def rd_dqc(infile=None, debug=None):
"""
read the dqc file
"""
print('dqc: ', infile)
if not os.path.exists(infile):
print(infile, 'does not exist')
print('Exiting')
sys.exit(0)
# open catalogue file handle
fh = pyfits.open(infile)
data = fh[1].data
print('Number of rows: ', len(data))
#help(data)
if debug: table_stats(infile)
#data['ra']=np.degrees(data['ra'])
#data['dec']=np.degrees(data['dec'])
return data
result.write('results1.fits', overwrite=True)
sys.exit()
# extract the project ID from the file
project = []
# table = ascii.read(infile, header_start=0, data_start=1)
# print()
# print(table[0])
# table = Table.read(infile)
table_stats('sources.fits', debug=False)
alma.info()
alma.info('stats')
Image_SourceStats(alma, filename=infile, verbose=False)
print(len(alma), 'Sources')
SourceStats(alma, verbose=False)
# limit to source with CUNIT3 == 'Hz' and CTYPE3 == 'FREQ'
itest = (alma['CTYPE3'] == 'FREQ') & (alma['NAXIS3'] == 1)
alma = alma[itest]
print('Number of sources with CTYPE3 = FREQ:', len(alma))
SourceStats(alma, verbose=False)
key=raw_input("Enter any key to continue: ")
logdata = "Delete lockfile %s " % lockfile
logger(flog, logdata)
logger(flogerr, logdata)
os.remove(lockfile)
continue
else:
logdata = "imcore_list Finished"
logger(flog, logdata)
hdulist = pyfits.open(outfile)
logdata = "Number of extensions: %d " % len(hdulist)
logger(flog, logdata)
n_ext = len(hdulist)
for ext in range(1, n_ext):
table_stats(outfile, ext=ext)
print "listdriven photometry completed"
# key=raw_input("Enter any key to continue: ")
print "Deleting data files used"
if os.path.exists(imagefile):
print "Remove the image file:" + imagefile
cmd = "rm -v " + imagefile
try:
result = os.popen(cmd)
except OSError as (errno, strerror):
logdata = "OS error({0}): {1}".format(errno, strerror)
logger(flogerr, logdata)
logdata = "error removing imagefile %s " % imagefile
logger(flogerr, logdata)
def imcore_list_run(args=None, imagefile=None,
confmapfile=None, listfile=None, outfile=None):
"""
runs imcore_list using subprocess
"""
# set the imcorelist parameters; maybe need to check these againsts
# values in the header of the catalogue file
nustep=-1
print('args.vhs: ', args.vhs)
print('args.cache: ', args.cache)
if not args.vhs:
nustep=pyfits.getval(imagefile,'NUSTEP',0)
print('nustep = ', nustep)
if args.vhs:
rcore = "3.0"
nbsize = "64"
threshold = "1.5"
# UKIDSS values
if (nustep==1):
rcore = "2.5"
nbsize = "64"
threshold = "1.5"
elif (nustep==4): # i.e., 2x2
rcore = "5.0"
nbsize = "128"
threshold = "1.25"
elif (nustep==9): # i.e., 3x3
rcore = "7.5"
nbsize = "192"
threshold = "1.25"
print('rcore, nbsize, threshold: ', rcore, nbsize, threshold)
# needs the binary location to be a parameter for portability
#command = 'time nice -n19 ' + IMCORE_LIST \
command = 'time nice -n19 /home/rgm/bin/imcore_list ' \
+ ' ' + imagefile \
+ ' ' + confmapfile \
+ ' ' + listfile \
+ ' ' + outfile \
+ ' ' + threshold \
+ ' --nbsize=' + nbsize \
+ ' --rcore=' + rcore \
+ ' --cattype=6 '
# + ' --verbose '
# save stdout and stderr to a logfile
stdoutlog = open(logpath+'Logfile_stdout', 'w+')
stderrlog = open(logpath+'Logfile_stderr', 'w+')
logdata=command
logger(flog, logdata)
# convert comamd to string list for subprocess
command = shlex.split(command)
