From 5a5b38e4b55145e0c40c2cf6f8c039e1bc7e8328 Mon Sep 17 00:00:00 2001
From: Alexander Drabent <alex@tls-tautenburg.de>
Date: Fri, 17 Apr 2020 15:51:56 +0200
Subject: [PATCH] add FR step
Former-commit-id: 10e38234f1a15e9c2fa893d6030980bc192684d0
---
lofar-cwl/steps/H5ParmCollector.cwl | 8 +-
lofar-cwl/steps/LoSoTo.Faraday.cwl | 12 +-
steps/h5parmcat.cwl | 55 ++--
subworkflow/apply_calibrate_fr.cwl | 115 +++++++
subworkflow/faraday_rotation.cwl | 174 ++++-------
workflows/prefactor_calibrator.cwl | 44 ++-
workflows/prefactor_calibrator/fr.cwl | 428 ++++++++++++++++++++++++++
workflows/prefactor_calibrator/pa.cwl | 7 +-
8 files changed, 686 insertions(+), 157 deletions(-)
create mode 100644 subworkflow/apply_calibrate_fr.cwl
create mode 100644 workflows/prefactor_calibrator/fr.cwl
diff --git a/lofar-cwl/steps/H5ParmCollector.cwl b/lofar-cwl/steps/H5ParmCollector.cwl
index 0ae9cf7b..31b1b945 100755
--- a/lofar-cwl/steps/H5ParmCollector.cwl
+++ b/lofar-cwl/steps/H5ParmCollector.cwl
@@ -12,7 +12,9 @@ baseCommand:
- H5parm_collector.py
inputs:
- id: h5parmFiles
- type: 'File[]'
+ type:
+ - 'File[]'
+ - File
format: lofar:#H5Parm
inputBinding:
position: 0
@@ -37,11 +39,13 @@ inputs:
position: 0
prefix: '--insoltab'
doc: Output solset name
-
- default: output.h5
id: outh5parmname
type: string
doc: Output h5parm name
+ inputBinding:
+ position: 0
+ prefix: '--outh5parm'
- id: squeeze
type: boolean
default: false
diff --git a/lofar-cwl/steps/LoSoTo.Faraday.cwl b/lofar-cwl/steps/LoSoTo.Faraday.cwl
index e3092536..85d949b6 100644
--- a/lofar-cwl/steps/LoSoTo.Faraday.cwl
+++ b/lofar-cwl/steps/LoSoTo.Faraday.cwl
@@ -32,7 +32,7 @@ arguments:
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
@@ -41,6 +41,9 @@ inputs:
- id: soltab
type: string
doc: "Solution table"
+ - id: soltabout
+ type: string?
+ doc: output table name (same solset)
- id: refAnt
type: string?
doc: Reference antenna, by default the first.
@@ -57,5 +60,12 @@ outputs:
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
+
$schema:
- https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
diff --git a/steps/h5parmcat.cwl b/steps/h5parmcat.cwl
index bd3861c1..861d08e7 100644
--- a/steps/h5parmcat.cwl
+++ b/steps/h5parmcat.cwl
@@ -1,19 +1,15 @@
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
+ lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
- lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
-$schema:
- - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
-
-id: h5parmcat
-
+id: h5parm_cat
baseCommand:
- H5parm_collector.py
inputs:
- - id: h5parmFiles
+ - format: 'lofar:#H5Parm'
+ id: h5parmFile
type: File
- format: lofar:#H5Parm
inputBinding:
position: 0
doc: List of h5parm files
@@ -37,17 +33,13 @@ inputs:
position: 0
prefix: '--insoltab'
doc: Output solset name
-
- - default: cal_solutions.h5
- id: outh5parmname
- type: string
- inputBinding:
- position: 0
- prefix: '--outh5parm'
+ - default: output.h5
+ id: input_file
+ type: File
doc: Output h5parm name
- - id: squeeze
+ - default: false
+ id: squeeze
type: boolean
- default: false
inputBinding:
position: 0
prefix: '-q'
@@ -59,29 +51,38 @@ inputs:
position: 0
prefix: '-v'
doc: verbose output
- - default: true
+ - default: false
id: clobber
type: boolean
inputBinding:
position: 0
prefix: '-c'
doc: overwrite output
-
outputs:
- id: outh5parm
doc: Output h5parm
type: File
- format: lofar:#H5Parm
outputBinding:
- glob: $(inputs.outh5parmname)
+ glob: $(inputs.input_file.basename)
+ format: lofar:#H5Parm
- id: log
type: File
outputBinding:
- glob: $(inputs.outh5parmname)-parm_collector_output.log
-label: H5parmcat
+ glob: parm_collector_output.log
+label: h5parm_cat
+arguments:
+ - position: 0
+ prefix: '-o'
