def main():
# ------------------------------------------------------------------------------
# Setup
INFRASTRUCTURE, CONTAINER_PATH = gen.set_infrastructure(sys.argv)
# Get paths from config and setup folders
CWD = cfg.CWD
OXKAT = cfg.OXKAT
PARSETS = cfg.PARSETS
TOOLS = cfg.TOOLS
GAINTABLES = cfg.GAINTABLES
IMAGES = cfg.IMAGES
LOGS = cfg.LOGS
SCRIPTS = cfg.SCRIPTS
gen.setup_dir(LOGS)
gen.setup_dir(SCRIPTS)
gen.setup_dir(IMAGES)
gen.setup_dir(GAINTABLES)
# Get containers needed for this script
CASA_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.CASA_PATTERN)
DDFACET_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.DDFACET_PATTERN)
TRICOLOUR_CONTAINER = gen.get_container(CONTAINER_PATH,
cfg.TRICOLOUR_PATTERN)
WSCLEAN_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.WSCLEAN_PATTERN)
# Set names of the run and kill files, open run file for writing
submit_file = 'submit_2GC_jobs.sh'
f = open(submit_file, 'w')
f.write('#!/usr/bin/env bash\n')
# Get target info from project_info.p
project_info = pickle.load(open('project_info.p', 'rb'), encoding='latin1')
targets = project_info['target_list']
SLURM_WSCLEAN_MOD = cfg.SLURM_WSCLEAN
SLURM_WSCLEAN_MOD['TIME'] = '18:00:00'
PBS_WSCLEAN_MOD = cfg.PBS_WSCLEAN
PBS_WSCLEAN_MOD['TIME'] = '18:00:00'
# Loop over targets
for target in targets:
targetname = target[0]
filename_targetname = gen.scrub_target_name(targetname)
code = gen.get_target_code(targetname)
myms = target[2].rstrip('/')
mask0 = sorted(
glob.glob(IMAGES + '/*' + filename_targetname + '*.mask.fits'))
print('------------------------------------------------------')
print(gen.now() + 'Target: ' + targetname)
print(gen.now() + 'MS: ' + myms)
if len(mask0) > 0:
mask = mask0[0]
else:
mask = 'auto'
print(gen.now() + 'Using mask: ' + mask)
kill_file = SCRIPTS + '/kill_2GC_jobs_' + filename_targetname + '.sh'
data_img_prefix = IMAGES + '/img_' + myms + '_datamask'
corr_img_prefix = IMAGES + '/img_' + myms + '_pcalmask'
# Initialise a list to hold all the job IDs
id_list = []
# ------------------------------------------------------------------------------
# STEP 1:
# Masked wsclean on DATA column
id_wsclean1 = 'WSDMA' + code
id_list.append(id_wsclean1)
syscall = 'singularity exec ' + WSCLEAN_CONTAINER + ' '
syscall += gen.generate_syscall_wsclean(mslist=[myms],
imgname=data_img_prefix,
briggs=-1.5,
multiscale=True,
scales='0,3,9',
niter=300000,
datacol='DATA',
bda=True,
mask=mask)
run_command = gen.job_handler(syscall=syscall,
jobname=id_wsclean1,
infrastructure=INFRASTRUCTURE,
slurm_config=SLURM_WSCLEAN_MOD,
pbs_config=PBS_WSCLEAN_MOD)
f.write(run_command + '\n')
# ------------------------------------------------------------------------------
# STEP 2:
# Predict MODEL_DATA
id_predict1 = 'WSDPR' + code
id_list.append(id_predict1)
syscall = 'singularity exec ' + WSCLEAN_CONTAINER + ' '
syscall += gen.generate_syscall_predict(msname=myms,
imgbase=data_img_prefix)
run_command = gen.job_handler(syscall=syscall,
jobname=id_predict1,
infrastructure=INFRASTRUCTURE,
dependency=id_wsclean1,
slurm_config=cfg.SLURM_WSCLEAN,
pbs_config=cfg.PBS_WSCLEAN)
f.write(run_command + '\n')
# ------------------------------------------------------------------------------
# STEP 3:
# Self-calibrate phases then amplitudes
id_selfcal = 'CLSLF' + code
id_list.append(id_selfcal)
casalog = LOGS + '/casa_2GC_' + id_selfcal + '.log'
syscall = 'singularity exec ' + CASA_CONTAINER + ' '
syscall += gen.generate_syscall_casa(
casascript=OXKAT + '/2GC_casa_selfcal_target_amp_phases.py',
casalogfile=casalog,
extra_args='mslist=' + myms + ' uvmin=300')
run_command = gen.job_handler(syscall=syscall,
jobname=id_selfcal,
infrastructure=INFRASTRUCTURE,
dependency=id_predict1)
f.write(run_command + '\n')
# ------------------------------------------------------------------------------
# STEP 4:
# Masked wsclean on CORRECTED_DATA column
id_wsclean2 = 'WSCMA' + code
id_list.append(id_wsclean2)
syscall = 'singularity exec ' + WSCLEAN_CONTAINER + ' '
syscall += gen.generate_syscall_wsclean(mslist=[myms],
imgname=corr_img_prefix,
datacol='CORRECTED_DATA',
briggs=-1.5,
multiscale=True,
scales='0,3,9',
niter=300000,
bda=True,
mask=mask)
run_command = gen.job_handler(syscall=syscall,
jobname=id_wsclean2,
infrastructure=INFRASTRUCTURE,
dependency=id_selfcal,
slurm_config=SLURM_WSCLEAN_MOD,
pbs_config=PBS_WSCLEAN_MOD)
f.write(run_command + '\n')
# ------------------------------------------------------------------------------
# STEP 5:
# Predict MODEL_DATA
id_predict2 = 'WSCPR' + code
id_list.append(id_predict2)
syscall = 'singularity exec ' + WSCLEAN_CONTAINER + ' '
syscall += gen.generate_syscall_predict(msname=myms,
imgbase=corr_img_prefix)
run_command = gen.job_handler(syscall=syscall,
jobname=id_predict2,
infrastructure=INFRASTRUCTURE,
dependency=id_wsclean2,
slurm_config=cfg.SLURM_WSCLEAN,
pbs_config=cfg.PBS_WSCLEAN)
f.write(run_command + '\n')
# ------------------------------------------------------------------------------
if INFRASTRUCTURE in ['idia', 'chpc']:
kill = 'echo "scancel "$' + '" "$'.join(
id_list) + ' > ' + kill_file
f.write(kill + '\n')
f.close()
def main():
USE_SINGULARITY = cfg.USE_SINGULARITY
gen.preamble()
print(gen.col() + '1GC (referenced calibration) setup')
gen.print_spacer()
# ------------------------------------------------------------------------------
#
# Setup paths, required containers, infrastructure
#
# ------------------------------------------------------------------------------
gen.setup_dir(cfg.LOGS)
