Running the pipeline

So you’re ready to run the pipeline? Make sure you’ve completed the Installation and Getting started steps first.

The Arrakis pipeline requires 36 calibrated MeasurementSets, one per ASKAP beam. You can obtain these from the Observatory (via CASDA) or produce them yourself with a pipline like Flint. You’ll need to have the visibilities stored in a single ‘working’ directory.

spice_process and spice_field orchestrate the pipeline flow using Prefect and Dask. These script calls the other arrakis modules to do the work. You can control which modules run in the configuration of spice_process or spice_field. spice_process operates on the level of a single RACS fields, whereas spice_field merges multiple fields togther. You will need to run spice_process on at least two fields before calling spice_field. After running spice_process or spice_field you can run spice_cat to produce a just a catalogue from the database values.

Details of each module can be found in the API documentation. But broadly the stages are:
  • Imaging - Create image cubes from visibilities using WSClean. This will also convolve the cubes to a common spatial resolution.

  • Cutout - Finds the position of the source in the image cubes and cuts out a square region around it.

  • LINMOS - Applies the primary beam and leakage correction to the cutout beam cubes, and then mosaics each into a single cube for each source per field.

  • FRion - Applies time-independent ionospheric Faraday rotation to the mosaicked cubes using FRion.

  • RM synthesis - Extracts 1D spectra for each component of each source and runs RM synthesis using RM-tools.

  • RM-CLEAN - Runs RM-CLEAN on the extracted 1D spectra using RM-tools.

  • Catalogue - Queries the database for a given field and constructs a polarisation catalogue for each component.

  • Clean up - Create a tarball of the the cutouts, and remove beam cubes.


With an initalised database you can call the pipeline on a single field:

(arrakis310) $ spice_process -h
usage: spice_process [-h] [--dask_config DASK_CONFIG] [--imager_dask_config IMAGER_DASK_CONFIG] [--imager_only] [--skip_imager] [--skip_cutout] [--skip_linmos]
                     [--skip_frion] [--skip_rmsynth] [--skip_rmclean] [--skip_cat] [--skip_cleanup] [--sbid SBID] [-s STOKESLIST [STOKESLIST ...]] [-e EPOCH] [-v]
                     [--host host] [--username USERNAME] [--password PASSWORD] [--limit LIMIT] [--database] [--temp_dir_wsclean TEMP_DIR_WSCLEAN]
                     [--temp_dir_images TEMP_DIR_IMAGES] [--psf_cutoff PSF_CUTOFF] [--robust ROBUST] [--nchan NCHAN] [--pols POLS] [--size SIZE] [--scale SCALE]
                     [--mgain MGAIN] [--niter NITER] [--nmiter NMITER] [--auto_mask AUTO_MASK] [--auto_threshold AUTO_THRESHOLD] [--local_rms]
                     [--local_rms_window LOCAL_RMS_WINDOW] [--force_mask_rounds FORCE_MASK_ROUNDS] [--gridder {direct-ft,idg,wgridder,tuned-wgridder,wstacking}]
                     [--taper TAPER] [--minuv MINUV] [--parallel PARALLEL] [--purge] [--mpi] [--multiscale] [--multiscale_scale_bias MULTISCALE_SCALE_BIAS]
                     [--multiscale_scales MULTISCALE_SCALES] [--absmem ABSMEM] [--make_residual_cubes] [--ms_glob_pattern MS_GLOB_PATTERN] [--data_column DATA_COLUMN]
                     [--no_mf_weighting] [--skip_fix_ms] [--hosted-wsclean HOSTED_WSCLEAN | --local_wsclean LOCAL_WSCLEAN] [-p PAD] [-d] [--holofile HOLOFILE]
                     [--yanda YANDA] [--yanda_image YANDA_IMAGE] [--ionex_server IONEX_SERVER] [--ionex_prefix IONEX_PREFIX] [--ionex_formatter IONEX_FORMATTER]
                     [--ionex_proxy_server IONEX_PROXY_SERVER] [--ionex_predownload] [--dimension DIMENSION] [--save_plots] [--rm_verbose] [--ion] [--tt0 TT0]
                     [--tt1 TT1] [--validate] [--own_fit] [--weight_type WEIGHT_TYPE] [--fit_function FIT_FUNCTION] [--fit_rmsf] [--phi_max PHI_MAX] [--dphi DPHI]
                     [--n_samples N_SAMPLES] [--poly_ord POLY_ORD] [--no_stokes_i] [--show_plots] [--not_rmsf] [--debug] [--cutoff CUTOFF] [--max_iter MAX_ITER]
                     [--gain GAIN] [--window WINDOW] [--leakage_degree LEAKAGE_DEGREE] [--leakage_bins LEAKAGE_BINS] [--leakage_snr LEAKAGE_SNR] [--write OUTFILE]
                     [--overwrite] [--config CONFIG]
                     datadir field msdir


