Advanced CLI¶
Calibration related CLI¶
To perform solar attenuation calibration using noise diode, use
run_fluxcal.
Click here to see parameters
usage: run_fluxcal [-h] --workdir WORKDIR --caldir CALDIR [--keep_backup]
[--cpu_frac CPU_FRAC] [--mem_frac MEM_FRAC]
[--logfile LOGFILE] [--jobid JOBID]
msname
Basic calibration using calibrators
options:
-h, --help show this help message and exit
###################
Essential parameters
###################:
msname Name of measurement set (required positional argument)
--workdir WORKDIR Working directory (default: auto-created next to MS)
(default: )
--caldir CALDIR Directory for calibration products (default: auto-
created in the workdir MS) (default: )
###################
Advanced parameters
###################:
--keep_backup Keep backup of measurement set after each round
###################
Hardware resource management parameters
###################:
--cpu_frac CPU_FRAC CPU fraction to use (default: 0.8)
--mem_frac MEM_FRAC Memory fraction to use (default: 0.8)
--logfile LOGFILE Path to log file (default: None)
--jobid JOBID Job ID for logging and tracking (default: 0)
Parition calibrator scans from main measurement set, use
run_partition.
Click here to see parameters
usage: run_partition [-h] [--outputms OUTPUTMS] --workdir WORKDIR
[--fields FIELDS] [--scans SCANS] [--width WIDTH]
[--timebin TIMEBIN] [--datacolumn DATACOLUMN]
[--split_fullpol] [--cpu_frac CPU_FRAC]
[--mem_frac MEM_FRAC] [--logfile LOGFILE] [--jobid JOBID]
msname
Partition measurement set in multi-MS format
options:
-h, --help show this help message and exit
###################
Essential parameters
###################:
msname Name of input measurement set (required positional
argument)
--outputms OUTPUTMS Name of output multi-MS (default: multi.ms)
--workdir WORKDIR Work directory (default: None)
###################
Advanced parameters
###################:
--fields FIELDS Comma-separated list of field IDs to split (default: )
--scans SCANS Comma-separated list of scans to split (default: )
--width WIDTH Number of spectral channels to average (default: 1)
--timebin TIMEBIN Time averaging bin (e.g., '10s', '1min') (default: )
--datacolumn DATACOLUMN
Datacolumn to split (default: data)
--split_fullpol Split all polarizations (default: False)
###################
Hardware resource management parameters
###################:
--cpu_frac CPU_FRAC CPU fraction to use (default: 0.8)
--mem_frac MEM_FRAC Memory fraction to use (default: 0.8)
--logfile LOGFILE Path to log file (default: None)
--jobid JOBID Job ID for process tracking (default: 0)
Flagging of calibrators, use
run_flag.
Click here to see parameters
usage: run_flag [-h] [--workdir WORKDIR] [--datacolumn DATACOLUMN]
[--no_flag_bad_ants] [--no_flag_bad_spw] [--use_tfcrop]
[--use_rflag] [--no_flag_autocorr] [--no_flagbackup]
[--flagdimension FLAGDIMENSION] [--cpu_frac CPU_FRAC]
[--mem_frac MEM_FRAC] [--logfile LOGFILE] [--jobid JOBID]
msname
Initial flagging of calibrator data
options:
-h, --help show this help message and exit
###################
Essential parameters
###################:
msname Name of measurement set
--workdir WORKDIR Name of work directory (default: )
--datacolumn DATACOLUMN
Name of the datacolumn (default: DATA)
###################
Advanced parameters
###################:
--no_flag_bad_ants Do not flag bad antennas
--no_flag_bad_spw Do not flag bad spectral windows
--use_tfcrop Use tfcrop flagging
--use_rflag Use rflag flagging
--no_flag_autocorr Do not flag auto-correlations
--no_flagbackup Do not backup flags
###################
Hardware resource management parameters
###################:
--flagdimension FLAGDIMENSION
Flag dimension (default: freqtime)
--cpu_frac CPU_FRAC CPU fraction to use (default: 0.8)
--mem_frac MEM_FRAC Memory fraction to use (default: 0.8)
--logfile LOGFILE Log file (default: None)
--jobid JOBID Job ID (default: 0)
Simulate visibilities for calibrators, use
import_model.