gen.setup_dir(cfg.SCRIPTS)
gen.setup_dir(cfg.GAINTABLES)
INFRASTRUCTURE, CONTAINER_PATH = gen.set_infrastructure(sys.argv)
if CONTAINER_PATH is not None:
CONTAINER_RUNNER = 'singularity exec '
else:
CONTAINER_RUNNER = ''
CASA_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.CASA_PATTERN,
USE_SINGULARITY)
MEQTREES_CONTAINER = gen.get_container(CONTAINER_PATH,
cfg.MEQTREES_PATTERN,
USE_SINGULARITY)
RAGAVI_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.RAGAVI_PATTERN,
USE_SINGULARITY)
SHADEMS_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.SHADEMS_PATTERN,
USE_SINGULARITY)
# ------------------------------------------------------------------------------
#
# 1GC recipe definition
#
# ------------------------------------------------------------------------------
original_ms = glob.glob('*.ms')[0]
code = gen.get_code(original_ms)
myms = original_ms.replace('.ms', '_' + str(cfg.PRE_NCHANS) + 'ch.ms')
steps = []
# _ ______ ___ _ _ ______
# | | | ___ \ / _ \ | \ | | | _ \
# | | ______ | |_/ / / /_\ \ | \| | | | | |
# | | |______| | ___ \ | _ | | . ` | | | | |
# | |____ | |_/ / | | | | | |\ | | |/ /
# \_____/ \____/ \_| |_/ \_| \_/ |___/
if cfg.BAND[0].upper() == 'L':
step = {}
step['step'] = 0
step['comment'] = 'Split and average master MS'
step['dependency'] = None
step['id'] = 'SPPRE' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(
casascript=cfg.OXKAT + '/PRE_casa_average_to_1k_add_wtspec.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 1
step['comment'] = 'Run setup script to generate project_info pickle'
step['dependency'] = 0
step['id'] = 'SETUP' + code
syscall = CONTAINER_RUNNER + MEQTREES_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += ' python ' + cfg.OXKAT + '/1GC_00_setup.py ' + myms
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 2
step[
'comment'] = 'Rephase primary calibrator visibilties in case of open-time offset problems'
step['dependency'] = 1
step['id'] = 'UVFIX' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(
casascript=cfg.OXKAT +
'/1GC_01_casa_rephase_primary_calibrator.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 3
step['comment'] = 'Apply basic flagging steps to all fields'
step['dependency'] = 2
step['id'] = 'FGBAS' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(casascript=cfg.OXKAT +
'/1GC_02_casa_basic_flags.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 4
step['comment'] = 'Run setjy for primary calibrator'
step['dependency'] = 3
step['id'] = 'SETJY' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(casascript=cfg.OXKAT +
'/1GC_04_casa_setjy.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 5
step['comment'] = 'Run auto-flaggers on calibrators'
step['dependency'] = 4
step['id'] = 'FGCAL' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(
casascript=cfg.OXKAT + '/1GC_05_casa_autoflag_cals_DATA.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 6
step['comment'] = 'Split off calibrator MS with 8 SPWs'
step['dependency'] = 5
step['id'] = 'SPCAL' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(
casascript=cfg.OXKAT + '/1GC_06_casa_split_calibrators.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 7
step['comment'] = 'Fit for intrinsic model of secondary calibrator'
step['dependency'] = 6
step['id'] = 'CLMOD' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(
casascript=cfg.OXKAT + '/1GC_07_casa_get_secondary_model.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 8
step[
'comment'] = 'Generate reference calibration solutions and apply to target(s)'
step['dependency'] = 7
step['id'] = 'CL1GC' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(
casascript=cfg.OXKAT +
'/1GC_08_casa_refcal_using_secondary_model.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 9
step['comment'] = 'Plot the gain solutions'
step['dependency'] = 8
step['id'] = 'PLTAB' + code
syscall = CONTAINER_RUNNER + RAGAVI_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += 'python3 ' + cfg.OXKAT + '/PLOT_gaintables.py cal_1GC_* cal_1GC_*calibrators.ms*'
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 10
step['comment'] = 'Split the corrected target data'
step['dependency'] = 8
step['id'] = 'SPTRG' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(casascript=cfg.OXKAT +
'/1GC_09_casa_split_targets.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 11
step['comment'] = 'Plot the corrected calibrator visibilities'
step['dependency'] = 10
step['id'] = 'PLVIS' + code
syscall = CONTAINER_RUNNER + SHADEMS_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += 'python3 ' + cfg.OXKAT + '/1GC_10_plot_visibilities.py'
step['syscall'] = syscall
steps.append(step)
# _ _ _ _ ______
# | | | | | | | | | ___|
# | | | | | |_| | | |_
# | | | | | _ | | _|
# | |_| | | | | | | |
# \___/ \_| |_/ \_|
elif cfg.BAND[0].upper() == 'U':
step = {}
step['step'] = 0
step['comment'] = 'Split and average master MS'
step['dependency'] = None
step['id'] = 'SPPRE' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(
casascript=cfg.OXKAT + '/PRE_casa_average_to_1k_add_wtspec.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 1
step['comment'] = 'Run setup script to generate project_info pickle'
step['dependency'] = 0
step['id'] = 'SETUP' + code
syscall = CONTAINER_RUNNER + MEQTREES_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += ' python ' + cfg.OXKAT + '/1GC_00_setup.py ' + myms