    mmm   mmm   mmm   mmm   mmm
    )-(   )-(   )-(   )-(   )-(
   ( S ) ( P ) ( I ) ( C ) ( E )
   |   | |   | |   | |   | |   |
   |___| |___| |___| |___| |___|
    mmm     mmm     mmm     mmm
    )-(     )-(     )-(     )-(
   ( R )   ( A )   ( C )   ( S )
   |   |   |   |   |   |   |   |
   |___|   |___|   |___|   |___|

    Arrakis pipeline.

    Before running make sure to start a session of mongodb e.g.
        $ mongod --dbpath=/path/to/database --bind_ip $(hostname -i)



options:
  -h, --help            show this help message and exit
  --hosted-wsclean HOSTED_WSCLEAN
                        Docker or Singularity image for wsclean (default: docker://alecthomson/wsclean:latest)
  --local_wsclean LOCAL_WSCLEAN
                        Path to local wsclean Singularity image (default: None)
  --config CONFIG       Config file path (default: None)

pipeline arguments:
  --dask_config DASK_CONFIG
                        Config file for Dask SlurmCLUSTER. (default: None)
  --imager_dask_config IMAGER_DASK_CONFIG
                        Config file for Dask SlurmCLUSTER. (default: None)
  --imager_only         Only run the imager component of the pipeline.  (default: False)
  --skip_imager         Skip imaging stage [False]. (default: False)
  --skip_cutout         Skip cutout stage [False]. (default: False)
  --skip_linmos         Skip LINMOS stage [False]. (default: False)
  --skip_frion          Skip cleanup stage [False]. (default: False)
  --skip_rmsynth        Skip RM Synthesis stage [False]. (default: False)
  --skip_rmclean        Skip RM-CLEAN stage [False]. (default: False)
  --skip_cat            Skip catalogue stage [False]. (default: False)
  --skip_cleanup        Skip cleanup stage [False]. (default: False)

workdir arguments:
  datadir               Directory to create/find full-size images and 'cutout' directory

generic arguments:
  field                 Name of field (e.g. RACS_2132-50).
  --sbid SBID           SBID of observation. (default: None)
  -s STOKESLIST [STOKESLIST ...], --stokes STOKESLIST [STOKESLIST ...]
                        List of Stokes parameters to image (default: ['I', 'Q', 'U'])
  -e EPOCH, --epoch EPOCH
                        Epoch of observation. (default: 0)
  -v                    Verbose output. (default: False)
  --host host           Host of mongodb (probably $hostname -i). (default: None)
  --username USERNAME   Username of mongodb. (default: None)
  --password PASSWORD   Password of mongodb. (default: None)
  --limit LIMIT         Limit the number of islands to process. (default: None)
  --database            Add data to MongoDB. (default: False)

