', e)
#display the image
if display_image:
print("Displaying %s" % outfile)
try:
display(outfile)
except Exception as e:
print(e)
#if the images are imaging data, run sextractor on them
name=iminfo[0]
propcode=iminfo[headerList.index('PROPID')].strip().upper()
obsmode=iminfo[headerList.index('OBSMODE')].strip().upper()
detmode=iminfo[headerList.index('DETMODE')].strip().upper()
obstype=iminfo[headerList.index('CCDTYPE')].strip().upper()
target=iminfo[headerList.index('OBJECT')].strip().upper()
lampid=iminfo[headerList.index('LAMPID')].strip().upper()
print(detmode)
if (obsmode=='IMAGING' or obsmode=='FABRY-PEROT' ) and (detmode=='NORMAL' or detmode=='FT' or detmode=='FRAME TRANSFER'):
i=headerList.index('CCDSUM')
ccdbin=int(iminfo[i].split()[0])
pix_scale=0.14*ccdbin
r_ap=1.5/pix_scale
#measure the photometry
print("RUNNING PHOTOMETRY")
quickphot(outfile, r_ap, pix_scale, self.sexfile, clobber, logfile, verbose)
#load the regions
#if display_image: regions(outfile)
#measure the background statistics
#hdu=pyfits.open(outfile)
#bmean, bmidpt, bstd=saltstat.iterstat(hdu[1].data, 5, 3)
bmean, bmidpt, bstd=(-1,-1,-1)
#hdu.close()
print("---------Background Statistics---------")
print("%10s %10s %10s" % ('Mean', 'MidPoint', 'STD'))
print("%10.2f %10.2f %10.2f" % (bmean, bmidpt, bstd))
iminfo[headerList.index('BMEAN')]='%f' % (bmean)
iminfo[headerList.index('BMIDPT')]='%f' % (bmidpt)
iminfo[headerList.index('BSTD')]='%f' % (bstd)
#measure the seeing
outtxt=outfile.replace('fits', 'cat')
try:
mag_arr, fwhm_arr=np.loadtxt(outtxt, usecols=(2,10), unpack=True)
mean, std, norm, peak=seeing_stats(fwhm_arr)
see=mean*pix_scale
nsources=len(mag_arr)
except:
see=-1
nsources=-1
iminfo[headerList.index('NSOURCES')]='%i' % nsources
iminfo[headerList.index('SEEING')]='%f' % see
#self.emit(QtCore.SIGNAL("updateimlist(str,str,str)"), (name, 'SEEING', '%f' % see))
#self.emit(QtCore.SIGNAL("updatespec(QString)"), name)
#If the images are spectral images, run specreduce on them
if obsmode=='SPECTROSCOPY': # and not(target in ['FLAT', 'BIAS']):
y1,y2=quickspec(outfile, lampid, objsection=self.objsection, findobj=True, clobber=True, logfile=logfile, verbose=verbose)
print(y1,y2)
specfile=outpath+'smbxp'+infile.split('.fits')[0]+'.txt'
#In here, so it doesn't break when the first checkdata runs
try:
self.specTab.updaterange(y1,y2)
self.emit(QtCore.SIGNAL("updatespec(QString)"), infile)
except Exception as e:
message="SALTFIRST--ERROR: Could not wavelength calibrate %s because %s" % (infile, e)
fout=open(logfile, 'a')
fout.write(message)
print(message)
if obsmode=='FABRY-PEROT' and obstype=='ARC':
try:
flatimage='/home/ccd/smc/FPFLAT.fits'
profile=os.path.basename(outfile)
fpcal(profile, flatimage=flatimage, minflat=18000, niter=5, bthresh=5, displayimage=True, clobber=True, logfile=logfile, verbose=verbose)
except Exception as e:
message="SALTFIRST--ERROR: Could not calibrate FP data te %s because %s" % (infile, e)
fout=open(logfile, 'a')
fout.write(message)
print(message)
#check for fast mode operation
if self.update:
runfast(name, propcode,self.obsdate,self.server, self.readme, self.sdbhost,self.sdbname, self.sdbuser, self.password)
return iminfo
readme = iraf.osfn('pipetools$html/readme.template')
if not os.path.isfile(nightlog):
nightlog = ''
message = 'No night log {} found'.format(nightlog)
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
