From 4e0c9a8908ea2fb09008834b9dba5936d916d21d Mon Sep 17 00:00:00 2001
From: Alexander Drabent <alex@tls-tautenburg.de>
Date: Wed, 15 Apr 2020 18:58:52 +0200
Subject: [PATCH] add losoto steps for PA
Former-commit-id: 247e0e9118f48386559cbf554430826cf6c4cde7
Former-commit-id: 56d7d7f7dfd500ff6f00776f5d63a5d953979ed0
---
lofar-cwl/steps/LoSoTo.Duplicate.cwl | 8 +-
lofar-cwl/steps/LoSoTo.Plot.cwl | 12 +-
lofar-cwl/steps/LoSoTo.Polalign.cwl | 8 +-
lofar-cwl/steps/LoSoTo.Residual.cwl | 10 +-
lofar-cwl/steps/ddecal.cwl | 2 +-
steps/h5parmcat.cwl | 87 +++++++
subworkflow/pol_align.cwl | 115 +++++----
workflows/HBA_calibrator.cwl | 47 ++--
workflows/prefactor_calibrator.cwl | 109 +++-----
workflows/prefactor_calibrator/pa.cwl | 315 ++++++++++++++++++++++++
workflows/prefactor_calibrator/prep.cwl | 61 +----
11 files changed, 572 insertions(+), 202 deletions(-)
create mode 100644 steps/h5parmcat.cwl
create mode 100644 workflows/prefactor_calibrator/pa.cwl
diff --git a/lofar-cwl/steps/LoSoTo.Duplicate.cwl b/lofar-cwl/steps/LoSoTo.Duplicate.cwl
index 2219758c..7fe56b03 100644
--- a/lofar-cwl/steps/LoSoTo.Duplicate.cwl
+++ b/lofar-cwl/steps/LoSoTo.Duplicate.cwl
@@ -30,7 +30,7 @@ arguments:
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
@@ -48,8 +48,12 @@ 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
$namespaces:
lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
$schema:
diff --git a/lofar-cwl/steps/LoSoTo.Plot.cwl b/lofar-cwl/steps/LoSoTo.Plot.cwl
index d3d07743..7f3a77e4 100644
--- a/lofar-cwl/steps/LoSoTo.Plot.cwl
+++ b/lofar-cwl/steps/LoSoTo.Plot.cwl
@@ -15,7 +15,7 @@ requirements:
InitialWorkDirRequirement:
listing:
- entryname: 'parset.config'
- entry: $(get_losoto_config().join('\n'))
+ entry: $(get_losoto_config('PLOT').join('\n'))
- entryname: $(inputs.input_h5parm.basename)
entry: $(inputs.input_h5parm)
writable: true
@@ -29,14 +29,14 @@ arguments:
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
type: File
format: lofar:#H5Parm
- id: soltab
- type: string[]
+ type: string
doc: "Tabs to plot"
- id: axesInPlot
@@ -125,6 +125,12 @@ outputs:
type: File[]
outputBinding:
glob: "$(inputs.prefix)*.png"
+ - id: logfile
+ type: File
+ outputBinding:
+ glob: $(inputs.input_h5parm.basename)-losoto.log
+
+stdout: $(inputs.input_h5parm.basename)-losoto.log
$namespaces:
diff --git a/lofar-cwl/steps/LoSoTo.Polalign.cwl b/lofar-cwl/steps/LoSoTo.Polalign.cwl
index a6a65068..0c53cba5 100755
--- a/lofar-cwl/steps/LoSoTo.Polalign.cwl
+++ b/lofar-cwl/steps/LoSoTo.Polalign.cwl
@@ -48,7 +48,7 @@ arguments:
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
@@ -88,5 +88,9 @@ 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
diff --git a/lofar-cwl/steps/LoSoTo.Residual.cwl b/lofar-cwl/steps/LoSoTo.Residual.cwl
index 9dd82a8a..7a8b8ba5 100644
--- a/lofar-cwl/steps/LoSoTo.Residual.cwl
+++ b/lofar-cwl/steps/LoSoTo.Residual.cwl
@@ -29,7 +29,7 @@ arguments:
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
@@ -49,9 +49,15 @@ inputs:
outputs:
- id: output_h5parm
type: File
- format: lofar#H5Parm
+ 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
$namespaces:
lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
diff --git a/lofar-cwl/steps/ddecal.cwl b/lofar-cwl/steps/ddecal.cwl
index cee6e89b..e2620ffe 100644
--- a/lofar-cwl/steps/ddecal.cwl
+++ b/lofar-cwl/steps/ddecal.cwl
@@ -14,7 +14,7 @@ requirements:
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
arguments:
- steps=[ddecal]
diff --git a/steps/h5parmcat.cwl b/steps/h5parmcat.cwl
new file mode 100644
index 00000000..bd3861c1
--- /dev/null
+++ b/steps/h5parmcat.cwl