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 2
step['comment'] = 'Apply basic flagging steps to all fields'
step['dependency'] = 1
step['id'] = 'FGBAS' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(casascript=cfg.OXKAT +
'/1GC_casa_UHF_basic_flags.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 3
step['comment'] = 'Run auto-flaggers on calibrators'
step['dependency'] = 2
step['id'] = 'FGCAL' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(
casascript=cfg.OXKAT + '/1GC_casa_UHF_autoflag_cals_DATA.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 4
step[
'comment'] = 'Generate reference calibration solutions and apply to target(s)'
step['dependency'] = 3
step['id'] = 'CL1GC' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(casascript=cfg.OXKAT +
'/1GC_casa_UHF_refcal.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 5
step['comment'] = 'Plot the gain solutions'
step['dependency'] = 4
step['id'] = 'PLTAB' + code
syscall = CONTAINER_RUNNER + RAGAVI_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += 'python3 ' + cfg.OXKAT + '/PLOT_gaintables.py cal_1GC_*'
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 6
step['comment'] = 'Split the corrected target data'
step['dependency'] = 4
step['id'] = 'SPTRG' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(casascript=cfg.OXKAT +
'/1GC_09_casa_split_targets.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 7
step['comment'] = 'Plot the corrected calibrator visibilities'
step['dependency'] = 6
step['id'] = 'PLVIS' + code
syscall = CONTAINER_RUNNER + SHADEMS_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += 'python3 ' + cfg.OXKAT + '/1GC_10_plot_visibilities.py'
step['syscall'] = syscall
steps.append(step)
# ------------------------------------------------------------------------------
#
# Write the run file and kill file based on the recipe
#
# ------------------------------------------------------------------------------
submit_file = 'submit_1GC_jobs.sh'
kill_file = cfg.SCRIPTS + '/kill_1GC_jobs.sh'
f = open(submit_file, 'w')
f.write('#!/usr/bin/env bash\n')
f.write('export SINGULARITY_BINDPATH=' + cfg.BINDPATH + '\n')
id_list = []
for step in steps:
step_id = step['id']
id_list.append(step_id)
if step['dependency'] is not None:
dependency = steps[step['dependency']]['id']
else:
dependency = None
syscall = step['syscall']
if 'slurm_config' in step.keys():
slurm_config = step['slurm_config']
else:
slurm_config = cfg.SLURM_DEFAULTS
if 'pbs_config' in step.keys():
pbs_config = step['pbs_config']
else:
pbs_config = cfg.PBS_DEFAULTS
comment = step['comment']
run_command = gen.job_handler(syscall=syscall,
jobname=step_id,
infrastructure=INFRASTRUCTURE,
dependency=dependency,
slurm_config=slurm_config,
pbs_config=pbs_config)
f.write('\n# ' + comment + '\n')
f.write(run_command)
if INFRASTRUCTURE == 'idia' or INFRASTRUCTURE == 'hippo':
kill = '\necho "scancel "$' + '" "$'.join(
id_list) + ' > ' + kill_file + '\n'
f.write(kill)
elif INFRASTRUCTURE == 'chpc':
kill = '\necho "qdel "$' + '" "$'.join(
id_list) + ' > ' + kill_file + '\n'
f.write(kill)
f.close()
gen.make_executable(submit_file)
gen.print_spacer()
print(gen.col('Run file') + submit_file)
gen.print_spacer()
def main():
# ------------------------------------------------------------------------------
# Setup
INFRASTRUCTURE, CONTAINER_PATH = gen.set_infrastructure(sys.argv)
# Get paths from config and setup folders
CWD = cfg.CWD
BIND = cfg.BIND
OXKAT = cfg.OXKAT
PARSETS = cfg.PARSETS
GAINTABLES = cfg.GAINTABLES
LOGS = cfg.LOGS
SCRIPTS = cfg.SCRIPTS
BINDPATH = '$PWD,'+CWD+','+BIND
gen.setup_dir(LOGS)
gen.setup_dir(SCRIPTS)
gen.setup_dir(GAINTABLES)
# Enable running without containers
if CONTAINER_PATH is not None:
CONTAINER_RUNNER='singularity exec '
else:
CONTAINER_RUNNER=''
# Get containers needed for this script
CASA_CONTAINER = gen.get_container(CONTAINER_PATH,cfg.CASA_PATTERN)
RAGAVI_CONTAINER = gen.get_container(CONTAINER_PATH,cfg.RAGAVI_PATTERN)
SHADEMS_CONTAINER = gen.get_container(CONTAINER_PATH,cfg.SHADEMS_PATTERN)
MEQTREES_CONTAINER = gen.get_container(CONTAINER_PATH,cfg.MEQTREES_PATTERN)
# Set names of the run and kill files, open run file for writing
submit_file = 'submit_1GC_jobs.sh'
kill_file = SCRIPTS+'/kill_1GC_jobs.sh'
f = open(submit_file,'w')
f.write('#!/usr/bin/env bash\n')
f.write('export SINGULARITY_BINDPATH='+BINDPATH+'\n')
# Get the MS name
original_ms = glob.glob('*.ms')[0]
code = gen.get_code(original_ms)
myms = original_ms.replace('.ms','_'+str(cfg.PRE_NCHANS)+'ch.ms')
# Initialise a list to hold all the job IDs
id_list = []
# ------------------------------------------------------------------------------
# Pre-processing:
# Duplicate orignal MS, average to 1k channels if required
id_average = 'SPPRE'+code
id_list.append(id_average)
casalog = LOGS+'/casa_1GC_'+id_average+'.log'
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' '
syscall += gen.generate_syscall_casa(casascript=OXKAT+'/PRE_casa_average_to_1k_add_wtspec.py',
casalogfile=casalog)
run_command = gen.job_handler(syscall=syscall,
jobname=id_average,
infrastructure=INFRASTRUCTURE)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 0:
# Examine MS and store relevant deductions in project_info.p
id_setup = 'SETUP'+code
id_list.append(id_setup)
syscall = CONTAINER_RUNNER+MEQTREES_CONTAINER+' '
syscall += 'python '+OXKAT+'/1GC_00_setup.py '+myms
