Target 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 target data in order to apply the direction-independent corrections from the calibrator pipeline. A first initial direction-independent self-calibration of the target field is performed, using a global sky model based on the TGSS ADR or the new Global Sky Model (GSM), and applied to the data.

This chapter will present the specific steps of the target 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 target, incl. “demixing” (prep)

This part of the pipeline prepares the target data in order to be calibration-ready for the first direction-independent phase-only self-calibration against a global sky model. This mainly includes mitigation of bad data (RFI, bad antennas, contaminations from A-Team sources), selection of the data to be calibrated (e.g. Dutch stations only), and some averaging to reduce data size and enhance the signal-to-noise ratio if applicable. Furthermore, for HBA observations ionospheric Rotation Measure corrections are applied, using RMextract The user can specify whether to do raw data or pre-processed data flagging. Demixing is performed only if the pointing is closer than 30 degress to an A-Team source if not specified by the user otherwise.

The basic workflows are:

• preparation of data (prep)

• concatenating and phase-only self-calibration against a global sky model (gsmcal)

• creating the finally calibrated data set, via applying the self-calibration solutions and compressing the data (finalize)

The workflow prep consists of:

• check for a potential station mismatch between calibrator solutions and the target data (step compare_station_list)

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

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

• getting ionospheric Rotation Measure corrections and adding it to the solutions (step createRMh5parm)

• basic flagging, applying solutions, and averaging (subworkflow dp3_prep_target)

  • 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)

  • applying calibrator solutions (steps applyPA, applybandpass, applyclock, applyphase, applybeam, applyRM)

  • averaging of the data in time and frequency

  • predicting impact of A-Team sources and write it to the MODEL_DATA column (step predict)

  • clipping time- and frequency chunks that are likely to be affected by A-Team sources and which have not been demixed before (step Ateamclipper)

Calibration against a global skymodel (gsmcal)

These steps aim for deriving a good first guess for the phase correction in the direction of the phase center (direction-independent phase correction).

Once this is done, the data is ready for further processing with direction-dependent calibration techniques, using software like Rapthor, factor or killMS.

The phase solutions derived from the gsmcal workflow are collected and loaded into LoSoTo to provide diagnostic plots:

• ph_freq??.png: matrix plot of the phase solutions with time for a particular chunk of target data, where both polarizations are colorcoded

  

• ph_poldif_freq??.png: matrix plot of the XX-YY phase solutions with time for a particular chunk of target data

  

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

  

• ph_poldif.png: matrix plot of the phase solutions for the XX-YY polarization

  

The workflow gsmcal consists of:

• retrieving and creating a global sky model (steps find_skymodel_target, make_sourcedb_target)

• identification of fully flagged antennas (step identify_bad_antennas)

• concatenating the data into chunks (subworkflow concat)

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

• checking for bad data chunks (step check_unflagged_fraction)

• perform the calibration against the global skymodel (subworkflow calibrate_target, baseline-dependend smoothing (step BLsmooth) if specified do_smooth : true)

• perform self-calibration against a skymodel derived from imaging the dataset (subworkflow selfcal_target_lba for LBA observations and selfcal_target_hba (optional) for HBA observations)

Self-calibration workflow for HBA observations (selfcal_target_hba)

The self-calibration procedure for LOFAR HBA observation is optional and highly recommended if the solutions derived from TGSS ADR or the new Global Sky Model (GSM) may have room for improvement.

• ??_??-MFS-image.fits: FITS image of the target field

The workflow selfcal_target_hba consists of:

• apply solutions derived from the calibration using TGSS ADR or the new Global Sky Model (GSM) (step apply_gsmcal)

• image target field and write clean component model into model data column (step image_target)

• perform the calibration against the model data column (subworkflow self_calibrate_target, baseline-dependend smoothing (step BLsmooth) if specified do_smooth : true)

Self-calibration workflow for LBA observations (selfcal_target_lba)

The self-calibration procedure for LOFAR LBA observations is run by default and aims for a more accurate determination of phase and amplitude corrections for the array than achieved using the Global Sky Model (GSM) only. It requires an additional round of parameter extraction similar to the calibrator pipeline, starting from the correction of the effects caused by Faraday Rotation (workflow fr) as well as the Total Electron Content (TEC) and amplitude fluctuations (workflow tec_and_amp). This is followed by imaging the calibrated data set at different resolutions to subtract the contamination from sources outside the primary beam of the telescope (workflow imaging_subtract) and update the skymodel in order to repeat the parameter extraction and correction (second iteration). The final data set will have the sources outside the primary beam subtracted.