Click here to see parameters
usage: import_model [-h] [--workdir WORKDIR] [--cpu_frac CPU_FRAC]
[--mem_frac MEM_FRAC] [--logfile LOGFILE] [--jobid JOBID]
msname
Import calibrator models
options:
-h, --help show this help message and exit
###################
Essential parameters
###################:
msname Name of measurement set
--workdir WORKDIR Name of work directory (default: )
###################
Hardware resource management parameters
###################:
--cpu_frac CPU_FRAC CPU fraction to use (default: 0.8)
--mem_frac MEM_FRAC Memory fraction to use (default: 0.8)
--logfile LOGFILE Log file (default: None)
--jobid JOBID Job ID (default: 0)
Perform basic calibration, use
run_basic_cal.
Click here to see parameters
usage: run_basic_cal [-h] --workdir WORKDIR --caldir CALDIR [--refant REFANT]
[--uvrange UVRANGE] [--do_delaycal] [--perform_polcal]
[--keep_backup] [--cpu_frac CPU_FRAC]
[--mem_frac MEM_FRAC] [--logfile LOGFILE] [--jobid JOBID]
msname
Basic calibration using calibrators
options:
-h, --help show this help message and exit
###################
Essential parameters
###################:
msname Name of measurement set (required positional argument)
--workdir WORKDIR Working directory for calibration outputs (default:
auto-created next to MS) (default: )
--caldir CALDIR Caltables directory (default: auto-created in the
workdir MS) (default: )
###################
Advanced calibration parameters
###################:
--refant REFANT Reference antenna (default: 1)
--uvrange UVRANGE UV range for calibration (e.g. '>100lambda') (default:
)
--do_delaycal Enable delay calibration
--perform_polcal Enable polarization calibration
--keep_backup Keep backup of measurement set after each calibration
round
###################
Hardware resource management parameters
###################:
--cpu_frac CPU_FRAC CPU fraction to use (default: 0.8)
--mem_frac MEM_FRAC Memory fraction to use (default: 0.8)
--logfile LOGFILE Optional path to log file (default: None)
--jobid JOBID Job ID for logging and PID tracking (default: 0)
Apply basic calibration solutions, use
run_apply_basiccal.
Click here to see parameters
usage: run_apply_basiccal [-h] [--workdir WORKDIR] [--caldir CALDIR]
[--use_only_bandpass] [--applymode APPLYMODE]
[--overwrite_datacolumn] [--force_apply]
[--do_post_flag] [--cpu_frac CPU_FRAC]
[--mem_frac MEM_FRAC] [--logfile LOGFILE]
[--jobid JOBID]
mslist
Apply basic calibration solutions to target scans
options:
-h, --help show this help message and exit
###################
Essential parameters
###################:
mslist Comma-separated list of measurement sets (required)
--workdir WORKDIR Working directory for intermediate files (default: )
--caldir CALDIR Directory containing calibration tables (default: )
###################
Advanced parameters
###################:
--use_only_bandpass Use only bandpass calibration solutions
--applymode APPLYMODE
Applycal mode (e.g. 'calonly', 'calflag') (default:
calflag)
--overwrite_datacolumn
Overwrite corrected data column in MS
--force_apply Force apply calibration even if already applied
--do_post_flag Perform post-calibration flagging
###################
Hardware resource management parameters
###################:
--cpu_frac CPU_FRAC CPU fraction to use (default: 0.8)
--mem_frac MEM_FRAC Memory fraction to use (default: 0.8)
--logfile LOGFILE Optional path to log file (default: None)
--jobid JOBID Job ID for logging and process tracking (default: 0)
Split measurement set for self-calibration or final imaging, use
run_target_split.