run_command = gen.job_handler(syscall=syscall,
jobname=id_setup,
infrastructure=INFRASTRUCTURE,
dependency=id_average)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 1:
# Rephase the primary calibrators to correct positions
id_fixvis = 'UVFIX'+code
id_list.append(id_fixvis)
casalog = LOGS+'/casa_1GC_'+id_fixvis+'.log'
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' '
syscall += gen.generate_syscall_casa(casascript=OXKAT+'/1GC_01_casa_rephase_primary_calibrator.py',
casalogfile=casalog)
run_command = gen.job_handler(syscall=syscall,
jobname=id_fixvis,
infrastructure=INFRASTRUCTURE,
dependency=id_setup)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 2:
# Apply basic flagging steps to all fields
id_basic = 'FGBAS'+code
id_list.append(id_basic)
casalog = LOGS+'/casa_1GC_'+id_basic+'.log'
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' '
syscall += gen.generate_syscall_casa(casascript=OXKAT+'/1GC_02_casa_basic_flags.py',
casalogfile=casalog)
run_command = gen.job_handler(syscall=syscall,
jobname=id_basic,
infrastructure=INFRASTRUCTURE,
dependency=id_fixvis)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 3:
# Run auto-flaggers on calibrators
id_autoflagcals = 'FGCAL'+code
id_list.append(id_autoflagcals)
casalog = LOGS+'/casa_1GC_'+id_autoflagcals+'.log'
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' '
syscall += gen.generate_syscall_casa(casascript=OXKAT+'/1GC_03_casa_autoflag_cals_DATA.py',
casalogfile=casalog)
run_command = gen.job_handler(syscall=syscall,
jobname=id_autoflagcals,
infrastructure=INFRASTRUCTURE,
dependency=id_basic)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 4:
# Split calibrators into a MS with 8 spectral windows
id_splitcals = 'SPCAL'+code
id_list.append(id_splitcals)
casalog = LOGS+'/casa_1GC_'+id_splitcals+'.log'
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' '
syscall += gen.generate_syscall_casa(casascript=OXKAT+'/1GC_04_casa_split_calibrators.py',
casalogfile=casalog)
run_command = gen.job_handler(syscall=syscall,
jobname=id_splitcals,
infrastructure=INFRASTRUCTURE,
dependency=id_autoflagcals)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 5:
# Derive an intrinsic spectral model for the secondary calibrator
id_secondarymodel = 'CLMOD'+code
id_list.append(id_secondarymodel)
casalog = LOGS+'/casa_1GC_'+id_secondarymodel+'.log'
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' '
syscall += gen.generate_syscall_casa(casascript=OXKAT+'/1GC_05_casa_get_secondary_model.py',
casalogfile=casalog)
run_command = gen.job_handler(syscall=syscall,
jobname=id_secondarymodel,
infrastructure=INFRASTRUCTURE,
dependency=id_splitcals)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 6: (1GC)
# Perform reference calibration steps and apply to target(s)
id_1GC = 'CL1GC'+code
id_list.append(id_1GC)
casalog = LOGS+'/casa_1GC_'+id_1GC+'.log'
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' '
syscall += gen.generate_syscall_casa(casascript=OXKAT+'/1GC_06_casa_refcal_using_secondary_model.py',
casalogfile=casalog)
run_command = gen.job_handler(syscall=syscall,
jobname=id_1GC,
infrastructure=INFRASTRUCTURE,
dependency=id_secondarymodel)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 7:
# Make gain table plots
id_gainplots = 'PLTAB'+code
id_list.append(id_gainplots)
syscall = CONTAINER_RUNNER+RAGAVI_CONTAINER+' '
syscall += 'python3 '+OXKAT+'/PLOT_gaintables.py cal_1GC_* cal_1GC_*calibrators.ms*'
run_command = gen.job_handler(syscall=syscall,
jobname=id_gainplots,
infrastructure=INFRASTRUCTURE,
dependency=id_1GC)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 8:
# Split the corrected target data into individual Measurement Sets
id_splittargets = 'SPTRG'+code
id_list.append(id_splittargets)
casalog = LOGS+'/casa_1GC_'+id_splittargets+'.log'
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' '
syscall += gen.generate_syscall_casa(casascript=OXKAT+'/1GC_07_casa_split_targets.py',
casalogfile=casalog)
run_command = gen.job_handler(syscall=syscall,
jobname=id_splittargets,
infrastructure=INFRASTRUCTURE,
dependency=id_1GC)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 9:
# Make visibility plots
id_visplots = 'PLVIS'+code
id_list.append(id_visplots)
syscall = CONTAINER_RUNNER+SHADEMS_CONTAINER+' '
syscall += 'python3 '+OXKAT+'/1GC_08_plot_visibilities.py'
run_command = gen.job_handler(syscall=syscall,
jobname=id_visplots,
infrastructure=INFRASTRUCTURE,
dependency=id_splittargets)
f.write(run_command)
# ------------------------------------------------------------------------------
if INFRASTRUCTURE == 'idia' or INFRASTRUCTURE == 'hippo':
kill = 'echo "scancel "$'+'" "$'.join(id_list)+' > '+kill_file+'\n'
f.write(kill)
elif INFRASTRUCTURE == 'chpc':
kill = 'echo "qdel "$'+'" "$'.join(id_list)+' > '+kill_file+'\n'
f.write(kill)
f.close()
gen.make_executable(submit_file)
def main():
# ------------------------------------------------------------------------------
# Setup
INFRASTRUCTURE, CONTAINER_PATH = gen.set_infrastructure(sys.argv)
# Get paths from config and setup folders
CWD = cfg.CWD
BIND = cfg.BIND
OXKAT = cfg.OXKAT
PARSETS = cfg.PARSETS
TOOLS = cfg.TOOLS
GAINTABLES = cfg.GAINTABLES
IMAGES = cfg.IMAGES
LOGS = cfg.LOGS
SCRIPTS = cfg.SCRIPTS
BINDPATH = '$PWD,' + CWD + ',' + BIND
gen.setup_dir(LOGS)
gen.setup_dir(SCRIPTS)
gen.setup_dir(IMAGES)
gen.setup_dir(GAINTABLES)
