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()