All solutions derived are loaded into LoSoTo to provide diagnostic plots:

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

• slowtec?_freq??.png: matrix plot of the derived slow varying TEC values at a given calibration iteration

  

• tec?_freq??.png: matrix plot of the derived fast varying TEC values at a given calibration iteration

  

• ??_mask-MFS-image.fits: shallowly cleaned image at high resolution used as an input for determining a cleaning mask

  

• ??.mask: derived cleaning mask from ??_mask-MFS-image.fits

  

• ??_hires-MFS-image.fits: deeply cleaned high-resolution image using ??.mask as a cleaning mask

  

• ??_tmp-image.fits: shallowly cleaned image at low resolution after subtracting a model derived from the high-resolution image as a reference for the primary beam mask

  

• ??_blank.fits: calculcated primary beam mask using ??_tmp-image.fits as a reference image

  

• ??_lowres-MFS-image.fits: deeply cleaned low-resolution image after subtracting a model derived from the high-resolution image using ??_blank.fits as a cleaning mask

  

• ??_large-MFS-image.fits: diagnostic wide-field image at high resolution after subtracting a model derived from the low- and the high-resolution images

  

The workflow selfcal_target_lba consists of:

• create and calibrate against model data for Faraday Rotation (subworkflow predict_calibrate_fr) and determination of the corresponding correction factors (subworkflow FaradayRot), create diagnostic plots (steps losoto_plot) (subworkflow fr)

• apply corrections for Faraday Rotation correction and calibrate and correct for slow and fast varying ionospheric effects caused by the ionosphere as well as amplitude fluctuations (steps apply_targ, calib_targ1, apply_targ1, calib_targ2, plus only in first loop apply_targ2, calib_targ_amp in subworkflow apply_calibrate_tec), create diagnostic plots (steps losoto_plot) (subworkflow tec_and_amp, baseline-dependend smoothing (step BLsmooth) is used.)

• correction of amplitude fluctuations (step apply_targ_amp)

• imaging at high-resolution (step image_hires) using an imaging mask (steps make_mask_image, make_mask), subtracting it from the data (steps predict_hires and subtract_hires), imaging at low resolution (step image_lowres) outside the primary beam using an imaging mask (steps image_tmp and blank_image_reg), subtracting it from the data (steps predict_lowres, subtract_lowres), flagging on the residual data (step aoflag_residual), reconstruct data set for second calibration iteration through subtracting the low-resolution model comprising of sources outside the primary beam from the data (steps corrupt_slowtec, corrupt_tec, corrupt_fr, corrupt_amp, subtract_model from the subworkflow corrupt_model), update the model data using the high-resolution image for the next calibration iteration (step recreate_model) (subworkflow imaging_subtract)

• correction of amplitude fluctuations again (step apply_targ_amp_2)

• second iteration of appyling corrections for Faraday Rotation and calibration of slow and fast varying ionospheric effects (subworkflow tec_and_amp_2)

Finalizing the LINC output (finalize)

These steps produce the final data output and many helpful diagnostics.

The workflow finalize consists of:

• adding missing stations to the solution set with zero phase and unit amplitude (for international stations, step add_missing_stations)

• applying the final (from the global skymodel or from self-calibration) phaseonly or (in case of LBA) TEC self-calibration solutions to the data and compress them (step apply_gsmcal)

• derive the structure function of the phases (step structure_function)

• make a fast image of the target field (steps average and wsclean)

• create plots of the uv-coverage of the final data set (step uvplot)

• create a summary file (step summary)

The last step also incorporates full Dysco compression to save disk space. The fully calibrated data is stored in the DATA column of the final data set.

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

• fully calibrated datasets in results, concatenated with num_SBs_per_group subbands per MS file and averaged, if desired (see averaging options below). The DATA column of each MS contains the calibrated data (with the direction-independent solutions applied).

