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)
# Get container needed for this script
WSCLEAN_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.WSCLEAN_PATTERN)
# Bump up the walltimes
SLURM_WSCLEAN_MOD = cfg.SLURM_WSCLEAN
SLURM_WSCLEAN_MOD['TIME'] = '18:00:00'
PBS_WSCLEAN_MOD = cfg.PBS_WSCLEAN
PBS_WSCLEAN_MOD['WALLTIME'] = '18:00:00'
# Set names of the run file, open for writing
submit_file = 'submit_2GC_continue_clean_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')
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]
filename_targetname = gen.scrub_target_name(targetname)
code = gen.get_target_code(targetname)
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)
corr_img_prefix = IMAGES + '/img_' + myms + '_pcalmask'
# ------------------------------------------------------------------------------
# STEP 1:
# Continue wsclean on CORRECTED_DATA column with additional scale
id_wsclean = 'WSCM2' + code
syscall = 'singularity exec ' + WSCLEAN_CONTAINER + ' '
syscall += gen.generate_syscall_wsclean(mslist=[myms],
imgname=corr_img_prefix,
continueclean=True,
datacol='CORRECTED_DATA',
briggs=-1.5,
multiscale=True,
scales='0,3,9,18',
niter=400000,
bda=False,
mask=mask)
run_command = gen.job_handler(syscall=syscall,
jobname=id_wsclean,
infrastructure=INFRASTRUCTURE,
slurm_config=SLURM_WSCLEAN_MOD,
pbs_config=PBS_WSCLEAN_MOD)
f.write(run_command + '\n')
f.close()
def main():
# ------------------------------------------------------------------------------
# Setup
INFRASTRUCTURE, CONTAINER_PATH = gen.set_infrastructure(sys.argv)
if INFRASTRUCTURE == 'idia':
myNCPU = 8
elif INFRASTRUCTURE == 'chpc':
myNCPU = 23
else:
myNCPU = 40
# 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)
# Enable running without containers
if CONTAINER_PATH is not None:
CONTAINER_RUNNER = 'singularity exec '
else:
CONTAINER_RUNNER = ''
# Get containers needed for this script
DDFACET_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.DDFACET_PATTERN)
KILLMS_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.KILLMS_PATTERN)
# Set names of the run and kill files, open run file for writing
submit_file = 'submit_3GC_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')
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)
mask1 = sorted(
glob.glob(IMAGES + '/*' + filename_targetname +
'*.mask1.zoom*.fits'))
if len(mask1) > 0:
mask = mask1[0]
else:
mask = 'auto'
region = glob.glob('*' + targetname + '*.reg')
if len(region) == 0:
print(gen.now() + 'Please provide a region file')
sys.exit()
else:
region = region[0]
print('------------------------------------------------------')
print(gen.now() + 'Target: ' + targetname)
print(gen.now() + 'MS: ' + myms)
print(gen.now() + 'Using mask: ' + mask)
print(gen.now() + 'Using region: ' + region)
f.write('\n# ' + targetname + '\n')
kill_file = SCRIPTS + '/kill_3GC_jobs_' + filename_targetname + '.sh'
ddf_img_prefix = IMAGES + '/img_' + myms + '_DDFpcal'
kms_img_prefix = IMAGES + '/img_' + myms + '_DDFkMS'
# Initialise a list to hold all the job IDs
id_list = []
# ------------------------------------------------------------------------------
# STEP 1:
# DDFacet on CORRECTED_DATA column
id_ddfacet1 = 'DDCMA' + code
id_list.append(id_ddfacet1)
syscall = CONTAINER_RUNNER + DDFACET_CONTAINER + ' '
syscall += gen.generate_syscall_ddfacet(
mspattern=myms,
imgname=ddf_img_prefix,
ncpu=myNCPU,
mask=mask,
sparsification='100,30,10,2')
run_command = gen.job_handler(syscall=syscall,
jobname=id_ddfacet1,
infrastructure=INFRASTRUCTURE,
slurm_config=cfg.SLURM_HIGHMEM,
pbs_config=cfg.PBS_WSCLEAN)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 2:
# Run killMS
id_killms = 'KILMS' + code
id_list.append(id_killms)
syscall = CONTAINER_RUNNER + KILLMS_CONTAINER + ' '
syscall += 'python3 ' + TOOLS + '/reg2npy.py ' + region + '\n '
