User Parameters - Preparation of the Science field dataΒΆ

These parameters govern the pre-processing needed for the science field, to split by beam, apply the bandpass (although none of the parameters listed here relate to that), flag, and average to continuum resolution.

The splitting is done by beam, and optionally by particular scans and/or fields (where the latter are selected on the basis of the FIELD NAME in the MS).

As noted in User Parameters - Data Location & Beam Selection, when an observation was taken in one-field-per-beam mode, and no selection on scans or channels is done, and there is only a single beam in the MS, then the beam MSs are copied instead of using mssplit. This will run much faster.

Once copied or split, the raw measurement set is first calibrated with the bandpass calibration table derived previously (see User Parameters - Bandpass Calibration). Once calibrated, the dataset will be flagged to remove interference.

As is the case for the bandpass calibrator dataset, the MS is flagged in two passes. First, a combination of selection rules (allowing flagging of channels, time ranges, antennas & baselines, and autocorrelations) and (optionally) a simple flat amplitude threshold are applied. Then a sequence of Stokes-V flagging and dynamic flagging of amplitudes is done, optionally integrating over or across individual spectra. Each of these steps is selectable via input parameters.

Again, there is an option to use the AOFlagger tool (written by Andre Offringa) to do the flagging. This can be turned on by FLAG_WITH_AOFLAGGER, or FLAG_SCIENCE_WITH_AOFLAGGER & FLAG_SCIENCE_AV_WITH_AOFLAGGER (to just do it for the full-spectral-resolution or averaged science data respectively). You can provide a strategy file via AOFLAGGER_STRATEGY or AOFLAGGER_STRATEGY_SCIENCE & AOFLAGGER_STRATEGY_SCIENCE_AV, with access to some of the aoflagger parameters provided - see the table below. These strategy files need to be created prior to running the pipeline.

The dataset used for continuum imaging is created by averaging the frequency channels. The averaging scale defaults to 54 channels, resulting in a 1MHz-resolution MS that can be imaged with cimager, although this averaging scale can be changed by the user.

Once the averaged dataset has been created, a second round of flagging can be done on it, to flag any additional features that the averaging process may have enhanced.

The default behaviour is to process all fields within the science MS (interleaving, for instance, makes use of multiple fields), with each field being processed in its own sub-directory. The field selection is done in the splitting task, at the same time as the beam selection. It is possible, however, to select a single field to process via the FIELD_SELECTION_SCIENCE parameter (by giving the field name).