+ valueFrom: $(inputs.input_file.basename)
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.input_file)
+ writable: true
+ - class: InlineJavascriptRequirement
hints:
- class: DockerRequirement
- dockerPull: 'lofareosc/prefactor:HBAcalibrator'
-stdout: $(inputs.outh5parmname)-parm_collector_output.log
-requirements:
- - class: InlineJavascriptRequirement
\ No newline at end of file
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: parm_collector_output.log
+$schema:
+ - 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
diff --git a/subworkflow/apply_calibrate_fr.cwl b/subworkflow/apply_calibrate_fr.cwl
new file mode 100644
index 00000000..f04c3dd0
--- /dev/null
+++ b/subworkflow/apply_calibrate_fr.cwl
@@ -0,0 +1,115 @@
+class: Workflow
+cwlVersion: v1.0
+id: apply_calibrate
+label: apply_calibrate
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: msin
+ type: Directory
+ 'sbg:x': -1000
+ 'sbg:y': -200
+ - id: do_smooth
+ type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': -100
+ - id: flagunconverged
+ type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': 100
+ - id: propagatesolutions
+ type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': 200
+ - id: input_h5parm
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': 300
+outputs:
+ - id: msout
+ outputSource:
+ - calib_cal/msout
+ type: Directory
+ 'sbg:x': 1000
+ 'sbg:y': -200
+ - id: BLsmooth.log
+ outputSource:
+ - BLsmooth/logfile
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': -100
+ - id: apply_cal.log
+ outputSource:
+ - applyFR/logfile
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: calib_cal.log
+ outputSource:
+ - calib_cal/logfile
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 100
+ - id: outh5parm
+ outputSource:
+ - calib_cal/h5parm
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 200
+steps:
+ - id: applyFR
+ in:
+ - id: msin
+ source: msin
+ - id: msin_datacolumn
+ default: CORRECTED_DATA
+ - id: parmdb
+ source: input_h5parm
+ - id: msout_datacolumn
+ default: CORRECTED_DATA
+ - id: correction
+ default: faraday
+ out:
+ - id: msout
+ - id: logfile
+ run: ../lofar-cwl/steps/applycal.cwl
+ label: applyFR
+ 'sbg:x': -400
+ 'sbg:y': 0
+ - id: BLsmooth
+ in:
+ - id: msin
+ source: applyFR/msout
+ - id: do_smooth
+ source: do_smooth
+ - id: in_column_name
+ default: CORRECTED_DATA
+ out:
+ - id: msout
+ - id: logfile
+ run: ../steps/blsmooth.cwl
+ label: BLsmooth
+ 'sbg:x': 0
+ 'sbg:y': 0
+ - id: calib_cal
+ in:
+ - id: msin
+ source: BLsmooth/msout
+ - id: msin_datacolumn
+ default: SMOOTHED_DATA
+ - id: msin_modelcolum
+ default: MODEL_DATA
+ - id: flagunconverged
+ source: flagunconverged
+ - id: propagate_solutions
+ source: propagatesolutions
+ - id: mode
+ default: diagonal
+ out:
+ - id: msout
+ - id: h5parm
+ - id: logfile
+ run: ../lofar-cwl/steps/ddecal.cwl
+ 'sbg:x': 500
+ 'sbg:y': 0
+requirements: []
diff --git a/subworkflow/faraday_rotation.cwl b/subworkflow/faraday_rotation.cwl
index 3f3fec4e..493146b3 100644
--- a/subworkflow/faraday_rotation.cwl
+++ b/subworkflow/faraday_rotation.cwl
@@ -4,147 +4,81 @@ id: faraday_rotation
label: faraday_rotation
$namespaces:
sbg: 'https://www.sevenbridges.com/'
+ lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+$schema:
+ - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
inputs:
- - id: msin
- type: 'Directory[]'
- 'sbg:x': -1017.7406616210938
- 'sbg:y': -230.76498413085938
- - id: do_smooth
- type: boolean
- 'sbg:x': -892.199951171875
- 'sbg:y': 63.25977325439453
- - id: propagate_solutions
- type: boolean
- 'sbg:x': -862.6722412109375
- 'sbg:y': -476.848876953125
- - id: flagunconverged
- type: boolean
- 'sbg:x': -719.998046875
- 'sbg:y': 88.66199493408203
- id: refAnt
type: string?