@@ -0,0 +1,87 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$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
+
+id: h5parmcat
+
+baseCommand:
+ - H5parm_collector.py
+inputs:
+ - id: h5parmFiles
+ type: File
+ format: lofar:#H5Parm
+ inputBinding:
+ position: 0
+ doc: List of h5parm files
+ - default: sol000
+ id: insolset
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--insolset'
+ doc: Input solset name
+ - default: sol000
+ id: outsolset
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--outsolset'
+ doc: Output solset name
+ - id: insoltab
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--insoltab'
+ doc: Output solset name
+
+ - default: cal_solutions.h5
+ id: outh5parmname
+ type: string
+ inputBinding:
+ position: 0
+ prefix: '--outh5parm'
+ doc: Output h5parm name
+ - id: squeeze
+ type: boolean
+ default: false
+ inputBinding:
+ position: 0
+ prefix: '-q'
+ doc: removes all axes with the length of 1
+ - default: true
+ id: verbose
+ type: boolean
+ inputBinding:
+ position: 0
+ prefix: '-v'
+ doc: verbose output
+ - default: true
+ 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)
+ - id: log
+ type: File
+ outputBinding:
+ glob: $(inputs.outh5parmname)-parm_collector_output.log
+label: H5parmcat
+hints:
+ - class: DockerRequirement
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
+stdout: $(inputs.outh5parmname)-parm_collector_output.log
+requirements:
+ - class: InlineJavascriptRequirement
\ No newline at end of file
diff --git a/subworkflow/pol_align.cwl b/subworkflow/pol_align.cwl
index 5a879a4e..ec67ee23 100644
--- a/subworkflow/pol_align.cwl
+++ b/subworkflow/pol_align.cwl
@@ -1,60 +1,83 @@
class: Workflow
cwlVersion: v1.0
-id: pa
-label: pa
+id: pol_align
+label: PolAlign
$namespaces:
sbg: 'https://www.sevenbridges.com/'
+ lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
inputs:
- - id: msin
- type: 'Directory[]'
- 'sbg:x': -1000
- 'sbg:y': -100
- - id: do_smooth
- type: boolean
- 'sbg:x': -1000
- 'sbg:y': 0
- - id: sourcedb
+ - id: refAnt
+ type: string?
+ 'sbg:x': -451.3746643066406
+ 'sbg:y': -493.92510986328125
+ - id: input_h5parm
type: File
- 'sbg:x': -1000
- 'sbg:y': 100
+ 'sbg:x': -743.1871948242188
+ 'sbg:y': -316.5615234375
outputs:
- - id: blsmooth.log
+ - id: output_h5parm
outputSource:
- - concat_logfiles_blsmooth/output
+ - losoto_residual/output_h5parm
type: File
- 'sbg:x': 1000
- 'sbg:y': 100
+ format: lofar:#H5Parm
+ 'sbg:x': 152.59103393554688
+ 'sbg:y': -289.2899169921875
+ - id: logfiles
+ outputSource:
+ - losoto_duplicate/log
+ - losoto_polalign/log
+ - losoto_residual/log
+ linkMerge: merge_flattened
+ type: 'File[]'
+
steps:
- - id: calibrate_first
+ - id: losoto_duplicate
+ in:
+ - id: input_h5parm
+ source: input_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': -423.6229248046875
+ 'sbg:y': -287.8958435058594
+ - id: losoto_polalign
in:
- - id: msin
- source: msin
- - id: do_smooth
- source: do_smooth
- - id: sourcedb
- source: sourcedb
+ - id: input_h5parm
+ source: losoto_duplicate/output_h5parm
+ - id: soltab
+ default: sol000/phase000
+ - id: soltabout
+ default: polalign
+ - id: average
+ default: true
+ - id: replace
+ default: true
+ - id: refAnt
+ source: refAnt
out:
- - id: msout
- - id: blsmooth.log
- run: ../subworkflow/calibrate_first.cwl
- label: calibrate_first
- scatter:
- - msin
- 'sbg:x': -500
- 'sbg:y': 0
- - id: concat_logfiles_blsmooth
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.Polalign.cwl
+ 'sbg:x': -203.663818359375
+ 'sbg:y': -292.61700439453125
+ - id: losoto_residual
in:
- - id: file_list
- source:
- - calibrate_first/blsmooth.log
- - id: file_prefix
- default: blsmooth
