Calibrator pipeline

Note

If you are running the deprecated genericpipeline version of the pipeline (prefactor 3.2 or older), please check the old instructions page.

This pipeline processes the calibrator data in order to derive direction-independent corrections. It will take into account the correct order of distortions to be calibrated for. This chapter will present the specific steps of the calibrator pipeline in more detail.

All results (diagnostic plots and calibration solutions) will be stored usually in the --outdir directory specified with your cwltool or toil command.

Prepare calibrator, incl. “demixing” (prep)

This part of the pipeline prepares the calibrator data in order to be calibration-ready. This mainly includes mitigation of bad data (RFI, bad antennas, contaminations from A-Team sources), selection of the data to be calibrated, and some averaging to reduce data size and enhance the signal-to-noise ratio. The user can specify whether to do raw data or pre-processed data flagging and whether demixing should be performed.

The basic workflows are:

• preparation of data (prep)

• correcting for polarization alignment (PA)

• correcting for Faraday Rotation (FR)

• correcting for bandpass (BP)

• correcting for ionospheric disturbances (ion)

The workflow prep consists of:

• determining suitable calibrator skymodel (steps find_skymodel_cal, make_sourcedb)

• checking for nearby A-Team sources (step check_Ateam_separation)

• creating a model of A-Team sources to be subtracted (step make_sourcedb_ateam)

• basic flagging and averaging (subworkflow dp3_prep_cal)

  • edges of the band (flagedge) – only used if raw_data : true

  • statistical flagging (aoflag) – only used in raw_data : true

  • baseline flagging (flagbaseline)

  • low elevation flagging (below 15 degress elevation) (flagelev)

  • low amplitude flagging (below 1e-30) (flagamp)

  • demix A-Team sources (demix) – only used if specified demix : true

  • averaging of the data in time and frequency

• wide-band statistical flagging (steps ms_concat and aoflag)

• write the calibrator skymodel into the MODEL_DATA column (step predict) and perform direction-independent phase-only calibration (diagonal terms + common rotation angle, step calib_cal) (subworkflow predict_cal, baseline-dependent smoothing (step BLsmooth) if specified do_smooth : true)

Calibration of the polarization alignment (PA)

The phase solutions derived from the preparation step are now collected and loaded into LoSoTo. LoSoTo will derive the polarizion alignment and provide diagnostic plots under inspection/:

• polalign_ph_pol??.png: matrix plot of the phase solutions for the XX and YY polarization

  

• polalign_ph_poldif.png: matrix plot of the phase solutions from XX-YY

  

• polalign_rotangle.png: matrix plot of the common rotation angle solutions

  

• polalign_amp_pol??.png: matrix plot of the amplitude solutions for the XX and YY polarization

  

• polalign.png: matrix plot of the derived polarization alignment between XX and YY

  

• polalign_ph-res_pol??.png: matrix plot of the residual phase solutions for the XX and YY polarization after subtraction the derived polarization alignment

• polalign_ph-res_poldif.png: matrix plot of the residual phase solutions for XX-YY after subtraction of the derived polarization alignment

The workflow PA consists of:

• deriving the polarization alignment from the calibration solutions (subworkflow PolAlign)

• creating diagnostic plots (steps losoto_plot)

• applying polarization alignment solutions (step applyPA) and the element beam correction (step applybeam) to the original data and re-calibrate (diagonal terms + common rotation angle, step calib_cal) (subworkflow apply_calibrate_pa, baseline-dependend smoothing (step BLsmooth) if specified do_smooth : true)

Calibration of the Faraday Rotation (FR)

The outcome of the re-calibration after correcting for the polarization alignment is again loaded into LoSoTo in order to derive corrections for Faraday Rotation. The following diagnostic plots are created:

• fr_ph_pol??.png: matrix plot of the phase solutions for the XX and YY polarization

• fr_ph_poldif.png: matrix plot of the phase solutions from XX-YY

• fr_rotangle.png: matrix plot of the common rotation angle solutions

• fr_amp_pol??.png: matrix plot of the amplitude solutions for the XX and YY polarization

