From 86c94e9402b29a3eebf1c29132c70cc37a29f48c Mon Sep 17 00:00:00 2001
From: Alexander Drabent <alex@tls-tautenburg.de>
Date: Fri, 24 Apr 2020 14:05:07 +0200
Subject: [PATCH] finish bandpass step
---
lofar-cwl/steps/H5ParmCollector.cwl | 5 +-
lofar-cwl/steps/LoSoTo.Abs.cwl | 3 +-
lofar-cwl/steps/LoSoTo.Clip.cwl | 3 +-
lofar-cwl/steps/LoSoTo.Duplicate.cwl | 6 +-
lofar-cwl/steps/LoSoTo.Faraday.cwl | 6 +-
lofar-cwl/steps/LoSoTo.Flag.cwl | 6 +-
lofar-cwl/steps/LoSoTo.FlagStation.cwl | 6 +-
lofar-cwl/steps/LoSoTo.Flagextend.cwl | 6 +-
lofar-cwl/steps/LoSoTo.Interpolate.cwl | 6 +-
lofar-cwl/steps/LoSoTo.Lofarbeam.cwl | 3 +-
lofar-cwl/steps/LoSoTo.Norm.cwl | 3 +-
lofar-cwl/steps/LoSoTo.Plot.cwl | 8 +-
lofar-cwl/steps/LoSoTo.Polalign.cwl | 6 +-
lofar-cwl/steps/LoSoTo.Replicateonaxis.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Reset.cwl | 3 +-
lofar-cwl/steps/LoSoTo.Residual.cwl | 6 +-
lofar-cwl/steps/LoSoTo.Reweight.cwl | 6 +-
lofar-cwl/steps/LoSoTo.Smooth.cwl | 1 +
lofar-cwl/steps/LoSoTo.Splitleak.cwl | 3 +-
lofar-cwl/steps/LoSoTo.Structure.cwl | 3 +-
lofar-cwl/steps/applybeam.cwl | 21 +--
lofar-cwl/steps/applycal.cwl | 4 +-
steps/check_ateam_separation.cwl | 0
steps/concatenate_files.cwl | 4 +-
steps/h5parm_pointingname.cwl | 47 ++++++
steps/transfer_solutions.cwl | 86 ++++++++++
subworkflow/apply_calibrate_bp.cwl | 8 +-
subworkflow/apply_calibrate_pa.cwl | 6 +-
workflows/HBA_calibrator.cwl | 5 +-
workflows/prefactor_calibrator.cwl | 12 +-
workflows/prefactor_calibrator/bp.cwl | 174 +++++++++++++++++++--
workflows/prefactor_calibrator/fr.cwl | 4 +-
workflows/prefactor_calibrator/pa.cwl | 4 +-
workflows/prefactor_calibrator/prep.cwl | 8 +-
34 files changed, 401 insertions(+), 73 deletions(-)
mode change 100755 => 100644 steps/check_ateam_separation.cwl
create mode 100644 steps/h5parm_pointingname.cwl
create mode 100644 steps/transfer_solutions.cwl
diff --git a/lofar-cwl/steps/H5ParmCollector.cwl b/lofar-cwl/steps/H5ParmCollector.cwl
index 31b1b945..5b6a2dcd 100755
--- a/lofar-cwl/steps/H5ParmCollector.cwl
+++ b/lofar-cwl/steps/H5ParmCollector.cwl
@@ -76,13 +76,14 @@ outputs:
outputBinding:
glob: $(inputs.outh5parmname)
- id: log
- type: File
+ type: File[]
outputBinding:
- glob: $(inputs.outh5parmname)-parm_collector_output.log
+ glob: '$(inputs.outh5parmname)-parm_collector_output*.log'
label: H5parm_collector
hints:
- class: DockerRequirement
dockerPull: 'lofareosc/prefactor:HBAcalibrator'
stdout: $(inputs.outh5parmname)-parm_collector_output.log
+stderr: $(inputs.outh5parmname)-parm_collector_output_err.log
requirements:
- class: InlineJavascriptRequirement
\ No newline at end of file
diff --git a/lofar-cwl/steps/LoSoTo.Abs.cwl b/lofar-cwl/steps/LoSoTo.Abs.cwl
index 69ec253b..4ce89e2b 100755
--- a/lofar-cwl/steps/LoSoTo.Abs.cwl
+++ b/lofar-cwl/steps/LoSoTo.Abs.cwl
@@ -25,12 +25,13 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
diff --git a/lofar-cwl/steps/LoSoTo.Clip.cwl b/lofar-cwl/steps/LoSoTo.Clip.cwl
index 867699da..d9cda245 100644
