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gsmcal.cwl 13.25 KiB
class: Workflow
cwlVersion: v1.2
id: gsmcal
label: gsmcal
inputs:
- id: msin
type: 'Directory[]'
- id: filter_baselines
type: string?
default: '[CR]S*&'
- id: num_SBs_per_group
type: int?
default: 10
- id: reference_stationSB
type: int?
default: null
- id: use_target
type: boolean?
default: true
- id: target_skymodel
type: File?
- id: skymodel_source
type: string?
default: 'TGSS'
- id: do_smooth
type: boolean?
default: false
- id: propagatesolutions
type: boolean?
default: true
- id: avg_timeresolution_concat
type: int?
default: 8
- id: avg_freqresolution_concat
type: string?
default: '97.64kHz'
- id: min_unflagged_fraction
type: float?
default: 0.5
- id: refant
type: string?
default: 'CS001HBA0'
- id: min_length
type: int?
default: 5
- id: overhead
type: float?
default: 0.8
- id: rfistrategy
type:
- File?
- string?
outputs:
- id: msout
outputSource:
- calibrate_target/msout
type: 'Directory[]'
- id: outh5parm
outputSource:
- h5parm_collector/outh5parm
type: File
- id: bad_antennas
outputSource:
- identifybadantennas_join/filter_out
type: string
- id: outh5parm_logfile
outputSource:
- concat_logfiles_losoto/output
type: File
- id: Ateam_flags_join_out outputSource:
- Ateam_flags_join/flagged_fraction_antenna
type: File
- id: inspection
outputSource:
- losoto_plot_P/output_plots
- losoto_plot_P2/output_plots
- losoto_plot_Pd/output_plots
- losoto_plot_Pd2/output_plots
- plot_unflagged/output_imag
type: 'File[]'
linkMerge: merge_flattened
- id: out_refant
outputSource:
- findRefAnt_join/refant
type: string
- id: logfiles
outputSource:
- concat_logfiles_identify/output
- concat_logfiles_RefAnt/output
- sort_times_into_freqGroups/logfile
- find_skymodel_target/logfile
- make_sourcedb_target/log
- concat_logfiles_calib/output
- concat_logfiles_dpppconcat/output
- concat_logfiles_blsmooth/output
- concat_logfiles_unflagged/output
- ms_concat/logfile
- aoflag/logfile
type: 'File[]'
linkMerge: merge_flattened
- id: removed_bands
outputSource:
- check_unflagged_fraction/filenames
type: 'string[]'
- id: total_bandwidth
outputSource:
- sort_times_into_freqGroups/total_bandwidth
type: int
steps:
- id: identifybadantennas
in:
- id: msin
source: msin
out:
- id: flaggedants
- id: logfile
run: ../../steps/identify_bad_antennas.cwl
label: identifybadantennas
scatter:
- msin
- id: identifybadantennas_join
in:
- id: flaggedants
source:
- identifybadantennas/flaggedants
- id: filter
source: filter_baselines
out:
- id: filter_out
- id: logfile
run: ../../steps/identify_bad_antennas_join.cwl
label: identifybadantennas_join
- id: findRefAnt_join
in:
- id: flagged_fraction_dict
source:
- concat/flagged_fraction_dict
- id: filter_station
source: refant out:
- id: refant
- id: logfile
run: ../../steps/findRefAnt_join.cwl
label: findRefAnt_join
- id: Ateam_flags_join
in:
- id: flagged_fraction_dict
source:
- concat/flagged_fraction_dict
- id: filter_station
default: ''
- id: state
default: 'concat'
out:
- id: flagged_fraction_antenna
run: ../../steps/findRefAnt_join.cwl
label: Ateam_flags_join
- id: sort_times_into_freqGroups
in:
- id: msin
source:
- msin
- id: numbands
source: num_SBs_per_group
- id: NDPPPfill
default: true
- id: stepname
default: .dpppconcat
- id: firstSB
source: reference_stationSB
- id: truncateLastSBs
default: false
out:
- id: filenames
- id: groupnames
- id: total_bandwidth