• fr: matrix plot of the derived differential Rotation Measure from Faraday Rotation

  

The workflow FR consists of:

• deriving the Faraday Rotation from the calibration solutions (subworkflow FaradayRot)

• creating diagnostic plots (steps losoto_plot)

• applying Faraday Rotation solutions (step applyFR) and re-calibrate (diagonal terms + common rotation angle, step calib_cal) (subworkflow apply_calibrate_fr, baseline-dependend smoothing (step BLsmooth) if specified do_smooth : true)

Calibration of the Bandpass (BP)

The outcome of the re-calibration after correcting for the polarization alignment and Faraday Rotation is loaded into LoSoTo in order to derive corrections for the bandpass. A robust flagging on the amplitude solutions as well as a Savitzky-Golay filter is applied in order to reject bad solutions and smooth the outcome. Frequency regimes up to a certain maximum width (parameter max2interpolate) will be interpolated if flagged. The following diagnostic plots are created:

• ampBFlag_??.png: matrix plot of the amplitude solutions for the XX and YY polarization before flagging

  

• ampAFlag_??.png: matrix plot of the amplitude solutions for the XX and YY polarization after flagging

  

• bandpass_pol??.png: the derived bandpass of all stations in the XX and YY polarization

• bandpass_time??.png: matrix plot of the derived bandpass, where both polarizations are colorcoded

  

• bandpass_time??_pol??.png: plot of the derived bandpass of the XX and YY polarization, where all stations are colorcoded

  

The workflow BP consists of:

• deriving the bandpass from the calibration solutions (subworkflow bandpass)

• creating diagnostic plots (steps losoto_plot)

• transfer solutions for international stations for non-trusted calibrator sources (step transfer_solutions), see parameters do_transfer and trusted_sources

• applying polarization alignment solutions (step applyPA), the bandpass (step applyBP), the element beam correction (step applybeam) and the Faraday Rotation solutions (applyFR) to the original data and calibrate (only single scalar phase, step calib_cal) (subworkflow apply_calibrate_bp, baseline-dependend smoothing (step BLsmooth) if specified do_smooth : true)

• deriving final amount of flags applied to the data (step final_flags)

Calibration of the instrumental and ionospheric delays (ion)

The outcome of the re-calibration after correcting for the polarization alignment, the bandpass and the Faraday Rotation is loaded into LoSoTo in order to derive corrections for the instrumental and ionospheric delays. A robust flagging on the amplitude solutions is applied in order to reject bad solutions. These flags are applied to the phase solutions. These phase solutions should be mainly affected by instrumental (clock) and ionospheric (TEC) delays. This LoSoTo step will aim to separate both effects (clock-TEC separation). The following diagnostic plots are created:

• ion_ph.png: matrix plot of the phase solutions

• clock.png: matrix plot of the derived (instrumental) clock offsets in seconds

  

• tec.png: matrix plot of the derived differential TEC in TECU

  

• ion_ph-res.png: matrix plot of the residual phase solutions after the subtraction of the derived instrumental and ionospheric delays

The workflow ion consists of:

• performing clock-TEC-separation from the calibration solutions (subworkflow clocktec)

• creating diagnostic plots (steps losoto_plot)

• create a summary file (step summary)

Note

All solutions are written in the h5parm file format via the steps H5parm_collector and called during all the workflows.

The solutions are stored in the final calibrator solution set cal_solutions.h5.

Further diagnostics

The results directory will contain all relevant outputs of the current LINC run, once the pipeline has finished:

• logfiles in logs

• summary file (JSON format) in ??_LINC_calibrator_summary.json

• calibration solutions in cal_solutions.h5

• inspection plots in inspection

Ateam_separation.png shows the distance and the elevation of A-Team sources with respect to the analyzed observation.