- 'sbg:x': -468.52337646484375
- 'sbg:y': -415.06396484375
+ 'sbg:x': -451.3746643066406
+ 'sbg:y': -493.92510986328125
+ - id: input_h5parm
+ type: File
+ 'sbg:x': -743.1871948242188
+ 'sbg:y': -316.5615234375
outputs:
- - id: msout
+ - id: output_h5parm
outputSource:
- - applycal/msout
- type: 'Directory[]'
- 'sbg:x': 481.69647216796875
- 'sbg:y': -386.3322448730469
+ - losoto_residual/output_h5parm
+ type: File
+ format: lofar:#H5Parm
+ 'sbg:x': 152.59103393554688
+ 'sbg:y': -289.2899169921875
+ - id: logfiles
+ outputSource:
+ - losoto_duplicate/log
+ - losoto_faraday/log
+ - losoto_residual/log
+ linkMerge: merge_flattened
+ type: 'File[]'
+ 'sbg:x': 300.59103393554688
+ 'sbg:y': 0
steps:
- - id: smooth_corrected
- in:
- - id: msin
- source: msin
- - id: do_smooth
- source: do_smooth
- - id: in_column_name
- default: CORRECTED_DATA
- - id: out_column
- default: SMOOTHED_DATA
- out:
- - id: msout
- run: ../steps/blsmooth.cwl
- label: smooth_corrected
- scatter:
- - msin
- 'sbg:x': -773.8645629882812
- 'sbg:y': -111.44158172607422
- - id: calib_cal
- in:
- - id: msin
- source: smooth_corrected/msout
- - id: msin_modelcolum
- default: SMOOTHED_DATA
- - id: output_name_h5parm
- default: output.h5
- - id: propagate_solutions
- source: propagate_solutions
- - id: flagunconverged
- default: true
- source: flagunconverged
- - id: flagdivergedonly
- default: true
- out:
- - id: msout
- - id: h5parm
- run: ../lofar-cwl/steps/calib_rot_diag.cwl
- scatter:
- - msin
- 'sbg:x': -568.359130859375
- 'sbg:y': -151.39132690429688
- - id: h5imp_cal_FR
+ - id: losoto_duplicate
in:
- - id: h5parmFiles
- linkMerge: merge_flattened
- source:
- - calib_cal/h5parm
- - id: squeeze
- default: true
- - id: verbose
- default: true
- - id: clobber
- default: true
+ - id: input_h5parm
+ source: input_h5parm
+ - id: soltab
+ default: sol000/phase000
+ - id: soltabOut
+ default: phaseOrig
out:
- - id: outh5parm
+ - id: output_h5parm
- id: log
- run: ../lofar-cwl/steps/H5ParmCollector.cwl
- label: h5imp_cal_FR
- 'sbg:x': -339.8519592285156
- 'sbg:y': -82.80227661132812
+ run: ../lofar-cwl/steps/LoSoTo.Duplicate.cwl
+ 'sbg:x': -423.6229248046875
+ 'sbg:y': -287.8958435058594
- id: losoto_faraday
in:
- id: input_h5parm
- source: h5imp_cal_FR/outh5parm
+ source: losoto_duplicate/output_h5parm
- id: soltab
- default: sol000/phase000
+ default: sol000/rotation000
+ - id: soltabout
+ default: faraday
- id: refAnt
source: refAnt
- id: maxResidual
- default: 1
+ default: 1.0
out:
- id: output_h5parm
+ - id: log
run: ../lofar-cwl/steps/LoSoTo.Faraday.cwl
'sbg:x': -99.27792358398438
'sbg:y': -126.80227661132812
- - id: h5exp_cal_FR
+ - id: losoto_residual
in:
- - id: h5parmFiles
- linkMerge: merge_flattened
- source:
- - losoto_faraday/output_h5parm
- - id: insolset
- default: sol000
- - id: squeeze
- default: true
- - id: verbose
- default: true
- - id: clobber