imaging arguments:
  msdir                 Directory containing MS files
  --temp_dir_wsclean TEMP_DIR_WSCLEAN
                        Temporary directory for WSClean to store intermediate files (default: None)
  --temp_dir_images TEMP_DIR_IMAGES
                        Temporary directory for to store intermediate image files (default: None)
  --psf_cutoff PSF_CUTOFF
                        Cutoff for smoothing in units of arcseconds.  (default: None)
  --robust ROBUST
  --nchan NCHAN
  --pols POLS
  --size SIZE
  --scale SCALE
  --mgain MGAIN
  --niter NITER
  --nmiter NMITER
  --auto_mask AUTO_MASK
  --auto_threshold AUTO_THRESHOLD
  --local_rms
  --local_rms_window LOCAL_RMS_WINDOW
  --force_mask_rounds FORCE_MASK_ROUNDS
  --gridder {direct-ft,idg,wgridder,tuned-wgridder,wstacking}
  --taper TAPER
  --minuv MINUV
  --parallel PARALLEL
  --purge               Purge intermediate files (default: False)
  --mpi                 Use MPI (default: False)
  --multiscale          Use multiscale clean (default: False)
  --multiscale_scale_bias MULTISCALE_SCALE_BIAS
                        The multiscale scale bias term provided to wsclean.  (default: None)
  --multiscale_scales MULTISCALE_SCALES
                        The scales used in the multiscale clean.  (default: 0,2,4,8,16,32,64,128)
  --absmem ABSMEM       Absolute memory limit in GB (default: None)
  --make_residual_cubes
                        Create residual cubes as well as cubes from restored images.  (default: False)
  --ms_glob_pattern MS_GLOB_PATTERN
                        The pattern used to search for measurement sets.  (default: scienceData*_averaged_cal.leakage.ms)
  --data_column DATA_COLUMN
                        Which column in the measurement set to image.  (default: CORRECTED_DATA)
  --no_mf_weighting     Do not use multi-frequency weighting.  (default: False)
  --skip_fix_ms         Do not apply the ASKAP MS corrections from the package fixms.  (default: False)

cutout arguments:
  -p PAD, --pad PAD     Number of beamwidths to pad around source [3]. (default: 3)
  -d, --dryrun          Do a dry-run [False]. (default: False)

linmos arguments:
  --holofile HOLOFILE   Path to holography image (default: None)
  --yanda YANDA         Yandasoft version to pull from DockerHub [1.3.0]. (default: 1.3.0)
  --yanda_image YANDA_IMAGE
                        Path to an existing yandasoft singularity container image.  (default: None)

frion arguments:
  --ionex_server IONEX_SERVER
                        IONEX server (default: ftp://ftp.aiub.unibe.ch/CODE/)
  --ionex_prefix IONEX_PREFIX
  --ionex_formatter IONEX_FORMATTER
                        IONEX formatter. (default: ftp.aiub.unibe.ch)
  --ionex_proxy_server IONEX_PROXY_SERVER
                        Proxy server. (default: None)
  --ionex_predownload   Pre-download IONEX files. (default: False)

common rm arguments:
  --dimension DIMENSION
                        How many dimensions for RMsynth '1d' or '3d'. (default: 1d)
  --save_plots          save the plots. (default: False)
  --rm_verbose          Verbose RMsynth/RMClean. (default: False)