Variable Default Parset equivalent Description
Job selection      
DO_SPLIT_SCIENCE true none Whether to split out the given beam from the science MS
JOB_TIME_SPLIT_SCIENCE JOB_TIME_DEFAULT (12:00:00) none Time request for splitting the science MS
DO_FLAG_SCIENCE true none Whether to flag the (splitted) science MS
JOB_TIME_FLAG_SCIENCE JOB_TIME_DEFAULT (12:00:00) none Time request for flagging the science MS
DO_APPLY_BANDPASS true none Whether to apply the bandpass calibration to the science observation
JOB_TIME_APPLY_BANDPASS JOB_TIME_DEFAULT (12:00:00) none Time request for applying the bandpass to the science data
NUM_CORES_CAL_APPLY 55 none Number of cores for the job to apply the bandpass to the science data.
DO_AVERAGE_CHANNELS true none Whether to average the science MS to continuum resolution
JOB_TIME_AVERAGE_MS JOB_TIME_DEFAULT (12:00:00) none Time request for averaging the channels of the science data
Data selection      
SCAN_SELECTION_SCIENCE no default (see description) scans (mssplit (Measurement Splitting/Averaging Utility)) This allows selection of particular scans from the science observation. If not provided, no scan selection is done (all scans are included in the output MS).
FIELD_SELECTION_SCIENCE no default (see description) fields (mssplit (Measurement Splitting/Averaging Utility)) This allows selection of particular FIELD NAMEs from the science observation. If not provided, all fields are done. The value must be just the field name - not surrounded by square brackets (which is a possible format for mssplit.fields). This is because the value iwll be matched to field names from the measurement set.
MS_BASE_SCIENCE scienceData_SB%s_%b.ms none Base name for the science observation measurement set after splitting. The wildcard %b will be replaced by the string “FIELD_beamBB”, where FIELD represents the FIELD id, and BB the (zero-based) beam number (scienceData_SB1234_LMC_beam00.ms etc), and the %s will be replaced by the scheduling block ID.
MS_SCIENCE_AVERAGE no default (see description) dataset (cimager) The name of the averaged measurement set that will be imaged by the continuum imager. Provide this if you want to skip the bandpass calibration and averaging steps (perhaps you’ve already done them). The wildcard %b, if present, will be replaced with “FIELD_beamBB”, as described above. If not provided, the averaged MS name will be derived from MS_BASE_SCIENCE, with ”.ms” replaced with “_averaged.ms”.
CHAN_RANGE_SCIENCE “” channel (mssplit (Measurement Splitting/Averaging Utility)) Range of channels in science observation (used in splitting and averaging). This must (for now) be the same as CHAN_RANGE_1934. The default is to use all available channels from the MS.
NUM_CHAN_TO_AVERAGE 54 stman.tilenchan (mssplit (Measurement Splitting/Averaging Utility)) Number of channels to be averaged to create continuum measurement set. Also determines the tile size when creating the MS.
Initial flagging      
FLAG_DO_DYNAMIC_AMPLITUDE_SCIENCE true none Whether to do the dynamic flagging, after the rule-based and simple flat-amplitude flagging is done
FLAG_THRESHOLD_DYNAMIC_SCIENCE 4.0 amplitude_flagger.threshold (cflag (Flagging Utility)) Dynamic threshold applied to amplitudes when flagging science field data [sigma]
FLAG_DYNAMIC_INTEGRATE_SPECTRA true amplitude_flagger.integrateSpectra (cflag (Flagging Utility)) Whether to integrate the spectra in time and flag channels during the dynamic flagging task.
FLAG_THRESHOLD_DYNAMIC_SCIENCE_SPECTRA 4.0 amplitude_flagger.integrateSpectra.threshold (cflag (Flagging Utility)) Dynamic threshold applied to amplitudes when flagging science field data in integrateSpectra mode [sigma]
FLAG_DYNAMIC_INTEGRATE_TIMES false amplitude_flagger.integrateTimes (cflag (Flagging Utility)) Whether to integrate across spectra and flag time samples during the dynamic flagging task.
FLAG_THRESHOLD_DYNAMIC_SCIENCE_TIMES 4.0 amplitude_flagger.integrateTimes.threshold (cflag (Flagging Utility)) Dynamic threshold applied to amplitudes when flagging science field data in integrateTimes mode [sigma]
FLAG_DO_STOKESV_SCIENCE true none Whether to do the Stokes-V flagging on the science data, after the rule-based and simple flat-amplitude flagging is done
