diff --git a/lofar-cwl/steps/LoSoTo.ClockTec.cwl b/lofar-cwl/steps/LoSoTo.ClockTec.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..6453badf4041d013d150b6c13a3b89832289692d
--- /dev/null
+++ b/lofar-cwl/steps/LoSoTo.ClockTec.cwl
@@ -0,0 +1,103 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+id: losoto_clocktec
+
+$namespaces:
+ lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+doc: |
+ Separate phase solutions into Clock and TEC.
+ The Clock and TEC values are stored in the specified output soltab with type 'clock', 'tec', 'tec3rd'.
+
+requirements:
+ InlineJavascriptRequirement:
+ expressionLib:
+ - { $include: utils.js}
+ InitialWorkDirRequirement:
+ listing:
+ - entryname: 'parset.config'
+ entry: $(get_losoto_config('CLOCKTEC').join('\n'))
+
+ - entryname: $(inputs.input_h5parm.basename)
+ entry: $(inputs.input_h5parm)
+ writable: true
+
+baseCommand: "losoto"
+
+arguments:
+ - '--verbose'
+ - $(inputs.input_h5parm.basename)
+ - parset.config
+
+hints:
+ DockerRequirement:
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+
+inputs:
+ - id: input_h5parm
+ type: File
+ format: lofar:#H5Parm
+ - id: soltab
+ type: string
+ doc: "Solution table"
+ - id: clocksoltabOut
+ doc: output soltab name for clock
+ type: string?
+ - id: tecsoltabOut
+ doc: output soltab name for tec
+ type: string?
+ - id: offsetsoltabOut
+ doc: output soltab name for phase offset
+ type: string?
+ - id: tec3rdsoltabOut
+ doc: output soltab name for tec3rd offset
+ type: string?
+ - id: flagBadChannels
+ type: boolean?
+ doc: Detect and remove bad channel before fitting, by default True.
+ - id: flagCut
+ type: float?
+ - id: chi2cut
+ type: float?
+ - id: combinePol
+ type: boolean?
+ doc: |
+ Find a combined polarization solution, by default False.
+ - id: removePhaseWraps
+ type: boolean?
+ doc: |
+ Detect and remove phase wraps, by default True.
+ - id: fit3rdorder
+ type: boolean?
+ doc: |
+ Fit a 3rd order ionospheric ocmponent (usefult <40 MHz). By default False.
+ - id: circular
+ type: boolean?
+ doc: |
+ Assume circular polarization with FR not removed. By default False.
+ - id: reverse
+ type: boolean?
+ doc:
+ Reverse the time axis. By default False.
+ - id: invertOffset
+ type: boolean?
+ doc: |
+ Invert (reverse the sign of) the phase offsets. By default False. Set to True
+ if you want to use them with the residuals operation.
+
+outputs:
+ - id: output_h5parm
+ type: File
+ format: lofar:#H5Parm
+ outputBinding:
+ glob: $(inputs.input_h5parm.basename)
+ - id: log
+ type: File[]
+ outputBinding:
+ glob: '$(inputs.input_h5parm.basename)-losoto*.log'
+
+stdout: $(inputs.input_h5parm.basename)-losoto.log
+stderr: $(inputs.input_h5parm.basename)-losoto_err.log
+$schema:
+ - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
diff --git a/subworkflow/clocktec.cwl b/subworkflow/clocktec.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..24fd219eac4aae763a13aedc3ec6c70674beda42
--- /dev/null
+++ b/subworkflow/clocktec.cwl
@@ -0,0 +1,209 @@
+class: Workflow
+cwlVersion: v1.0
+id: losoto_ion
+label: losoto_ion
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: input_h5parm
+ type: File
+ 'sbg:x': -588.3988647460938
+ 'sbg:y': -147.5
+ - id: fit3rdorder
+ type: boolean?
+ 'sbg:x': 83.60113525390625
+ 'sbg:y': 53.5
+ - id: refAnt
+ type: string?