Click here to see parameters
usage: run_target_split [-h] [--workdir WORKDIR] [--datacolumn DATACOLUMN]
[--spw SPW] [--scans SCANS (Comma seperated)]
[--time_window Float] [--time_interval Float]
[--quack_timestamps Integer] [--spectral_chunk Float]
[--n_spectral_chunk Integer] [--freqres Float]
[--timeres Float] [--prefix PREFIX] [--split_fullpol]
[--merge_spws] [--cpu_frac Float] [--mem_frac Float]
[--max_cpu_frac Float] [--max_mem_frac Float]
[--logfile LOGFILE] [--jobid JOBID]
msname
Split target scans
options:
-h, --help show this help message and exit
###################
Essential parameters
###################:
msname Name of measurement set (required positional argument)
--workdir WORKDIR Name of work directory (default: )
###################
Advanced parameters
###################:
--datacolumn DATACOLUMN
Data column to split (default: data)
--spw SPW Spectral window to split (default: )
--scans SCANS (Comma seperated)
Target scan list (default: all) (default: )
--time_window Float Time window in seconds (default: -1)
--time_interval Float
Time interval in seconds (default: -1)
--quack_timestamps Integer
Time stamps to ignore at the start and end of the each
scan (default: -1)
--spectral_chunk Float
Spectral chunk in MHz (default: -1)
--n_spectral_chunk Integer
Numbers of spectral chunks to split (default: -1)
--freqres Float Frequency to average in MHz (default: -1)
--timeres Float Time bin to average in seconds (default: -1)
--prefix PREFIX Splited ms prefix name (default: targets)
--split_fullpol Split full polar data
--merge_spws Merge spectral windows
###################
Hardware resource management parameters
###################:
--cpu_frac Float CPU fraction to use (default: 0.8)
--mem_frac Float Memory fraction to use (default: 0.8)
--max_cpu_frac Float Maximum CPU fraction to use (default: 0.8)
--max_mem_frac Float Maximum memory fraction to use (default: 0.8)
--logfile LOGFILE Log file (default: None)
--jobid JOBID Job ID (default: 0)
Perform self-calibration, use
run_selfcal.
Click here to see parameters
usage: run_selfcal [-h] --workdir WORKDIR --caldir CALDIR
[--start_thresh Float] [--stop_thresh Float]
[--max_iter Integer] [--max_DR Float] [--min_iter Integer]
[--conv_frac Float] [--solint SOLINT] [--uvrange UVRANGE]
[--minuv Float] [--weight WEIGHT] [--robust Float]
[--applymode String] [--min_tol_factor Float] [--no_apcal]
[--no_solar_selfcal] [--keep_backup] [--cpu_frac Float]
[--mem_frac Float] [--jobid JOBID]
mslist
Self-calibration
options:
-h, --help show this help message and exit
###################
Essential parameters
###################:
mslist Comma-separated list of measurement sets (required
positional argument)
--workdir WORKDIR Working directory (default: )
--caldir CALDIR Caltable directory (default: )
###################
Advanced calibration and imaging parameters
###################:
--start_thresh Float Starting CLEANing threshold (default: 5)
--stop_thresh Float Stop CLEANing threshold (default: 3)
--max_iter Integer Maximum number of selfcal iterations (default: 100)
--max_DR Float Maximum dynamic range (default: 1000)
--min_iter Integer Minimum number of selfcal iterations (default: 2)
--conv_frac Float Fractional change in DR to determine convergence
(default: 0.3)
--solint SOLINT Solution interval (default: 60s)
--uvrange UVRANGE Calibration UV-range (CASA format) (default: )
--minuv Float Minimum UV-lambda used for imaging (default: 0)
--weight WEIGHT Imaging weight (default: briggs)
--robust Float Robust parameter for briggs weight (default: 0.0)
--applymode String Solution apply mode (default: calonly)
--min_tol_factor Float
Minimum tolerable variation in temporal direction in
percentage (default: 1.0)
--no_apcal Do not perform ap-selfcal
--no_solar_selfcal Do not perform solar self-calibration
--keep_backup Keep backup of self-calibration rounds
###################
Hardware resource management parameters
###################:
--cpu_frac Float CPU fraction to use (default: 0.8)
--mem_frac Float Memory fraction to use (default: 0.8)
--jobid JOBID Job ID (default: 0)
Apply self-calibration solutions, use
run_apply_selfcal.