--- a/lofar-cwl/steps/LoSoTo.Clip.cwl
+++ b/lofar-cwl/steps/LoSoTo.Clip.cwl
@@ -26,12 +26,13 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
diff --git a/lofar-cwl/steps/LoSoTo.Duplicate.cwl b/lofar-cwl/steps/LoSoTo.Duplicate.cwl
index 7fe56b03..55208333 100644
--- a/lofar-cwl/steps/LoSoTo.Duplicate.cwl
+++ b/lofar-cwl/steps/LoSoTo.Duplicate.cwl
@@ -25,6 +25,7 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
@@ -49,11 +50,12 @@ outputs:
outputBinding:
glob: $(inputs.input_h5parm.basename)
- id: log
- 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
$namespaces:
lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
$schema:
diff --git a/lofar-cwl/steps/LoSoTo.Faraday.cwl b/lofar-cwl/steps/LoSoTo.Faraday.cwl
index 85d949b6..c015e412 100644
--- a/lofar-cwl/steps/LoSoTo.Faraday.cwl
+++ b/lofar-cwl/steps/LoSoTo.Faraday.cwl
@@ -27,6 +27,7 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
@@ -61,11 +62,12 @@ outputs:
outputBinding:
glob: $(inputs.input_h5parm.basename)
- id: log
- 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/lofar-cwl/steps/LoSoTo.Flag.cwl b/lofar-cwl/steps/LoSoTo.Flag.cwl
index 7e058ad1..302bc825 100644
--- a/lofar-cwl/steps/LoSoTo.Flag.cwl
+++ b/lofar-cwl/steps/LoSoTo.Flag.cwl
@@ -27,6 +27,7 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
@@ -102,10 +103,11 @@ outputs:
outputBinding:
glob: $(inputs.input_h5parm.basename)
- id: log
- 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/lofar-cwl/steps/LoSoTo.FlagStation.cwl b/lofar-cwl/steps/LoSoTo.FlagStation.cwl
index 42ee7fbe..be98dbb4 100644
--- a/lofar-cwl/steps/LoSoTo.FlagStation.cwl
+++ b/lofar-cwl/steps/LoSoTo.FlagStation.cwl
@@ -26,6 +26,7 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
@@ -101,10 +102,11 @@ outputs:
outputBinding:
glob: $(inputs.input_h5parm.basename)
- id: log
- 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/lofar-cwl/steps/LoSoTo.Flagextend.cwl b/lofar-cwl/steps/LoSoTo.Flagextend.cwl
index 20d48f24..c64fae49 100644
--- a/lofar-cwl/steps/LoSoTo.Flagextend.cwl
+++ b/lofar-cwl/steps/LoSoTo.Flagextend.cwl
@@ -28,6 +28,7 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
@@ -68,10 +69,11 @@ outputs:
outputBinding:
glob: $(inputs.input_h5parm.basename)
- id: log
- 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/lofar-cwl/steps/LoSoTo.Interpolate.cwl b/lofar-cwl/steps/LoSoTo.Interpolate.cwl
index 15d5f32e..f2fee5dc 100644
--- a/lofar-cwl/steps/LoSoTo.Interpolate.cwl
+++ b/lofar-cwl/steps/LoSoTo.Interpolate.cwl
@@ -29,6 +29,7 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
@@ -79,10 +80,11 @@ 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/lofar-cwl/steps/LoSoTo.Lofarbeam.cwl b/lofar-cwl/steps/LoSoTo.Lofarbeam.cwl
index ce421868..ffdc5dcc 100644
--- a/lofar-cwl/steps/LoSoTo.Lofarbeam.cwl
+++ b/lofar-cwl/steps/LoSoTo.Lofarbeam.cwl
@@ -25,12 +25,13 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
diff --git a/lofar-cwl/steps/LoSoTo.Norm.cwl b/lofar-cwl/steps/LoSoTo.Norm.cwl
index e9cadbd6..f193e64c 100644