+ 'sbg:x': 500.74346923828125
+ 'sbg:y': -382.8847351074219
+ - id: maxStddev
+ type: float?
+ 'sbg:x': 374.1950988769531
+ 'sbg:y': -308.9609069824219
+outputs:
+ - id: output_h5parm
+ outputSource:
+ - losoto_flagstation/output_h5parm
+ type: File
+ 'sbg:x': 775
+ 'sbg:y': -169
+ - id: logfiles
+ outputSource:
+ - flag/log
+ - flagextend/log
+ - merge/log
+ - flagextend/log
+ - merge/log
+ - duplicatePbkp/log
+ - losoto_clocktec/log
+ - smooth/logfile
+ - losoto_residual/log
+ - losoto_flagstation/log
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 775
+ 'sbg:y': 169
+steps:
+ - id: flag
+ in:
+ - id: input_h5parm
+ source: input_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: axesToFlag
+ default:
+ - time
+ - freq
+ - id: order
+ default:
+ - 100
+ - 40
+ - id: maxCycles
+ default: 1
+ - id: maxRms
+ default: 5
+ - id: mode
+ default: smooth
+ out:
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.Flag.cwl
+ 'sbg:x': -442.3984375
+ 'sbg:y': -138.5
+ - id: flagextend
+ in:
+ - id: input_h5parm
+ source: flag/output_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: axesToExt
+ default:
+ - time
+ - freq
+ - id: size
+ default:
+ - 200
+ - 80
+ - id: percent
+ default: 50
+ - id: maxCycles
+ default: 2
+ out:
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.Flagextend.cwl
+ 'sbg:x': -255
+ 'sbg:y': -160
+ - id: merge
+ in:
+ - id: input_h5parm
+ source: flagextend/output_h5parm
+ - id: soltab
+ default: sol000/phase000
+ - id: mode
+ default: copy
+ - id: soltabImport
+ default: amplitude000
+ out:
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.Reweight.cwl
+ 'sbg:x': -94
+ 'sbg:y': -162
+ - id: duplicatePbkp
+ in:
+ - id: input_h5parm
+ source: merge/output_h5parm
+ - id: soltab
+ default: sol000/phase000
+ - id: soltabOut
+ default: phaseOrig
+ out:
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.Duplicate.cwl
+ 'sbg:x': 69
+ 'sbg:y': -162
+ - id: losoto_flagstation
+ in:
+ - id: input_h5parm
+ source: losoto_residual/output_h5parm
+ - id: soltab
+ default: sol000/phase000
+ - id: mode
+ default: bandpass
+ - id: maxStddev
+ source: maxStddev
+ - id: refAnt
+ source: refAnt
+ - id: soltabExport
+ default: clock
+ out:
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.FlagStation.cwl
+ 'sbg:x': 587
+ 'sbg:y': -172
+ - id: losoto_clocktec
+ in:
+ - id: input_h5parm
+ source: duplicatePbkp/output_h5parm
+ - id: soltab
+ default: sol000/phase000
+ - id: clocksoltabOut
+ default: clock
+ - id: tecsoltabOut
+ default: tec
+ - id: offsetsoltabOut
+ default: phase_offset
+ - id: tec3rdsoltabOut
+ default: tec3rd
+ - id: combinePol
+ default: true
+ - id: fit3rdorder
+ source: fit3rdorder
+ out:
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.ClockTec.cwl
+ 'sbg:x': 217.72296142578125
+ 'sbg:y': -230.69259643554688
+ - id: smooth
+ in:
+ - id: input_h5parm
+ source: losoto_clocktec/output_h5parm
+ - id: soltab
+ default: sol000/clock
+ - id: axesToSmooth
+ default:
+ - time
+ - id: mode
+ default: median
+ - id: replace
+ default: true
+ - id: log
+ default: false
+ out:
+ - id: output_h5parm
+ - id: logfile
+ run: ../lofar-cwl/steps/LoSoTo.Smooth.cwl
+ 'sbg:x': 301.4368591308594
+ 'sbg:y': -51.11399841308594
+ - id: losoto_residual
+ in:
+ - id: input_h5parm
+ source: smooth/output_h5parm
+ - id: soltab
+ default: sol000/phase000
+ - id: soltabsToSub
+ source:
+ - fit3rdorder
+ valueFrom: '$(self ? ["tec", "clock", "tec3rd"] : ["tec", "clock"])'
+ out:
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.Residual.cwl
+ 'sbg:x': 411.0426330566406
+ 'sbg:y': -168.98934936523438
+requirements: []
diff --git a/workflows/HBA_calibrator.cwl b/workflows/HBA_calibrator.cwl
index ad68fdbdb72cdfb2709fc070cbde391691b0f967..35432e92bb5f26f42b877ce11751774509e72e13 100644
--- a/workflows/HBA_calibrator.cwl
+++ b/workflows/HBA_calibrator.cwl
@@ -170,26 +170,21 @@ inputs:
type: File?
