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Commit 119c0e20 authored by alex's avatar alex
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fix clocktec

parent e0d43703
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2 merge requests!69Change the name of the pre-calibrated output MS,!20Merge request HBA_calibrator to master
Pipeline #1509 failed
Stage: validate_cwl_scripts
Stage: test_steps
Stage: integration_test
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lofar-cwl/steps/LoSoTo.ClockTec.cwl
+ 8
− 4
View file @ 119c0e20
...@@ -53,14 +53,14 @@ inputs: ...@@ -53,14 +53,14 @@ inputs:
- id: tec3rdsoltabOut - id: tec3rdsoltabOut
doc: output soltab name for tec3rd offset doc: output soltab name for tec3rd offset
type: string? type: string?
- id: flagBadChannels - id: FlagBadChannels
type: boolean? type: boolean?
doc: Detect and remove bad channel before fitting, by default True. doc: Detect and remove bad channel before fitting, by default True.
- id: flagCut - id: flagCut
type: float? type: float?
- id: chi2cut - id: chi2cut
type: float? type: float?
- id: combinePol - id: CombinePol
type: boolean? type: boolean?
doc: | doc: |
Find a combined polarization solution, by default False. Find a combined polarization solution, by default False.
...@@ -68,11 +68,11 @@ inputs: ...@@ -68,11 +68,11 @@ inputs:
type: boolean? type: boolean?
doc: | doc: |
Detect and remove phase wraps, by default True. Detect and remove phase wraps, by default True.
- id: fit3rdorder - id: Fit3rdOrder
type: boolean? type: boolean?
doc: | doc: |
Fit a 3rd order ionospheric ocmponent (usefult <40 MHz). By default False. Fit a 3rd order ionospheric ocmponent (usefult <40 MHz). By default False.
- id: circular - id: Circular
type: boolean? type: boolean?
doc: | doc: |
Assume circular polarization with FR not removed. By default False. Assume circular polarization with FR not removed. By default False.
...@@ -92,6 +92,10 @@ outputs: ...@@ -92,6 +92,10 @@ outputs:
format: lofar:#H5Parm format: lofar:#H5Parm
outputBinding: outputBinding:
glob: $(inputs.input_h5parm.basename) glob: $(inputs.input_h5parm.basename)
- id: parset
type: File
outputBinding:
glob: parset.config
- id: log - id: log
type: File[] type: File[]
outputBinding: outputBinding:
......
lofar-cwl/steps/LoSoTo.Smooth.cwl
+ 3
− 2
View file @ 119c0e20
...@@ -96,10 +96,11 @@ outputs: ...@@ -96,10 +96,11 @@ outputs:
outputBinding: outputBinding:
glob: $(inputs.input_h5parm.basename) glob: $(inputs.input_h5parm.basename)
- id: logfile - id: logfile
type: File type: File[]
outputBinding: outputBinding:
glob: $(inputs.input_h5parm.basename)-losoto.log glob: '$(inputs.input_h5parm.basename)-losoto*.log'
stdout: $(inputs.input_h5parm.basename)-losoto.log stdout: $(inputs.input_h5parm.basename)-losoto.log
stderr: $(inputs.input_h5parm.basename)-losoto_err.log
$schema: $schema:
- https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
subworkflow/apply_calibrate_bp.cwl
+ 7
− 1
View file @ 119c0e20
...@@ -68,6 +68,12 @@ outputs: ...@@ -68,6 +68,12 @@ outputs:
type: File type: File
'sbg:x': 1000 'sbg:x': 1000
'sbg:y': 300 'sbg:y': 300
- id: applybeam.log
outputSource:
- concat_logfiles_applybeam/output
type: File
'sbg:x': 1000
'sbg:y': 400
steps: steps:
- id: applyPA - id: applyPA
in: in:
...@@ -254,7 +260,7 @@ steps: ...@@ -254,7 +260,7 @@ steps:
out: out:
- id: output - id: output
run: ../steps/concatenate_files.cwl run: ../steps/concatenate_files.cwl
label: concat_logfiles_applBP label: concat_logfiles_applyBP
'sbg:x': 0 'sbg:x': 0
'sbg:y': 200 'sbg:y': 200
- id: concat_logfiles_applyPA - id: concat_logfiles_applyPA
......