--- a/lofar-cwl/steps/LoSoTo.Norm.cwl
+++ b/lofar-cwl/steps/LoSoTo.Norm.cwl
@@ -26,12 +26,13 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
diff --git a/lofar-cwl/steps/LoSoTo.Plot.cwl b/lofar-cwl/steps/LoSoTo.Plot.cwl
index a9e82d36..c8533dbe 100644
--- a/lofar-cwl/steps/LoSoTo.Plot.cwl
+++ b/lofar-cwl/steps/LoSoTo.Plot.cwl
@@ -24,6 +24,7 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
@@ -130,11 +131,16 @@ outputs:
outputBinding:
glob: "$(inputs.prefix)*.png"
- id: logfile
+ type: File[]
+ outputBinding:
+ glob: '$(inputs.input_h5parm.basename)-losoto*.log'
+ - id: parset
type: File
outputBinding:
- glob: $(inputs.input_h5parm.basename)-losoto.log
+ glob: parset.config
stdout: $(inputs.input_h5parm.basename)-losoto.log
+stderr: $(inputs.input_h5parm.basename)-losoto_err.log
$namespaces:
diff --git a/lofar-cwl/steps/LoSoTo.Polalign.cwl b/lofar-cwl/steps/LoSoTo.Polalign.cwl
index 0c53cba5..fa4bfe34 100755
--- a/lofar-cwl/steps/LoSoTo.Polalign.cwl
+++ b/lofar-cwl/steps/LoSoTo.Polalign.cwl
@@ -43,6 +43,7 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
@@ -89,8 +90,9 @@ outputs:
outputBinding:
glob: $(inputs.input_h5parm.basename)
- id: log
- 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
diff --git a/lofar-cwl/steps/LoSoTo.Replicateonaxis.cwl b/lofar-cwl/steps/LoSoTo.Replicateonaxis.cwl
index f7512ea6..3f953a16 100644
--- a/lofar-cwl/steps/LoSoTo.Replicateonaxis.cwl
+++ b/lofar-cwl/steps/LoSoTo.Replicateonaxis.cwl
@@ -42,7 +42,7 @@ arguments:
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
diff --git a/lofar-cwl/steps/LoSoTo.Reset.cwl b/lofar-cwl/steps/LoSoTo.Reset.cwl
index 887b0b81..ea6e06cb 100644
--- a/lofar-cwl/steps/LoSoTo.Reset.cwl
+++ b/lofar-cwl/steps/LoSoTo.Reset.cwl
@@ -24,12 +24,13 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
diff --git a/lofar-cwl/steps/LoSoTo.Residual.cwl b/lofar-cwl/steps/LoSoTo.Residual.cwl
index 7a8b8ba5..6642f7ec 100644
--- a/lofar-cwl/steps/LoSoTo.Residual.cwl
+++ b/lofar-cwl/steps/LoSoTo.Residual.cwl
@@ -24,6 +24,7 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
@@ -53,11 +54,12 @@ outputs:
outputBinding:
glob: $(inputs.input_h5parm.basename)
- id: log
- 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
$namespaces:
lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
diff --git a/lofar-cwl/steps/LoSoTo.Reweight.cwl b/lofar-cwl/steps/LoSoTo.Reweight.cwl
index 054add11..e8f02761 100644
--- a/lofar-cwl/steps/LoSoTo.Reweight.cwl
+++ b/lofar-cwl/steps/LoSoTo.Reweight.cwl
@@ -27,6 +27,7 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
@@ -78,10 +79,11 @@ outputs:
outputBinding:
glob: $(inputs.input_h5parm.basename)
- id: log
- 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/lofar-cwl/steps/LoSoTo.Smooth.cwl b/lofar-cwl/steps/LoSoTo.Smooth.cwl
index d1b095a8..9117c041 100644
--- a/lofar-cwl/steps/LoSoTo.Smooth.cwl
+++ b/lofar-cwl/steps/LoSoTo.Smooth.cwl
@@ -30,6 +30,7 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
diff --git a/lofar-cwl/steps/LoSoTo.Splitleak.cwl b/lofar-cwl/steps/LoSoTo.Splitleak.cwl