sdb=saltmysql.connectdb(sdbhost, sdbname, sdbuser, sdbpass)
if (rssrawnum > 0 or scmrawnum > 0 or hrsrawnum>0):
propids=saltmysql.getpropcodes(sdb, obsdate)
for pid in propids:
try:
saltelsdata(pid, obsdate, elshost, elsname, elsuser, elspass,
sdbhost,sdbname,sdbuser, sdbpass, clobber, logfile,verbose)
except:
continue
try:
outfile='%s_%s_elsdata.fits' % (pid, obsdate)
outdir='%s/doc/' % (pid)
shutil.move(outfile, outdir)
except:
os.remove(outfile)
def findcal(obsdate, sdbhost, sdbname, sdbuser, password):
"""Find all of the unique configuration settings used on a night
and insert it into the database
obsdate--Observation date in YYYYMMDD
sdbhost--host name for sdb
sdbname--name of the sdb
sdbuser--user for the sdb
password--sdb password
"""
#connect to the db
sdb = saltmysql.connectdb(sdbhost, sdbname, sdbuser, password)
#get the nightinfo id
logic = "Date='%4s-%2s-%2s'" % (obsdate[0:4], obsdate[4:6], obsdate[6:8])
results = saltmysql.select(sdb, 'NightInfo_Id', 'NightInfo', logic)
night_id = results[0][0]
#select all the scam data from this obsdate
cmd_select = 'd.FileName, d.FileData_Id, f.CCDTYPE, d.DETMODE, CCDSUM, GAINSET, ROSPEED, FILTER'
cmd_table = ''' FileData as d
left join FitsHeaderImage as f using (FileData_Id)
left join FitsHeaderSalticam using (FileData_Id)
'''
cmd_logic = "d.FileName like 'S" + obsdate + "%' and f.CCDTYPE='OBJECT'"
results = saltmysql.select(sdb, cmd_select, cmd_table, cmd_logic)
#loop through all the results and return only the Set of identical results
caldict = create_caldict(results)
#insert the results into the database
for k in caldict:
#first check to see if it has already been entered
record = saltmysql.select(sdb, 'FileData_Id',
'SalticamNightlyCalibration',
'FileData_Id=%i' % k)
if len(record) < 1:
#check for block_id
blockid = saltmysql.select(sdb, 'Block_Id', 'FileData',
'FileData_Id=%i' % k)[0][0]
#get the calibration types requested
if blockid:
request = saltmysql.select(sdb, 'SalticamCalibrationType_Id',
'SalitcamCalibration',
'Block_Id=%i' % blockid)
for cid in request:
cid = cid[0]
cmd_insert = 'NightInfo_Id=%i, FileData_Id=%i, SatlicamCalibrationType_Id=%i' % (
night_id, k, cid)
#saltmysql.insert(sdb, cmd_insert, 'SalitcamNightlyCalibration')
print k, " ".join([str(k) for k in caldict[k]])
#list of rss calibration types
#+-----------------------+----------------------------------+
#| RssCalibrationType_Id | CalibrationType |
#+-----------------------+----------------------------------+
#| 2 | Arc |
#| 1 | Bias |
#| 14 | Imaging flat - Lamp |
#| 15 | Imaging flat - Twilight |
#| 3 | Spectroscopic flat - Lamp |
#| 4 | Spectroscopic flat - Twilight |
#| 12 | Standard - Circular polarimetric |
#| 13 | Standard - Lick |
#| 9 | Standard - Linear polarimetric |
#| 5 | Standard - Photometric |
#| 8 | Standard - RV |
#| 11 | Standard - Smooth spectrum |
#| 7 | Standard - Spectrophotometric |
#| 6 | Standard - Spectroscopic |
#| 10 | Standard - Unpolarised |
#+-----------------------+----------------------------------+
#select all the RSS data from this obsdate
rssheaderlist = 'f.CCDTYPE, d.DETMODE, d.OBSMODE, CCDSUM, GAINSET, ROSPEED, FILTER, GRATING, GRTILT, AR_STA, MASKID'
cmd_select = 'd.FileName,d.FileData_Id, %s' % rssheaderlist
# CCDTYPE, DETMODE, OBSMODE, CCDSUM, GAINSET, ROSPEED, FILTER, GRATING, GR_STA, AR_STA, MASKID'
cmd_table = ''' FileData as d
left join FitsHeaderImage as f using (FileData_Id)