- id: logfile
run: ../../steps/sort_times_into_freqGroups.cwl
label: sorttimesintofreqGroups
- id: find_skymodel_target
in:
- id: msin
source:
- msin
- id: SkymodelPath
source: target_skymodel
- id: Radius
default: 5
- id: Source
source: skymodel_source
- id: DoDownload
source: use_target
out:
- id: skymodel
- id: logfile
run: ../../steps/find_skymodel_target.cwl
label: find_skymodel_target
- id: make_sourcedb_target
in:
- id: sky_model
source: find_skymodel_target/skymodel
- id: output_file_name
default: target.sourcedb
- id: logname
default: make_sourcedb_target.log
out:
- id: sourcedb
- id: log
run: ../../steps/makesourcedb.cwl label: make_sourcedb_target
- id: concat_logfiles_dpppconcat
in:
- id: file_list
source:
- concat/dpppconcat.log
- id: file_prefix
default: dpppconcat
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_dpppconcat
- id: concat_logfiles_blsmooth
in:
- id: file_list
source:
- calibrate_target/BLsmooth.log
- id: file_prefix
default: blsmooth_target
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_blsmooth
- id: concat_logfiles_calib
in:
- id: file_list
source:
- calibrate_target/gaincal.log
- id: file_prefix
default: gaincal
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_calib
- id: concat_logfiles_losoto
in:
- id: file_list
linkMerge: merge_flattened
source:
- h5parm_collector/log
- losoto_plot_P/logfile
- losoto_plot_P2/logfile
- losoto_plot_Pd/logfile
- losoto_plot_Pd2/logfile
- id: file_prefix
default: losoto_gsmcal
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_losoto
- id: concat_logfiles_unflagged
in:
- id: file_list
linkMerge: merge_flattened
source:
- merge_array_files/output
- plot_unflagged/logfile
- id: file_prefix
default: check_unflagged_fraction
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_unflagged
- id: concat_logfiles_identify
in:
- id: file_list
linkMerge: merge_flattened
source:
- identifybadantennas/logfile
- identifybadantennas_join/logfile - id: file_prefix
default: identifyBadAntennas
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_identify
- id: concat_logfiles_RefAnt
in:
- id: file_list
linkMerge: merge_flattened
source:
- findRefAnt_join/logfile
- id: file_prefix
default: findRefAnt
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_RefAnt
- id: concat
in:
- id: msin
source:
- msin
- id: group_id
source: sort_times_into_freqGroups/groupnames
- id: groups_specification
source: sort_times_into_freqGroups/filenames
- id: filter_baselines
source: identifybadantennas_join/filter_out
- id: avg_timeresolution_concat
source: avg_timeresolution_concat
- id: avg_freqresolution_concat
source: avg_freqresolution_concat
out:
- id: msout
- id: flagged_fraction_dict
- id: dpppconcat.log
run: ./concat.cwl
label: concat
scatter:
- group_id
- id: ms_concat
in:
- id: min_length
source: min_length
- id: overhead
source: overhead
- id: msin
source:
- concat/msout
out:
- id: concat_meta_ms
- id: concat_additional_ms
- id: ms_outs
- id: logfile
run: ../../steps/ms_concat.cwl
label: ms_concat
- id: aoflag
in:
- id: msin
source:
- ms_concat/ms_outs
- id: concat_meta_ms
source: ms_concat/concat_meta_ms
- id: concat_additional_ms
source: ms_concat/concat_additional_ms
- id: verbose
default: true
- id: combine-spws
default: true - id: strategy
source: rfistrategy
out:
- id: output_ms
- id: logfile
run: ../../steps/aoflag.cwl
label: aoflag
- id: check_unflagged_fraction
in:
- id: msin