print('Print command as args: ')
print(command)
result = subprocess.call(command, \
stderr=stderrlog, stdout=stdoutlog)
Popen=False
if Popen:
result = subprocess.Popen(command, shell=True,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
print('Using subprocess.Popen and communicate')
output, errors = result.communicate()
result=subprocess.check_output(command)
#help(result)
print('subprocesss output: ', output)
print('subprocess errors: ', errors)
#logdata='subprocess error status: ' + str(result)
#logger(flog, logdata)
trace = traceback.extract_stack()[-1]
print(os.path.basename(trace[0]), ' line :', str(trace[1]))
#if result is not 0: print(len(result))
#print(result)
result=0
if result is not 0:
print(result)
trace = traceback.extract_stack()[-1]
print(os.path.basename(trace[0]), ' line :', str(trace[1]))
print('Something went wrong: ', args)
logger(flogerr, logdata)
logdata = 'Something went wrong: ' + command
logger(flogerr, logdata)
logger(flogerr, line_save)
logger(flogerr, command)
while True:
line = result.readline()
if line == "": break
logdata = line
logger(flog, logdata)
print(line,)
if debug: key=raw_input("Enter any key to continue: ")
# delete the outfile if created
if os.path.exists(outfile):
logdata = "Delete %s " % outfile
logger(flog, logdata)
logger(flogerr, logdata)
os.remove(outfile)
if os.path.exists(lockfile):
logdata = "Delete lockfile %s " % lockfile
logger(flog, logdata)
logger(flogerr, logdata)
os.remove(lockfile)
#continue
usage = resource.getrusage(resource.RUSAGE_CHILD)
for name, desc in [
('ru_utime', 'User time'),
('ru_stime', 'System time'),
]:
print('%-25s (%-10s) = %s' % (desc, name, getattr(usage, name)))
else:
logdata='imcore_list Finished'
logger(flog, logdata)
print('Read back the results and check integrity: ', outfile)
if not os.path.exists(outfile):
print('File does not exist: ', outfile)
try:
hdulist = pyfits.open(outfile)
except:
traceback.print_exc(file=sys.stdout)
logdata= 'Number of extensions: %d ' % len(hdulist)
logger(flog, logdata)
n_ext=len(hdulist)
for ext in range(1, n_ext):
table_stats(outfile, ext=ext)
print('listdriven photometry completed')
debug = False
verbose = False
inpath = '/data/vhs/dqc/vsa/2014/VHSv20140409/'
filename = 'vhs_vsa_dqc_tiles_fs_metadata.fits'
dqcfile = inpath + filename
print('Elpased time: %.2f seconds' % (time.time() - t0))
print('Get table stats: ', dqcfile)
dqc = libdqc.rd_dqc(infile=dqcfile)
table_stats(dqcfile)
print('Elpased time: %.2f seconds' % (time.time() - t0))
#libdqc.dqc_stats(dqc=dqc)
test = False
if test:
test = (data['nite'] >= '20120901') & (data['nite'] <= '20130401')
data = data[test]
interactive = True
showplots = True
t0 = time.time()
debug=False
verbose=False
inpath= '/data/vhs/dqc/vsa/2014/VHSv20140409/'
filename= 'vhs_vsa_dqc_tiles_fs_metadata.fits'
dqcfile= inpath + filename
print('Elpased time: %.2f seconds' %(time.time() - t0))
print('Get table stats: ', dqcfile)
dqc = libdqc.rd_dqc(infile=dqcfile)
table_stats(dqcfile)
print('Elpased time: %.2f seconds' %(time.time() - t0))
#libdqc.dqc_stats(dqc=dqc)
test=False
if test:
test = (data['nite'] >= '20120901') & (data['nite'] <= '20130401')
data=data[test]
interactive=True
showplots=True