left join FitsHeaderRss using (FileData_Id)
join ProposalCode using (ProposalCode_Id)
'''
cmd_logic = "d.FileName like 'P" + obsdate + "%' and CCDTYPE='OBJECT' and Proposal_Code not like 'CAL_SPST' and GRTILT > 0"
results = saltmysql.select(sdb, cmd_select, cmd_table, cmd_logic)
#loop through all the results and return only the Set of identical results
caldict = create_caldict(results)
#insert the rss results into the database
for k in caldict:
#first check to see if it has already been entered
record = saltmysql.select(sdb, 'FileData_Id', 'RssNightlyCalibration',
'FileData_Id=%i' % k)
if len(record) < 1:
#period for checking for SPST. If the uses requests this, it gets set to
# 7 days, but the default is taken within the last month for non-requests
period = 30
#check for block_id
blockid = saltmysql.select(sdb, 'Block_Id', 'FileData',
'FileData_Id=%i' % k)[0][0]
#get the calibration types requested
if blockid:
request = saltmysql.select(sdb, 'RssCalibrationType_Id',
'RssCalibration',
'Block_Id=%i' % blockid)
for cid in request:
cid = cid[0]
#check to see if the request is already in the database or if a similar request has
#been taken recently
if cid == 1: #bias
if not checkforbias(sdb, k):
cmd_insert = 'NightInfo_Id=%i, FileData_Id=%i, RssCalibrationType_Id=%i' % (
night_id, k, cid)
saltmysql.insert(sdb, cmd_insert,
'RssNightlyCalibration')
elif cid in [3, 4]: #flats
if not checkforflats(sdb,
k,
cid,
rssheaderlist,
instr='rss',
keylist=caldict[k],
period=90):
cmd_insert = 'NightInfo_Id=%i, FileData_Id=%i, RssCalibrationType_Id=%i' % (
night_id, k, cid)
saltmysql.insert(sdb, cmd_insert,
'RssNightlyCalibration')
elif cid == 7: #specstand
period = 7
#print period, k, caldict[k]
if not checkforspst(
sdb, k, caldict[k], rssheaderlist,
period=period):
cmd_insert = 'NightInfo_Id=%i, FileData_Id=%i, RssCalibrationType_Id=7' % (
night_id, k)
saltmysql.insert(sdb, cmd_insert,
'RssNightlyCalibration')
else:
cmd_insert = 'NightInfo_Id=%i, FileData_Id=%i, RssCalibrationType_Id=%i' % (
night_id, k, cid)
saltmysql.insert(sdb, cmd_insert,
'RssNightlyCalibration')
print k, cid, " ".join([str(w) for w in caldict[k]])
#select all the HRS data from this obsdate
#+-----------------------+-------------------------------+
#| HrsCalibrationType_Id | CalibrationType |
#+-----------------------+-------------------------------+
#| 3 | Arc - Calsys |
#| 2 | Arc - Internal |
#| 1 | Bias |
#| 4 | Spectroscopic flat - Lamp |
#| 5 | Spectroscopic flat - Twilight |
#| 11 | Standard - Lick |
#| 6 | Standard - Photometric |
#| 9 | Standard - RV |
#| 10 | Standard - Smooth spectrum |
#| 8 | Standard - Spectrophotometric |
#| 7 | Standard - Spectroscopic |
#+-----------------------+-------------------------------+
hrsheaderlist = 'f.CCDTYPE, d.DETMODE, d.OBSMODE, CCDSUM, GAINSET, ROSPEED'
cmd_select = 'd.FileName,d.FileData_Id, %s' % hrsheaderlist
cmd_table = ''' FileData as d
left join FitsHeaderImage as f using (FileData_Id)
left join FitsHeaderHrs using (FileData_Id)
join ProposalCode using (ProposalCode_Id)
'''
cmd_logic = "d.FileName like 'H" + obsdate + "%' and CCDTYPE='Science' and Proposal_Code not like 'CAL_SPST'"
results = saltmysql.select(sdb, cmd_select, cmd_table, cmd_logic)
#loop through all the results and return only the Set of identical results
caldict = create_caldict(results)
for k in caldict:
#first check to see if it has already been entered