subworkflow/clocktec.cwl
+ 92
− 63
View file @ 119c0e20
...@@ -7,47 +7,53 @@ $namespaces: ...@@ -7,47 +7,53 @@ $namespaces:
inputs: inputs:
- id: input_h5parm - id: input_h5parm
type: File type: File
'sbg:x': -588.3988647460938 'sbg:x': -700
'sbg:y': -147.5 'sbg:y': -400
- id: fit3rdorder - id: fit3rdorder
type: boolean? type: boolean?
'sbg:x': 83.60113525390625 'sbg:x': -700
'sbg:y': 53.5 'sbg:y': -200
- id: refAnt - id: refAnt
type: string? type: string?
'sbg:x': 500.74346923828125 'sbg:x': -700
'sbg:y': -382.8847351074219 'sbg:y': 0
- id: maxStddev - id: maxStddev
type: float? type: float?
'sbg:x': 374.1950988769531 'sbg:x': -700
'sbg:y': -308.9609069824219 'sbg:y': 200
- id: clock_smooth - id: clock_smooth
type: boolean? type: boolean?
'sbg:x': 10.164066314697266 'sbg:x': -700
'sbg:y': -342.3074035644531 'sbg:y': 400
outputs: outputs:
- id: output_h5parm - id: output_h5parm
outputSource: outputSource:
- losoto_flagstation/output_h5parm - losoto_flagstation/output_h5parm
type: File type: File
'sbg:x': 775 'sbg:x': 1500
'sbg:y': -169 'sbg:y': 0
- id: logfiles - id: logfiles
outputSource: outputSource:
- duplicateAbkp/log
- flag/log - flag/log
- flagextend/log - flagextend/log
- merge/log - merge/log
- flagextend/log
- merge/log
- duplicatePbkp/log - duplicatePbkp/log
- losoto_clocktec/log - losoto_clocktec/log
- smooth/logfile
- losoto_residual/log - losoto_residual/log
- duplicateCbkp/log
- smooth/logfile
- losoto_flagstation/log - losoto_flagstation/log
type: 'File[]' type: 'File[]'
linkMerge: merge_flattened linkMerge: merge_flattened
'sbg:x': 775 'sbg:x': 1500
'sbg:y': 169 'sbg:y': -200
- id: parset
outputSource:
- losoto_residual/output_h5parm
type: File
'sbg:x': 1500
'sbg:y': 200
steps: steps:
- id: duplicateAbkp - id: duplicateAbkp
in: in:
...@@ -56,13 +62,13 @@ steps: ...@@ -56,13 +62,13 @@ steps:
- id: soltab - id: soltab
default: sol000/amplitude000 default: sol000/amplitude000
- id: soltabOut - id: soltabOut
default: amplitudeOrig000 default: amplitudeOrig
out: out:
- id: output_h5parm - id: output_h5parm
- id: log - id: log
run: ../lofar-cwl/steps/LoSoTo.Duplicate.cwl run: ../lofar-cwl/steps/LoSoTo.Duplicate.cwl
'sbg:x': -542.3984375 'sbg:x': -500
'sbg:y': -138.5 'sbg:y': 0
- id: flag - id: flag
in: in:
- id: input_h5parm - id: input_h5parm
...@@ -81,14 +87,18 @@ steps: ...@@ -81,14 +87,18 @@ steps:
default: 1 default: 1
- id: maxRms - id: maxRms
default: 5 default: 5
- id: replace
default: false
- id: preflagzeros
default: false
- id: mode - id: mode
default: smooth default: smooth
out: out:
- id: output_h5parm - id: output_h5parm
- id: log - id: log
run: ../lofar-cwl/steps/LoSoTo.Flag.cwl run: ../lofar-cwl/steps/LoSoTo.Flag.cwl
'sbg:x': -442.3984375 'sbg:x': -300
'sbg:y': -138.5 'sbg:y': 0
- id: flagextend - id: flagextend
in: in:
- id: input_h5parm - id: input_h5parm