- default: false
+ - id: input_h5parm
+ source: losoto_faraday/output_h5parm
+ - id: soltab
+ default: sol000/phase000
+ - id: soltabsToSub
+ default:
+ - faraday
out:
- - id: outh5parm
+ - id: output_h5parm
- id: log
- run: ../lofar-cwl/steps/H5ParmCollector.cwl
- label: H5parm_collector
- 'sbg:x': 56.72110366821289
- 'sbg:y': -198
- - id: applycal
- in:
- - id: msin
- source: msin
- - id: msin_datacolumn
- default: CORRECTED_DATA
- - id: parmdb
- source: h5exp_cal_FR/outh5parm
- - id: correction
- default: rotationmeasure000
- out:
- - id: msout
- run: ../lofar-cwl/steps/applycal.cwl
- scatter:
- - msin
- 'sbg:x': 291.55780029296875
- 'sbg:y': -384.2626647949219
-requirements:
- - class: ScatterFeatureRequirement
+ run: ../lofar-cwl/steps/LoSoTo.Residual.cwl
+ 'sbg:x': -0.012040258385241032
+ 'sbg:y': -287.7294006347656
+requirements: []
diff --git a/workflows/prefactor_calibrator.cwl b/workflows/prefactor_calibrator.cwl
index 083d9683..a21a2560 100644
--- a/workflows/prefactor_calibrator.cwl
+++ b/workflows/prefactor_calibrator.cwl
@@ -197,18 +197,19 @@ outputs:
outputSource:
- prep/check_Ateam_separation.png
- pa/inspection
+ - fr/inspection
type: File[]
'sbg:x': 1000
'sbg:y': -600
- id: solutions
outputSource:
- - pa/solutions
+ - fr/outsolutions
type: File
'sbg:x': 1000
'sbg:y': -500
- id: msout
outputSource:
- - pa/msout
+ - fr/msout
type: 'Directory[]'
'sbg:x': 1000
'sbg:y': 0
@@ -222,6 +223,7 @@ outputs:
outputSource:
- prep/logfiles
- pa/logfiles
+ - fr/logfiles
type: 'File[]'
linkMerge: merge_flattened
'sbg:x': 1000
@@ -308,12 +310,46 @@ steps:
source: do_smooth
out:
- id: msout
- - id: solutions
+ - id: outsolutions
- id: inspection
- id: logfiles
+ - id: outh5parm
+ - id: outh5parm_logfile
run: ./prefactor_calibrator/pa.cwl
label: PA
- 'sbg:x': 500
+ 'sbg:x': 400
+ 'sbg:y': 0
+ - id: fr
+ in:
+ - id: msin
+ source:
+ - pa/msout
+ - id: h5parm
+ source:
+ - pa/outh5parm
+ - id: refant
+ source: refant
+ - id: inh5parm_logfile
+ source:
+ - pa/outh5parm_logfile
+ - id: flagunconverged
+ source: flagunconverged
+ - id: propagatesolutions
+ source: propagatesolutions
+ - id: do_smooth
+ source: do_smooth
+ - id: insolutions
+ source: pa/outsolutions
+ out:
+ - id: msout
+ - id: outsolutions
+ - id: inspection
+ - id: logfiles
+ - id: outh5parm
+ - id: outh5parm_logfile
+ run: ./prefactor_calibrator/fr.cwl
+ label: FR
+ 'sbg:x': 700
'sbg:y': 0
requirements:
- class: SubworkflowFeatureRequirement
diff --git a/workflows/prefactor_calibrator/fr.cwl b/workflows/prefactor_calibrator/fr.cwl
new file mode 100644
index 00000000..6c8a01c7
--- /dev/null
+++ b/workflows/prefactor_calibrator/fr.cwl
@@ -0,0 +1,428 @@
+class: Workflow
+cwlVersion: v1.0
+id: fr
+label: FR
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: flagunconverged
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -300
+ - id: propagatesolutions
+ type: boolean?
