fix clocktec

Former-commit-id: 119c0e20

lofar-cwl/steps/LoSoTo.ClockTec.cwl

@@ -53,14 +53,14 @@ inputs:
   - id: tec3rdsoltabOut
     doc: output soltab name for tec3rd offset
     type: string?
-  - id: flagBadChannels
+  - 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
+  - id: CombinePol
     type: boolean?
     doc: |
       Find a combined polarization solution, by default False.
@@ -68,11 +68,11 @@ inputs:
     type: boolean?
     doc: |
       Detect and remove phase wraps, by default True.
-  - id: fit3rdorder
+  - id: Fit3rdOrder
     type: boolean?
     doc: |
       Fit a 3rd order ionospheric ocmponent (usefult <40 MHz). By default False.
-  - id: circular
+  - id: Circular
     type: boolean?
     doc: |
       Assume circular polarization with FR not removed. By default False.
@@ -92,6 +92,10 @@ outputs:
     format: lofar:#H5Parm
     outputBinding:
       glob: $(inputs.input_h5parm.basename)
+  - id: parset
+    type: File
+    outputBinding:
+      glob: parset.config
   - id: log
     type: File[]
     outputBinding:

lofar-cwl/steps/LoSoTo.Smooth.cwl

@@ -96,10 +96,11 @@ outputs:
     outputBinding:
       glob: $(inputs.input_h5parm.basename)
   - id: logfile
-    type: File
+    type: File[]
     outputBinding:
-      glob: $(inputs.input_h5parm.basename)-losoto.log
+      glob: '$(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

subworkflow/apply_calibrate_bp.cwl

@@ -68,6 +68,12 @@ outputs:
     type: File
     'sbg:x': 1000
     'sbg:y': 300
+  - id: applybeam.log
+    outputSource:
+      - concat_logfiles_applybeam/output
+    type: File
+    'sbg:x': 1000
+    'sbg:y': 400
 steps:
   - id: applyPA
     in:
@@ -254,7 +260,7 @@ steps:
     out:
       - id: output
     run: ../steps/concatenate_files.cwl
-    label: concat_logfiles_applBP
+    label: concat_logfiles_applyBP
     'sbg:x': 0
     'sbg:y': 200
   - id: concat_logfiles_applyPA