'sbg:x': -1000
'sbg:y': 1500
- - id: cal_solutions
- type: string?
- default: cal_solutions.h5
- 'sbg:x': -1000
- 'sbg:y': 1600
- id: avg_timeresolution
type: float?
default: 4
'sbg:x': -1000
- 'sbg:y': 1700
+ 'sbg:y': 1600
- id: avg_freqresolution
type: string?
default: 48.82kHz
'sbg:x': -1000
- 'sbg:y': 1800
+ 'sbg:y': 1700
- id: bandpass_freqresolution
type: string?
default: 195.3125kHz
'sbg:x': -1000
- 'sbg:y': 1900
+ 'sbg:y': 1800
outputs:
- id: solutions
outputSource:
@@ -294,8 +289,6 @@ steps:
source: calibrator_path_skymodel
- id: A-Team_skymodel
source: A-Team_skymodel
- - id: cal_solutions
- source: cal_solutions
- id: avg_timeresolution
source: avg_timeresolution
- id: avg_freqresolution
diff --git a/workflows/prefactor_calibrator.cwl b/workflows/prefactor_calibrator.cwl
index 18d50c141ff4c20e951a887ec8662fe20dd15d54..a1e71b9c84aaf3d94304123aab9ffaac6f5af7f9 100644
--- a/workflows/prefactor_calibrator.cwl
+++ b/workflows/prefactor_calibrator.cwl
@@ -170,26 +170,21 @@ inputs:
type: File?
'sbg:x': -1000
'sbg:y': 1500
- - id: cal_solutions
- type: string?
- default: cal_solutions.h5
- 'sbg:x': -1000
- 'sbg:y': 1600
- id: avg_timeresolution
type: float?
default: 4
'sbg:x': -1000
- 'sbg:y': 1700
+ 'sbg:y': 1600
- id: avg_freqresolution
type: string?
default: 48.82kHz
'sbg:x': -1000
- 'sbg:y': 1800
+ 'sbg:y': 1700
- id: bandpass_freqresolution
type: string?