index 34059375..c29e1da6 100644
--- a/lofar-cwl/steps/LoSoTo.Splitleak.cwl
+++ b/lofar-cwl/steps/LoSoTo.Splitleak.cwl
@@ -24,12 +24,13 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
diff --git a/lofar-cwl/steps/LoSoTo.Structure.cwl b/lofar-cwl/steps/LoSoTo.Structure.cwl
index cdf29c2f..639a7e7d 100644
--- a/lofar-cwl/steps/LoSoTo.Structure.cwl
+++ b/lofar-cwl/steps/LoSoTo.Structure.cwl
@@ -27,12 +27,13 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
diff --git a/lofar-cwl/steps/applybeam.cwl b/lofar-cwl/steps/applybeam.cwl
index 6c7baccf..81559884 100644
--- a/lofar-cwl/steps/applybeam.cwl
+++ b/lofar-cwl/steps/applybeam.cwl
@@ -45,29 +45,30 @@ inputs:
inputBinding:
prefix: msout.storagemanager=
- id: updateweights
- type: boolean?
+ type: string?
inputBinding:
position: 0
- prefix: -applybeam.updateweights=
+ prefix: applybeam.updateweights=
separate: false
- - id: beammode
+ - id: usechannelfreq
type: string?
inputBinding:
position: 0
- prefix: -applybeam.beammode=
+ prefix: applybeam.usechannelfreq=
separate: false
- - id: usechannelfreq
- type: boolean?
+ - id: invert
+ type: string?
inputBinding:
position: 0
- prefix: -applybeam.usechannelfreq=
+ prefix: applybeam.invert=
separate: false
- - id: invert
- type: boolean?
+ - id: beammode
+ type: string?
inputBinding:
position: 0
- prefix: -applybeam.invert=
+ prefix: applybeam.beammode=
separate: false
+
outputs:
- id: msout
doc: Output Measurement Set
diff --git a/lofar-cwl/steps/applycal.cwl b/lofar-cwl/steps/applycal.cwl
index 49b7af68..03f258d0 100644
--- a/lofar-cwl/steps/applycal.cwl
+++ b/lofar-cwl/steps/applycal.cwl
@@ -54,10 +54,10 @@ inputs:
inputBinding:
prefix: msout.storagemanager=
- id: updateweights
- type: boolean?
+ type: string?
inputBinding:
position: 0
- prefix: -applycal.updateweights=
+ prefix: applycal.updateweights=
separate: false
outputs:
- id: msout
diff --git a/steps/check_ateam_separation.cwl b/steps/check_ateam_separation.cwl
old mode 100755
new mode 100644
diff --git a/steps/concatenate_files.cwl b/steps/concatenate_files.cwl
index eaae4ab1..ba9c5f64 100644
--- a/steps/concatenate_files.cwl
+++ b/steps/concatenate_files.cwl
@@ -2,7 +2,7 @@ class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
-id: bulk_rename
+id: concatfiles
baseCommand:
- bash
- bulk_rename.sh
@@ -21,7 +21,7 @@ outputs:
type: File
outputBinding:
glob: "$(inputs.file_prefix).$(inputs.file_suffix)"
-label: bulk_rename
+label: concatfiles
requirements:
- class: InitialWorkDirRequirement
listing:
diff --git a/steps/h5parm_pointingname.cwl b/steps/h5parm_pointingname.cwl
new file mode 100644
index 00000000..21a1b263
--- /dev/null
+++ b/steps/h5parm_pointingname.cwl
@@ -0,0 +1,47 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: h5parm_pointingname
+baseCommand:
+ - python3
+ - /usr/local/bin/h5parm_pointingname.py
+inputs:
+ - id: h5parm
+ type: File
+ inputBinding:
+ position: 1
+ doc: H5parm whose pointing direction should be corrected the solutions should be transferred.