Click here to see parameters
usage: run_apply_selfcal [-h] [--workdir WORKDIR] [--caldir CALDIR]
[--applymode APPLYMODE] [--overwrite_datacolumn]
[--force_apply] [--cpu_frac CPU_FRAC]
[--mem_frac MEM_FRAC] [--logfile LOGFILE]
[--jobid JOBID]
mslist
Apply self-calibration solutions to target scans
options:
-h, --help show this help message and exit
###################
Essential parameters
###################:
mslist Comma-separated list of measurement sets (required)
--workdir WORKDIR Working directory for intermediate files (default: )
--caldir CALDIR Directory containing self-calibration tables (default:
)
###################
Advanced parameters
###################:
--applymode APPLYMODE
Applycal mode (e.g. 'calonly', 'calflag') (default:
calonly)
--overwrite_datacolumn
Overwrite corrected data column in MS
--force_apply Force apply calibration even if already applied
###################
Hardware resource management parameters
###################:
--cpu_frac CPU_FRAC CPU fraction to use (default: 0.8)
--mem_frac MEM_FRAC Memory fraction to use (default: 0.8)
--logfile LOGFILE Optional path to log file (default: None)
--jobid JOBID Job ID for logging and PID tracking (default: 0)
Solar specific CLI¶
To correct sidereal motion of the Sun, if the Sun is not tracked by the correlator delay center, use
run_solar_siderealcor. This is useful for observations where the Sun is in sidelobe of the telescope primary beam.
Click here to see parameters
usage: run_solar_siderealcor [-h] [--workdir WORKDIR] [--cpu_frac Float]
[--mem_frac Float] [--max_cpu_frac Float]
[--max_mem_frac Float] [--logfile LOGFILE]
[--jobid JOBID]
mslist
Correct measurement sets for sidereal motion
options:
-h, --help show this help message and exit
###################
Essential parameters
###################:
mslist Comma-separated list of measurement sets (required
positional argument)
--workdir WORKDIR Working directory (default: )
###################
Hardware resource management parameters
###################:
--cpu_frac Float CPU fraction to use (default: 0.8)
--mem_frac Float Memory fraction to use (default: 0.8)
--max_cpu_frac Float Maximum CPU fraction to use (default: 0.8)
--max_mem_frac Float Maximum memory fraction to use (default: 0.8)
--logfile LOGFILE Log file (default: None)
--jobid JOBID Job ID (default: 0)
Make dynamic spectra of solar scans, use
run_makeds.
Click here to see parameters
usage: run_makeds [-h] --workdir WORKDIR --outdir OUTDIR
[--extension EXTENSION] [--target_scans [TARGET_SCANS ...]]
[--no_merge] [--no_seperate] [--cpu_frac CPU_FRAC]
[--mem_frac MEM_FRAC] [--logfile LOGFILE] [--jobid JOBID]
msname
Make dynamic spectra of solar scans
options:
-h, --help show this help message and exit
###################
Essential parameters
###################:
msname Measurement set name
--workdir WORKDIR Working directory (default: None)
--outdir OUTDIR Output directory (default: None)
###################
Advanced parameters
###################:
--extension EXTENSION
Save file extension (default: png)
--target_scans [TARGET_SCANS ...]
List of target scans to process (space-separated, e.g.
3 5 7) (default: [])
--no_merge Do not merge scans
--no_seperate Do not seperate scans
###################
Hardware resource management parameters
###################:
--cpu_frac CPU_FRAC Fraction of CPU usuage per node (default: 0.8)
--mem_frac MEM_FRAC Fraction of memory usuage per node (default: 0.8)
--logfile LOGFILE Optional path to log file (default: None)
--jobid JOBID Job ID for logging and PID tracking (default: 0)
Imaging related CLI¶
Perform spectro-polarimetric snapshot imaging, use
run_imaging.
