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():
USE_SINGULARITY = cfg.USE_SINGULARITY
gen.preamble()
print(gen.col() + '3GC (facet-based corrections) setup')
gen.print_spacer()
# ------------------------------------------------------------------------------
#
# Setup paths, required containers, infrastructure
#
# ------------------------------------------------------------------------------
OXKAT = cfg.OXKAT
DATA = cfg.DATA
GAINTABLES = cfg.GAINTABLES
IMAGES = cfg.IMAGES
SCRIPTS = cfg.SCRIPTS
TOOLS = cfg.TOOLS
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 INFRASTRUCTURE == 'idia':
myNCPU = 8 # Dial back the parallelism for IDIA nodes
elif INFRASTRUCTURE == 'chpc':
myNCPU = 23 # Kind of meaningless as this stuff probably won't ever run on CHPC
else:
myNCPU = 40 # Assumed NCPU for standalone nodes
if CONTAINER_PATH is not None:
CONTAINER_RUNNER = 'singularity exec '
else:
CONTAINER_RUNNER = ''
DDFACET_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.DDFACET_PATTERN,
USE_SINGULARITY)
KILLMS_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.KILLMS_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']
# ------------------------------------------------------------------------------
#
# 3GC peeling 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 zoomed FITS mask for this target
mask1 = sorted(
glob.glob(IMAGES + '/*' + filename_targetname +
'*.mask1.zoom*.fits'))
if len(mask1) > 0:
mask = mask1[0]
else:
mask = 'auto'
# Look for the DS9 region file that defines the tessel centres for this target
region = glob.glob('*' + targetname + '*.reg')
if len(region) == 0:
gen.print_spacer()
print(gen.col() + 'Please provide a region file of the form:')
print(gen.col() + ' *' + targetname + '*.reg')
print(gen.col() + 'for this field.')
gen.print_spacer()
sys.exit()
else:
region = region[0]
gen.print_spacer()
print(gen.col('Target') + targetname)
print(gen.col('Measurement Set') + myms)
print(gen.col('Code') + code)
print(gen.col('Mask') + mask)
print(gen.col('Region') + region)
# Image prefixes
ddf_img_prefix = IMAGES + '/img_' + myms + '_DDFpcal'
kms_img_prefix = IMAGES + '/img_' + myms + '_DDFkMS'
# Target-specific kill file
kill_file = SCRIPTS + '/kill_3GC_facet_jobs_' + filename_targetname + '.sh'
step = {}
step['step'] = 0
step[
'comment'] = 'Run DDFacet, masked deconvolution of CORRECTED_DATA column of ' + myms
step['dependency'] = None
step['id'] = 'DDCMA' + code
step['slurm_config'] = cfg.SLURM_WSCLEAN
step['pbs_config'] = cfg.PBS_WSCLEAN
syscall = CONTAINER_RUNNER + DDFACET_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_ddfacet(mspattern=myms,
imgname=ddf_img_prefix,
ncpu=myNCPU,
mask=mask,
sparsification='50,20,5,2')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 1
step[
'comment'] = 'Convert the DS9 region into a numpy file that killMS will recognise'
step['dependency'] = 0
step['id'] = 'RG2NP' + code
syscall = CONTAINER_RUNNER + DDFACET_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += 'python3 ' + TOOLS + '/reg2npy.py ' + region
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 2
step['comment'] = 'Run killMS'
step['dependency'] = 1
step['id'] = 'KILMS' + code
syscall = CONTAINER_RUNNER + KILLMS_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_killms(myms=myms,
baseimg=ddf_img_prefix,
ncpu=myNCPU,
outsols='killms-cohjones',
nodesfile=region + '.npy')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 3
step[
'comment'] = 'Run DDFacet on CORRECTED_DATA of ' + myms + ', applying killMS solutions'
step['dependency'] = 2
step['id'] = 'DDKMA' + code
syscall = CONTAINER_RUNNER + DDFACET_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_ddfacet(
mspattern=myms,
imgname=kms_img_prefix,
chunkhours=1,
ncpu=myNCPU,
initdicomodel=ddf_img_prefix + '.DicoModel',
hogbom_maxmajoriter=0,
hogbom_maxminoriter=1000,
mask=mask,
ddsols='killms-cohjones')
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_3GC_facet_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
gen.preamble()
print(gen.col() + 'FLAG (target flagging & initial mask-making) setup')
gen.print_spacer()
# ------------------------------------------------------------------------------
#
# Setup paths, required containers, infrastructure
#
# ------------------------------------------------------------------------------
OXKAT = cfg.OXKAT
DATA = cfg.DATA
IMAGES = cfg.IMAGES
SCRIPTS = cfg.SCRIPTS
TOOLS = cfg.TOOLS
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)
CUBICAL_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.CUBICAL_PATTERN,
USE_SINGULARITY)
MAKEMASK_CONTAINER = gen.get_container(CONTAINER_PATH,
cfg.MAKEMASK_PATTERN,
USE_SINGULARITY)
TRICOLOUR_CONTAINER = gen.get_container(CONTAINER_PATH,
cfg.TRICOLOUR_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']