rm-synth arguments:
  --ion                 Use ionospheric-corrected data. (default: False)
  --tt0 TT0             TT0 MFS image -- will be used for model of Stokes I -- also needs --tt1. (default: None)
  --tt1 TT1             TT1 MFS image -- will be used for model of Stokes I -- also needs --tt0. (default: None)
  --validate            Run on Stokes I. (default: False)
  --own_fit             Use own Stokes I fit function. (default: False)
  --weight_type WEIGHT_TYPE
                        weighting (inverse) 'variance' or 'uniform' (all 1s). (default: variance)
  --fit_function FIT_FUNCTION
                        Stokes I fitting function: 'linear' or 'log' polynomials. (default: log)
  --fit_rmsf            Fit a Gaussian to the RMSF (default: False)
  --phi_max PHI_MAX     Absolute max Faraday depth sampled (in rad/m^2) (overrides NSAMPLES). (default: None)
  --dphi DPHI           Width of Faraday depth channel. (default: None)
  --n_samples N_SAMPLES
                        Number of samples across the FWHM RMSF. (default: 5)
  --poly_ord POLY_ORD   polynomial order to fit to I spectrum. (default: 3)
  --no_stokes_i         ignore the Stokes I spectrum. (default: False)
  --show_plots          show the plots. (default: False)
  --not_rmsf            Skip calculation of RMSF? (default: False)
  --debug               turn on debugging messages & plots. (default: False)

rm-clean arguments:
  --cutoff CUTOFF       CLEAN cutoff (+ve = absolute, -ve = sigma). (default: -3)
  --max_iter MAX_ITER   maximum number of CLEAN iterations. (default: 10000)
  --gain GAIN           CLEAN loop gain. (default: 0.1)
  --window WINDOW       Further CLEAN in mask to this threshold. (default: None)

catalogue arguments:
  --leakage_degree LEAKAGE_DEGREE
                        Degree of leakage polynomial fit. (default: 4)
  --leakage_bins LEAKAGE_BINS
                        Number of bins for leakage fit. (default: 16)
  --leakage_snr LEAKAGE_SNR
                        SNR cut for leakage fit. (default: 30.0)
  --write OUTFILE       File to save table to. (default: None)

cleanup arguments:
  --overwrite           Overwrite existing tarball (default: False)

Args that start with '--' can also be set in a config file (/scratch3/projects/spiceracs/arrakis/arrakis/.default_config.yaml or specified via --config). Config file
syntax allows: key=value, flag=true, stuff=[a,b,c] (for details, see syntax at https://goo.gl/R74nmi). In general, command-line values override config file values which
override defaults.

You can optionally pass a configuration file (with the --config argument) to set the options you prefer. An example file in contained in arrakis/.default_config.yaml:

# options:
hosted-wsclean: docker://alecthomson/wsclean:latest # Docker or Singularity image for wsclean (default: docker://alecthomson/wsclean:latest)
local_wsclean: null # Path to local wsclean Singularity image (default: None)

# pipeline arguments:
dask_config: null # Config file for Dask SlurmCLUSTER. (default: None)
imager_dask_config: null #Config  file for Dask SlurmCLUSTER. (default: None)
imager_only: false # Only run the imager component of the pipeline.  (default: False)
skip_imager: false #Skip imaging stage [False]. (default: False)
skip_cutout: false #Skip cutout stage [False]. (default: False)
skip_linmos: false #Skip LINMOS stage [False]. (default: False)
skip_frion: false #Skip cleanup stage [False]. (default: False)
skip_rmsynth: false #Skip RM Synthesis stage [False]. (default: False)
skip_rmclean: false #Skip RM-CLEAN stage [False]. (default: False)
skip_cat: false #Skip catalogue stage [False]. (default: False)
skip_cleanup: false #Skip cleanup stage [False]. (default: False)

# generic null arguments:
sbid: null #SBID of observation. (default: None)
stokes: # List of Stokes parameters to image (default: ['I', 'Q', 'U'])
  - I
  - Q
  - U
epoch: 0 # Epoch of observation. (default: 0)
host: null # Host of mongodb (probably $hostname -i). (default: None)
username: null # Username of mongodb. (default: None)
password: # Password of mongodb. (default: None)
limit: null # Limit the number of islands to process. (default: None)
database: false # Add data to MongoDB. (default: False)