+ - id: solsetName
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--solsetName'
+ doc: Name of the input h5parm solution set
+ - id: pointing
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--pointing'
+ doc: Name of the output h5parm solution set
+outputs:
+ - id: outh5parm
+ type: File
+ outputBinding:
+ glob: $(inputs.h5parm.basename)
+ - id: log
+ type: File[]
+ outputBinding:
+ glob: 'h5parm_name*.log'
+stdout: h5parm_name.log
+stderr: h5parm_name_err.log
+label: h5parm_pointingname
+hints:
+ - class: DockerRequirement
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.h5parm)
+ writable: true
\ No newline at end of file
diff --git a/steps/transfer_solutions.cwl b/steps/transfer_solutions.cwl
new file mode 100644
index 00000000..995a8d47
--- /dev/null
+++ b/steps/transfer_solutions.cwl
@@ -0,0 +1,86 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: transfer_solutions
+baseCommand:
+ - python3
+ - /usr/local/bin/transfer_solutions.py
+inputs:
+ - default: output.h5
+ id: h5parm
+ type: File
+ inputBinding:
+ position: 1
+ doc: H5parm to which the solutions should be transferred.
+ - id: refh5parm
+ type:
+ - File?
+ - string?
+ default: '/data/solutions/3C48.h5'
+ inputBinding:
+ position: 0
+ prefix: '--refh5parm'
+ doc: Name of the h5parm from which the solutions should be transferred.
+ - id: insolset
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--insolset'
+ doc: Name of the input h5parm solution set
+ - id: outsolset
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--outsolset'
+ doc: Name of the output h5parm solution set
+ - id: insoltab
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--insoltab'
+ doc: Name of the input h5parm solution set
+ - id: outsoltab
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--outsoltab'
+ doc: Name of the output h5parm solution set
+ - id: antenna
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--antenna'
+ doc: Regular expression of antenna solutions to be transferred
+ - id: parset
+ type: File?
+ inputBinding:
+ position: 0
+ prefix: '--parset'
+ doc: Parset for plotting diagnostic plots after transfer with LoSoTo
+outputs:
+ - id: outh5parm
+ type: File
+ outputBinding:
+ glob: $(inputs.h5parm.basename)
+ - id: log
+ type: File[]
+ outputBinding:
+ glob: 'transfer_solutions*.log'
+ - id: plots
+ type: File[]
+ outputBinding:
+ glob: "*.png"
+
+stdout: transfer_solutions.log
+stderr: transfer_solutions_err.log
+label: transfer_solutions
+hints:
+ - class: DockerRequirement
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.h5parm)
+ writable: true
diff --git a/subworkflow/apply_calibrate_bp.cwl b/subworkflow/apply_calibrate_bp.cwl
index 3d08649c..0f21d792 100644
--- a/subworkflow/apply_calibrate_bp.cwl
+++ b/subworkflow/apply_calibrate_bp.cwl
@@ -95,7 +95,7 @@ steps:
- id: msin_datacolumn
default: CORRECTED_DATA
- id: updateweights
- default: true
+ default: 'True'
- id: parmdb
source: input_h5parm
- id: msout_datacolumn
@@ -116,13 +116,13 @@ steps:
- id: msout_datacolumn
