def runPipeline():
# the terminal object is used for printing to the screen
term = Terminal()
# create instance of CommandLine object to parse input, then
# parse all the input parameters and store them as attributes in
# cl_params structure
cl = commandline.CommandLine()
cl_params = cl.read(sys)
# create a directory for storing log files
mkdir_p('log')
# instantiate a log object for log files and screen output
log = Logging(cl_params, 'pipeline')
# print a command summary to log file/terminal
command_summary(cl_params, term, log)
log.doMessage('INFO', '{t.underline}Start '
'calibration.{t.normal}'.format(t=term))
# calibrated_maps will contain a list of tuples each with a
# MappingPipeline instance, window id, feed id and polarization id
calibrated_maps = []
# check to see if the infile parameter is a directory. This is the
# default case for vegas data processing. If we have a directory of
# files, we calibrate each input file separately, then perform the
# imaging step on all the calibrated outputs.
if os.path.isdir(cl_params.infilename):
log.doMessage('INFO', 'Infile name is a directory')
input_directory = cl_params.infilename
# calibrate one raw SDFITS file at a time
for infilename in glob.glob(input_directory + '/' +
os.path.basename(input_directory) +
'*.fits'):
log.doMessage('INFO', '\nCalibrating', infilename.rstrip('.fits'))
# change the infilename in the params structure to the
# current infile in the directory for each iteration
cl_params.infilename = infilename
calibrated_maps_this_file = calibrate_file(term, log, cl_params)
calibrated_maps.extend(calibrated_maps_this_file)
else:
calibrated_maps_this_file = calibrate_file(term, log, cl_params)
calibrated_maps.extend(calibrated_maps_this_file)
# if we are doing imaging
if not cl_params.imagingoff:
# instantiate an Imaging object
imag = Imaging()
# image all the calibrated maps
imag.run(log, term, cl_params, calibrated_maps)
sys.stdout.write('\n')
def runPipeline():
# the blessings.Terminal object is used for printing to the screen
terminal = blessings.Terminal()
term = terminal
# create instance of CommandLine object to parse input, then
# parse all the input parameters and store them as attributes in
# cl_params structure
cl = commandline.CommandLine()
cl_params = cl.read(sys)
# create a directory for storing log files
mkdir_p('log')
# instantiate a log object for log files and screen output
log = Logging(cl_params, 'pipeline')
# print a command summary to log file/terminal
command_summary(cl_params, term, log)
if not cl_params.imagingoff:
# instantiate an Imaging object
imag = Imaging.Imaging()
else:
imag = None
log.doMessage('INFO', '{t.underline}Start '
'calibration.{t.normal}'.format(t=term))
# calibrated_maps will contain a list of tuples each with a
# MappingPipeline instance, window id, feed id and polarization id
calibrated_maps = []
# check to see if the infile parameter is a directory. This is the
# default case for vegas data processing. If we have a directory of
# files, we calibrate each input file separately, then perform the
# imaging step on all the calibrated outputs.
if os.path.isdir(cl_params.infilename):
log.doMessage('INFO', 'Infile name is a directory')
input_directory = cl_params.infilename
# Instantiate a SdFits object for I/O and interpreting the
# contents of the index file
sdf = SdFits()
# generate a name for the index file based on the name of the
# raw SDFITS file. The index file simply has a different extension
directory_name = os.path.basename(cl_params.infilename.rstrip('/'))
indexfile = cl_params.infilename + '/' + directory_name + '.index'
try:
# create a structure that lists the raw SDFITS rows for
# each scan/window/feed/polarization
row_list, summary = sdf.parseSdfitsIndex(indexfile, cl_params.mapscans)
except IOError:
log.doMessage('ERR', 'Could not open index file', indexfile)
sys.exit()
quitcal = False
if cl_params.window and set(cl_params.window).isdisjoint(set(row_list.windows())):
log.doMessage('ERR', 'no given WINDOW(S)', cl_params.window, 'in dataset')
quitcal = True
if cl_params.feed and set(cl_params.feed).isdisjoint(set(row_list.feeds())):
log.doMessage('ERR', 'no given FEED(S)', cl_params.feed, 'in dataset')
quitcal = True
if cl_params.pol and set(cl_params.pol).isdisjoint(set(row_list.pols())):
log.doMessage('ERR', 'no given POL(S)', cl_params.pol, 'in dataset')
quitcal = True
if cl_params.mapscans and set(cl_params.mapscans).isdisjoint(set(row_list.scans())):
log.doMessage('ERR', 'no given MAPSCAN(S)', cl_params.mapscans, 'in dataset')
quitcal = True
if cl_params.refscans and set(cl_params.refscans).isdisjoint(set(row_list.scans())):
log.doMessage('ERR', 'no given REFSCAN(S)', cl_params.refscans, 'in dataset')
quitcal = True
if quitcal:
sys.exit(12)
# calibrate one raw SDFITS file at a time
for infilename in glob.glob(input_directory + '/' +
os.path.basename(input_directory) +
'*.fits'):
log.doMessage('DBG', 'Attempting to calibrate', os.path.basename(infilename).rstrip('.fits'))