syscall += CONTAINER_RUNNER + KILLMS_CONTAINER + ' '
syscall += gen.generate_syscall_killms(myms=myms,
baseimg=ddf_img_prefix,
ncpu=myNCPU,
outsols='killms-cohjones',
nodesfile=region + '.npy')
run_command = gen.job_handler(syscall=syscall,
jobname=id_killms,
dependency=id_ddfacet1,
infrastructure=INFRASTRUCTURE,
slurm_config=cfg.SLURM_HIGHMEM,
pbs_config=cfg.PBS_WSCLEAN)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 3:
# DDFacet on CORRECTED_DATA column, apply killMS solutions
id_ddfacet2 = 'DDKMA' + code
id_list.append(id_ddfacet1)
syscall = CONTAINER_RUNNER + DDFACET_CONTAINER + ' '
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')
run_command = gen.job_handler(syscall=syscall,
jobname=id_ddfacet2,
dependency=id_killms,
infrastructure=INFRASTRUCTURE,
slurm_config=cfg.SLURM_HIGHMEM,
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()
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)
# Get container needed for this script
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_GC_continue_clean_job.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('/')
print('------------------------------------------------------')
print(gen.now() + 'Target: ' + targetname)
print(gen.now() + 'MS: ' + myms)
corr_img_prefix = IMAGES + '/img_' + myms + '_pcalmask'
# ------------------------------------------------------------------------------
# STEP 1:
# Continue wsclean on CORRECTED_DATA column with additional scale
id_wsclean = 'WSCN3' + code
syscall = 'singularity exec ' + WSCLEAN_CONTAINER + ' '
syscall += gen.generate_syscall_wsclean(mslist=[myms],
imgname=corr_img_prefix,
continueclean=True,
datacol='CORRECTED_DATA',
briggs=-1.5,
multiscale=True,
scales='0,3,9,18',
niter=300000,
bda=False,
mask='none')
run_command = gen.job_handler(syscall=syscall,
jobname=id_wsclean,
infrastructure=INFRASTRUCTURE,
slurm_config=SLURM_WSCLEAN_MOD,
pbs_config=PBS_WSCLEAN_MOD)
f.write(run_command + '\n')
f.close()
def main():
USE_SINGULARITY = cfg.USE_SINGULARITY
gen.preamble()
print(gen.now() + 'Imaging secondary calibrators')
# ------------------------------------------------------------------------------
#
# Setup paths, required containers, infrastructure
#
# ------------------------------------------------------------------------------
OXKAT = cfg.OXKAT
IMAGES = cfg.IMAGES
SCRIPTS = cfg.SCRIPTS
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 = ''
WSCLEAN_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.WSCLEAN_PATTERN,
USE_SINGULARITY)
# Get secondary calibrator information from project pickle
project_info = pickle.load(open('project_info.p', 'rb'), encoding='latin1')
myms = project_info['master_ms']
pcal_names = project_info['secondary_names']
pcal_ids = project_info['secondary_ids']
# ------------------------------------------------------------------------------
#
# Image calibrators -- recipe definition
#
# ------------------------------------------------------------------------------
cal_steps = []
codes = []
ii = 1
# Loop over secondaries
for i in range(0, len(pcal_ids)):
field = pcal_ids[i]
calname = pcal_names[i]
steps = []
filename_calname = gen.scrub_target_name(calname)
code = gen.get_target_code(calname)
if code in codes:
code += '_' + str(ii)
ii += 1
codes.append(code)
gen.print_spacer()
print(gen.now() + 'Secondary | ' + calname)
print(gen.now() + 'Code | ' + code)
# Image prefix
img_prefix = IMAGES + '/img_' + myms + '_' + filename_calname + '_corrblind'
step = {}
step['step'] = i
step[
'comment'] = 'Run wsclean, blind deconvolution of the CORRECTED_DATA for ' + calname
if i == 0:
step['dependency'] = None
else:
step['dependency'] = i - 1
step['id'] = 'WSCMA' + code
step['slurm_config'] = cfg.SLURM_WSCLEAN
step['pbs_config'] = cfg.PBS_WSCLEAN
syscall = CONTAINER_RUNNER + WSCLEAN_CONTAINER + ' ' if USE_SINGULARITY else ''