default: CORRECTED_DATA
- id: updateweights
- default: true
+ default: 'true'
- id: invert
- default: true
+ default: 'true'
- id: beammode
default: element
- id: usechannelfreq
- default: false
+ default: 'false'
- id: msin
source: applyBP/msout
- id: type
diff --git a/subworkflow/apply_calibrate_pa.cwl b/subworkflow/apply_calibrate_pa.cwl
index f13f9282..02c9d1e5 100644
--- a/subworkflow/apply_calibrate_pa.cwl
+++ b/subworkflow/apply_calibrate_pa.cwl
@@ -89,13 +89,13 @@ steps:
- id: msout_datacolumn
default: CORRECTED_DATA
- id: updateweights
- default: true
+ default: 'true'
- id: invert
- default: true
+ default: 'true'
- id: beammode
default: element
- id: usechannelfreq
- default: false
+ default: 'false'
- id: msin
source: applyPA/msout
- id: type
diff --git a/workflows/HBA_calibrator.cwl b/workflows/HBA_calibrator.cwl
index cd03d8c1..ad68fdbd 100644
--- a/workflows/HBA_calibrator.cwl
+++ b/workflows/HBA_calibrator.cwl
@@ -45,7 +45,7 @@ inputs:
'sbg:x': -1000
'sbg:y': -1000
- id: ampRange
- type: 'int[]?'
+ type: 'float[]?'
default:
- 0
- 0
@@ -77,8 +77,7 @@ inputs:
'sbg:x': -1000
'sbg:y': -400
- id: solutions2transfer
- type: string?
- default: /data/solutions/3C48.h5
+ type: File?
'sbg:x': -1000
'sbg:y': -300
- id: antennas2transfer
diff --git a/workflows/prefactor_calibrator.cwl b/workflows/prefactor_calibrator.cwl
index 22c1943c..18d50c14 100644
--- a/workflows/prefactor_calibrator.cwl
+++ b/workflows/prefactor_calibrator.cwl
@@ -45,7 +45,7 @@ inputs:
'sbg:x': -1000
'sbg:y': -1000
- id: ampRange
- type: 'int[]?'
+ type: 'float[]?'
default:
- 0
- 0
@@ -77,8 +77,7 @@ inputs:
'sbg:x': -1000
'sbg:y': -400
- id: solutions2transfer
- type: string?
- default: /data/solutions/3C48.h5
+ type: File?
'sbg:x': -1000
'sbg:y': -300
- id: antennas2transfer
@@ -289,6 +288,7 @@ steps:
- id: check_Ateam_separation.png
- id: msout
- id: parset
+ - id: calibrator_name
run: ./prefactor_calibrator/prep.cwl
label: prep
'sbg:x': 0
@@ -386,6 +386,12 @@ steps:
source: do_smooth
- id: insolutions
source: fr/outsolutions
+ - id: solutions2transfer
+ source: solutions2transfer
+ - id: antennas2transfer
+ source: antennas2transfer
+ - id: calibrator_name
+ source: prep/calibrator_name
out:
- id: msout
- id: outsolutions
diff --git a/workflows/prefactor_calibrator/bp.cwl b/workflows/prefactor_calibrator/bp.cwl
index 7a7d1bc7..a5019e8f 100644
--- a/workflows/prefactor_calibrator/bp.cwl
+++ b/workflows/prefactor_calibrator/bp.cwl
@@ -5,6 +5,10 @@ label: BP
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
+ - id: calibrator_name
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': -700
- id: ampRange
type: 'float[]?'
'sbg:x': -1000
@@ -43,8 +47,12 @@ inputs:
type: File
'sbg:x': -1000
'sbg:y': 200
+ - id: solutions2transfer
+ type: File?
+ 'sbg:x': -1000
+ 'sbg:y': 300
- id: inh5parm_logfile
- type: File
+ type: File[]
'sbg:x': -1000
'sbg:y': 400
- id: do_smooth
@@ -56,6 +64,10 @@ inputs:
type: File
'sbg:x': -1000
'sbg:y': 600
+ - id: antennas2transfer
+ type: string?