# imaging arguments:
temp_dir_wsclean: null # Temporary directory for WSClean to store intermediate files (default: None)
temp_dir_images: null # Temporary directory for to store intermediate image files (default: None)
psf_cutoff: null # Cutoff for smoothing in units of arcseconds.  (default: None)
robust: -0.5 # ROBUST
nchan: 36 # NCHAN
pols: IQU # POLS
size: 6144 # SIZE
scale: 2.5 # SCALE
mgain: 0.7 # MGAIN
niter: 500_000 # NITER
nmiter: 15 # NMITER
auto_mask: 4 # AUTO_MASK
auto_threshold: 1 # AUTO_THRESHOLD
local_rms: true #
local_rms_window: 60 # LOCAL_RMS_WINDOW
force_mask_rounds: 8 # FORCE_MASK_ROUNDS
gridder: wgridder # {direct-ft,idg,wgridder,tuned-wgridder,wstacking}
taper: null # TAPER
minuv: 200 # MINUV
parallel: null # PARALLEL
mpi: false #                 Use MPI (default: False)
purge: false # Purge intermediate files (default: False)
multiscale: false # Use multiscale clean (default: False)
multiscale_scale_bias: null # The multiscale scale bias term provided to wsclean.  (default: None)
multiscale_scales: 0,2,4,8,16,32,64,12 # The scales used in the multiscale clean.  (default: 0,2,4,8,16,32,64,128)
absmem: null # ABSMEM       Absolute memory limit in GB (default: None)
make_residual_cubes: false # Create residual cubes as well as cubes from restored images.  (default: False)
ms_glob_pattern: scienceData*_averaged_cal.leakage.ms # The pattern used to search for measurement sets.  (default: scienceData*_averaged_cal.leakage.ms)
data_column: CORRECTED_DATA # Which column in the measurement set to image.  (default: CORRECTED_DATA)
no_mf_weighting: false # Do not use multi-frequency weighting.  (default: False)
skip_fix_ms: false # Do not apply the ASKAP MS corrections from the package fixms.  (default: False)

# cutout arguments:
pad: 3 # Number of beamwidths to pad around source [3]. (default: 3)
dryrun: false # Do a dry-run [False]. (default: False)

# linmos null arguments:
holofile: null #Path to holography image (default: None)
yanda: 1.3.0 # Yandasoft version to pull from DockerHub [1.3.0]. (default: 1.3.0)
yanda_image: null #Path to an existing yandasoft singularity container image.  (default: None)

# frion arguments:
ionex_server: ftp://ftp.aiub.unibe.ch/CODE/ # IONEX server (default: ftp://ftp.aiub.unibe.ch/CODE/)
ionex_prefix: codg # IONEX_PREFIX
ionex_formatter: null # IONEX formatter. (default: ftp.aiub.unibe.ch)
ionex_proxy_server: null # Proxy server. (default: None)
ionex_predownload: false # Pre-download IONEX files. (default: False)

# common rm arguments:
dimension: 1d # How many dimensions for RMsynth '1d' or '3d'. (default: 1d)
save_plots: false #          save the plots. (default: False)
rm_verbose: false #          Verbose RMsynth/RMClean. (default: False)

# rm-synth arguments:
ion: false # Use ionospheric-corrected data. (default: False)
tt0: null # TT0 MFS image -- will be used for model of Stokes I -- also needs --tt1. (default: None)
tt1: null # TT1 MFS image -- will be used for model of Stokes I -- also needs --tt0. (default: None)
validate: false # Run on Stokes I. (default: False)
own_fit: false # Use own Stokes I fit function. (default: False)
weight_type: # weighting (inverse) 'variance' or 'uniform' (all 1s). (default: variance)
fit_function: # Stokes I fitting function: 'linear' or 'log' polynomials. (default: log)
fit_rmsf: false # Fit a Gaussian to the RMSF (default: False)
phi_max: null # Absolute max Faraday depth sampled (in rad/m^2) (overrides NSAMPLES). (default: None)
dphi: null # Width of Faraday depth channel. (default: None)
n_samples: # Number of samples across the FWHM RMSF. (default: 5)
poly_ord: # polynomial order to fit to I spectrum. (default: 3)
no_stokes_i: false # ignore the Stokes I spectrum. (default: False)
show_plots: false # show the plots. (default: False)
not_rmsf: false # Skip calculation of RMSF? (default: False)
debug: false # turn on debugging messages & plots. (default: False)