# Enable running without containers
if CONTAINER_PATH is not None:
CONTAINER_RUNNER = 'singularity exec '
else:
CONTAINER_RUNNER = ''
# Get containers needed for this script
CASA_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.CASA_PATTERN)
DDFACET_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.DDFACET_PATTERN)
MAKEMASK_CONTAINER = gen.get_container(CONTAINER_PATH,
cfg.MAKEMASK_PATTERN)
RAGAVI_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.RAGAVI_PATTERN)
TRICOLOUR_CONTAINER = gen.get_container(CONTAINER_PATH,
cfg.TRICOLOUR_PATTERN)
WSCLEAN_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.WSCLEAN_PATTERN)
# Set names of the run and kill files, open run file for writing
submit_file = 'submit_2GC_jobs.sh'
f = open(submit_file, 'w')
f.write('#!/usr/bin/env bash\n')
f.write('export SINGULARITY_BINDPATH=' + BINDPATH + '\n')
# Get target info from project_info.p
project_info = pickle.load(open('project_info.p', 'rb'), encoding='latin1')
target_ids = project_info['target_ids']
target_names = project_info['target_names']
target_ms = project_info['target_ms']
# Loop over targets
codes = []
ii = 1
for tt in range(0, len(target_ids)):
targetname = target_names[tt]
myms = target_ms[tt]
if not o.isdir(myms):
print('------------------------------------------------------')
print(gen.now() + myms + ' not found, skipping ' + targetname)
else:
filename_targetname = gen.scrub_target_name(targetname)
code = gen.get_target_code(targetname)
if code in codes:
code += '_' + str(ii)
ii += 1
codes.append(code)
mask0 = sorted(
glob.glob(IMAGES + '/*' + filename_targetname +
'*.mask0.fits'))
if len(mask0) > 0:
mask = mask0[0]
else:
mask = 'auto'
print('------------------------------------------------------')
print(gen.now() + 'Target: ' + targetname)
print(gen.now() + 'MS: ' + myms)
print(gen.now() + 'Using mask: ' + mask)
f.write('\n# ' + targetname + '\n')
kill_file = SCRIPTS + '/kill_2GC_jobs_' + filename_targetname + '.sh'
data_img_prefix = IMAGES + '/img_' + myms + '_datamask'
corr_img_prefix = IMAGES + '/img_' + myms + '_pcalmask'
# Initialise a list to hold all the job IDs
id_list = []
# ------------------------------------------------------------------------------
# STEP 1:
# Masked wsclean on DATA column
id_wsclean1 = 'WSDMA' + code
id_list.append(id_wsclean1)
syscall = CONTAINER_RUNNER + WSCLEAN_CONTAINER + ' '
syscall += gen.generate_syscall_wsclean(mslist=[myms],
imgname=data_img_prefix,
datacol='DATA',
bda=True,
mask=mask)
run_command = gen.job_handler(syscall=syscall,
jobname=id_wsclean1,
infrastructure=INFRASTRUCTURE,
slurm_config=cfg.SLURM_WSCLEAN,
pbs_config=cfg.PBS_WSCLEAN)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 2:
# Predict MODEL_DATA
id_predict1 = 'WSDPR' + code
id_list.append(id_predict1)
syscall = CONTAINER_RUNNER + WSCLEAN_CONTAINER + ' '
syscall += gen.generate_syscall_predict(msname=myms,
imgbase=data_img_prefix)
run_command = gen.job_handler(syscall=syscall,
jobname=id_predict1,
infrastructure=INFRASTRUCTURE,
dependency=id_wsclean1,
slurm_config=cfg.SLURM_WSCLEAN,
pbs_config=cfg.PBS_WSCLEAN)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 3:
# Self-calibrate phases then amplitudes
id_selfcal = 'CL2GC' + code
id_list.append(id_selfcal)
casalog = LOGS + '/casa_2GC_' + id_selfcal + '.log'
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' '
syscall += gen.generate_syscall_casa(
casascript=OXKAT + '/2GC_casa_selfcal_target_amp_phases.py',
casalogfile=casalog,
extra_args='mslist=' + myms)
run_command = gen.job_handler(syscall=syscall,
jobname=id_selfcal,
infrastructure=INFRASTRUCTURE,
dependency=id_predict1)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 4:
# Make gain table plots
id_gainplots = 'PLTAB' + code
id_list.append(id_gainplots)
syscall = CONTAINER_RUNNER + RAGAVI_CONTAINER + ' '
syscall += 'python3 ' + OXKAT + '/PLOT_gaintables.py cal_2GC_*' + myms + '*'
run_command = gen.job_handler(syscall=syscall,
jobname=id_gainplots,
infrastructure=INFRASTRUCTURE,
dependency=id_selfcal)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 5:
# Masked wsclean on CORRECTED_DATA column
id_wsclean2 = 'WSCMA' + code
id_list.append(id_wsclean2)
syscall = CONTAINER_RUNNER + WSCLEAN_CONTAINER + ' '
syscall += gen.generate_syscall_wsclean(mslist=[myms],
imgname=corr_img_prefix,
datacol='CORRECTED_DATA',
bda=True,
mask=mask)
run_command = gen.job_handler(syscall=syscall,
jobname=id_wsclean2,
infrastructure=INFRASTRUCTURE,
dependency=id_selfcal,
slurm_config=cfg.SLURM_WSCLEAN,
pbs_config=cfg.PBS_WSCLEAN)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 6:
# Make a FITS mask
syscall = CONTAINER_RUNNER + MAKEMASK_CONTAINER + ' '
syscall += gen.generate_syscall_makemask(
restoredimage=corr_img_prefix + '-MFS-image.fits',
outfile=corr_img_prefix + '-MFS-image.mask1.fits',
thresh=5.5,
zoompix=cfg.DDF_NPIX)[0]
id_makemask = 'MASK1' + code
id_list.append(id_makemask)
run_command = gen.job_handler(syscall=syscall,
jobname=id_makemask,
infrastructure=INFRASTRUCTURE,
dependency=id_wsclean2)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 7:
# Predict MODEL_DATA
id_predict2 = 'WSCPR' + code
id_list.append(id_predict2)
syscall = CONTAINER_RUNNER + WSCLEAN_CONTAINER + ' '
syscall += gen.generate_syscall_predict(msname=myms,
imgbase=corr_img_prefix)
run_command = gen.job_handler(syscall=syscall,
jobname=id_predict2,
infrastructure=INFRASTRUCTURE,
dependency=id_wsclean2,
slurm_config=cfg.SLURM_WSCLEAN,