+ 'sbg:x': -1000
+ 'sbg:y': 700
outputs:
- id: outh5parm
outputSource:
@@ -76,13 +88,14 @@ outputs:
- losoto_plot_B1/output_plots
- losoto_plot_B2/output_plots
- losoto_plot_B3/output_plots
- type: 'File[]'
+ - transfer_solutions/plots
+ type: 'File[]?'
linkMerge: merge_flattened
'sbg:x': 1000
'sbg:y': 0
- id: outsolutions
outputSource:
- - write_solutions/outh5parm
+ - transfer_solutions/outh5parm
type: File
'sbg:x': 1000
'sbg:y': 100
@@ -101,7 +114,7 @@ outputs:
- id: outh5parm_logfile
outputSource:
- h5parm_collector/log
- type: File
+ type: File[]
'sbg:x': 1000
'sbg:y': 300
steps:
@@ -147,7 +160,7 @@ steps:
- id: logfile
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_A1
- 'sbg:x': 0
+ 'sbg:x': -200
'sbg:y': -200
- id: losoto_plot_A2
in:
@@ -170,7 +183,7 @@ steps:
- id: logfile
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_A2
- 'sbg:x': 0
+ 'sbg:x': -200
'sbg:y': -100
- id: losoto_plot_B1
in:
@@ -193,7 +206,7 @@ steps:
- id: logfile
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_B1
- 'sbg:x': 0
+ 'sbg:x': -200
'sbg:y': 0
- id: losoto_plot_B2
in:
@@ -222,7 +235,7 @@ steps:
- id: logfile
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_B2
- 'sbg:x': 0
+ 'sbg:x': -200
'sbg:y': 100
- id: losoto_plot_B3
in:
@@ -249,8 +262,84 @@ steps:
- id: logfile
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_B3
- 'sbg:x': 0
+ 'sbg:x': -200
'sbg:y': 200
+ - id: losoto_plot_B1_trans
+ in:
+ - id: input_h5parm
+ source: bandpass/output_h5parm
+ - id: soltab
+ default: sol000/bandpass
+ - id: axesInPlot
+ default:
+ - time
+ - freq
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: true
+ - id: prefix
+ default: bandpass_transfer_
+ out:
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_B1_trans
+ 'sbg:x': -200
+ 'sbg:y': 300
+ - id: losoto_plot_B2_trans
+ in:
+ - id: input_h5parm
+ source: bandpass/output_h5parm
+ - id: soltab
+ default: sol000/bandpass
+ - id: axesInPlot
+ default:
+ - freq
+ - id: axisInTable
+ default: ant
+ - id: axisInCol
+ default: pol
+ - id: plotFlag
+ default: true
+ - id: time.minmaxstep
+ default:
+ - 0
+ - 1e20
+ - 500000
+ - id: prefix
+ default: bandpass_transfer_
+ out:
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_B2_trans
+ 'sbg:x': -200
+ 'sbg:y': 400
+ - id: losoto_plot_B3_trans
+ in:
+ - id: input_h5parm
+ source: bandpass/output_h5parm
+ - id: soltab
+ default: sol000/bandpass
+ - id: axesInPlot
+ default:
+ - freq
+ - id: axisInCol
+ default: ant
+ - id: plotFlag
+ default: true
+ - id: time.minmaxstep
+ default:
+ - 0
+ - 1e20
+ - 500000
+ - id: prefix
+ default: bbandpass_transfer_
+ out:
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_B3_trans
+ 'sbg:x': -200
+ 'sbg:y': 500
- id: concat_logfiles_bp
in:
- id: file_list
@@ -264,6 +353,8 @@ steps:
- losoto_plot_B2/logfile
- losoto_plot_B3/logfile
- write_solutions/log
+ - h5parm_pointingname/log
+ - transfer_solutions/log
- id: file_prefix
default: losoto_bandpass
out:
@@ -293,8 +384,8 @@ steps:
- id: log
run: ../../steps/h5parmcat.cwl