subworkflow/clocktec.cwl

@@ -7,47 +7,53 @@ $namespaces:
 inputs:
   - id: input_h5parm
     type: File
-    'sbg:x': -588.3988647460938
-    'sbg:y': -147.5
+    'sbg:x': -700
+    'sbg:y': -400
   - id: fit3rdorder
     type: boolean?
-    'sbg:x': 83.60113525390625
-    'sbg:y': 53.5
+    'sbg:x': -700
+    'sbg:y': -200
   - id: refAnt
     type: string?
-    'sbg:x': 500.74346923828125
-    'sbg:y': -382.8847351074219
+    'sbg:x': -700
+    'sbg:y': 0
   - id: maxStddev
     type: float?
-    'sbg:x': 374.1950988769531
-    'sbg:y': -308.9609069824219
+    'sbg:x': -700
+    'sbg:y': 200
   - id: clock_smooth
     type: boolean?
-    'sbg:x': 10.164066314697266
-    'sbg:y': -342.3074035644531
+    'sbg:x': -700
+    'sbg:y': 400
 outputs:
   - id: output_h5parm
     outputSource:
       - losoto_flagstation/output_h5parm
     type: File
-    'sbg:x': 775
-    'sbg:y': -169
+    'sbg:x': 1500
+    'sbg:y': 0
   - id: logfiles
     outputSource:
+      - duplicateAbkp/log
       - flag/log
       - flagextend/log
       - merge/log
-      - flagextend/log
-      - merge/log
       - duplicatePbkp/log
       - losoto_clocktec/log
-      - smooth/logfile
       - losoto_residual/log
+      - duplicateCbkp/log
+      - smooth/logfile
       - losoto_flagstation/log
     type: 'File[]'
     linkMerge: merge_flattened
-    'sbg:x': 775
-    'sbg:y': 169
+    'sbg:x': 1500
+    'sbg:y': -200
+  - id: parset
+    outputSource:
+      - losoto_residual/output_h5parm
+    type: File
+    'sbg:x': 1500
+    'sbg:y': 200
 steps:
   - id: duplicateAbkp
     in:
@@ -56,13 +62,13 @@ steps:
       - id: soltab
         default: sol000/amplitude000
       - id: soltabOut
-        default: amplitudeOrig000
+        default: amplitudeOrig
     out:
       - id: output_h5parm
       - id: log
     run: ../lofar-cwl/steps/LoSoTo.Duplicate.cwl
-    'sbg:x': -542.3984375
-    'sbg:y': -138.5
+    'sbg:x': -500
+    'sbg:y': 0
   - id: flag
     in:
       - id: input_h5parm
@@ -81,14 +87,18 @@ steps:
         default: 1
       - id: maxRms
         default: 5
+      - id: replace
+        default: false
+      - id: preflagzeros
+        default: false
       - 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
+    'sbg:x': -300
+    'sbg:y': 0
   - id: flagextend
     in:
       - id: input_h5parm
@@ -111,8 +121,8 @@ steps:
       - id: output_h5parm
       - id: log
     run: ../lofar-cwl/steps/LoSoTo.Flagextend.cwl
-    'sbg:x': -255
-    'sbg:y': -160
+    'sbg:x': -100
+    'sbg:y': 0
   - id: merge
     in:
       - id: input_h5parm
@@ -127,8 +137,8 @@ steps:
       - id: output_h5parm
       - id: log
     run: ../lofar-cwl/steps/LoSoTo.Reweight.cwl
-    'sbg:x': -94
-    'sbg:y': -162
+    'sbg:x': 100
+    'sbg:y': 0
   - id: duplicatePbkp
     in:
       - id: input_h5parm
@@ -141,28 +151,8 @@ steps:
       - 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
+    'sbg:x': 300
+    'sbg:y': 0
   - id: losoto_clocktec
     in:
       - id: input_h5parm
@@ -177,20 +167,55 @@ steps:
         default: phase_offset
       - id: tec3rdsoltabOut
         default: tec3rd
-      - id: combinePol
+      - id: FlagBadChannels
+        default: false
+      - id: CombinePol
         default: true
-      - id: fit3rdorder
+      - id: Fit3rdOrder
         source: fit3rdorder
+      - id: Circular
+        default: false
     out:
       - id: output_h5parm
+      - id: parset
       - id: log
     run: ../lofar-cwl/steps/LoSoTo.ClockTec.cwl
-    'sbg:x': 217.72296142578125
-    'sbg:y': -230.69259643554688
-  - id: smooth
+    'sbg:x': 500
+    'sbg:y': 0
+  - id: losoto_residual
     in:
       - id: input_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
         source: clock_smooth
       - id: soltab
@@ -208,24 +233,28 @@ steps:
       - id: output_h5parm
       - id: logfile
     run: ../lofar-cwl/steps/LoSoTo.Smooth.cwl
-    'sbg:x': 301.4368591308594
-    'sbg:y': -51.11399841308594
-  - id: losoto_residual
+    'sbg:x': 1100
+    'sbg:y': 0
+  - id: losoto_flagstation
     in:
       - id: input_h5parm
         source: smooth/output_h5parm
       - id: soltab
         default: sol000/phase000
-      - id: soltabsToSub
-        source:
-          - fit3rdorder
-        valueFrom: '$(self ? ["tec", "clock", "tec3rd"] : ["tec", "clock"])'
+      - id: mode
+        default: resid
+      - id: maxStddev
+        source: maxStddev
+      - id: refAnt
+        source: refAnt
+      - id: soltabExport
+        default: clock
     out:
       - id: output_h5parm
       - id: log
-    run: ../lofar-cwl/steps/LoSoTo.Residual.cwl
-    'sbg:x': 411.0426330566406
-    'sbg:y': -168.98934936523438
+    run: ../lofar-cwl/steps/LoSoTo.FlagStation.cwl
+    'sbg:x': 1300
+    'sbg:y': 0
 requirements:
   - class: StepInputExpressionRequirement
   - class: InlineJavascriptRequirement