pbs_config=cfg.PBS_WSCLEAN)
f.write(run_command)
# ------------------------------------------------------------------------------
if INFRASTRUCTURE == 'idia':
kill = 'echo "scancel "$' + '" "$'.join(
id_list) + ' > ' + kill_file + '\n'
f.write(kill)
elif INFRASTRUCTURE == 'chpc':
kill = 'echo "qdel "$' + '" "$'.join(
id_list) + ' > ' + kill_file + '\n'
f.write(kill)
f.close()
gen.make_executable(submit_file)
def main():
USE_SINGULARITY = cfg.USE_SINGULARITY
gen.preamble()
print(gen.col() + '2GC (direction independent selfcal) setup')
gen.print_spacer()
# ------------------------------------------------------------------------------
#
# Setup paths, required containers, infrastructure
#
# ------------------------------------------------------------------------------
OXKAT = cfg.OXKAT
DATA = cfg.DATA
GAINTABLES = cfg.GAINTABLES
IMAGES = cfg.IMAGES
SCRIPTS = cfg.SCRIPTS
gen.setup_dir(GAINTABLES)
gen.setup_dir(IMAGES)
gen.setup_dir(cfg.LOGS)
gen.setup_dir(cfg.SCRIPTS)
INFRASTRUCTURE, CONTAINER_PATH = gen.set_infrastructure(sys.argv)
if CONTAINER_PATH is not None:
CONTAINER_RUNNER = 'singularity exec '
else:
CONTAINER_RUNNER = ''
CASA_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.CASA_PATTERN,
USE_SINGULARITY)
MAKEMASK_CONTAINER = gen.get_container(CONTAINER_PATH,
cfg.MAKEMASK_PATTERN,
USE_SINGULARITY)
RAGAVI_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.RAGAVI_PATTERN,
USE_SINGULARITY)
WSCLEAN_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.WSCLEAN_PATTERN,
USE_SINGULARITY)
# Get target information from project pickle
project_info = pickle.load(open('project_info.p', 'rb'), encoding='latin1')
target_ids = project_info['target_ids']
target_names = project_info['target_names']
target_ms = project_info['target_ms']
# ------------------------------------------------------------------------------
#
# 2GC recipe definition
#
# ------------------------------------------------------------------------------
target_steps = []
codes = []
ii = 1
# Loop over targets
for tt in range(0, len(target_ids)):
targetname = target_names[tt]
myms = target_ms[tt]
if not o.isdir(myms):
gen.print_spacer()
print(gen.col('Target') + targetname)
print(gen.col('MS') + 'not found, skipping')
else:
steps = []
filename_targetname = gen.scrub_target_name(targetname)
code = gen.get_target_code(targetname)
if code in codes:
code += '_' + str(ii)
ii += 1
codes.append(code)
# Look for the FITS mask for this target
mask0 = sorted(
glob.glob(IMAGES + '/*' + filename_targetname +
'*.mask0.fits'))
if len(mask0) > 0:
mask = mask0[0]
else:
mask = 'auto'
gen.print_spacer()
print(gen.col('Target') + targetname)
print(gen.col('Measurement Set') + myms)
print(gen.col('Code') + code)
print(gen.col('Mask') + mask)
# Image prefixes
data_img_prefix = IMAGES + '/img_' + myms + '_datamask'
corr_img_prefix = IMAGES + '/img_' + myms + '_pcalmask'
# Target-specific kill file
kill_file = SCRIPTS + '/kill_2GC_jobs_' + filename_targetname + '.sh'
step = {}
step['step'] = 0
step[
'comment'] = 'Run wsclean, masked deconvolution of the DATA column of ' + myms
step['dependency'] = None
step['id'] = 'WSDMA' + code
step['slurm_config'] = cfg.SLURM_WSCLEAN
step['pbs_config'] = cfg.PBS_WSCLEAN
absmem = gen.absmem_helper(step, INFRASTRUCTURE, cfg.WSC_ABSMEM)
syscall = CONTAINER_RUNNER + WSCLEAN_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_wsclean(mslist=[myms],
imgname=data_img_prefix,
datacol='DATA',
bda=True,
automask=False,
autothreshold=False,
localrms=False,
mask=mask,
absmem=absmem)
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 1
step[
'comment'] = 'Predict model visibilities from imaging of the DATA column'
step['dependency'] = 0
step['id'] = 'WSDPR' + code
step['slurm_config'] = cfg.SLURM_WSCLEAN
step['pbs_config'] = cfg.PBS_WSCLEAN
absmem = gen.absmem_helper(step, INFRASTRUCTURE, cfg.WSC_ABSMEM)
syscall = CONTAINER_RUNNER + WSCLEAN_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_predict(msname=myms,
imgbase=data_img_prefix,
absmem=absmem)
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 2
step['comment'] = 'Run CASA self-calibration script'
step['dependency'] = 1
step['id'] = 'CL2GC' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(
casascript=OXKAT + '/2GC_casa_selfcal_target_amp_phases.py',
extra_args='mslist=' + myms)
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 3
step['comment'] = 'Plot the self-calibration gain solutions'
step['dependency'] = 2
step['id'] = 'PLTAB' + code
syscall = CONTAINER_RUNNER + RAGAVI_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += 'python3 ' + OXKAT + '/PLOT_gaintables.py cal_2GC_*' + myms + '*'
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 4
step[
'comment'] = 'Run wsclean, masked deconvolution of the CORRECTED_DATA column of ' + myms
step['dependency'] = 2
step['id'] = 'WSCMA' + code
step['slurm_config'] = cfg.SLURM_WSCLEAN
step['pbs_config'] = cfg.PBS_WSCLEAN
absmem = gen.absmem_helper(step, INFRASTRUCTURE, cfg.WSC_ABSMEM)
syscall = CONTAINER_RUNNER + WSCLEAN_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_wsclean(mslist=[myms],
imgname=corr_img_prefix,
datacol='CORRECTED_DATA',
bda=True,
automask=False,
autothreshold=False,
localrms=False,
mask=mask,
absmem=absmem)
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 5
step[
'comment'] = 'Refine the cleaning mask for ' + targetname + ', crop for use with DDFacet'
step['dependency'] = 4