label: write_solutions
- 'sbg:x': 0
- 'sbg:y': 500
+ 'sbg:x': -200
+ 'sbg:y': 700
- id: apply_calibrate_bp
in:
- id: msin
@@ -306,7 +397,7 @@ steps:
- id: propagatesolutions
source: propagatesolutions
- id: input_h5parm
- source: write_solutions/outh5parm
+ source: transfer_solutions/outh5parm
out:
- id: msout
- id: BLsmooth.log
@@ -404,6 +495,65 @@ steps:
label: H5parm_collector
'sbg:x': 750
'sbg:y': -300
+ - 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': 300
+ - id: transfer_solutions
+ in:
+ - id: h5parm
+ source: h5parm_pointingname/outh5parm
+ - id: refh5parm
+ source: solutions2transfer
+ - id: insolset
+ default: calibrator
+ - id: outsolset
+ default: calibrator
+ - id: insoltab
+ default: bandpass
+ - id: outsoltab
+ default: bandpass
+ - id: antenna
+ source: antennas2transfer
+ - id: parset
+ source: concat_parset/output
+ out:
+ - id: outh5parm
+ - id: log
+ - id: plots
+ run: ../../steps/transfer_solutions.cwl
+ label: transfer_solutions
+ 'sbg:x': 200
+ 'sbg:y': 300
+ - id: concat_parset
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - losoto_plot_B1_trans/parset
+ - losoto_plot_B2_trans/parset
+ - losoto_plot_B3_trans/parset
+ - id: file_prefix
+ default: losoto
+ - id: file_suffix
+ default: parset
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_parset
+ 'sbg:x': 0
+ 'sbg:y': 500
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
diff --git a/workflows/prefactor_calibrator/fr.cwl b/workflows/prefactor_calibrator/fr.cwl
index 6c8a01c7..b907a043 100644
--- a/workflows/prefactor_calibrator/fr.cwl
+++ b/workflows/prefactor_calibrator/fr.cwl
@@ -28,7 +28,7 @@ inputs:
'sbg:x': -1000
'sbg:y': 100
- id: inh5parm_logfile
- type: File
+ type: File[]
'sbg:x': -1000
'sbg:y': 200
- id: do_smooth
@@ -85,7 +85,7 @@ outputs:
- id: outh5parm_logfile
outputSource:
- h5parm_collector/log
- type: File
+ type: File[]
'sbg:x': 1000
'sbg:y': 300
steps:
diff --git a/workflows/prefactor_calibrator/pa.cwl b/workflows/prefactor_calibrator/pa.cwl
index 7ff28e55..6a6e66cd 100644
--- a/workflows/prefactor_calibrator/pa.cwl
+++ b/workflows/prefactor_calibrator/pa.cwl
@@ -28,7 +28,7 @@ inputs:
'sbg:x': -1000
'sbg:y': 100
- id: inh5parm_logfile
- type: File
+ type: File[]
'sbg:x': -1000
'sbg:y': 200
- id: do_smooth
@@ -82,7 +82,7 @@ outputs:
- id: outh5parm_logfile
outputSource:
- h5parm_collector/log
- type: File
+ type: File[]
'sbg:x': 1000
'sbg:y': 300
steps:
diff --git a/workflows/prefactor_calibrator/prep.cwl b/workflows/prefactor_calibrator/prep.cwl
index 950f70d6..313b1474 100644
--- a/workflows/prefactor_calibrator/prep.cwl
+++ b/workflows/prefactor_calibrator/prep.cwl
@@ -134,10 +134,16 @@ outputs:
type: 'File[]'
'sbg:x': 1000
'sbg:y': 200
+ - id: calibrator_name
+ outputSource:
+ - find_skymodel_cal/model_name
+ type: string
+ 'sbg:x': 1000
+ 'sbg:y': 400
- id: outh5parm_logfile
outputSource:
- h5parm_collector/log
- type: File
+ type: File[]
'sbg:x': 1000
'sbg:y': 650
- id: logfiles
--
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