• logfiles in logs

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

• calibration solutions in cal_solutions.h5

• inspection plots in inspection

The following diagnostic help to assess the quality of the data reduction:

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

  

• Ateamclipper.png: fraction of flagged data due to their potential contamination from A-Team sources versus frequency

  

• unflagged_fraction.png: fraction of remaining unflagged data versus frequency

  

• ??_uv-coverage_uvdist.png: fraction of remaining unflagged data versus uv-distance

  

• ??_uv_coverage.png: the uv-coverage of the final data set

  

• ??_structure.png: plot of the ionospheric structure function of the processed target field

  

• ??-MFS-image.fits: FITS image of the target field

  

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, 372 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: 0.014%

Solution table 'polalign' (type: phase): 120 times, 60 ants, 1484 freqs, 2 pols
    Flagged data: 0.000%

Solution set 'target':
======================

Directions: P000+00

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 'RMextract' (type: rotationmeasure): 60 ants, 119 times
    Flagged data: 0.000%

Solution table 'TGSSphase' (type: phase): 3446 times, 58 ants, 1 freq, 2 pols
    Flagged data: 0.000%
    History: 2021-07-30 11:25:44: Bad stations 'CS006HBA1', 'CS006HBA0' have not been added
                                  back.

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

$ cat logs/???_summary.log

************************************
*** LINC target pipeline summary ***
************************************

Field name: P000+00

User-specified baseline filter: [CR]S*&
Additional antennas removed from the data: CS006HBA1, CS006HBA0
A-Team sources close to the phase reference center: NONE

XX diffractive scale: 4.4 km
YY diffractive scale: 4.0 km

Changes applied to cal_solutions.h5:
2021-07-30 11:25:44: Bad stations 'CS006HBA1', 'CS006HBA0' have not been added back.

Amount of flagged solutions per station and solution table:
Station   bandpass    clock    faraday  polalign  RMextract TGSSphase
CS001HBA0    0.29%     0.00%     0.00%     0.00%     0.00%     0.00%
CS001HBA1    0.29%     0.00%     0.00%     0.00%     0.00%     0.00%
CS002HBA0    0.29%     0.00%     0.00%     0.00%     0.00%     0.05%
CS002HBA1    0.29%     0.00%     0.00%     0.00%     0.00%     0.00%
CS003HBA0    0.29%     0.00%     0.00%     0.00%     0.00%     0.00%
CS003HBA1    0.29%     0.00%     0.00%     0.00%     0.00%     0.05%
CS004HBA0    0.29%     0.00%     0.00%     0.00%     0.00%     0.05%
CS004HBA1    6.05%     0.00%     0.00%     0.00%     0.00%     0.05%
CS005HBA0    0.29%     0.00%     0.00%     0.00%     0.00%     0.05%
CS005HBA1    0.39%     0.00%     0.00%     0.00%     0.00%     0.00%
CS006HBA0    0.29%     0.00%     0.00%     0.00%     0.00%
CS006HBA1    0.29%     0.00%     0.00%     0.00%     0.00%

Amount of flagged data per station at a given state:
Station    initial  prep    Ateam   final
CS001HBA0   5.13%   5.41%  11.12%  22.74%
CS001HBA1   5.13%   5.41%  11.03%  22.51%
CS002HBA0   5.12%   5.39%  11.39%  23.18%
CS002HBA1   5.12%   5.40%  21.09%  29.95%
CS003HBA0   5.12%   5.39%   9.92%  22.58%
CS003HBA1   5.12%   5.40%  11.37%  23.95%
CS004HBA0   5.12%   5.40%  13.27%  24.62%
CS004HBA1   5.12%   5.40%  12.24%  23.53%
CS005HBA0   5.12%   5.40%  11.59%  23.38%
CS005HBA1   5.12%  15.36%  20.07%  30.09%
CS006HBA0 100.00% 100.00% 100.00%
CS006HBA1 100.00% 100.00% 100.00%

**********
Summary file is written to: ???_LINC_target_summary.json
Summary has been created.

User-defined parameter configuration

Parameters you will need to adjust

Location of the target data and calibrator solutions

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

• cal_solutions: location of the calibrator solutions, 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_target: 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: [CR]S*&)

• 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: [CR]S*&)

• 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)

• min_unflagged_fraction: minimal fraction of unflagged data to be accepted for further processing of the data chunk (default: 0.5)