+ - id: input_h5parm
+ source: losoto_polalign/output_h5parm
+ - id: soltab
+ default: sol000/phase000
+ - id: soltabsToSub
+ default:
+ - polalign
out:
- - id: output
- run: ../steps/concatenate_files.cwl
- label: concat_logfiles_blsmooth
- 'sbg:x': 0
- 'sbg:y': 300
-requirements:
- - class: SubworkflowFeatureRequirement
- - class: ScatterFeatureRequirement
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.Residual.cwl
+ 'sbg:x': -0.012040258385241032
+ 'sbg:y': -287.7294006347656
+requirements: []
diff --git a/workflows/HBA_calibrator.cwl b/workflows/HBA_calibrator.cwl
index 835efc46..fda22fbe 100644
--- a/workflows/HBA_calibrator.cwl
+++ b/workflows/HBA_calibrator.cwl
@@ -192,10 +192,10 @@ inputs:
'sbg:x': -1000
'sbg:y': 1900
outputs:
- - id: instrument.h5
+ - id: solutions
outputSource:
- - prefactor/instrument.h5
- type: File
+ - save_solutions/log_dir
+ type: Directory
'sbg:x': 1500
'sbg:y': -200
- id: msout
@@ -304,19 +304,11 @@ steps:
- id: bandpass_freqresolution
source: bandpass_freqresolution
out:
- - id: check_Ateam_separation.png
- - id: check_Ateam_separation.log
- - id: make_sourcedb_ateam.log
+ - id: logfiles
- id: msout
- - id: logfile_prep_cal
- id: parset
- - id: find_skymodel_cal.log
- - id: make_sourcedb.log
- - id: BLsmooth.log
- - id: predict_cal.log
- - id: calib_cal.log
- - id: h5parm_collector.log
- id: instrument.h5
+ - id: inspection
run: ./prefactor_calibrator.cwl
label: prefactor_calibrator
'sbg:x': 0
@@ -326,17 +318,9 @@ steps:
- id: log_files
linkMerge: merge_flattened
source:
- - prefactor/check_Ateam_separation.log
- - prefactor/make_sourcedb_ateam.log
- - prefactor/find_skymodel_cal.log
- - prefactor/make_sourcedb.log
- - prefactor/logfile_prep_cal
- - prefactor/BLsmooth.log
- - prefactor/predict_cal.log
- - prefactor/calib_cal.log
- - prefactor/h5parm_collector.log
+ - prefactor/logfiles
- id: sub_directory_name
- default: logs
+ default: results/logs
out:
- id: log_dir
run: ./../steps/collectlog.cwl
@@ -348,15 +332,28 @@ steps:
- id: log_files
linkMerge: merge_flattened
source:
- - prefactor/check_Ateam_separation.png
+ - prefactor/inspection
- id: sub_directory_name
- default: inspection
+ default: results/inspection
out:
- id: log_dir
run: ./../steps/collectlog.cwl
label: save_inspection
'sbg:x': 1000
'sbg:y': 1200
+ - id: save_solutions
+ in:
+ - id: log_files
+ source:
+ - prefactor/instrument.h5
+ - id: sub_directory_name
+ default: results/cal_values
+ out:
+ - id: log_dir
+ run: ./../steps/collectlog.cwl
+ label: save_solutions
+ 'sbg:x': 1000
+ 'sbg:y': 1400
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
diff --git a/workflows/prefactor_calibrator.cwl b/workflows/prefactor_calibrator.cwl
index ff1b5c5e..04316e70 100644
--- a/workflows/prefactor_calibrator.cwl
+++ b/workflows/prefactor_calibrator.cwl
@@ -192,84 +192,40 @@ inputs:
'sbg:x': -1000
'sbg:y': 1900
outputs:
- - id: instrument.h5
- outputSource:
- - prep/instrument.h5
- type: File
- 'sbg:x': 1000
- 'sbg:y': -500
- - id: h5parm_collector.log
- outputSource:
- - prep/h5parm_collector.log
- type: File
- 'sbg:x': 1000
- 'sbg:y': -400
- - id: check_Ateam_separation.png
+ - id: inspection
+ linkMerge: merge_flattened
outputSource:
- - prep/check_Ateam_separation.png
- type: File
+ - prep/check_Ateam_separation.png
+ - pa/inspection
+ type: File[]
'sbg:x': 1000
- 'sbg:y': -300
- - id: check_Ateam_separation.log
+ 'sbg:y': -600
+ - id: instrument.h5
outputSource:
- - prep/check_Ateam_separation.log
+ - pa/output_h5parm
type: File
'sbg:x': 1000
- 'sbg:y': -200
- - id: make_sourcedb_ateam.log
- outputSource:
- - prep/make_sourcedb_ateam.log
- type: File?