record = saltmysql.select(sdb, 'FileData_Id', 'HrsNightlyCalibration',
'FileData_Id=%i' % k)
if len(record) < 1:
#period for checking for SPST. If the uses requests this, it gets set to
# 7 days, but the default is taken within the last month for non-requests
period = 30
#check for block_id
blockid = saltmysql.select(sdb, 'Block_Id', 'FileData',
'FileData_Id=%i' % k)[0][0]
#get the calibration types requested
if not checkforbias(sdb, k, instr='hrs'):
cmd_insert = 'NightInfo_Id=%i, FileData_Id=%i, HrsCalibrationType_Id=%i' % (
night_id, k, 1)
saltmysql.insert(sdb, cmd_insert, 'HrsNightlyCalibration')
return
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 saltfast(obsdate, readme, emailserver, username,password, bcc, sdbhost,
sdbname,sdbuser, clobber,logfile,verbose):
# set up
nightlog = ''
with logging(logfile,debug) as log:
# determine current directory
workdir = os.getcwd()
logfile = workdir + '/' + os.path.basename(logfile)
#log into the database
sdb=saltmysql.connectdb(sdbhost,sdbname,sdbuser,password)
#query the data base for all of the data taken last night and the proposal codes
select='FileName, Target_Name, Proposal_Code'
table='FileData join ProposalCode using (ProposalCode_Id)'
logic="FileName like '%"+obsdate+"%'"
records=saltmysql.select(sdb, select, table, logic)
if len(records)==0:
message='No data taken on %s\n' % obsdate
log.message(message)
return
#determine the list of files, targets, and propcodes
file_list=[]
target_list=[]
propcode_list=[]
propcode_dict={}
for name,targ,pid in records:
file_list.append(name)
target_list.append(targ)
propcode_list.append(pid)
try:
propcode_dict[pid].append(targ)
except KeyError:
propcode_dict[pid]=[targ]
# check to see if any of the PI directories requires fast response
for pid in propcode_dict.keys():
target=set(propcode_dict[pid])
if checkforfast(pid, target, sdb):
#log the move
message='Copying data from %s to the ftp site' % pid
log.message(message, with_stdout=verbose)
#get the username
piptuser=saltmysql.getpiptusername(sdb, pid)
#create the fast directory
fastdir='/salt/ftparea/%s/FAST/' % piptuser
if os.path.isdir(fastdir): saltio.deletedir(fastdir)
os.mkdir(fastdir)
for i in range(len(file_list)):
if propcode_list[i]==pid:
#create the data filename
if file_list[i].startswith('S'):
instr='scam'
elif file_list[i].startswith('P'):
instr='rss'
filepath='/salt/%s/data/%s/%s/raw/%s' % (instr, obsdate[0:4], obsdate[4:8], file_list[i])
saltio.copy(filepath, fastdir)
#make the temporary readme
mailmessage = maketempreadmefast(pid, sdb, readme)
#send the email
subject='SALT Raw Data available for %s' % pid
sender='*****@*****.**'
recipient=saltmysql.getpiptemail(sdb, piptuser)
bcc='*****@*****.**'#[email protected]'
#if detmode=='FT' or detmode=='FRAME TRANSFER': return iminfo
#reduce the data
if reduce_image:
try:
quickclean(filename, interp, cleanup, clobber, logfile, verbose)
except Exception, e:
print e
return iminfo
#load the data into the SDB
if self.sdbhost and self.update:
try:
log=None #open(logfile, 'a')
sdb=saltmysql.connectdb(self.sdbhost, self.sdbname, self.sdbuser, self.password)
sdbloadfits(filename, sdb, log, False)
print 'SDBLOADFITS: SUCCESS'
except Exception, e:
print 'SDBLOADFITSERROR:', e
#display the image
if display_image:
print "Displaying %s" % outfile
try:
display(outfile)
except Exception, e:
print e
#if the images are imaging data, run sextractor on them
