From 290a0848e2de283219d60a87975b058e2c0246e0 Mon Sep 17 00:00:00 2001
From: Alexander Drabent <alex@tls-tautenburg.de>
Date: Wed, 13 May 2020 11:07:16 +0200
Subject: [PATCH] fix clocktec
Former-commit-id: 119c0e20cf4b04303d114f7f5ad85be37b55f149
---
lofar-cwl/steps/LoSoTo.ClockTec.cwl | 12 +-
lofar-cwl/steps/LoSoTo.Smooth.cwl | 5 +-
subworkflow/apply_calibrate_bp.cwl | 8 +-
subworkflow/clocktec.cwl | 155 +++++++++++++++----------
workflows/prefactor_calibrator.cwl | 5 +-
workflows/prefactor_calibrator/bp.cwl | 15 +++
workflows/prefactor_calibrator/ion.cwl | 36 +++++-
7 files changed, 160 insertions(+), 76 deletions(-)
diff --git a/lofar-cwl/steps/LoSoTo.ClockTec.cwl b/lofar-cwl/steps/LoSoTo.ClockTec.cwl
index 6453badf..a02a92a0 100644
--- a/lofar-cwl/steps/LoSoTo.ClockTec.cwl
+++ b/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:
diff --git a/lofar-cwl/steps/LoSoTo.Smooth.cwl b/lofar-cwl/steps/LoSoTo.Smooth.cwl
index d902c0b2..7f0d07e3 100644
--- a/lofar-cwl/steps/LoSoTo.Smooth.cwl
+++ b/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
diff --git a/subworkflow/apply_calibrate_bp.cwl b/subworkflow/apply_calibrate_bp.cwl
index 66362f93..5aca7b54 100644
--- a/subworkflow/apply_calibrate_bp.cwl
+++ b/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
diff --git a/subworkflow/clocktec.cwl b/subworkflow/clocktec.cwl
index 102a1481..77eb284a 100644
--- a/subworkflow/clocktec.cwl
+++ b/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
diff --git a/workflows/prefactor_calibrator.cwl b/workflows/prefactor_calibrator.cwl
index dcf2f263..7bd24145 100644
--- a/workflows/prefactor_calibrator.cwl
+++ b/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
diff --git a/workflows/prefactor_calibrator/bp.cwl b/workflows/prefactor_calibrator/bp.cwl
index a5019e8f..aabd0ff3 100644
--- a/workflows/prefactor_calibrator/bp.cwl
+++ b/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
diff --git a/workflows/prefactor_calibrator/ion.cwl b/workflows/prefactor_calibrator/ion.cwl
index eab2b718..cb4b7cb0 100644
--- a/workflows/prefactor_calibrator/ion.cwl
+++ b/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
--
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