...@@ -111,8 +121,8 @@ steps: ...@@ -111,8 +121,8 @@ steps:
- id: output_h5parm - id: output_h5parm
- id: log - id: log
run: ../lofar-cwl/steps/LoSoTo.Flagextend.cwl run: ../lofar-cwl/steps/LoSoTo.Flagextend.cwl
'sbg:x': -255 'sbg:x': -100
'sbg:y': -160 'sbg:y': 0
- id: merge - id: merge
in: in:
- id: input_h5parm - id: input_h5parm
...@@ -127,8 +137,8 @@ steps: ...@@ -127,8 +137,8 @@ steps:
- id: output_h5parm - id: output_h5parm
- id: log - id: log
run: ../lofar-cwl/steps/LoSoTo.Reweight.cwl run: ../lofar-cwl/steps/LoSoTo.Reweight.cwl
'sbg:x': -94 'sbg:x': 100
'sbg:y': -162 'sbg:y': 0
- id: duplicatePbkp - id: duplicatePbkp
in: in:
- id: input_h5parm - id: input_h5parm
...@@ -141,28 +151,8 @@ steps: ...@@ -141,28 +151,8 @@ steps:
- id: output_h5parm - id: output_h5parm
- id: log - id: log
run: ../lofar-cwl/steps/LoSoTo.Duplicate.cwl run: ../lofar-cwl/steps/LoSoTo.Duplicate.cwl
'sbg:x': 69 'sbg:x': 300
'sbg:y': -162 'sbg:y': 0
- 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 - id: losoto_clocktec
in: in:
- id: input_h5parm - id: input_h5parm
...@@ -177,20 +167,55 @@ steps: ...@@ -177,20 +167,55 @@ steps:
default: phase_offset default: phase_offset
- id: tec3rdsoltabOut - id: tec3rdsoltabOut
default: tec3rd default: tec3rd
- id: combinePol - id: FlagBadChannels
default: false
- id: CombinePol
default: true default: true
- id: fit3rdorder - id: Fit3rdOrder
source: fit3rdorder source: fit3rdorder
- id: Circular
default: false
out: out:
- id: output_h5parm - id: output_h5parm
- id: parset
- id: log - id: log
run: ../lofar-cwl/steps/LoSoTo.ClockTec.cwl run: ../lofar-cwl/steps/LoSoTo.ClockTec.cwl
'sbg:x': 217.72296142578125 'sbg:x': 500
'sbg:y': -230.69259643554688 'sbg:y': 0
- id: smooth - id: losoto_residual
in: in:
- id: input_h5parm - id: input_h5parm
source: losoto_clocktec/output_h5parm source: losoto_clocktec/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': 700
'sbg:y': 0
- id: duplicateCbkp
in:
- id: input_h5parm
source: losoto_residual/output_h5parm
- id: soltab
default: sol000/clock
- id: soltabOut
default: clockOrig
out:
- id: output_h5parm
- id: log
run: ../lofar-cwl/steps/LoSoTo.Duplicate.cwl
'sbg:x': 900
'sbg:y': 0
- id: smooth
in:
- id: input_h5parm
source: duplicateCbkp/output_h5parm
- id: execute - id: execute
source: clock_smooth source: clock_smooth
- id: soltab - id: soltab
...@@ -208,24 +233,28 @@ steps: ...@@ -208,24 +233,28 @@ steps:
- id: output_h5parm - id: output_h5parm
- id: logfile - id: logfile
run: ../lofar-cwl/steps/LoSoTo.Smooth.cwl run: ../lofar-cwl/steps/LoSoTo.Smooth.cwl
'sbg:x': 301.4368591308594 'sbg:x': 1100
'sbg:y': -51.11399841308594 'sbg:y': 0
- id: losoto_residual - id: losoto_flagstation
in: in:
- id: input_h5parm - id: input_h5parm
source: smooth/output_h5parm source: smooth/output_h5parm
- id: soltab - id: soltab