default: 195.3125kHz
'sbg:x': -1000
- 'sbg:y': 1900
+ 'sbg:y': 1800
outputs:
- id: inspection
linkMerge: merge_flattened
@@ -198,12 +193,13 @@ outputs:
- pa/inspection
- fr/inspection
- bp/inspection
+ - ion/inspection
type: File[]
'sbg:x': 2000
'sbg:y': -600
- id: solutions
outputSource:
- - bp/outsolutions
+ - ion/outsolutions
type: File
'sbg:x': 2000
'sbg:y': -500
@@ -225,6 +221,7 @@ outputs:
- pa/logfiles
- fr/logfiles
- bp/logfiles
+ - ion/logfiles
type: 'File[]'
linkMerge: merge_flattened
'sbg:x': 2000
@@ -403,5 +400,31 @@ steps:
label: BP
'sbg:x': 1000
'sbg:y': 0
+ - id: ion
+ in:
+ - id: h5parm
+ source:
+ - bp/outh5parm
+ - id: refant
+ source: refant
+ - id: inh5parm_logfile
+ source:
+ - bp/outh5parm_logfile
+ - id: insolutions
+ source: bp/outsolutions
+ - id: maxStddev
+ source: maxStddev
+ - id: ion_3rd
+ source: ion_3rd
+ - id: tables2export
+ source: tables2export
+ out:
+ - id: outsolutions
+ - id: inspection
+ - id: logfiles
+ run: ./prefactor_calibrator/ion.cwl
+ label: ion
+ 'sbg:x': 1300
+ 'sbg:y': 0
requirements:
- class: SubworkflowFeatureRequirement
diff --git a/workflows/prefactor_calibrator/ion.cwl b/workflows/prefactor_calibrator/ion.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..2998d82dad4dd4759c0e485b6eea9f59a22cabc9
--- /dev/null
+++ b/workflows/prefactor_calibrator/ion.cwl
@@ -0,0 +1,382 @@
+class: Workflow
+cwlVersion: v1.0
+id: ion
+label: ion
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: ion_3rd
+ type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: refant
+ type: string?
+ 'sbg:x': -1000
+ 'sbg:y': 100
+ - id: h5parm
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': 200
+ - id: tables2export
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': 300
+ - id: inh5parm_logfile
+ type: 'File[]'
+ 'sbg:x': -1000
+ 'sbg:y': 400
+ - id: maxStddev
+ type: float
+ 'sbg:x': -1000
+ 'sbg:y': 500
+ - id: insolutions
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': 600
+outputs:
+ - id: inspection
+ outputSource:
+ - losoto_plot_A1/output_plots
+ - losoto_plot_A2/output_plots
+ - losoto_plot_P3/output_plots
+ - losoto_plot_Pd/output_plots
+ - losoto_plot_tec/output_plots
+ - losoto_plot_tec3rd/output_plots
+ - losoto_plot_clock/output_plots
+ - losoto_plot_Pr/output_plots
+ - losoto_plot_Pr3/output_plots
+ type: 'File[]?'
+ linkMerge: merge_flattened
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: outsolutions
+ outputSource:
+ - write_solutions/outh5parm
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 100
+ - id: logfiles
+ outputSource:
+ - concat_logfiles_ion/output
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 1000
+ 'sbg:y': 200
+steps:
+ - id: clocktec
+ in:
+ - id: input_h5parm
+ source: h5parm
+ - id: maxStddev
+ source: maxStddev
+ - id: fit3rdorder
+ source: ion_3rd
+ out:
+ - id: output_h5parm
+ - id: logfiles
+ run: ../../subworkflow/clocktec.cwl
+ label: clocktec
+ 'sbg:x': -500
+ 'sbg:y': 0
+ - id: losoto_plot_A1
+ in:
+ - id: input_h5parm
+ source: clocktec/output_h5parm
+ - id: soltab
+ default: sol000/amplitudeOrig000
+ - id: axesInPlot
+ default:
+ - time
+ - freq
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: true
+ - id: prefix
+ default: ion_ampBFlag_
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_A1
+ 'sbg:x': 0
+ 'sbg:y': -400
+ - id: losoto_plot_A2
+ in:
+ - id: input_h5parm
+ source: clocktec/output_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: axesInPlot
+ default:
+ - time
+ - freq
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: true
+ - id: prefix
+ default: ion_ampAFlag_
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_A2
+ 'sbg:x': 0
+ 'sbg:y': -300
+ - id: losoto_plot_P3
+ in:
+ - id: input_h5parm
