Docs

arrakis/.default_config.cfg

@@ -1,56 +1,102 @@
 # Arrakis default config
-[General options]
-# host: # Host of mongodb.
-# username: # Username of mongodb.
-# password: # Password of mongodb.
-# dask_config: # Config file for Dask SlurmCLUSTER.
-# holofile:
-yanda: "1.3.0"
-
-[Flow options]
+
+## Note 'None' will be interpreated as a string, not a NoneType
+## If you want to use the default value, just leave the line blank
+
+[Imaging options]
+# temp_dir: None
+# psf_cutoff: None
+robust: -0.5
+nchan: 36
+pols: 'IQU'
+size: 4096
+scale: 2.5
+mgain: 0.8
+niter: 100000
+# nmiter: None
+auto_mask: 3.0
+auto_threshold: 1.0
+local_rms: False
+# local_rms_window: None
+# force_mask_rounds: None
+# gridder: None
+# taper: None
+minuv: 0.0
+# parallel: None
+purge: False
+mpi: False
+multiscale: False
+# multiscale_scale_bias: None
+multiscale_scales: '0,2,4,8,16,32,64,128'
+# absmem: None
+make_residual_cubes: False
+ms_glob_pattern: 'scienceData*_averaged_cal.leakage.ms'
+data_column: 'CORRECTED_DATA'
+no_mf_weighting: False
+skip_fix_ms: False
+hosted-wsclean: 'docker://alecthomson/wsclean:latest'
+# local_wsclean: None
+
+[Pipeline options]
+# config: None
+epoch: 0
+# host: None
+# username: None
+# password: None
+# dask_config: None
+# imager_dask_config: None
+# holofile: None
+yanda: '1.3.0'
+# yanda_image: None
+imager_only: False
+skip_imager: False
 skip_cutout: False
 skip_linmos: False
 skip_cleanup: False
+skip_frion: False
 skip_rmsynth: False
 skip_rmclean: False
 skip_cat: False
-
-[Output options]
-verbose: True # Verbose output
-verbose_worker: False # Verbose worker output
+verbose: False
 
 [Cutout options]
-pad: 3 # Number of beamwidths to pad around source
-dryrun: False # Do a dry-run
-
-[RM-synth/CLEAN options]
-dimension: 1d # How many dimensions for RMsynth [1d] or '3d'
-database: True # Add RMsynth data to MongoDB
-# tt0: # TT0 MFS image -- will be used for model of Stokes I -- also needs --tt1.
-# tt1: # TT1 MFS image -- will be used for model of Stokes I -- also needs --tt0.
-validate: False # Run on RMsynth Stokes I
-# limit: # Limit number of sources
-own_fit: False # Use own fit for RMsynth Stokes I
-
-[RM-tools options]
-savePlots: False # save the plots
-weightType: variance # weighting [uniform] (all 1s) or 'variance'
-fit_function: log # Stokes I fitting function
-fitRMSF: True # Fit a gaussian to the RMSF
-# phiMax_radm2: # Absolute max Faraday depth sampled (overrides NSAMPLES)
-# dPhi_radm2: # Width of Faraday depth channel
-nSamples: 5 # Number of samples across the FWHM RMSF
-polyOrd: -3 # polynomial order to fit to I spectrum
-noStokesI: False # ignore the Stokes I spectrum
-showPlots: False # show the plots
-not_RMSF: False # Skip calculation of RMSF
-rm_verbose: False # Verbose RMsynth/CLEAN
-debug: False # turn on debugging messages & plots
-cutoff: -3 # CLEAN cutoff (+ve = absolute, -ve = sigma)
-maxIter: 10000 # maximum number of CLEAN iterations
-gain: 0.1 # CLEAN loop gain
-window: False # use a windowed CLEAN
-
-[Catalogue options]
-# outfile: # File to save table to
-format: fits # Format for output file
+pad: 5
+dryrun: False
+
+[RMsynth options]
+dimension: '1d'
+database: False
+# tt0: None
+# tt1: None
+validate: False
+# limit: None
+own_fit: False
+savePlots: False
+weightType: 'variance'
+fit_function: 'log'
+fitRMSF: False
+# phiMax_radm2: None
+# dPhi_radm2: None
+nSamples: 5
+polyOrd: 3
+noStokesI: False
+showPlots: False
+not_RMSF: False
+rm_verbose: False
+debug: False
+
+[RMclean options]
+cutoff: -3
+maxIter: 10000
+gain: 0.1
+# window: None
+
+[FRion options]
+ionex_server: 'ftp://ftp.aiub.unibe.ch/CODE/'
+ionex_prefix: 'codg'
+# ionex_proxy_server: None
+# ionex_formatter: None
+ionex_predownload: False
+
+[Catalog options]
+# outfile: None

arrakis/process_region.py

@@ -9,7 +9,7 @@
 from prefect import flow
 
 from arrakis import makecat, merge_fields, process_spice, rmclean_oncuts, rmsynth_oncuts
-from arrakis.logger import logger
+from arrakis.logger import UltimateHelpFormatter, logger
 from arrakis.utils.database import test_db
 from arrakis.utils.pipeline import logo_str
 
@@ -164,7 +164,7 @@ def cli():
     parser = configargparse.ArgParser(
         default_config_files=[".default_field_config.txt"],
         description=descStr,
-        formatter_class=configargparse.ArgumentDefaultsHelpFormatter,
+        formatter_class=UltimateHelpFormatter,
     )
     parser.add("--config", required=False, is_config_file=True, help="Config file path")
 

arrakis/process_spice.py

@@ -22,7 +22,7 @@
     rmclean_oncuts,
     rmsynth_oncuts,
 )
-from arrakis.logger import logger
+from arrakis.logger import UltimateHelpFormatter, logger
 from arrakis.utils.database import test_db
 from arrakis.utils.pipeline import logo_str
 
@@ -343,9 +343,9 @@ def cli():
 
     # Parse the command line options
     parser = configargparse.ArgParser(
-        default_config_files=[".default_config.txt"],
+        default_config_files=[".default_config.cfg"],
         description=descStr,
-        formatter_class=configargparse.ArgumentDefaultsHelpFormatter,
+        formatter_class=UltimateHelpFormatter,
         parents=[imager_parser],
     )
     parser.add("--config", required=False, is_config_file=True, help="Config file path")
@@ -631,6 +631,7 @@ def cli():
         "--outfile", default=None, type=str, help="File to save table to [None]."
     )
     args = parser.parse_args()
+
     parser.print_values()
 
     verbose = args.verbose