Click here to see parameters
usage: run_imaging [-h] --workdir WORKDIR --outdir OUTDIR
[--freqrange FREQRANGE] [--timerange TIMERANGE]
[--datacolumn DATACOLUMN] [--pol POL] [--freqres FREQRES]
[--timeres TIMERES] [--weight WEIGHT] [--robust ROBUST]
[--minuv_l MINUV] [--threshold THRESHOLD] [--band BAND]
[--cutout_rsun CUTOUT_RSUN] [--no_multiscale]
[--no_solar_mask] [--no_savemodel] [--no_saveres]
[--no_make_overlay] [--no_make_plots] [--cpu_frac CPU_FRAC]
[--mem_frac MEM_FRAC] [--jobid JOBID]
mslist
Perform spectropolarimetric snapshot imaging
options:
-h, --help show this help message and exit
###################
Essential parameters
###################:
mslist Comma-separated list of measurement sets (required)
--workdir WORKDIR Work directory for imaging (default: )
--outdir OUTDIR Output directory for imaging products (default: )
###################
Advanced imaging parameters
###################:
--freqrange FREQRANGE
Frequency range to image (default: )
--timerange TIMERANGE
Time range to image (default: )
--datacolumn DATACOLUMN
Data column to use for imaging (default:
CORRECTED_DATA)
--pol POL Stokes parameters to image (default: I)
--freqres FREQRES Frequency resolution per chunk in MHz (-1 for full)
(default: -1)
--timeres TIMERES Time resolution per chunk in seconds (-1 for full)
(default: -1)
--weight WEIGHT Imaging weighting scheme (default: briggs)
--robust ROBUST Briggs robust parameter (default: 0.0)
--minuv_l MINUV Minimum UV distance in wavelengths (default: 0.0)
--threshold THRESHOLD
CLEAN threshold in Jy (default: 1.0)
--band BAND Band name label for output (default: )
--cutout_rsun CUTOUT_RSUN
Cutout radius for images (solar radii) (default: 2.5)
--no_multiscale Do not use multiscale CLEAN
--no_solar_mask Do not use solar disk mask for CLEANing
--no_savemodel Do no save model images
--no_saveres Do not save residual images
--no_make_overlay Do not generate overlay with SUVI images
--no_make_plots Do not make generate helioprojective plots
###################
Hardware resource management parameters
###################:
--cpu_frac CPU_FRAC Fraction of available CPU to use (default: 0.8)
--mem_frac MEM_FRAC Fraction of available memory to use (default: 0.8)
--jobid JOBID Job ID for process tracking and logging (default: 0)
Perform primary beam correction of MeerKAT primary beam, for a single image, use
run_single_meerpbcor.
Click here to see parameters
usage: run_single_meerpbcor [-h] [--pbdir PBDIR] [--pbcor_dir PBCOR_DIR]
[--no_save_beam] [--band BAND] [--no_apply_parang]
[--verbose] [--ncpu Integer] [--jobid JOBID]
imagename
Correct image for full-polar antenna averaged MeerKAT primary beam
options:
-h, --help show this help message and exit
###################
Essential parameters
###################:
imagename Name of image (required positional argument)
--pbdir PBDIR Name of primary beam directory (default: )
--pbcor_dir PBCOR_DIR
Name of primary beam corrected image directory
(default: )
###################
Advanced parameters
###################:
--no_save_beam Do not save beam to disk
--band BAND Band name (default: )
--no_apply_parang Do not apply parallactic angle correction
--verbose Verbose output
###################
Hardware resource management parameters
###################:
--ncpu Integer Number of CPU threads to use (default: 8)
--jobid JOBID Job ID (default: 0)
Perform primary beam corrections of MeerKAT primary beam for all images in a directory, use
run_meerpbcor.
Click here to see parameters
usage: run_meerpbcor [-h] [--workdir WORKDIR] [--no_make_TB] [--no_make_plots]
[--no_apply_parang] [--cpu_frac CPU_FRAC]
[--mem_frac MEM_FRAC] [--logfile LOGFILE] [--jobid JOBID]
imagedir
Correct all images for MeerKAT full-pol averaged primary beam
options:
-h, --help show this help message and exit
###################
Essential parameters
###################:
imagedir Path to image directory
--workdir WORKDIR Path to work directory (default: )
###################
Advanced parameters
###################:
--no_make_TB Do not generate brightness temperature map
--no_make_plots Do not make png and pdf plots
--no_apply_parang Do not apply parallactic angle correction
###################
Hardware resource management parameters
###################:
--cpu_frac CPU_FRAC CPU usage fraction (default: 0.8)
--mem_frac MEM_FRAC Memory usage fraction (default: 0.8)
--logfile LOGFILE Path to log file (default: None)
--jobid JOBID Job ID for logging and PID tracking (default: 0)