FLAG_USE_ROBUST_STATS_STOKESV_SCIENCE true stokesv_flagger.useRobustStatistics (cflag (Flagging Utility)) Whether to use robust statistics (median and inter-quartile range) in computing the Stokes-V statistics.
FLAG_THRESHOLD_STOKESV_SCIENCE 4.0 stokesv_flagger.threshold (cflag (Flagging Utility)) Threshold applied to amplitudes when flagging the Stokes-V for the science field data [sigma]
FLAG_STOKESV_INTEGRATE_SPECTRA true stokesv_flagger.integrateSpectra (cflag (Flagging Utility)) Whether to integrate the spectra in time and flag channels during the Stokes-V flagging task.
FLAG_THRESHOLD_STOKESV_SCIENCE_SPECTRA 4.0 stokesv_flagger.integrateSpectra.threshold (cflag (Flagging Utility)) Threshold applied to amplitudes when flagging the Stokes-V for the science field data in integrateSpectra mode [sigma]
FLAG_STOKESV_INTEGRATE_TIMES false stokesv_flagger.integrateTimes (cflag (Flagging Utility)) Whether to integrate across spectra and flag time samples during the Stokes-V flagging task.
FLAG_THRESHOLD_STOKESV_SCIENCE_TIMES 4.0 stokesv_flagger.integrateTimes.threshold (cflag (Flagging Utility)) Threshold applied to amplitudes when flagging the Stokes-V for the science field data in integrateTimes mode [sigma]
FLAG_DO_FLAT_AMPLITUDE_SCIENCE false none Whether to apply a flag amplitude flux threshold to the data.
FLAG_THRESHOLD_AMPLITUDE_SCIENCE
amplitude_flagger.high (cflag (Flagging Utility)) Simple amplitude threshold applied when flagging science field data. If set to blank (FLAG_THRESHOLD_AMPLITUDE_SCIENCE_LOW=""), then no minimum value is applied.
`FLAG_THRESHOLD_AMPLITUDE_SCIENCE_LOW “” amplitude_flagger.low (cflag (Flagging Utility)) Lower threshold for the simple amplitude flagging. If set to blank (FLAG_THRESHOLD_AMPLITUDE_SCIENCE_LOW=""), then no minimum value is applied.
ANTENNA_FLAG_SCIENCE “” selection_flagger.<rule>.antenna (cflag (Flagging Utility)) Allows flagging of antennas or baselines. For example, to flag out the 1-3 baseline, set this to “ak01&&ak03” (with the quote marks). See documentation for further details on format.
CHANNEL_FLAG_SCIENCE “” selection_flagger.<rule>.spw (cflag (Flagging Utility)) Allows flagging of a specified range of channels. For example, to flag out the first 100 channnels, use “0:0~16” (with the quote marks). See the documentation for further details on the format.
TIME_FLAG_SCIENCE “” selection_flagger.<rule>.timerange (cflag (Flagging Utility)) Allows flagging of a specified time range(s). The string given is passed directly to the timerange option of cflag’s selection flagger. For details on the possible syntax, consult the MS selection documentation.
FLAG_AUTOCORRELATION_SCIENCE false selection_flagger.<rule>.autocorr If true, then autocorrelations will be flagged.
Flagging of averaged data      
FLAG_AFTER_AVERAGING true none Whether to do an additional step of flagging on the channel-averaged MS proior to imaging.
FLAG_DO_DYNAMIC_AMPLITUDE_SCIENCE_AV true none Whether to do the dynamic flagging on the averaged science data, after the simple flat-amplitude flagging is done
FLAG_THRESHOLD_DYNAMIC_SCIENCE_AV 4.0 amplitude_flagger.threshold (cflag (Flagging Utility)) Dynamic threshold applied to amplitudes when flagging the averaged science field data [sigma]
FLAG_DYNAMIC_INTEGRATE_SPECTRA_AV true amplitude_flagger.integrateSpectra (cflag (Flagging Utility)) Whether to integrate the spectra in time and flag channels during the dynamic flagging task.
FLAG_THRESHOLD_DYNAMIC_SCIENCE_SPECTRA_AV 4.0 amplitude_flagger.integrateSpectra.threshold (cflag (Flagging Utility)) Dynamic threshold applied to amplitudes when flagging the averaged science field data in integrateSpectra mode [sigma]
FLAG_DYNAMIC_INTEGRATE_TIMES_AV false amplitude_flagger.integrateTimes (cflag (Flagging Utility)) Whether to integrate across spectra and flag time samples during the dynamic flagging task.
FLAG_THRESHOLD_DYNAMIC_SCIENCE_TIMES_AV 4.0 amplitude_flagger.integrateTimes.threshold (cflag (Flagging Utility)) Dynamic threshold applied to amplitudes when flagging the averaged science field data in integrateTimes mode [sigma]