+ source: clocktec/output_h5parm
+ - id: soltab
+ default: sol000/phaseOrig
+ - id: axesInPlot
+ default:
+ - time
+ - freq
+ - id: axisInTable
+ default: ant
+ - id: minmax
+ default:
+ - -3.14
+ - 3.14
+ - id: plotFlag
+ default: true
+ - id: refAnt
+ source: refant
+ - id: prefix
+ default: ion_ph_
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_P3
+ 'sbg:x': 0
+ 'sbg:y': -200
+ - id: losoto_plot_Pd
+ in:
+ - id: input_h5parm
+ source: clocktec/output_h5parm
+ - id: soltab
+ default: sol000/phaseOrig
+ - 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: refant
+ - id: prefix
+ default: ion_ph_poldif
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_Pd
+ 'sbg:x': 0
+ 'sbg:y': -100
+ - id: losoto_plot_tec
+ in:
+ - id: input_h5parm
+ source: clocktec/output_h5parm
+ - id: soltab
+ default: sol000/tec
+ - id: axesInPlot
+ default:
+ - time
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: false
+ - id: refAnt
+ source: refant
+ - id: prefix
+ default: tec
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_tec
+ 'sbg:x': 0
+ 'sbg:y': 0
+ - id: losoto_plot_tec3rd
+ in:
+ - id: input_h5parm
+ source: clocktec/output_h5parm
+ - id: soltab
+ source:
+ - ion_3rd
+ valueFrom: '$(self ? "sol000/tec3rd" : sol000/tec)'
+ - id: axesInPlot
+ default:
+ - time
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: false
+ - id: refAnt
+ source: refant
+ - id: prefix
+ source:
+ - ion_3rd
+ valueFrom: '$(self ? "tec3rd" : "tec")'
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_tec3rd
+ 'sbg:x': 0
+ 'sbg:y': 100
+ - id: losoto_plot_clock
+ in:
+ - id: input_h5parm
+ source: clocktec/output_h5parm
+ - id: soltab
+ default: sol000/clock
+ - id: axesInPlot
+ default:
+ - time
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: false
+ - id: refAnt
+ source: refant
+ - id: prefix
+ default: clock
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_clock
+ 'sbg:x': 0
+ 'sbg:y': 200
+ - id: losoto_plot_Pr
+ in:
+ - id: input_h5parm
+ source: clocktec/output_h5parm
+ - 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: refant
+ - id: prefix
+ default: ion_ph-res_poldif
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_Pr
+ 'sbg:x': 0
+ 'sbg:y': 300
+ - id: losoto_plot_Pr3
+ in:
+ - id: input_h5parm
+ source: clocktec/output_h5parm
+ - id: soltab
+ default: sol000/phase000
+ - id: axesInPlot
+ default:
+ - time
+ - freq
+ - id: axisInTable
+ default: ant
+ - id: axisInCol
+ default: pol
+ - id: minmax
+ default:
+ - -3.14
+ - 3.14
+ - id: plotFlag
+ default: true
+ - id: refAnt
+ source: refant
+ - id: prefix
+ default: ion_ph-res_
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_Pr3
+ 'sbg:x': 0
+ 'sbg:y': 400
+ - id: concat_logfiles_ion
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - inh5parm_logfile
+ - clocktec/logfiles
+ - losoto_plot_A1/logfile
+ - losoto_plot_A2/logfile
+ - losoto_plot_P3/logfile
+ - losoto_plot_Pd/logfile
+ - losoto_plot_tec/logfile
+ - losoto_plot_tec3rd/logfile
+ - losoto_plot_clock/logfile
+ - losoto_plot_Pr/logfile
+ - losoto_plot_Pr3/logfile
+ - write_solutions/log
+ - id: file_prefix
+ default: losoto_ion
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_ion
+ 'sbg:x': 500
+ 'sbg:y': 500
+ - id: write_solutions
+ in:
+ - id: h5parmFile
+ source: clocktec/output_h5parm
+ - id: outsolset
+ default: calibrator
+ - id: insoltab
+ source: tables2export
+ - id: input_file
+ source: insolutions
+ - id: squeeze
+ default: true
+ - id: verbose
+ default: true
+ out:
+ - id: outh5parm
+ - id: log
+ run: ../../steps/h5parmcat.cwl
+ label: write_solutions
+ 'sbg:x': -200
+ 'sbg:y': 700
+requirements:
+ - class: SubworkflowFeatureRequirement
+ - class: MultipleInputFeatureRequirement