workflows/prefactor_calibrator.cwl

@@ -211,7 +211,7 @@ outputs:
     'sbg:y': 0
   - id: parset
     outputSource:
-      - prep/parset
+      - ion/parsets
     type: 'File[]'
     'sbg:x': 2000
     'sbg:y': 200
@@ -420,10 +420,13 @@ steps:
         source: tables2export
       - id: clock_smooth
         source: clock_smooth
+      - id: calibrator_name
+        source: prep/calibrator_name
     out:
       - id: outsolutions
       - id: inspection
       - id: logfiles
+      - id: parsets
     run: ./prefactor_calibrator/ion.cwl
     label: ion
     'sbg:x': 1300

workflows/prefactor_calibrator/bp.cwl

@@ -107,6 +107,7 @@ outputs:
       - concat_logfiles_apply/output
       - concat_logfiles_apply_pa/output
       - concat_logfiles_apply_fr/output
+      - concat_logfiles_beam/output
     type: 'File[]'
     linkMerge: merge_flattened
     'sbg:x': 1000
@@ -405,6 +406,7 @@ steps:
       - id: apply_pa.log
       - id: apply_fr.log
       - id: calib_cal.log
+      - id: applybeam.log
       - id: outh5parm
     run: ../../subworkflow/apply_calibrate_bp.cwl
     label: apply_calibrate_bp
@@ -464,6 +466,19 @@ steps:
     label: concat_logfiles_apply
     'sbg:x': 750
     '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
     in:
       - id: file_list

workflows/prefactor_calibrator/ion.cwl

@@ -5,6 +5,10 @@ label: ion
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 inputs:
+  - id: calibrator_name
+    type: string
+    'sbg:x': -1000
+    'sbg:y': -200
   - id: clock_smooth
     type: boolean
     'sbg:x': -1000
@@ -55,7 +59,7 @@ outputs:
     'sbg:y': 0
   - id: outsolutions
     outputSource:
-      - write_solutions/outh5parm
+      - h5parm_pointingname/outh5parm
     type: File
     'sbg:x': 1000
     'sbg:y': 100
@@ -66,6 +70,13 @@ outputs:
     linkMerge: merge_flattened
     'sbg:x': 1000
     'sbg:y': 200
+  - id: parsets
+    outputSource:
+      - clocktec/parset
+    type: 'File[]'
+    linkMerge: merge_flattened
+    'sbg:x': 1000
+    'sbg:y': 300
 steps:
   - id: clocktec
     in:
@@ -80,6 +91,7 @@ steps:
     out:
       - id: output_h5parm
       - id: logfiles
+      - id: parset
     run: ../../subworkflow/clocktec.cwl
     label: clocktec
     'sbg:x': -500
@@ -89,7 +101,7 @@ steps:
       - id: input_h5parm
         source: clocktec/output_h5parm
       - id: soltab
-        default: sol000/amplitudeOrig000
+        default: sol000/amplitudeOrig
       - id: axesInPlot
         default:
           - time
@@ -251,7 +263,7 @@ steps:
       - id: input_h5parm
         source: clocktec/output_h5parm
       - id: soltab
-        default: sol000/clock
+        default: sol000/clockOrig
       - id: axesInPlot
         default:
           - time
@@ -315,8 +327,6 @@ steps:
           - freq
       - id: axisInTable
         default: ant
-      - id: axisInCol
-        default: pol
       - id: minmax
         default:
           - -3.14
@@ -352,6 +362,7 @@ steps:
           - losoto_plot_Pr/logfile
           - losoto_plot_Pr3/logfile
           - write_solutions/log
+          - h5parm_pointingname/log
       - id: file_prefix
         default: losoto_ion
     out:
@@ -381,6 +392,21 @@ steps:
     label: write_solutions
     'sbg:x': -200
     '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:
   - class: SubworkflowFeatureRequirement
   - class: MultipleInputFeatureRequirement