Add WSClean QU imaging step

[vijaymahatma]

In the steps/ folder we need a separate CWL script that runs WSClean for QU imaging only. This will be used by the polarization_imaging.cwl workflow as a step to run.

[dalonsolopez17]

We have created a step called wsclean_pol.cwl to make polarization channel images. There's a decision to be made regarding beam size, i.e., such that all channel images have the same (common lowest) resolution. When using Gaussian tapering there is an option to specify beam size -taper-gaussian , so that "A Gaussian taper in uv space will be calculated such that the FWHM of the Gaussian in real space has the given beam size.". So we need to decide if it's necessary to add -beam-size separately to the -taper-gaussian, or doing only -taper gaussian does both things at once in a more robust way

[emaderubeis]

New WSClean step for polarization imaging: https://github.com/LOFAR-VLBI/pilot/blob/add_qu_imaging/steps/wsclean_pol.cwl

[emaderubeis]

Outputs are now compatible with the main CWL workflow.

[vijaymahatma]

The updated flocs vlbi-cwl runner is now able to execute the pipeline to start QU imaging:

(flocs-runners_patch) [mahatmav@node078 vlbi-polarization-test]$ flocs-run vlbi polarization-imaging --msin=../Delay-Calibration_3C351_ep1_delaycal_ddf/facetselfcal/delaycal_ddf.ms.copy.avg --num-channels 210
2026-02-12 12:36:29 [info     ] Generating VLBI polarization-imaging config
2026-02-12 12:36:29 [info     ] Using ms: ../Delay-Calibration_3C351_ep1_delaycal_ddf/facetselfcal/delaycal_ddf.ms.copy.avg for polarization imaging
2026-02-12 12:36:29 [info     ] Found 1 files                 
2026-02-12 12:36:31 [info     ] Using existing /beegfs/general/mahatmav/lofar/long_baseline/pipeline/LINC/.versions
2026-02-12 12:36:31 [info     ] Written configuration to mslist_VLBI_polarization-imaging.json
2026-02-12 12:36:31 [info     ] Running workflow with cwltool under singleMachine in /beegfs/general/mahatmav/lofar/long_baseline/3C351/vlbi-polarization-test/tmp.VLBI_polarization-imaging.8w61w4ji
2026-02-12 12:36:31 [info     ] Running command:
cwltool --parallel --timestamps --disable-pull --singularity --tmpdir-prefix=/beegfs/general/mahatmav/lofar/long_baseline/3C351/vlbi-polarization-test/tmp.VLBI_polarization-imaging.8w61w4ji/tmpdir_VLBI_polarization-imaging/ --outdir=/beegfs/general/mahatmav/lofar/long_baseline/3C351/vlbi-polarization-test/tmp.VLBI_polarization-imaging.8w61w4ji/results_VLBI_polarization-imaging/ --log-dir=/beegfs/general/mahatmav/lofar/long_baseline/3C351/vlbi-polarization-test/tmp.VLBI_polarization-imaging.8w61w4ji/logs_VLBI_polarization-imaging/ /beegfs/general/mahatmav/lofar/long_baseline/pipeline/pilot/workflows/polarization-imaging.cwl mslist_VLBI_polarization-imaging.json
[2026-02-12 12:36:32] INFO /beegfs/general/mahatmav/soft/conda/miniconda3/envs/flocs-runners_patch/bin/cwltool 3.1.20260108082145
[2026-02-12 12:36:32] INFO Resolved '/beegfs/general/mahatmav/lofar/long_baseline/pipeline/pilot/workflows/polarization-imaging.cwl' to 'file:///beegfs/general/mahatmav/lofar/long_baseline/pipeline/pilot/workflows/polarization-imaging.cwl'
[2026-02-12 12:36:33] INFO [workflow ] starting step image_qu
[2026-02-12 12:36:33] INFO [workflow ] start
[2026-02-12 12:36:33] INFO [step image_qu] start
[2026-02-12 12:36:33] INFO Using local copy of Singularity image vlbi-cwl_latest.sif found in /beegfs/general/mahatmav/lofar/long_baseline/pipeline
[2026-02-12 12:37:44] INFO [job image_qu] /beegfs/general/mahatmav/lofar/long_baseline/3C351/vlbi-polarization-test/tmp.VLBI_polarization-imaging.8w61w4ji/tmpdir_VLBI_polarization-imaging/10hz66jz$ singularity \
    --quiet \
    run \
    --contain \
    --ipc \
    --cleanenv \
    --no-eval \
    --userns \
    --home \
    /beegfs/general/mahatmav/lofar/long_baseline/3C351/vlbi-polarization-test/tmp.VLBI_polarization-imaging.8w61w4ji/tmpdir_VLBI_polarization-imaging/10hz66jz:/TjuthQ \
    --mount=type=bind,source=/beegfs/general/mahatmav/lofar/long_baseline/3C351/vlbi-polarization-test/tmp.VLBI_polarization-imaging.8w61w4ji/tmpdir_VLBI_polarization-imaging/zksu8qp4,target=/tmp \
    --mount=type=bind,source=/beegfs/general/mahatmav/lofar/long_baseline/3C351/Delay-Calibration_3C351_ep1_delaycal_ddf/facetselfcal/delaycal_ddf.ms.copy.avg,target=/TjuthQ/delaycal_ddf.ms.copy.avg,readonly \
    --pwd \
    /TjuthQ \
    --net \
    --network \
    none \
    /beegfs/general/mahatmav/lofar/long_baseline/pipeline/vlbi-cwl_latest.sif \
    /bin/sh \
    -c \
    wsclean -verbose -log-time -no-update-model-required -apply-primary-beam -auto-mask 3.0 -auto-threshold 1.0 -baseline-averaging 7.74 -beam-size 0.3asec -channels-out 210 -j 24 -data-column DATA -deconvolution-channels 3 -fit-spectral-pol 3 -gridder wgridder -join-channels -join-polarizations -mgain 0.7 -minuv-l 80.0 -multiscale -multiscale-max-scales 9 -multiscale-scale-bias 0.6 -name image -niter 150000 -nmiter 9 -parallel-deconvolution 2600 -parallel-gridding 4 -parallel-reordering 6 -pol IQUV -scale 0.075arcsec -size 2000 2000 -squared-channel-joining -taper-gaussian 0.3arcsec -temp-dir . -use-differential-lofar-beam -weight briggs -1.5 /TjuthQ/delaycal_ddf.ms.copy.avg > /beegfs/general/mahatmav/lofar/long_baseline/3C351/vlbi-polarization-test/tmp.VLBI_polarization-imaging.8w61w4ji/logs_VLBI_polarization-imaging//image_qu/wsclean_qu.log 2> /beegfs/general/mahatmav/lofar/long_baseline/3C351/vlbi-polarization-test/tmp.VLBI_polarization-imaging.8w61w4ji/logs_VLBI_polarization-imaging//image_qu/wsclean_qu_err.log