syscall = 'singularity exec ' + WSCLEAN_CONTAINER + ' '
syscall += gen.generate_syscall_wsclean(mslist=[myms],
imgname=img_prefix,
field=field,
datacol='CORRECTED_DATA',
imsize=8192,
niter=40000,
gain=0.2,
mgain=0.9,
bda=True,
mask='none')
step['syscall'] = syscall
steps.append(step)
# ------------------------------------------------------------------------------
#
# Write the run file and kill file based on the recipe
#
# ------------------------------------------------------------------------------
submit_file = 'submit_image_secondary_jobs.sh'
kill_file = cfg.SCRIPTS + '/kill_image_secondary_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.now() + 'Created ' + 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():
# ------------------------------------------------------------------------------
# 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)
# Get containers needed for this script
CASA_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.CASA_PATTERN)
CUBICAL_CONTAINER = gen.get_container(CONTAINER_PATH, cfg.CUBICAL_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 = 'singularity exec ' + 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 = '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)
# ------------------------------------------------------------------------------
# STEP 3:
# Self-calibrate phases then amplitudes
id_selfcal = 'CL2GC' + code
id_list.append(id_selfcal)
syscall = 'singularity exec ' + CUBICAL_CONTAINER + ' '
syscall += gen.generate_syscall_cubical(parset=PARSETS +
'/cubical/phasecal.parset',
myms=myms)
run_command = gen.job_handler(syscall=syscall,
jobname=id_selfcal,
infrastructure=INFRASTRUCTURE,
dependency=id_predict1,
slurm_config=cfg.SLURM_WSCLEAN,
pbs_config=cfg.PBS_WSCLEAN)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 4:
# Make gain table plots
# id_gainplots = 'PLTAB'+code
# id_list.append(id_gainplots)
# syscall = 'singularity exec '+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 = 'singularity exec ' + 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 = 'singularity exec ' + 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 = '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)
# ------------------------------------------------------------------------------
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()
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
IMAGES = cfg.IMAGES
LOGS = cfg.LOGS
SCRIPTS = cfg.SCRIPTS
gen.setup_dir(LOGS)
gen.setup_dir(SCRIPTS)
gen.setup_dir(IMAGES)
# 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)
# Get target information from project pickle
project_info = pickle.load(open('project_info.p','rb'),encoding='latin1')
targets = project_info['target_list']
# Set names of the run file, open for writing
submit_file = 'submit_flag_jobs.sh'
f = open(submit_file,'w')
f.write('#!/usr/bin/env bash\n')
codes = []
ii = 1
# Loop over targets
for target in targets:
myms = target[2].rstrip('/')
targetname = target[0]
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)
# Image prefix
img_prefix = IMAGES+'/img_'+myms+'_datablind'
# Target-specific kill file
kill_file = SCRIPTS+'/kill_flag_jobs_'+filename_targetname+'.sh'
# Initialise a list to hold all the job IDs
id_list = []
# ------------------------------------------------------------------------------
# STEP 1:
# Run Tricolour on targets
syscall = 'singularity exec '+TRICOLOUR_CONTAINER+' '
syscall += gen.generate_syscall_tricolour(myms = myms,
config = PARSETS+'/target_flagging_1_narrow.yaml',
datacol = 'DATA',
fields = '0',
strategy = 'polarisation')
id_tricolour = 'TRICO'+code
id_list.append(id_tricolour)
run_command = gen.job_handler(syscall = syscall,
jobname = id_tricolour,
infrastructure = INFRASTRUCTURE,
slurm_config = cfg.SLURM_TRICOLOUR,