FLAG_DO_STOKESV_SCIENCE_AV true none Whether to do the Stokes-V flagging on the averaged science data, after the rule-based and simple flat-amplitude flagging is done
FLAG_USE_ROBUST_STATS_STOKESV_SCIENCE_AV true stokesv_flagger.useRobustStatistics (cflag (Flagging Utility)) Whether to use robust statistics (median and inter-quartile range) in computing the Stokes-V statistics.
FLAG_THRESHOLD_STOKESV_SCIENCE_AV 4.0 stokesv_flagger.threshold (cflag (Flagging Utility)) Threshold applied to amplitudes when flagging the Stokes-V for the averaged science field data [sigma]
FLAG_STOKESV_INTEGRATE_SPECTRA_AV true stokesv_flagger.integrateSpectra (cflag (Flagging Utility)) Whether to integrate the spectra in time and flag channels during the Stokes-V flagging task.
FLAG_THRESHOLD_STOKESV_SCIENCE_SPECTRA_AV 4.0 stokesv_flagger.integrateSpectra.threshold (cflag (Flagging Utility)) Threshold applied to amplitudes when flagging the Stokes-V for the averaged science field data in integrateSpectra mode [sigma]
FLAG_STOKESV_INTEGRATE_TIMES_AV false stokesv_flagger.integrateTimes (cflag (Flagging Utility)) Whether to integrate across spectra and flag time samples during the Stokes-V flagging task.
FLAG_THRESHOLD_STOKESV_SCIENCE_TIMES_AV 4.0 stokesv_flagger.integrateTimes.threshold (cflag (Flagging Utility)) Threshold applied to amplitudes when flagging the Stokes-V for the averaged science field data in integrateTimes mode [sigma]
FLAG_DO_FLAT_AMPLITUDE_SCIENCE_AV false none Whether to apply a flag amplitude flux threshold to the averaged science data.
FLAG_THRESHOLD_AMPLITUDE_SCIENCE_AV
amplitude_flagger.high (cflag (Flagging Utility)) Simple amplitude threshold applied when flagging the averaged science field data. If set to blank (FLAG_THRESHOLD_AMPLITUDE_SCIENCE_LOW=""), then no minimum value is applied. [value in flux-calibrated units]
FLAG_THRESHOLD_AMPLITUDE_SCIENCE_LOW_AV “” amplitude_flagger.low (cflag (Flagging Utility)) Lower threshold for the simple amplitude flagging on the averaged data. If set to blank (FLAG_THRESHOLD_AMPLITUDE_SCIENCE_LOW=""), then no minimum value is applied. [value in flux-calibrated units]
CHANNEL_FLAG_SCIENCE_AV “” selection_flagger.<rule>.spw (cflag (Flagging Utility)) Allows flagging of a specified range of channels. For example, to flag out the first 100 channnels, use “0:0~16” (with the quote marks). See the docuemntation for further details on the format.
TIME_FLAG_SCIENCE_AV “” selection_flagger.<rule>.timerange (cflag (Flagging Utility)) Allows flagging of a specified time range(s). The string given is passed directly to the timerange option of cflag’s selection flagger. For details on the possible syntax, consult the MS selection documentation.
Using AOFlagger for flagging      
FLAG_WITH_AOFLAGGER false none Use AOFlagger for all flagging tasks in the pipeline. This overrides the individual task level switches.
FLAG_SCIENCE_WITH_AOFLAGGER false none Use AOFlagger for the flagging of the full-spectral-resolution science dataset. This and the next parameter allows differentiation between the different flagging tasks in the pipeline.
FLAG_SCIENCE_AV_WITH_AOFLAGGER false none Use AOFlagger for the flagging of the averaged science dataset.
AOFLAGGER_STRATEGY “” none The strategy file to use for all AOFlagger tasks in the pipeline. Giving this a value will apply this one strategy file to all flagging jobs. The strategy file needs to be provided by the user.
AOFLAGGER_STRATEGY_SCIENCE “” none The strategy file to be used for the full-spectral-resolution science dataset. This will be overridden by AOFLAGGER_STRATEGY.
AOFLAGGER_STRATEGY_SCIENCE_AV “” none The strategy file to be used for the averaged science dataset. This will be overridden by AOFLAGGER_STRATEGY.
AOFLAGGER_VERBOSE true none Verbose output for AOFlagger
AOFLAGGER_READ_MODE auto none Read mode for AOflagger. This can take the value of one of “auto”, “direct”, “indirect”, or “memory”. These trigger the following respective command-line options for AOflagger: “-auto-read-mode”, “-direct-read”, “-indirect-read”, “-memory-read”.
AOFLAGGER_UVW false none When true, the command-line argument “-uvw” is added to the AOFlagger command. This reads uvw values (some exotic strategies require these).

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