default: sol000/phase000 default: sol000/phase000
- id: soltabsToSub - id: mode
source: default: resid
- fit3rdorder - id: maxStddev
valueFrom: '$(self ? ["tec", "clock", "tec3rd"] : ["tec", "clock"])' source: maxStddev
- id: refAnt
source: refAnt
- id: soltabExport
default: clock
out: out:
- id: output_h5parm - id: output_h5parm
- id: log - id: log
run: ../lofar-cwl/steps/LoSoTo.Residual.cwl run: ../lofar-cwl/steps/LoSoTo.FlagStation.cwl
'sbg:x': 411.0426330566406 'sbg:x': 1300
'sbg:y': -168.98934936523438 'sbg:y': 0
requirements: requirements:
- class: StepInputExpressionRequirement - class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement - class: InlineJavascriptRequirement
workflows/prefactor_calibrator.cwl
+ 4
− 1
View file @ 119c0e20
...@@ -211,7 +211,7 @@ outputs: ...@@ -211,7 +211,7 @@ outputs:
'sbg:y': 0 'sbg:y': 0
- id: parset - id: parset
outputSource: outputSource:
- prep/parset - ion/parsets
type: 'File[]' type: 'File[]'
'sbg:x': 2000 'sbg:x': 2000
'sbg:y': 200 'sbg:y': 200
...@@ -420,10 +420,13 @@ steps: ...@@ -420,10 +420,13 @@ steps:
source: tables2export source: tables2export
- id: clock_smooth - id: clock_smooth
source: clock_smooth source: clock_smooth
- id: calibrator_name
source: prep/calibrator_name
out: out:
- id: outsolutions - id: outsolutions
- id: inspection - id: inspection
- id: logfiles - id: logfiles
- id: parsets
run: ./prefactor_calibrator/ion.cwl run: ./prefactor_calibrator/ion.cwl
label: ion label: ion
'sbg:x': 1300 'sbg:x': 1300
......
workflows/prefactor_calibrator/bp.cwl
+ 15
− 0
View file @ 119c0e20
...@@ -107,6 +107,7 @@ outputs: ...@@ -107,6 +107,7 @@ outputs:
- concat_logfiles_apply/output - concat_logfiles_apply/output
- concat_logfiles_apply_pa/output - concat_logfiles_apply_pa/output
- concat_logfiles_apply_fr/output - concat_logfiles_apply_fr/output
- concat_logfiles_beam/output
type: 'File[]' type: 'File[]'
linkMerge: merge_flattened linkMerge: merge_flattened
'sbg:x': 1000 'sbg:x': 1000
...@@ -405,6 +406,7 @@ steps: ...@@ -405,6 +406,7 @@ steps:
- id: apply_pa.log - id: apply_pa.log
- id: apply_fr.log - id: apply_fr.log
- id: calib_cal.log - id: calib_cal.log
- id: applybeam.log
- id: outh5parm - id: outh5parm
run: ../../subworkflow/apply_calibrate_bp.cwl run: ../../subworkflow/apply_calibrate_bp.cwl
label: apply_calibrate_bp label: apply_calibrate_bp
...@@ -464,6 +466,19 @@ steps: ...@@ -464,6 +466,19 @@ steps:
label: concat_logfiles_apply label: concat_logfiles_apply
'sbg:x': 750 'sbg:x': 750
'sbg:y': 600 'sbg:y': 600
- id: concat_logfiles_beam
in:
- id: file_list
source:
- apply_calibrate_bp/applybeam.log
- id: file_prefix
default: applybeam_BP
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_beam
'sbg:x': 750
'sbg:y': 700
- id: concat_logfiles_calib - id: concat_logfiles_calib
in: in:
- id: file_list - id: file_list
......