You can also check the calibration solutions for more details:

$ losoto -i cal_solutions.h5

Summary of cal_solutions.h5

Solution set 'calibrator':
==========================

Directions: 3c286

Stations: CS001HBA0     CS001HBA1       CS002HBA0       CS002HBA1
          CS003HBA0     CS003HBA1       CS004HBA0       CS004HBA1
          CS005HBA0     CS005HBA1       CS006HBA0       CS006HBA1
          CS007HBA0     CS007HBA1       CS011HBA0       CS011HBA1
          CS017HBA0     CS017HBA1       CS021HBA0       CS021HBA1
          CS024HBA0     CS024HBA1       CS026HBA0       CS026HBA1
          CS028HBA0     CS028HBA1       CS030HBA0       CS030HBA1
          CS031HBA0     CS031HBA1       CS032HBA0       CS032HBA1
          CS101HBA0     CS101HBA1       CS103HBA0       CS103HBA1
          CS201HBA0     CS201HBA1       CS301HBA0       CS301HBA1
          CS302HBA0     CS302HBA1       CS401HBA0       CS401HBA1
          CS501HBA0     CS501HBA1       RS106HBA        RS205HBA
          RS208HBA      RS210HBA        RS305HBA        RS306HBA
          RS307HBA      RS310HBA        RS406HBA        RS407HBA
          RS409HBA      RS503HBA        RS508HBA        RS509HBA

Solution table 'bandpass' (type: amplitude): 120 times, 11 freqs, 60 ants, 2 pols
    Flagged data: 0.000%

Solution table 'clock' (type: clock): 120 times, 60 ants
    Flagged data: 0.000%

Solution table 'faraday' (type: rotationmeasure): 60 ants, 120 times
    Flagged data: 0.222%

Solution table 'polalign' (type: phase): 120 times, 60 ants, 40 freqs, 2 pols
    Flagged data: 0.000%

For an overall summary it is advised to check the summary logfile:

$ cat logs/3c286_summary.log

****************************************
*** LINC calibrator pipeline summary ***
****************************************

Field name: 3c286

User-specified baseline filter: *&
Additional antennas removed from the data: NONE
A-Team sources close to the phase reference center: VirA
    Of which were demixed: NONE
    Of which were clipped: NONE

Amount of flagged solutions per station and solution table:
Station   bandpass  clock   faraday  polalign
CS001HBA0   9.08%  100.00%    0.00%    0.00%
CS001HBA1   9.08%  100.00%    0.00%    0.00%
CS002HBA0   9.08%  100.00%    0.00%    0.00%
CS002HBA1   9.08%  100.00%    0.00%    0.00%
CS003HBA0   9.08%  100.00%    0.00%    0.00%
CS003HBA1   9.08%  100.00%    0.00%    0.00%

Amount of flagged data per station at a given state:
Station    initial  final
CS001HBA0   3.18%   3.96%
CS001HBA1   2.98%   3.97%
CS002HBA0   3.18%   4.42%
CS002HBA1   2.95%   3.67%
CS003HBA0   2.96%   3.94%
CS003HBA1   3.10%   4.21%

**********
Summary file is written to: 3c286_LINC_calibrator_summary.json
Summary has been created.

User-defined parameter configuration

Parameters you will need to adjust

Location of the calibrator solutions

• msin: location of the input calibrator data, for instructions look at the configuration instructions page

Parameters you may need to adjust

Data selection and calibration options

• refant: regular expression of the stations that are allowed to be selected as a reference antenna by the pipeline (default: CS00.*)

• flag_baselines: DP3-compatible pattern for baselines or stations to be flagged (may be an empty list, i.e.: [] )

• process_baselines_cal: performs A-Team-clipping/demixing and direction-independent phase-only self-calibration only on these baselines. Choose [CR]S*& if you want to process only cross-correlations and remove international stations (default: *&)

• filter_baselines: selects only this set of baselines to be processed. Choose [CR]S*& if you want to process only cross-correlations and remove international stations (default: *&)

• do_smooth: enable or disable baseline-based smoothing (default: false)

• rfistrategy: strategy to be applied with the statistical flagger (AOFlagger, default: $LINC_DATA_ROOT/rfistrategies/lofar-hba-wideband.lua)

• max2interpolate: amount of channels in which interpolation should be performed for deriving the bandpass (default: 30)