- 'sbg:x': 1000
- 'sbg:y': -100
+ 'sbg:y': -500
- id: msout
outputSource:
- - prep/msout
+ - pa/msout
type: 'Directory[]'
'sbg:x': 1000
'sbg:y': 0
- - id: logfile_prep_cal
- outputSource:
- - prep/logfile_prep_cal
- type: File
- 'sbg:x': 1000
- 'sbg:y': 100
- id: parset
outputSource:
- prep/parset
type: 'File[]'
'sbg:x': 1000
'sbg:y': 200
- - id: find_skymodel_cal.log
- outputSource:
- - prep/find_skymodel_cal.log
- type: File
- 'sbg:x': 1000
- 'sbg:y': 300
- - id: make_sourcedb.log
+ - id: logfiles
outputSource:
- - prep/make_sourcedb.log
- type: File
- 'sbg:x': 1000
- 'sbg:y': 400
- - id: BLsmooth.log
- outputSource:
- - prep/BLsmooth.log
- type: File
- 'sbg:x': 1000
- 'sbg:y': 500
- - id: predict_cal.log
- outputSource:
- - prep/predict_cal.log
- type: File
+ - prep/logfiles
+ - pa/logfiles
+ type: 'File[]'
+ linkMerge: merge_flattened
'sbg:x': 1000
'sbg:y': 600
- - id: calib_cal.log
- outputSource:
- - prep/calib_cal.log
- type: File
- 'sbg:x': 1000
- 'sbg:y': 700
steps:
- id: prep
in:
@@ -278,8 +234,6 @@ steps:
- msin
- id: filter_baselines
source: filter_baselines
- - id: do_smooth
- source: do_smooth
- id: raw_data
source: raw_data
- id: propagatesolutions
@@ -316,28 +270,41 @@ steps:
source: overhead
- id: min_separation
source: min_separation
+ - id: do_smooth
+ source: do_smooth
- id: max_separation_arcmin
source: max_separation_arcmin
- id: A-Team_skymodel
source: A-Team_skymodel
out:
+ - id: instrument.h5
+ - id: logfiles
- id: check_Ateam_separation.png
- - id: check_Ateam_separation.log
- - id: make_sourcedb_ateam.log
- id: msout
- - id: logfile_prep_cal
- id: parset
- - id: find_skymodel_cal.log
- - id: make_sourcedb.log
- id: sourcedb
- - id: BLsmooth.log
- - id: predict_cal.log
- - id: calib_cal.log
- - id: h5parm_collector.log
- - id: instrument.h5
run: ./prefactor_calibrator/prep.cwl
label: prep
'sbg:x': 0
'sbg:y': 0
+ - id: pa
+ in:
+ - id: msin
+ source:
+ - prep/msout
+ - id: h5parm
+ source:
+ - prep/instrument.h5
+ - id: refant
+ source: refant
+ out:
+ - id: msout
+ - id: output_h5parm
+ - id: inspection
+ - id: logfiles
+ run: ./prefactor_calibrator/pa.cwl
+ label: PA
+ 'sbg:x': 500
+ 'sbg:y': 0
requirements:
- class: SubworkflowFeatureRequirement
diff --git a/workflows/prefactor_calibrator/pa.cwl b/workflows/prefactor_calibrator/pa.cwl
new file mode 100644
index 00000000..c2951b3d
--- /dev/null
+++ b/workflows/prefactor_calibrator/pa.cwl
@@ -0,0 +1,315 @@
+class: Workflow
+cwlVersion: v1.0
+id: pa
+label: PA
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - 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
+outputs:
+ - id: msout
+ outputSource:
+ - msin
+ 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_Align/output_plots
+ - losoto_plot_Pr/output_plots
+ - losoto_plot_Pr2/output_plots
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: output_h5parm
+ outputSource:
+ - write_solutions/outh5parm
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 100
+ - id: logfiles
+ outputSource:
+ - concat_logfiles_pa/output
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 1000
+ 'sbg:y': 200
+steps:
+ - id: pol_align
+ in:
+ - id: refAnt
+ default: CS001HBA0
+ source: refant
+ - id: input_h5parm
+ source: h5parm
+ out:
+ - id: output_h5parm
+ - id: logfiles
+ run: ../../subworkflow/pol_align.cwl
+ label: PolAlign
+ 'sbg:x': -500
+ 'sbg:y': 0
+ - id: losoto_plot_P3
+ in:
+ - id: input_h5parm
+ source: pol_align/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: polalign_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: pol_align/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: polalign_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: pol_align/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: polalign_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: pol_align/output_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: axesInPlot