# rm-clean arguments:
cutoff: -8 # CLEAN cutoff (+ve = absolute, -ve = sigma). (default: -3)
max_iter: 10000 # maximum number of CLEAN iterations. (default: 10000)
gain: 0.1 # CLEAN loop gain. (default: 0.1)
window: null # Further CLEAN in mask to this threshold. (default: None)

# catalogue arguments:
leakage_degree: 4 # Degree of leakage polynomial fit. (default: 4)
leakage_bins: 16 # Number of bins for leakage fit. (default: 16)
leakage_snr: 30 # SNR cut for leakage fit. (default: 30.0)
write: null # File to save table to. (default: None)

# cleanup arguments:
overwrite: false # Overwrite existing tarball (default: False)

For extra information you can refer to the API:

Similarly, you can merge multiple fields togther using:

(arrakis310) $ spice_region -h
usage: spice_region [-h] [--dask_config DASK_CONFIG] [--skip_frion] [--skip_rmsynth] [--skip_rmclean] [--skip_cat] [--skip_cleanup] [--merge_name MERGE_NAME]
                    [--fields FIELDS [FIELDS ...]] [--datadirs DATADIRS [DATADIRS ...]] [--output_dir OUTPUT_DIR] [-e EPOCH] [--host host] [--username USERNAME]
                    [--password PASSWORD] [--holofile HOLOFILE] [--yanda YANDA] [--yanda_image YANDA_IMAGE] [--dimension DIMENSION] [--save_plots] [--rm_verbose]
                    [--ion] [--tt0 TT0] [--tt1 TT1] [--validate] [--own_fit] [--weight_type WEIGHT_TYPE] [--fit_function FIT_FUNCTION] [--fit_rmsf] [--phi_max PHI_MAX]
                    [--dphi DPHI] [--n_samples N_SAMPLES] [--poly_ord POLY_ORD] [--no_stokes_i] [--show_plots] [--not_rmsf] [--debug] [--cutoff CUTOFF]
                    [--max_iter MAX_ITER] [--gain GAIN] [--window WINDOW] [--leakage_degree LEAKAGE_DEGREE] [--leakage_bins LEAKAGE_BINS] [--leakage_snr LEAKAGE_SNR]
                    [--write OUTFILE] [--overwrite] [--config CONFIG]


    mmm   mmm   mmm   mmm   mmm
    )-(   )-(   )-(   )-(   )-(
   ( S ) ( P ) ( I ) ( C ) ( E )
   |   | |   | |   | |   | |   |
   |___| |___| |___| |___| |___|
    mmm     mmm     mmm     mmm
    )-(     )-(     )-(     )-(
   ( R )   ( A )   ( C )   ( S )
   |   |   |   |   |   |   |   |
   |___|   |___|   |___|   |___|

    Arrakis regional pipeline.

    Before running make sure to start a session of mongodb e.g.
        $ mongod --dbpath=/path/to/database --bind_ip $(hostname -i)



options:
  -h, --help            show this help message and exit
  --config CONFIG       Config file path (default: None)

pipeline arguments:
  --dask_config DASK_CONFIG
                        Config file for Dask SlurmCLUSTER. (default: None)
  --skip_frion          Skip cleanup stage [False]. (default: False)
  --skip_rmsynth        Skip RM Synthesis stage [False]. (default: False)
  --skip_rmclean        Skip RM-CLEAN stage [False]. (default: False)
  --skip_cat            Skip catalogue stage [False]. (default: False)
  --skip_cleanup        Skip cleanup stage [False]. (default: False)