workflows/prefactor_calibrator/ion.cwl
+ 31
− 5
View file @ 119c0e20
...@@ -5,6 +5,10 @@ label: ion ...@@ -5,6 +5,10 @@ label: ion
$namespaces: $namespaces:
sbg: 'https://www.sevenbridges.com/' sbg: 'https://www.sevenbridges.com/'
inputs: inputs:
- id: calibrator_name
type: string
'sbg:x': -1000
'sbg:y': -200
- id: clock_smooth - id: clock_smooth
type: boolean type: boolean
'sbg:x': -1000 'sbg:x': -1000
...@@ -55,7 +59,7 @@ outputs: ...@@ -55,7 +59,7 @@ outputs:
'sbg:y': 0 'sbg:y': 0
- id: outsolutions - id: outsolutions
outputSource: outputSource:
- write_solutions/outh5parm - h5parm_pointingname/outh5parm
type: File type: File
'sbg:x': 1000 'sbg:x': 1000
'sbg:y': 100 'sbg:y': 100
...@@ -66,6 +70,13 @@ outputs: ...@@ -66,6 +70,13 @@ outputs:
linkMerge: merge_flattened linkMerge: merge_flattened
'sbg:x': 1000 'sbg:x': 1000
'sbg:y': 200 'sbg:y': 200
- id: parsets
outputSource:
- clocktec/parset
type: 'File[]'
linkMerge: merge_flattened
'sbg:x': 1000
'sbg:y': 300
steps: steps:
- id: clocktec - id: clocktec
in: in:
...@@ -80,6 +91,7 @@ steps: ...@@ -80,6 +91,7 @@ steps:
out: out:
- id: output_h5parm - id: output_h5parm
- id: logfiles - id: logfiles
- id: parset
run: ../../subworkflow/clocktec.cwl run: ../../subworkflow/clocktec.cwl
label: clocktec label: clocktec
'sbg:x': -500 'sbg:x': -500
...@@ -89,7 +101,7 @@ steps: ...@@ -89,7 +101,7 @@ steps:
- id: input_h5parm - id: input_h5parm
source: clocktec/output_h5parm source: clocktec/output_h5parm
- id: soltab - id: soltab
default: sol000/amplitudeOrig000 default: sol000/amplitudeOrig
- id: axesInPlot - id: axesInPlot
default: default:
- time - time
...@@ -251,7 +263,7 @@ steps: ...@@ -251,7 +263,7 @@ steps:
- id: input_h5parm - id: input_h5parm
source: clocktec/output_h5parm source: clocktec/output_h5parm
- id: soltab - id: soltab
default: sol000/clock default: sol000/clockOrig
- id: axesInPlot - id: axesInPlot
default: default:
- time - time
...@@ -315,8 +327,6 @@ steps: ...@@ -315,8 +327,6 @@ steps:
- freq - freq
- id: axisInTable - id: axisInTable
default: ant default: ant
- id: axisInCol
default: pol
- id: minmax - id: minmax
default: default:
- -3.14 - -3.14
...@@ -352,6 +362,7 @@ steps: ...@@ -352,6 +362,7 @@ steps:
- losoto_plot_Pr/logfile - losoto_plot_Pr/logfile
- losoto_plot_Pr3/logfile - losoto_plot_Pr3/logfile
- write_solutions/log - write_solutions/log
- h5parm_pointingname/log
- id: file_prefix - id: file_prefix
default: losoto_ion default: losoto_ion
out: out:
...@@ -381,6 +392,21 @@ steps: ...@@ -381,6 +392,21 @@ steps:
label: write_solutions label: write_solutions
'sbg:x': -200 'sbg:x': -200
'sbg:y': 700 'sbg:y': 700
- id: h5parm_pointingname
in:
- id: h5parm
source: write_solutions/outh5parm
- id: solsetName
default: calibrator
- id: pointing
source: calibrator_name
out:
- id: outh5parm
- id: log
run: ../../steps/h5parm_pointingname.cwl
label: h5parm_pointingname
'sbg:x': 0
'sbg:y': 700
requirements: requirements:
- class: SubworkflowFeatureRequirement - class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement - class: MultipleInputFeatureRequirement
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