step['id'] = 'MASK1' + code
syscall = CONTAINER_RUNNER + MAKEMASK_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_makemask(
restoredimage=corr_img_prefix + '-MFS-image.fits',
outfile=corr_img_prefix + '-MFS-image.mask1.fits',
thresh=5.5,
zoompix=cfg.DDF_NPIX)[0]
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 6
step[
'comment'] = 'Predict model visibilities from imaging of the CORRECTED_DATA column'
step['dependency'] = 4
step['id'] = 'WSCPR' + code
step['slurm_config'] = cfg.SLURM_WSCLEAN
step['pbs_config'] = cfg.PBS_WSCLEAN
absmem = gen.absmem_helper(step, INFRASTRUCTURE, cfg.WSC_ABSMEM)
syscall = CONTAINER_RUNNER + WSCLEAN_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_predict(msname=myms,
imgbase=corr_img_prefix,
absmem=absmem)
step['syscall'] = syscall
steps.append(step)
target_steps.append((steps, kill_file, targetname))
# ------------------------------------------------------------------------------
#
# Write the run file and kill file based on the recipe
#
# ------------------------------------------------------------------------------
submit_file = 'submit_2GC_jobs.sh'
f = open(submit_file, 'w')
f.write('#!/usr/bin/env bash\n')
f.write('export SINGULARITY_BINDPATH=' + cfg.BINDPATH + '\n')
for content in target_steps:
steps = content[0]
kill_file = content[1]
targetname = content[2]
id_list = []
f.write('\n#---------------------------------------\n')
f.write('# ' + targetname)
f.write('\n#---------------------------------------\n')
for step in steps:
step_id = step['id']
id_list.append(step_id)
if step['dependency'] is not None:
dependency = steps[step['dependency']]['id']
else:
dependency = None
syscall = step['syscall']
if 'slurm_config' in step.keys():
slurm_config = step['slurm_config']
else:
slurm_config = cfg.SLURM_DEFAULTS
if 'pbs_config' in step.keys():
pbs_config = step['pbs_config']
else:
pbs_config = cfg.PBS_DEFAULTS
comment = step['comment']
run_command = gen.job_handler(syscall=syscall,
jobname=step_id,
infrastructure=INFRASTRUCTURE,
dependency=dependency,
slurm_config=slurm_config,
pbs_config=pbs_config)
f.write('\n# ' + comment + '\n')
f.write(run_command)
if INFRASTRUCTURE != 'node':
f.write('\n# Generate kill script for ' + targetname + '\n')
if INFRASTRUCTURE == 'idia' or INFRASTRUCTURE == 'hippo':
kill = 'echo "scancel "$' + '" "$'.join(
id_list) + ' > ' + kill_file + '\n'
f.write(kill)
elif INFRASTRUCTURE == 'chpc':
kill = 'echo "qdel "$' + '" "$'.join(
id_list) + ' > ' + kill_file + '\n'
f.write(kill)
f.close()
gen.make_executable(submit_file)
gen.print_spacer()
print(gen.col('Run file') + submit_file)
gen.print_spacer()
def main():
USE_SINGULARITY = cfg.USE_SINGULARITY
if cfg.BAND[0].upper() == 'U':
print(gen.col()+'Full-field primary models not available for UHF yet')
gen.print_spacer()
sys.exit()
gen.preamble()
print(gen.col()+'1GC (referenced calibration) setup')
print(gen.col()+'Note that this recipe uses a full-field model for PKS B1934-638.')
print(gen.col()+'This is somewhat experimental!')
gen.print_spacer()
# ------------------------------------------------------------------------------
#
# Setup paths, required containers, infrastructure
#
# ------------------------------------------------------------------------------
gen.setup_dir(cfg.LOGS)
gen.setup_dir(cfg.SCRIPTS)
gen.setup_dir(cfg.GAINTABLES)
INFRASTRUCTURE, CONTAINER_PATH = gen.set_infrastructure(sys.argv)
if CONTAINER_PATH is not None:
CONTAINER_RUNNER='singularity exec '
else:
CONTAINER_RUNNER=''
CASA_CONTAINER = gen.get_container(CONTAINER_PATH,cfg.CASA_PATTERN,USE_SINGULARITY)
MEQTREES_CONTAINER = gen.get_container(CONTAINER_PATH,cfg.MEQTREES_PATTERN,USE_SINGULARITY)
RAGAVI_CONTAINER = gen.get_container(CONTAINER_PATH,cfg.RAGAVI_PATTERN,USE_SINGULARITY)
SHADEMS_CONTAINER = gen.get_container(CONTAINER_PATH,cfg.SHADEMS_PATTERN,USE_SINGULARITY)
WSCLEAN_CONTAINER = gen.get_container(CONTAINER_PATH,cfg.WSCLEAN_PATTERN,USE_SINGULARITY)
# ------------------------------------------------------------------------------
#
# 1GC recipe definition
#
# ------------------------------------------------------------------------------
original_ms = glob.glob('*.ms')[0]
code = gen.get_code(original_ms)
myms = original_ms.replace('.ms','_'+str(cfg.PRE_NCHANS)+'ch.ms')
steps = []
step = {}
step['step'] = 0
step['comment'] = 'Split and average master MS'
step['dependency'] = None
step['id'] = 'SPPRE'+code
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(casascript=cfg.OXKAT+'/PRE_casa_average_to_1k_add_wtspec.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 1
step['comment'] = 'Run setup script to generate project_info pickle'
step['dependency'] = 0
step['id'] = 'SETUP'+code
syscall = CONTAINER_RUNNER+MEQTREES_CONTAINER+' ' if USE_SINGULARITY else ''
syscall += 'python '+cfg.OXKAT+'/1GC_00_setup.py '+myms
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 2
step['comment'] = 'Rephase primary calibrator visibilties in case of open-time offset problems'
step['dependency'] = 1
step['id'] = 'UVFIX'+code
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(casascript=cfg.OXKAT+'/1GC_01_casa_rephase_primary_calibrator.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 3
step['comment'] = 'Apply basic flagging steps to all fields'
step['dependency'] = 2
step['id'] = 'FGBAS'+code
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(casascript=cfg.OXKAT+'/1GC_02_casa_basic_flags.py')