name=iminfo[0]
def saltnightinfo(
obsdate,
sdbhost="sdb.saao",
sdbname="sdb",
sdbuser="",
password="",
clobber=False,
logfile="saltlog.log",
verbose=True,
):
"""Update the nightinfo table from the SOMMI log
"""
with logging(logfile, debug) as log:
# connect the database
sdb = saltmysql.connectdb(sdbhost, sdbname, sdbuser, password)
# get the nightinfo_id
night_id = saltmysql.getnightinfoid(sdb, obsdate)
print night_id
# get the start and end of twilight
nightstart = saltmysql.select(sdb, "EveningTwilightEnd", "NightInfo", "NightInfo_Id=%i" % night_id)[0][0]
nightend = saltmysql.select(sdb, "MorningTwilightStart", "NightInfo", "NightInfo_Id=%i" % night_id)[0][0]
print nightstart
print nightend
print (nightend - nightstart).seconds
# download the SOMMI log from the night
try:
sommi_log = saltmysql.select(sdb, "SONightLog", "NightLogs", "NightInfo_Id=%i" % night_id)[0][0]
except:
raise SaltError("Unable to read SOMMI log in the database for %s" % obsdate)
# set up the time for the night
try:
ntime = (nightend - nightstart).seconds
except:
raise SaltError("Unable to read night length from database for %s" % obsdate)
# parse the sommi log
slog = sommi_log.split("\n")
stime = 0
for i in range(len(slog)):
if slog[i].count("Science Time:"):
stime = extractinformation(slog[i])
if slog[i].count("Engineering Time:") and not slog[i].count("Non-observing Engineering Time"):
etime = extractinformation(slog[i])
if slog[i].count("Time lost to Weather:"):
wtime = extractinformation(slog[i])
if slog[i].count("Time lost to Tech. Problems:"):
ttime = extractinformation(slog[i])
if slog[i].count("Non-observing Engineering Time:"):
ltime = extractinformation(slog[i])
print etime
tot_time = stime + etime + wtime + ttime
print night_id, ntime, stime, etime, wtime, ttime, ltime, tot_time
# insert the information into the database
print tot_time, ntime
if abs(tot_time - ntime) < 900:
message = "Updating NightInfo Table with the following Times:\n"
message += "Science Time=%i\n" % stime
message += "Engineeringh=%i\n" % etime
message += "Time lost to Weather=%i\n" % wtime
message += "Time lost to Tech. Problems=%i\n" % ttime
message += "Non-observing Engineering Time=%i\n" % ltime
log.message(message)
insert_state = (
"ScienceTime=%i, EngineeringTime=%i, TimeLostToWeather=%i, TimeLostToProblems=%i, NonObservingEngineeringTime=%i"
% (stime, etime, wtime, ttime, ltime)
)
table_state = "NightInfo"
logic_state = "NightInfo_Id=%i" % night_id
saltmysql.update(sdb, insert_state, table_state, logic_state)
else:
message = "The total time for the night is not equal to the length of the night\n"
message += "Night Length=%i\n--------------------\n" % ntime
message += "Science Time=%i\n" % stime
message += "Engineeringh=%i\n" % etime
message += "Time lost to Weather=%i\n" % wtime
message += "Time lost to Tech. Problems=%i\n" % ttime
message += "Non-observing Engineering Time=%i\n" % ltime
message += "Total time for the Night=%i\n" % tot_time
log.message(message)
def saltquery(selection, logic, startdate, enddate, outfile=None, sdbhost='sdb.saao', sdbname='sdb', \
sdbuser='', password='', clobber=False, logfile='saltlog.log', verbose=True):
"""Query the salt database for FITS files
"""
with logging(logfile,debug) as log:
#check the outfiles
if not saltio.checkfornone(outfile):
outfile=None
#check that the output file can be deleted
if outfile:
saltio.overwrite(outfile, clobber)