# ------------------------------------------------------------------------------
#
# FLAG 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)
# Image prefix
img_prefix = IMAGES + '/img_' + myms + '_datablind'
# Target-specific kill file
kill_file = SCRIPTS + '/kill_flag_jobs_' + filename_targetname + '.sh'
gen.print_spacer()
print(gen.col('Target') + targetname)
print(gen.col('Measurement Set') + myms)
print(gen.col('Code') + code)
step = {}
step['step'] = 0
step['comment'] = 'Run Tricolour on ' + myms
step['dependency'] = None
step['id'] = 'TRIC0' + code
step['slurm_config'] = cfg.SLURM_TRICOLOUR
step['pbs_config'] = cfg.PBS_TRICOLOUR
syscall = CONTAINER_RUNNER + TRICOLOUR_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_tricolour(
myms=myms,
config=DATA + '/tricolour/target_flagging_1_narrow.yaml',
datacol='DATA',
fields='0',
strategy='polarisation')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 1
step['comment'] = 'Blind wsclean on DATA column of ' + myms
step['dependency'] = 0
step['id'] = 'WSDBL' + 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=img_prefix,
datacol='DATA',
bda=True,
automask=False,
autothreshold=False,
localrms=False,
mask=False,
absmem=absmem)
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 2
step['comment'] = 'Make initial cleaning mask for ' + targetname
step['dependency'] = 1
step['id'] = 'MASK0' + code
syscall = CONTAINER_RUNNER + MAKEMASK_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_makemask(
restoredimage=img_prefix + '-MFS-image.fits',
outfile=img_prefix + '-MFS-image.mask0.fits',
zoompix='')[0]
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 3
step['comment'] = 'Backup flag table for ' + myms
step['dependency'] = 1
step['id'] = 'SAVFG' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += 'casa -c ' + OXKAT + '/FLAG_casa_backup_flag_table.py --nologger --log2term --nogui '
syscall += 'versionname=tricolour1 mslist=' + myms
step['syscall'] = syscall
steps.append(step)
# step = {}
# step['step'] = 4
# step['comment'] = 'Add CORRECTED_DATA column to '+myms
# step['dependency'] = 3
# step['id'] = 'ADCOR'+code
# syscall = CONTAINER_RUNNER+CUBICAL_CONTAINER+' ' if USE_SINGULARITY else ''
# syscall += 'python '+TOOLS+'/add_MS_column.py '
# syscall += '--colname CORRECTED_DATA '
# syscall += myms
# step['syscall'] = syscall
# steps.append(step)
# step = {}
# step['step'] = 5
# step['comment'] = 'Copy DATA to CORRECTED_DATA for '+myms
# step['dependency'] = 4
# step['id'] = 'CPDAT'+code
# syscall = CONTAINER_RUNNER+CUBICAL_CONTAINER+' ' if USE_SINGULARITY else ''
# syscall += 'python '+TOOLS+'/copy_MS_column.py '
# syscall += '--fromcol DATA '
# syscall += '--tocol CORRECTED_DATA '
# syscall += myms
# 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_flag_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
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
gen.preamble()
print(gen.col() + 'FLAG (target flagging) setup')
gen.print_spacer()
# ------------------------------------------------------------------------------
#
# Setup paths, required containers, infrastructure
#
# ------------------------------------------------------------------------------
OXKAT = cfg.OXKAT
DATA = cfg.DATA
SCRIPTS = cfg.SCRIPTS
TOOLS = cfg.TOOLS
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)
TRICOLOUR_CONTAINER = gen.get_container(CONTAINER_PATH,
cfg.TRICOLOUR_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']
# ------------------------------------------------------------------------------
#
# FLAG 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)
# Target-specific kill file
kill_file = SCRIPTS + '/kill_flag_jobs_' + filename_targetname + '.sh'
gen.print_spacer()
print(gen.col('Target') + targetname)
print(gen.col('Measurement Set') + myms)
print(gen.col('Code') + code)
step = {}
step['step'] = 0
step['comment'] = 'Run Tricolour on ' + myms
step['dependency'] = None
step['id'] = 'TRIC0' + code
step['slurm_config'] = cfg.SLURM_TRICOLOUR
step['pbs_config'] = cfg.PBS_TRICOLOUR
syscall = CONTAINER_RUNNER + TRICOLOUR_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += gen.generate_syscall_tricolour(
myms=myms,
config=DATA + '/tricolour/target_flagging_1_narrow.yaml',
datacol='DATA',
fields='0',
strategy='polarisation')
step['syscall'] = syscall
steps.append(step)
step = {}
step['step'] = 1
step['comment'] = 'Backup flag table for ' + myms
step['dependency'] = 0
step['id'] = 'SAVFG' + code
syscall = CONTAINER_RUNNER + CASA_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall += 'casa -c ' + OXKAT + '/FLAG_casa_backup_flag_table.py --nologger --log2term --nogui '
syscall += 'versionname=tricolour1 mslist=' + myms
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_flag_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()