• fit_offset_PA: assume that together with a delay each station has also a differential phase offset (important for old LBA observations, default: false)

• interp_windowsize: size of the window over which a value is interpolated. Should be odd. (default: 15)

• ampRange: range of median amplitudes accepted per station (default: [0,0])

• skip_international: skip fitting the bandpass for international stations (this avoids flagging them in many cases, default: true)

• raw_data: use autoweight, set to True in case you are using raw data (default: false)

• propagatesolutions: use already derived solutions as initial guess for the upcoming time slot (default: true)

• flagunconverged : flag solutions for solves that did not converge (if they were also detected to diverge, default: false)

• maxStddev: maximum allowable standard deviation when outlier clipping is done. For phases, this should value should be in radians, for amplitudes in log(amp). If None (or negative), a value of 0.1 rad is used for phases and 0.01 for amplitudes (default: -1.0)

• solutions2transfer: provide own solutions from a reference calibrator observation in case calibrator source is not trusted

• antennas2transfer: DP3-compatible baseline pattern for those stations who should get calibration solutions from a reference solution set in case calibrator source is not trusted (default: [FUSPID].*)

• do_transfer: enable solutions transfer for non-trusted calibrator sources (default: false)

• trusted_sources: comma-separated list of trusted calibrator sources. Solutions are only transferred from a reference solution set in case the observed calibrator is not among them (default: 3C48,3C147,3C196,3C295,3C380)

• ion_3rd: take into account also 3rd-order effects for the clock-TEC separation (ionospheric calibration, default: false)

• clock_smooth: only take the median of the derived clock solutions (enable this in case of non-joint observations, default: true)

• remove_phase_wraps: detect and remove phase wraps in the clock-TEC separation (default: false)

A comprehensive explanation of the baseline selection syntax can be found here.

Demixing options (only used if demix step is added to the prep_cal_strategy variable)

• demix_sources: choose sources to demix (provided as list), e.g., [CasA,CygA]

• demix_freqres: frequency resolution used when demixing (default: 48.82kHz, which translates to 4 channels per subband)

• demix_timeres : time resolution used when demixing in seconds (default: 10)

• demix: if true force demixing using all sources of demix_sources, if false do not demix (default: null, automatically determines sources to be demixed according to min_separation)

• lbfgs_historysize: for the LBFGS solver: the history size, specified as a multiple of the parameter vector, to use to approximate the inverse Hessian (default: 10)

• lbfgs_robustdof: for the LBFGS solver: the degrees of freedom (DOF) given to the noise model (default: 200)

Further pipeline options

• min_separation: minimum accepted distance to an A-team source on the sky in degrees (will raise a WARNING, default: 30)

• tables2export: choose which tables to export to the solutions file after the ionospheric calibration (default: clock)

Parameters for pipeline performance

• max_dp3_threads: number of threads per process for DP3 (default: 10)

• memoryperc: maximum of memory used for aoflagger in raw_flagging mode in percent (default: 20)

• aoflag_reorder: make aoflagger reorder the measurement set before running the detection. This prevents that aoflagger will use its memory reading mode, which is faster but uses more memory (default: false, see the AOFlagger manual`_)

• aoflag_chunksize: this will split the set into intervals with the given maximum size, and flag each interval independently. This lowers the amount of memory required (default: 2000)

Parameters you may want to adjust

Skymodel directory

• calibrator_path_skymodel: location of the calibrator skymodels

• max_separation_arcmin: maximum separation between phase center of the observation and the patch of a calibrator skymodel which is accepted to be chosen as a skymodel (default: 1.0)

• A-Team_skymodel: location of the A-Team skymodels

Averaging for the calibrator data

• avg_timeresolution: final time resolution of the data in seconds after averaging (default: 4)

• avg_freqresolution : final frequency resolution of the data after averaging (default: 48.82kHz, which translates to 4 channels per subband)

• bandpass_freqresolution: frequency resolution of the bandpass solution table (default: 195.3125kHz, which translates to 1 channel per subband)