merge arguments:
  --merge_name MERGE_NAME
                        Name of the merged region (default: None)
  --fields FIELDS [FIELDS ...]
                        RACS fields to mosaic - e.g. RACS_2132-50A. (default: None)
  --datadirs DATADIRS [DATADIRS ...]
                        Directories containing cutouts (in subdir outdir/cutouts).. (default: None)
  --output_dir OUTPUT_DIR
                        Path to save merged data (in output_dir/merge_name/cutouts) (default: None)
  -e EPOCH, --epoch EPOCH
                        Epoch of observation. (default: 0)
  --host host           Host of mongodb (probably $hostname -i). (default: None)
  --username USERNAME   Username of mongodb. (default: None)
  --password PASSWORD   Password of mongodb. (default: None)

linmos arguments:
  --holofile HOLOFILE   Path to holography image (default: None)
  --yanda YANDA         Yandasoft version to pull from DockerHub [1.3.0]. (default: 1.3.0)
  --yanda_image YANDA_IMAGE
                        Path to an existing yandasoft singularity container image.  (default: None)

common rm arguments:
  --dimension DIMENSION
                        How many dimensions for RMsynth '1d' or '3d'. (default: 1d)
  --save_plots          save the plots. (default: False)
  --rm_verbose          Verbose RMsynth/RMClean. (default: False)

rm-synth arguments:
  --ion                 Use ionospheric-corrected data. (default: False)
  --tt0 TT0             TT0 MFS image -- will be used for model of Stokes I -- also needs --tt1. (default: None)
  --tt1 TT1             TT1 MFS image -- will be used for model of Stokes I -- also needs --tt0. (default: None)
  --validate            Run on Stokes I. (default: False)
  --own_fit             Use own Stokes I fit function. (default: False)
  --weight_type WEIGHT_TYPE
                        weighting (inverse) 'variance' or 'uniform' (all 1s). (default: variance)
  --fit_function FIT_FUNCTION
                        Stokes I fitting function: 'linear' or 'log' polynomials. (default: log)
  --fit_rmsf            Fit a Gaussian to the RMSF (default: False)
  --phi_max PHI_MAX     Absolute max Faraday depth sampled (in rad/m^2) (overrides NSAMPLES). (default: None)
  --dphi DPHI           Width of Faraday depth channel. (default: None)
  --n_samples N_SAMPLES
                        Number of samples across the FWHM RMSF. (default: 5)
  --poly_ord POLY_ORD   polynomial order to fit to I spectrum. (default: 3)
  --no_stokes_i         ignore the Stokes I spectrum. (default: False)
  --show_plots          show the plots. (default: False)
  --not_rmsf            Skip calculation of RMSF? (default: False)
  --debug               turn on debugging messages & plots. (default: False)

rm-clean arguments:
  --cutoff CUTOFF       CLEAN cutoff (+ve = absolute, -ve = sigma). (default: -3)
  --max_iter MAX_ITER   maximum number of CLEAN iterations. (default: 10000)
  --gain GAIN           CLEAN loop gain. (default: 0.1)
  --window WINDOW       Further CLEAN in mask to this threshold. (default: None)

catalogue arguments:
  --leakage_degree LEAKAGE_DEGREE
                        Degree of leakage polynomial fit. (default: 4)
  --leakage_bins LEAKAGE_BINS
                        Number of bins for leakage fit. (default: 16)
  --leakage_snr LEAKAGE_SNR
                        SNR cut for leakage fit. (default: 30.0)
  --write OUTFILE       File to save table to. (default: None)

cleanup arguments:
  --overwrite           Overwrite existing tarball (default: False)

Args that start with '--' can also be set in a config file (.default_config.cfg or specified via --config). Config file syntax allows: key=value, flag=true,
stuff=[a,b,c] (for details, see syntax at https://goo.gl/R74nmi). In general, command-line values override config file values which override defaults.

Helper scripts (mostly for bespoke purposes) are available on the commandline. See the API reference for more details.