#open outfile
if outfile:
fout=saltio.openascii(outfile, 'w')
#connect to the database
sdb=saltmysql.connectdb(sdbhost,sdbname,sdbuser,password)
#Create a list of the selection and then unpack it
selection_list = saltio.argunpack('Selection', selection)
selection=','.join(selection_list)
#write out the header for the outfile
outstr='#'+' '.join(['%s' % x for x in selection_list])
if outfile:
fout.write(outstr+'\n')
else:
print outstr
#set up the table
rsstable=''' FileData
left join FitsHeaderImage using (FileData_Id)
inner join FitsHeaderRss using (FileData_Id)
'''
#set up the table
scamtable=''' FileData
left join FitsHeaderImage using (FileData_Id)
inner join FitsHeaderSalticam using (FileData_Id)
'''
#set up the logic
logic=makelogic(logic, startdate, enddate)
for tab in [rsstable, scamtable]:
msg='''
Mysql querying data is:
SELECT %s
FROM %s
WHERE %s
''' % (selection, tab, logic)
log.message(msg, with_stdout=verbose)
record=saltmysql.select(sdb, selection, tab, logic)
print record
for r in record:
outstr=' '.join(['%s' % x for x in r])
if outfile:
fout.write(outstr+'\n')
else:
print outstr
#close outfile
if outfile: fout.close()
def saltadvance(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', sdbhost='',sdbname='',sdbuser='', password='',
clobber=False, cleanup=True, logfile='salt.log', verbose=True):
"""SALTADVANCE provides advanced data 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)
infiles.sort()
# create list of output files
outpath=saltio.abspath(outpath)
#log into the database
sdb=saltmysql.connectdb(sdbhost, sdbname, sdbuser, password)
#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')
obsmode=obsstruct.data.field('OBSMODE')
ccdtype=obsstruct.data.field('CCDTYPE')
propcode=obsstruct.data.field('PROPID')
masktype=obsstruct.data.field('MASKTYP')
#set the bias list of objects
biaslist=filename[(ccdtype=='ZERO')*(propcode=='CAL_BIAS')]
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=True, 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)
#update the database
updatedq(os.path.basename(img), struct, sdb)
#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=True, 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)
#update the database
updatedq(os.path.basename(img), struct, sdb)
#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 arc data
arclist=filename[(ccdtype=='ARC') * (obsmode=='SPECTROSCOPY') * (masktype=='LONGSLIT')]
for i, img in enumerate(infiles):
nimg=os.path.basename(img)
if nimg in arclist:
#open the image
struct=fits.open(img)
simg=outpath+'bxgp'+os.path.basename(img)
obsdate=os.path.basename(img)[1:9]
#print the message
if log:
message='Processing ARC frame %s' % img
log.message(message, with_stdout=verbose)
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 FITS file
saltio.writefits(struct,simg, clobber=clobber)
saltio.closefits(struct)
#mosaic the images
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)
#measure the arcdata
arcimage=outpath+'mbxgp'+nimg
dbfile=outpath+obsdate+'_specid.db'
lamp = obsstruct.data.field('LAMPID')[i]
lamp = lamp.replace(' ', '')
lampfile = iraf.osfn("pysalt$data/linelists/%s.salt" % lamp)
print arcimage, lampfile, os.getcwd()
specidentify(arcimage, lampfile, dbfile, guesstype='rss',
guessfile='', automethod='Matchlines', function='legendre',
order=3, rstep=100, rstart='middlerow', mdiff=20, thresh=3,