step['syscall'] = syscall
steps.append(step)
# step = {}
# step['step'] = 4
# step['comment'] = 'Add CORRECTED_DATA and MODEL_DATA columns'
# step['dependency'] = 3
# step['id'] = 'ADCOL'+code
# syscall = CONTAINER_RUNNER+MEQTREES_CONTAINER+' ' if USE_SINGULARITY else ''
# syscall += 'python '+cfg.TOOLS+'/add_MS_column.py --colname CORRECTED_DATA,MODEL_DATA '+myms
# step['syscall'] = syscall
# steps.append(step)
step = {}
step['step'] = 4
step['comment'] = 'Predict field sources for primary if required'
step['dependency'] = 3 # change back to 4 if above step is required
step['id'] = 'SETCC'+code
step['slurm_config'] = cfg.SLURM_WSCLEAN
step['pbs_config'] = cfg.PBS_WSCLEAN
syscall = CONTAINER_RUNNER+WSCLEAN_CONTAINER+' ' if USE_SINGULARITY else ''
syscall += 'python2 '+cfg.OXKAT+'/1GC_03_primary_cal_field_sources.py'
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 5
step['comment'] = 'Copy MODEL_DATA to CORRECTED_DATA (temp storage for primary field sources)'
step['dependency'] = 4
step['id'] = 'CPCOL'+code
syscall = CONTAINER_RUNNER+MEQTREES_CONTAINER+' ' if USE_SINGULARITY else ''
syscall += 'python '+cfg.TOOLS+'/copy_MS_column.py --fromcol MODEL_DATA --tocol CORRECTED_DATA '+myms
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 6
step['comment'] = 'Run setjy for primary calibrator'
step['dependency'] = 5
step['id'] = 'SETJY'+code
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(casascript=cfg.OXKAT+'/1GC_04_casa_setjy.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 7
step['comment'] = 'Add field source model in CORRECTED_DATA to component model in MODEL_DATA'
step['dependency'] = 6
step['id'] = 'SMCOL'+code
syscall = CONTAINER_RUNNER+MEQTREES_CONTAINER+' ' if USE_SINGULARITY else ''
syscall += 'python '+cfg.TOOLS+'/sum_MS_columns.py --src CORRECTED_DATA --dest MODEL_DATA '+myms
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 8
step['comment'] = 'Run auto-flaggers on calibrators'
step['dependency'] = 7
step['id'] = 'FGCAL'+code
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(casascript=cfg.OXKAT+'/1GC_05_casa_autoflag_cals_DATA.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 9
step['comment'] = 'Split off calibrator MS with 8 SPWs'
step['dependency'] = 8
step['id'] = 'SPCAL'+code
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(casascript=cfg.OXKAT+'/1GC_06_casa_split_calibrators.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 10
step['comment'] = 'Fit for intrinsic model of secondary calibrator'
step['dependency'] = 9
step['id'] = 'CLMOD'+code
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(casascript=cfg.OXKAT+'/1GC_07_casa_get_secondary_model.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 11
step['comment'] = 'Generate reference calibration solutions and apply to target(s)'
step['dependency'] = 10
step['id'] = 'CL1GC'+code
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(casascript=cfg.OXKAT+'/1GC_08_casa_refcal_using_secondary_model.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 12
step['comment'] = 'Plot the gain solutions'
step['dependency'] = 11
step['id'] = 'PLTAB'+code
syscall = CONTAINER_RUNNER+RAGAVI_CONTAINER+' ' if USE_SINGULARITY else ''
syscall += 'python3 '+cfg.OXKAT+'/PLOT_gaintables.py cal_1GC_* cal_1GC_*calibrators.ms*'
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 13
step['comment'] = 'Split the corrected target data'
step['dependency'] = 11
step['id'] = 'SPTRG'+code
syscall = CONTAINER_RUNNER+CASA_CONTAINER+' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_casa(casascript=cfg.OXKAT+'/1GC_09_casa_split_targets.py')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 14
step['comment'] = 'Plot the corrected calibrator visibilities'
step['dependency'] = 13
step['id'] = 'PLVIS'+code
syscall = CONTAINER_RUNNER+SHADEMS_CONTAINER+' ' if USE_SINGULARITY else ''
syscall += 'python3 '+cfg.OXKAT+'/1GC_10_plot_visibilities.py'
step['syscall'] = syscall
steps.append(step)
# ------------------------------------------------------------------------------
#
# Write the run file and kill file based on the recipe
#
# ------------------------------------------------------------------------------
submit_file = 'submit_1GC_jobs.sh'
kill_file = cfg.SCRIPTS+'/kill_1GC_jobs.sh'
f = open(submit_file,'w')
f.write('#!/usr/bin/env bash\n')
f.write('export SINGULARITY_BINDPATH='+cfg.BINDPATH+'\n')
id_list = []
for step in steps:
step_id = step['id']
id_list.append(step_id)
if step['dependency'] is not None:
dependency = steps[step['dependency']]['id']
else:
dependency = None
syscall = step['syscall']
if 'slurm_config' in step.keys():
slurm_config = step['slurm_config']
else:
slurm_config = cfg.SLURM_DEFAULTS
if 'pbs_config' in step.keys():
pbs_config = step['pbs_config']
else:
pbs_config = cfg.PBS_DEFAULTS
comment = step['comment']
run_command = gen.job_handler(syscall = syscall,
jobname = step_id,
infrastructure = INFRASTRUCTURE,
dependency = dependency,
slurm_config = slurm_config,
pbs_config = pbs_config)
f.write('\n# '+comment+'\n')
f.write(run_command)
if INFRASTRUCTURE == 'idia' or INFRASTRUCTURE == 'hippo':
kill = '\necho "scancel "$'+'" "$'.join(id_list)+' > '+kill_file+'\n'
f.write(kill)
elif INFRASTRUCTURE == 'chpc':
kill = '\necho "qdel "$'+'" "$'.join(id_list)+' > '+kill_file+'\n'
f.write(kill)
f.close()
gen.make_executable(submit_file)
gen.print_spacer()
print(gen.col('Run file')+submit_file)
gen.print_spacer()