+ default:
+ - time
+ - freq
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: true
+ - id: prefix
+ default: polalign_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_Align
+ in:
+ - id: input_h5parm
+ source: pol_align/output_h5parm
+ - id: soltab
+ default: sol000/polalign
+ - 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: polalign
+ out:
+ - id: output_plots
+ - id: logfile
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_Align
+ 'sbg:x': 0
+ 'sbg:y': 200
+ - id: losoto_plot_Pr
+ in:
+ - id: input_h5parm
+ source: pol_align/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: polalign_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: pol_align/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: polalign_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_pa
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - pol_align/logfiles
+ - losoto_plot_P3/logfile
+ - losoto_plot_Pd/logfile
+ - losoto_plot_Rot3/logfile
+ - losoto_plot_A3/logfile
+ - losoto_plot_Align/logfile
+ - losoto_plot_Pr/logfile
+ - losoto_plot_Pr2/logfile
+ - write_solutions/log
+ - id: file_prefix
+ default: losoto_PA
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_PA
+ 'sbg:x': 500
+ 'sbg:y': 500
+ - id: write_solutions
+ in:
+ - id: h5parmFiles
+ source:
+ - pol_align/output_h5parm
+ - id: outh5parmname
+ default: cal_solutions.h5
+ - id: outsolset
+ default: calibrator
+ - id: insoltab
+ default: polalign
+ - 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
+requirements:
+ - class: SubworkflowFeatureRequirement
+ - class: MultipleInputFeatureRequirement
diff --git a/workflows/prefactor_calibrator/prep.cwl b/workflows/prefactor_calibrator/prep.cwl
index 8e121862..538c2be3 100644
--- a/workflows/prefactor_calibrator/prep.cwl
+++ b/workflows/prefactor_calibrator/prep.cwl
@@ -116,82 +116,43 @@ outputs:
type: File
'sbg:x': 1000
'sbg:y': -500
- - id: h5parm_collector.log
- outputSource:
- - h5parm_collector/log
- type: File
- 'sbg:x': 1000
- 'sbg:y': -400
- id: check_Ateam_separation.png
outputSource:
- check_ateam_separation/output_imag
type: File
'sbg:x': 1000
'sbg:y': -300
- - id: check_Ateam_separation.log
- outputSource:
- - check_ateam_separation/logfile
- type: File
- 'sbg:x': 1000
- 'sbg:y': -200
- - id: make_sourcedb_ateam.log
- outputSource:
- - make_sourcedb_ateam/log
- type: File?
- 'sbg:x': 1000
- 'sbg:y': -100
- id: msout
outputSource:
- predict_calibrate/msout
type: 'Directory[]'
'sbg:x': 1000
'sbg:y': 0
- - id: logfile_prep_cal
- outputSource:
- - concat_logfiles_prep_cal/output
- type: File
- 'sbg:x': 1000
- 'sbg:y': 100
- id: parset
outputSource:
- ndppp_prep_cal/parset
type: 'File[]'
'sbg:x': 1000
'sbg:y': 200
- - id: find_skymodel_cal.log
- outputSource:
- - find_skymodel_cal/logfile
- type: File
- 'sbg:x': 1000
- 'sbg:y': 300
- - id: make_sourcedb.log
- outputSource:
- - make_sourcedb/log
- type: File
- 'sbg:x': 1000
- 'sbg:y': 400
- id: sourcedb
outputSource:
- make_sourcedb/sourcedb
type: File
'sbg:x': 1000
'sbg:y': 500
- - id: BLsmooth.log
- outputSource:
- - concat_logfiles_blsmooth/output
- type: File
- 'sbg:x': 1000
- 'sbg:y': 600
- - id: predict_cal.log
- outputSource:
- - concat_logfiles_predict/output
- type: File
- 'sbg:x': 1000
- 'sbg:y': 700
- - id: calib_cal.log
+ - id: logfiles
+ linkMerge: merge_flattened
outputSource:
- concat_logfiles_calib/output
- type: File
+ - concat_logfiles_predict/output
+ - concat_logfiles_blsmooth/output
+ - make_sourcedb/log
+ - find_skymodel_cal/logfile
+ - concat_logfiles_prep_cal/output
+ - make_sourcedb_ateam/log
+ - check_ateam_separation/logfile
+ - h5parm_collector/log
+ type: 'File[]'
'sbg:x': 1000
'sbg:y': 800
steps:
--
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