# change the infilename in the params structure to the
# current infile in the directory for each iteration
cl_params.infilename = infilename
# copy the cl_params structure so we can modify it during calibration
# for each seperate file.
commandline_options = copy.deepcopy(cl_params)
calibrated_maps_this_file = calibrate_file(term, log, commandline_options)
if calibrated_maps_this_file:
calibrated_maps.extend(calibrated_maps_this_file)
else:
commandline_options = copy.deepcopy(cl_params)
calibrated_maps_this_file = calibrate_file(term, log, commandline_options)
if calibrated_maps_this_file:
calibrated_maps.extend(calibrated_maps_this_file)
if not calibrated_maps:
log.doMessage('ERR', 'No calibrated spectra. Check inputs and try again')
sys.exit(-1)
# if we are doing imaging
if not cl_params.imagingoff:
# image all the calibrated maps
import itertools
calibrated_maps = list(itertools.chain(*calibrated_maps))
imag.run(log, term, cl_params, calibrated_maps)
sys.stdout.write('\n')
def runPipeline():
# the blessings.Terminal object is used for printing to the screen
terminal = blessings.Terminal()
term = terminal
# create instance of CommandLine object to parse input, then
# parse all the input parameters and store them as attributes in
# cl_params structure
cl = commandline.CommandLine()
cl_params = cl.read(sys)
# create a directory for storing log files
mkdir_p('log')
# instantiate a log object for log files and screen output
log = Logging(cl_params, 'pipeline')
# print a command summary to log file/terminal
command_summary(cl_params, term, log)
if not cl_params.imagingoff:
# instantiate an Imaging object
imag = Imaging.Imaging()
else:
imag = None
log.doMessage(
'INFO', '{t.underline}Start '
'calibration.{t.normal}'.format(t=term))
# calibrated_maps will contain a list of tuples each with a
# MappingPipeline instance, window id, feed id and polarization id
calibrated_maps = []
# check to see if the infile parameter is a directory. This is the
# default case for vegas data processing. If we have a directory of
# files, we calibrate each input file separately, then perform the
# imaging step on all the calibrated outputs.
if os.path.isdir(cl_params.infilename):
log.doMessage('INFO', 'Infile name is a directory')
input_directory = cl_params.infilename
# Instantiate a SdFits object for I/O and interpreting the
# contents of the index file
sdf = SdFits()
# generate a name for the index file based on the name of the
# raw SDFITS file. The index file simply has a different extension
directory_name = os.path.basename(cl_params.infilename.rstrip('/'))
indexfile = cl_params.infilename + '/' + directory_name + '.index'
try:
# create a structure that lists the raw SDFITS rows for
# each scan/window/feed/polarization
row_list, summary = sdf.parseSdfitsIndex(indexfile,
cl_params.mapscans)
except IOError:
log.doMessage('ERR', 'Could not open index file', indexfile)
sys.exit()
quitcal = False
if cl_params.window and set(cl_params.window).isdisjoint(
set(row_list.windows())):
log.doMessage('ERR', 'no given WINDOW(S)', cl_params.window,
'in dataset')
quitcal = True
if cl_params.feed and set(cl_params.feed).isdisjoint(
set(row_list.feeds())):
log.doMessage('ERR', 'no given FEED(S)', cl_params.feed,
'in dataset')
quitcal = True
if cl_params.pol and set(cl_params.pol).isdisjoint(set(
row_list.pols())):
log.doMessage('ERR', 'no given POL(S)', cl_params.pol,
'in dataset')
quitcal = True
if cl_params.mapscans and set(cl_params.mapscans).isdisjoint(
set(row_list.scans())):
log.doMessage('ERR', 'no given MAPSCAN(S)', cl_params.mapscans,
'in dataset')
quitcal = True
if cl_params.refscans and set(cl_params.refscans).isdisjoint(
set(row_list.scans())):
log.doMessage('ERR', 'no given REFSCAN(S)', cl_params.refscans,
'in dataset')
quitcal = True
if quitcal:
sys.exit(12)
# calibrate one raw SDFITS file at a time
for infilename in glob.glob(input_directory + '/' +
os.path.basename(input_directory) +
'*.fits'):
log.doMessage('DBG', 'Attempting to calibrate',
os.path.basename(infilename).rstrip('.fits'))
# change the infilename in the params structure to the
# current infile in the directory for each iteration
cl_params.infilename = infilename
# copy the cl_params structure so we can modify it during calibration
# for each seperate file.
commandline_options = copy.deepcopy(cl_params)
calibrated_maps_this_file = calibrate_file(term, log,
commandline_options)
if calibrated_maps_this_file:
calibrated_maps.extend(calibrated_maps_this_file)
else:
commandline_options = copy.deepcopy(cl_params)
calibrated_maps_this_file = calibrate_file(term, log,
commandline_options)
if calibrated_maps_this_file:
calibrated_maps.extend(calibrated_maps_this_file)
if not calibrated_maps:
log.doMessage('ERR',
'No calibrated spectra. Check inputs and try again')
sys.exit(-1)
# if we are doing imaging
if not cl_params.imagingoff:
# image all the calibrated maps
import itertools
calibrated_maps = list(itertools.chain(*calibrated_maps))
imag.run(log, term, cl_params, calibrated_maps)
sys.stdout.write('\n')