pbs_config = cfg.PBS_TRICOLOUR)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 2:
# wsclean with blind deconvolution
syscall = 'singularity exec '+WSCLEAN_CONTAINER+' '
syscall += gen.generate_syscall_wsclean(mslist = [myms],
imgname = img_prefix,
datacol = 'DATA',
bda = True,
niter = 100000,
autothreshold = 1.0,
mask = 'none')
id_wsclean = 'WSDBL'+code
id_list.append(id_wsclean)
run_command = gen.job_handler(syscall = syscall,
jobname = id_wsclean,
infrastructure = INFRASTRUCTURE,
dependency = id_tricolour,
slurm_config = cfg.SLURM_WSCLEAN,
pbs_config = cfg.PBS_WSCLEAN)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 3:
# Make a FITS mask
syscall = 'singularity exec '+DDFACET_CONTAINER+' '
syscall += gen.generate_syscall_makemask(restoredimage = img_prefix+'-MFS-image.fits',
suffix = 'mask0',
zoompix = '')[0]
id_makemask = 'MASK0'+code
id_list.append(id_makemask)
run_command = gen.job_handler(syscall = syscall,
jobname = id_makemask,
infrastructure = INFRASTRUCTURE,
dependency = id_wsclean)
f.write(run_command)
# ------------------------------------------------------------------------------
# STEP 4:
# Backup the flag table
syscall = 'singularity exec '+CASA_CONTAINER+' '
syscall += 'casa -c '+OXKAT+'/FLAG_casa_backup_flag_table.py --nologger --log2term --nogui '
syscall += 'versionname=tricolour1 '
id_saveflags = 'SAVFG'+code
id_list.append(id_saveflags)
run_command = gen.job_handler(syscall = syscall,
jobname = id_saveflags,
infrastructure =INFRASTRUCTURE,
dependency = id_wsclean)
f.write(run_command)
# ------------------------------------------------------------------------------
if INFRASTRUCTURE in ['idia','chpc']:
kill = 'echo "scancel "$'+'" "$'.join(id_list)+' > '+kill_file
f.write(kill+'\n')
f.write('\n')
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():
# ------------------------------------------------------------------------------
# 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']
# Loop over targets
codes = []
ii = 1
for target in targets:
targetname = target[0]
myms = target[2].rstrip('/')
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 = 'singularity exec ' + 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 = '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)
# ------------------------------------------------------------------------------
# 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)
run_command = gen.job_handler(syscall=syscall,
jobname=id_selfcal,
infrastructure=INFRASTRUCTURE,
dependency=id_predict1)
f.write(run_command)
# ------------------------------------------------------------------------------
# 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',
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 5:
# Make a FITS mask
syscall = 'singularity exec ' + DDFACET_CONTAINER + ' '
syscall += gen.generate_syscall_makemask(
restoredimage=corr_img_prefix + '-MFS-image.fits',
suffix='mask1',
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 6:
# 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)
# ------------------------------------------------------------------------------
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() + '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():
# ------------------------------------------------------------------------------
# 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)
# Bump up the walltimes
SLURM_WSCLEAN_MOD = cfg.SLURM_WSCLEAN
SLURM_WSCLEAN_MOD['TIME'] = '18:00:00'
PBS_WSCLEAN_MOD = cfg.PBS_WSCLEAN
PBS_WSCLEAN_MOD['WALLTIME'] = '18:00:00'
# Set names of the run file, open 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')
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]
filename_targetname = gen.scrub_target_name(targetname)
code = gen.get_target_code(targetname)
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()