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': -200
+ - id: msin
+ type: 'Directory[]'
+ 'sbg:x': -1000
+ 'sbg:y': -100
+ - id: h5parm
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: refant
+ type: string?
+ 'sbg:x': -1000
+ 'sbg:y': 100
+ - id: inh5parm_logfile
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': 200
+ - id: do_smooth
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': 300
+ - id: insolutions
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': 400
+outputs:
+ - id: outh5parm
+ outputSource:
+ - h5parm_collector/outh5parm
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': -200
+ - id: msout
+ outputSource:
+ - apply_calibrate_fr/msout
+ type: 'Directory[]'
+ 'sbg:x': 1000
+ 'sbg:y': -100
+ - id: inspection
+ outputSource:
+ - losoto_plot_P3/output_plots
+ - losoto_plot_Pd/output_plots
+ - losoto_plot_Rot3/output_plots
+ - losoto_plot_A3/output_plots
+ - losoto_plot_fr/output_plots
+ - losoto_plot_Pr/output_plots
+ - losoto_plot_Pr2/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_fr/output
+ - concat_logfiles_calib/output
+ - concat_logfiles_blsmooth/output
+ - concat_logfiles_apply/output
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 1000
+ 'sbg:y': 200
+ - id: outh5parm_logfile
+ outputSource:
+ - h5parm_collector/log
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 300
+steps:
+ - id: faraday_rot
+ in:
+ - id: refAnt
+ default: CS001HBA0
+ source: refant
+ - id: input_h5parm
+ source: h5parm
+ out:
+ - id: output_h5parm
+ - id: logfiles
+ run: ../../subworkflow/faraday_rotation.cwl
+ label: FaradayRot
+ 'sbg:x': -500
+ 'sbg:y': 0
+ - id: losoto_plot_P3
+ in:
+ - id: input_h5parm
+ source: faraday_rot/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: fr_ph_
+ out:
+ - id: output_plots
+ - id: logfile
+ 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: faraday_rot/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: fr_ph_poldif
+ out:
+ - id: output_plots
+ - id: logfile
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_Pd
+ 'sbg:x': 0
+ 'sbg:y': -100
+ - id: losoto_plot_Rot3
+ in:
+ - id: input_h5parm
+ source: faraday_rot/output_h5parm
+ - id: soltab
+ default: sol000/rotation000
+ - id: axesInPlot
+ default:
+ - time
+ - freq
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: true
+ - id: refAnt
+ source: refant
+ - id: prefix
+ default: fr_rotangle
+ out:
+ - id: output_plots
+ - id: logfile
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_Rot3
+ 'sbg:x': 0
+ 'sbg:y': 0
+ - id: losoto_plot_A3
+ in:
+ - id: input_h5parm
+ source: faraday_rot/output_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: axesInPlot
+ default:
+ - time
+ - freq
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: true
+ - id: prefix
+ default: fr_amp
+ out:
+ - id: output_plots
+ - id: logfile
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_A3
+ 'sbg:x': 0
+ 'sbg:y': 100
+ - id: losoto_plot_fr
+ in:
+ - id: input_h5parm
+ source: faraday_rot/output_h5parm
+ - id: soltab
+ default: sol000/faraday
+ - id: axesInPlot
+ default:
+ - time
+ - id: axisInTable
+ default: ant
+ - id: refAnt
+ source: refant
+ - id: prefix
+ default: fr
+ out:
+ - id: output_plots
+ - id: logfile
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_fr
+ 'sbg:x': 0
+ 'sbg:y': 200
+ - id: losoto_plot_Pr
+ in:
+ - id: input_h5parm
+ source: faraday_rot/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: fr_ph-res_poldif
+ out:
+ - id: output_plots
+ - id: logfile
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_Pr
+ 'sbg:x': 0
+ 'sbg:y': 300
+ - id: losoto_plot_Pr2
+ in:
+ - id: input_h5parm