startext=0, niter=5, smooth=3, inter=False, clobber=True, logfile=logfile,
verbose=verbose)
try:
ximg = outpath+'xmbxgp'+os.path.basename(arcimage)
specrectify(images=arcimage, outimages=ximg, outpref='', solfile=dbfile, caltype='line',
function='legendre', order=3, inttype='interp', w1=None, w2=None, dw=None,
nw=None, blank=0.0, conserve=True, nearest=True, clobber=True,
logfile=logfile, verbose=verbose)
except:
pass
#process the science data
for i, img in enumerate(infiles):
nimg=os.path.basename(img)
if not (nimg in flatlist or nimg in biaslist or nimg in arclist):
#open the image
struct=fits.open(img)
if struct[0].header['PROPID'].count('CAL_GAIN'): continue
simg=outpath+'bxgp'+os.path.basename(img)
#print the message
if log:
message='Processing science frame %s' % img
log.message(message, with_stdout=verbose)
#Check to see if it is RSS 2x2 and add bias subtraction
instrume=saltkey.get('INSTRUME', struct[0]).strip()
gainset = saltkey.get('GAINSET', struct[0])
rospeed = saltkey.get('ROSPEED', struct[0])
target = saltkey.get('OBJECT', struct[0]).strip()
exptime = saltkey.get('EXPTIME', struct[0])
obsmode = saltkey.get('OBSMODE', struct[0]).strip()
detmode = saltkey.get('DETMODE', struct[0]).strip()
masktype = saltkey.get('MASKTYP', struct[0]).strip()
xbin, ybin = saltkey.ccdbin( struct[0], img)
obsdate=os.path.basename(img)[1:9]
bstruct=None
crtype=None
thresh=5
mbox=11
bthresh=5.0,
flux_ratio=0.2
bbox=25
gain=1.0
rdnoise=5.0
fthresh=5.0
bfactor=2
gbox=3
maxiter=5
subbias=False
if instrume=='RSS' and gainset=='FAINT' and rospeed=='SLOW':
bfile='P%sBiasNM%ix%iFASL.fits' % (obsdate, xbin, ybin)
if os.path.exists(bfile):
bstruct=fits.open(bfile)
subbias=True
if detmode=='Normal' and target!='ARC' and xbin < 5 and ybin < 5:
crtype='edge'
thresh=5
mbox=11
bthresh=5.0,
flux_ratio=0.2
bbox=25
gain=1.0
rdnoise=5.0
fthresh=5.0
bfactor=2
gbox=3
maxiter=3
#process the image
struct=clean(struct, createvar=True, badpixelstruct=None, mult=True,
dblist=dblist, xdict=xdict, subover=subover, trim=trim, subbias=subbias,
bstruct=bstruct, median=median, function=function, order=order,
rej_lo=rej_lo, rej_hi=rej_hi, niter=niter, plotover=plotover,
crtype=crtype,thresh=thresh,mbox=mbox, bbox=bbox, \
bthresh=bthresh, flux_ratio=flux_ratio, gain=gain, rdnoise=rdnoise,
bfactor=bfactor, fthresh=fthresh, gbox=gbox, maxiter=maxiter,
log=log, verbose=verbose)
#update the database
updatedq(os.path.basename(img), struct, sdb)
#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,fill=True, cleanup=True,clobber=clobber,logfile=logfile,
verbose=verbose)
#remove the intermediate steps
saltio.delete(simg)
#if the file is spectroscopic mode, apply the wavelength correction
if obsmode == 'SPECTROSCOPY' and masktype.strip()=='LONGSLIT':
dbfile=outpath+obsdate+'_specid.db'
try:
ximg = outpath+'xmbxgp'+os.path.basename(img)
specrectify(images=mimg, outimages=ximg, outpref='', solfile=dbfile, caltype='line',
function='legendre', order=3, inttype='interp', w1=None, w2=None, dw=None,
nw=None, blank=0.0, conserve=True, nearest=True, clobber=True,
logfile=logfile, verbose=verbose)
except Exception, e:
log.message('%s' % e)
#clean up the results
if cleanup:
#clean up the bias frames
for i in masterbias_dict.keys():
blist=masterbias_dict[i][1:]
for b in blist: saltio.delete(b)
#clean up the flat frames
for i in masterflat_dict.keys():
flist=masterflat_dict[i][1:]
for f in flist: saltio.delete(f)