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

• compression_bitrate: defines the bitrate of Dysco compression of the data after the final step, choose 0 if you do NOT want to compress the data

• propagatesolutions: use already derived solutions as initial guess for the upcoming time slot

• apply_tec: apply TEC solutions from the calibrator (default: false)

• apply_clock: apply clock solutions from the calibrator (default: true)

• apply_phase: apply full phase solutions from the calibrator (default: false)

• apply_RM: apply ionospheric Rotation Measure from RMextract (default: true)

• apply_beam: apply element beam corrections (default: true)

• gsmcal_step: type of calibration to be performed in the self-calibration step (default: phase)

• updateweights: update WEIGHT_SPECTRUM column in a way consistent with the weights being inverse proportional to the autocorrelations (default: true)

• use_target: enable downloading of a target skymodel (default: true)

• skymodel_source: choose the target skymodel from TGSS ADR or the new Global Sky Model (GSM) (default: TGSS)

• skymodel_fluxlimit: limits the input skymodel to sources that exceed the given flux density limit in Jy (default: None for HBA, i.e. all sources of the catalogue will be kept, and 1.0 for LBA)

• selfcal: perform self-calibration (default: false)

• selfcal_strategy: sets the strategy for selfcal. If set to HBA. If set to LBA, selfcal will perform extensive self-calibration according to the LiLF scheme (recommended for LBA observations). (default: HBA)

• selfcal_region: ds9-compatible region file to select the image regions used for the self-calibration in case of LBA self-calibration.

• selfcal_hba_uvlambdamin: specify the minimum uv-distance in units of wavelength to be used when performing selfcal with HBA (default: 200)

• selfcal_hba_imsize: specifies the image size in pixels, as a list, to use during HBA self-calibration (default: [20000, 20000]).

• output_channels_per_chunk: HBA only. Sets the number of frequency channels to chunk data in after self-calibration (default: 20).

• calib_nchan: number of channels to be combined when calibration (default: 0 (one solution per group) if selfcal = false, otherwise 1 (one solution per channel))

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

Demixing and clipping options

• 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)

• demix_sources: choose sources to demix (provided as list), e.g., [CasA,CygA] (default: [VirA_4_patch,CygAGG,CasA_4_patch,TauAGG])

• 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)

• 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)

• clipAteam : enables A-Team clipping using the source list from clip_sources (default: true)

• clip_sources: list of the skymodel patches to be used for Ateamclipping, except those which are chosen to be demixed. An empty list means including all sources (enforced, not taking care whether demix is performed or not). (default: [VirA_4_patch,CygAGG,CasA_4_patch,TauAGG])

Further pipeline options

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

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)

• aoflag_freqconcat: concatenate all subbands on-the-fly before performing flagging. Disable if you use time-chunked input data (see chunkduration) (default: true)

• wsclean_tmpdir: Set the temporary directory of wsclean used when reordering files (default: /tmp). CAUTION: This directory needs to be visible for LINC, in particular if you use Docker or Singularity.

• make_structure_plot: Calculate and plot the structure function of the gsmcal_step (only if gsmcal_step is set to phase, default: true)

Skymodel directory

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

• target_skymodel: location of a user-defined target skymodel used for the self-calibration

Averaging for the target data

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

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

• avg_timeresolution_concat: final time resolution of the data in seconds after averaging and concatenation (default: 8)

• avg_freqresolution_concat: final frequency resolution of the data after averaging and concatenation (default: 97.64kHz, which translates to 2 channels per subband)

Concatenating of the target data

• num_SBs_per_group: make concatenated measurement-sets with that many subbands (default: 10 normally, -1 for HBA selfcal)

• reference_stationSB: station-subband number to use as reference for grouping (default: None -> use lowest frequency input data as reference)

• chunkduration: Duration (in seconds) after which to start writing a next measurement set while concatenating (default: 0.0, no chunking in time)

RMextract settings

• ionex_server: URL of the IONEX server (default: "ftp://gssc.esa.int/gnss/products/ionex/")

• ionex_prefix: the prefix of the IONEX files (default: UQRG)

• proxy_server: specify URL or IP of proxy server if needed

• proxy_port: port of proxy server if needed

• proxy_user: user name of proxy server if needed

• proxy_pass: password of proxy server if needed