source: aoflag/output_ms
- id: min_fraction
source: min_unflagged_fraction
out:
- id: msout
- id: unflagged_fraction
- id: filenames
- id: logfile
run: ../../steps/check_unflagged_fraction.cwl
label: check_unflagged_fraction
scatter:
- msin
- id: merge_array
in:
- id: input
source:
- check_unflagged_fraction/msout
out:
- id: output
run: ../../steps/merge_array.cwl
label: merge_array
- id: merge_array_files
in:
- id: input
source:
- check_unflagged_fraction/logfile
out:
- id: output
run: ../../steps/merge_array_files.cwl
label: merge_array_files
- id: check_filtered_MS_array
in:
- id: input
source: merge_array/output
out:
- id: output
run: ../../steps/check_filtered_MS_array.cwl
label: check_filtered_MS_array
- id: calibrate_target
in:
- id: msin
source: check_filtered_MS_array/output
- id: skymodel
source: make_sourcedb_target/sourcedb
- id: do_smooth
source: do_smooth
- id: propagatesolutions
source: propagatesolutions
out:
- id: msout
- id: BLsmooth.log
- id: gaincal.log
- id: outh5parm
run: ./calib_targ.cwl
label: calibrate_target
scatter:
- msin
- id: h5parm_collector
in:
- id: h5parmFiles source:
- calibrate_target/outh5parm
- id: squeeze
default: true
- id: verbose
default: true
- id: clobber
default: true
out:
- id: outh5parm
- id: log
run: ../../steps/H5ParmCollector.cwl
label: H5parm_collector
- id: plot_unflagged
in:
- id: msin
source:
- concat/msout
- id: unflagged_fraction
source:
- check_unflagged_fraction/unflagged_fraction
out:
- id: output_imag
- id: logfile
run: ../../steps/plot_unflagged.cwl
label: plot_unflagged
- id: losoto_plot_P
in:
- id: input_h5parm
source: h5parm_collector/outh5parm
- id: soltab
default: sol000/phase000
- id: axesInPlot
default:
- time
- freq
- id: axisInTable
default: ant
- id: minmax
default:
- -3.14
- 3.14
- id: plotFlag
default: true
- id: refAnt
source: findRefAnt_join/refant
- id: prefix
default: ph_
out:
- id: output_plots
- id: logfile
- id: parset
run: ../../steps/LoSoTo.Plot.cwl
label: losoto_plot_P
- id: losoto_plot_P2
in:
- id: input_h5parm
source: h5parm_collector/outh5parm
- id: soltab
default: sol000/phase000
- id: axesInPlot
default:
- time
- id: axisInTable
default: ant
- id: axisInCol
default: pol
- id: minmax
default:
- -3.14 - 3.14
- id: plotFlag
default: true
- id: refAnt
source: findRefAnt_join/refant
- id: prefix
default: ph_
out:
- id: output_plots
- id: logfile
- id: parset
run: ../../steps/LoSoTo.Plot.cwl
label: losoto_plot_P2
- id: losoto_plot_Pd
in:
- id: input_h5parm
source: h5parm_collector/outh5parm
- id: soltab
default: sol000/phase000
- id: axesInPlot
default:
- time
- freq
- id: axisInTable
default: ant
- id: axisDiff
default: pol
- id: minmax
default:
- -3.14
- 3.14
- id: plotFlag
default: true
- id: refAnt
source: findRefAnt_join/refant
- id: prefix
default: ph_poldif
out:
- id: output_plots
- id: logfile
- id: parset
run: ../../steps/LoSoTo.Plot.cwl
label: losoto_plot_Pd
- id: losoto_plot_Pd2
in:
- id: input_h5parm
source: h5parm_collector/outh5parm
- id: soltab
default: sol000/phase000
- id: axesInPlot
default:
- time
- id: axisInTable
default: ant
- id: axisDiff
default: pol
- id: minmax
default:
- -3.14
- 3.14
- id: plotFlag
default: true
- id: refAnt
source: findRefAnt_join/refant
- id: prefix
default: ph_poldif_
out:
- id: output_plots
- id: logfile
- id: parset run: ../../steps/LoSoTo.Plot.cwl
label: losoto_plot_Pd2
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement