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.
The DO_PREFLAG_SCIENCE parameter allows user to flag science data based on already available information from processing of the bandpass data. At this stage this is used to flag really bad antennas using robust outlier detection methods.
The USER_DEFINED_FLAGS parameter further allows users to specify rule-based flagging directives using an ascii FLAG_DIRECTIVE_FILE that the pipeline can interpret and use for flagging the specified data. The directive file can have as many rows as the number of rules necessary.
The first column must be used to specify the beam and the subsequent part of a row specifies elements corresponding to that beam that one wants flagged. Currently supported rules for flagging include:
The formats for each of these selections (Antenna, SPW, TimeRange, etc.) must be compatible with Cflag. For details on how to specify these, see: http://www.aoc.nrao.edu/~sbhatnag/misc/msselection/msselection.html
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).
SPEEDING up processing: The pipeline has an option to speed up processing by splitting the msdata in time. If sought, the timewise splitting of the measurement sets for each beam are done upfront at the copy/split step. This allows parallel execution of the non-imaging tasks (BandpassApplication, Flagging, Averaging and ContinuumSubtraction) on the cluster, and helps attain a massive reduction in processing times. The imaging is done per beam using data in ALL the TimeWindows either by combining the TimeWise split data in an intermediate step, or by passing to imager the list of the TimeWise split measurement sets (the latter is being experimented and should help reduce some duplication of data as well as save some time in the combining process). For details on making use of this feature, see the section on Processing by splitting data in time in the table below.
| 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 (24:00:00) | none | Time request for splitting the science MS |
| DO_PREFLAG_SCIENCE | false | none | Whether to propagate flags from Bandpass data to the splitted science MS. Currently, only BAD antenna flags are propagated |
| USER_DEFINED_FLAGS | false | none | Whether to propagate flag directives specified in an ASCII file: FLAG_DIRECTIVE_FILE |
| FLAG_DIRECTIVE_FILE | "" | none | ASCII file with each row specifying a Beam number and flagging criteria for that beam. For example:
In general each directive should be specified in a single row as:
|
| DO_FLAG_SCIENCE | true | none | Whether to flag the (splitted) science MS |
| JOB_TIME_FLAG_SCIENCE | JOB_TIME_DEFAULT (24:00:00) | 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 (24:00:00) | none | Time request for applying the bandpass to the science data |
| NUM_CORES_CAL_APPLY | 19 | 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 (24:00:00) | 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 | width (mssplit (Measurement Splitting/Averaging Utility)) | Number of channels to be averaged to create continuum measurement set. |
| TILENCHAN_AV | 1 | stman.tilenchan (mssplit (Measurement Splitting/Averaging Utility)) | The number of channels in the tile size used for the averaged 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. |
| ELEVATION_FLAG_SCIENCE_LOW | "" | elevation_flagger.low (cflag (Flagging Utility)) | Visibilities below this elevation (degrees) will be flagged. If set to blank (ELEVATION_FLAG_SCIENCE_LOW=""), then no flagging based on low elevation limit will be applied. |
| ELEVATION_FLAG_SCIENCE_HIGH | "" | elevation_flagger.high (cflag (Flagging Utility)) | Visibilities above this elevation (degrees) will be flagged. If set to blank (ELEVATION_FLAG_SCIENCE_HIGH=""), then no flagging based on high elevation limit will be 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. |
| UVRANGE_FLAG_SCIENCE | "" | selection_flagger.<rule>.uvrange (cflag (Flagging Utility)) | Allows flagging of a specified UV range(s). The string given is passed directly to the uvrange 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 documentation 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. |
| UVRANGE_FLAG_SCIENCE_AV | "" | selection_flagger.<rule>.uvrange (cflag (Flagging Utility)) | Allows flagging of a specified UV range(s). The string given is passed directly to the uvrange 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). |
| Processing by splitting data in time | |||
| DO_SPLIT_TIMEWISE | true | none | By default, the non-imaging jobs – bandpass application, flagging, averaging, ccontsubtract – will be done in data that has been split into TimeWindows (see below for TimeWindow interval selection param). This will speed-up the processing, especially when the observation duration exceeds a few hours. |
| SPLIT_INTERVAL_MINUTES | 60 | none | If DO_SPLIT_TIMEWISE is set to true, the pipeline will split data in to T/SPLIT_INTERVAL_MINUTES time-windows (where, T=total obs time in minutes. The pipleine ensures that the time intervals are equal to a second, and so the specified interval may get modified from what had been specified. |