+ source: faraday_rot/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: fr_ph-res_
+ out:
+ - id: output_plots
+ - id: logfile
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_Pr2
+ 'sbg:x': 0
+ 'sbg:y': 400
+ - id: concat_logfiles_fr
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - inh5parm_logfile
+ - faraday_rot/logfiles
+ - losoto_plot_P3/logfile
+ - losoto_plot_Pd/logfile
+ - losoto_plot_Rot3/logfile
+ - losoto_plot_A3/logfile
+ - losoto_plot_fr/logfile
+ - losoto_plot_Pr/logfile
+ - losoto_plot_Pr2/logfile
+ - write_solutions/log
+ - id: file_prefix
+ default: losoto_FR
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_FR
+ 'sbg:x': 500
+ 'sbg:y': 500
+ - id: write_solutions
+ in:
+ - id: h5parmFile
+ source: faraday_rot/output_h5parm
+ - id: input_file
+ source: insolutions
+ - id: outsolset
+ default: calibrator
+ - id: insoltab
+ default: faraday
+ - id: outh5parmname
+ default: cal_solutions.h5
+ - id: squeeze
+ default: true
+ - id: verbose
+ default: true
+ out:
+ - id: outh5parm
+ - id: log
+ run: ../../steps/h5parmcat.cwl
+ label: write_solutions
+ 'sbg:x': 0
+ 'sbg:y': 500
+ - id: apply_calibrate_fr
+ in:
+ - id: msin
+ source: msin
+ - id: do_smooth
+ source: do_smooth
+ - id: flagunconverged
+ source: flagunconverged
+ - id: propagatesolutions
+ source: propagatesolutions
+ - id: input_h5parm
+ source: write_solutions/outh5parm
+ out:
+ - id: msout
+ - id: BLsmooth.log
+ - id: apply_cal.log
+ - id: calib_cal.log
+ - id: outh5parm
+ run: ../../subworkflow/apply_calibrate_fr.cwl
+ label: apply_calibrate_fr
+ scatter:
+ - msin
+ 'sbg:x': 500
+ 'sbg:y': 0
+ - id: concat_logfiles_blsmooth
+ in:
+ - id: file_list
+ source:
+ - apply_calibrate_fr/BLsmooth.log
+ - id: file_prefix
+ default: blsmooth_FR
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_blsmooth
+ 'sbg:x': 750
+ 'sbg:y': 300
+ - id: concat_logfiles_apply
+ in:
+ - id: file_list
+ source:
+ - apply_calibrate_fr/apply_cal.log
+ - id: file_prefix
+ default: apply_cal_FR
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_apply
+ 'sbg:x': 750
+ 'sbg:y': 600
+ - id: concat_logfiles_calib
+ in:
+ - id: file_list
+ source:
+ - apply_calibrate_fr/calib_cal.log
+ - id: file_prefix
+ default: calib_cal_FR
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_calib
+ 'sbg:x': 750
+ 'sbg:y': 800
+ - id: h5parm_collector
+ in:
+ - id: h5parmFiles
+ source:
+ - apply_calibrate_fr/outh5parm
+ - id: squeeze
+ default: true
+ - id: verbose
+ default: true
+ - id: clobber
+ default: true
+ out:
+ - id: outh5parm
+ - id: log
+ run: ../../lofar-cwl/steps/H5ParmCollector.cwl
+ label: H5parm_collector
+ 'sbg:x': 750
+ 'sbg:y': -300
+requirements:
+ - class: SubworkflowFeatureRequirement
+ - class: ScatterFeatureRequirement
+ - class: MultipleInputFeatureRequirement
diff --git a/workflows/prefactor_calibrator/pa.cwl b/workflows/prefactor_calibrator/pa.cwl
index 9bdac658..7ff28e55 100644
--- a/workflows/prefactor_calibrator/pa.cwl
+++ b/workflows/prefactor_calibrator/pa.cwl
@@ -62,7 +62,7 @@ outputs:
linkMerge: merge_flattened
'sbg:x': 1000
'sbg:y': 0
- - id: solutions
+ - id: outsolutions
outputSource:
- write_solutions/outh5parm
type: File
@@ -327,7 +327,8 @@ steps:
- id: write_solutions
in:
- id: h5parmFiles
- source: pol_align/output_h5parm
+ source:
+ - pol_align/output_h5parm
- id: outsolset
default: calibrator
- id: insoltab
@@ -341,7 +342,7 @@ steps:
out:
- id: outh5parm
- id: log
- run: ../../steps/h5parmcat.cwl
+ run: ../../lofar-cwl/steps/H5ParmCollector.cwl
label: write_solutions
'sbg:x': 0
'sbg:y': 500
--
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