diff --git a/Docker/Dockerfile b/Docker/Dockerfile
index 1c67fe4191987e7e13a880192093711613926bf8..005ac10fc653f5891eb96b475f29a38172ebbd11 100644
--- a/Docker/Dockerfile
+++ b/Docker/Dockerfile
@@ -1,13 +1,14 @@
FROM lofareosc/lofar-pipeline:latest
USER root
+
+RUN apt update && apt install -y vim wget casacore-tools && rm -rf /var/cache/apt
+RUN pip3 install --upgrade pip && pip3 install --upgrade numpy scipy
COPY prefactor/scripts/* /opt/lofar/scripts/
COPY prefactor/skymodels/* /data/skymodels/
COPY prefactor/rfistrategies/* /data/rfistrategies/
-COPY prefactor/solutions/ /data/solutions/*
-RUN apt update && apt install -y vim
-RUN pip3 install --upgrade pip && pip3 install --upgrade numpy scipy
-RUN ln -sf /opt/lofar/scripts/* /usr/local/bin/
+COPY prefactor/solutions/* /data/solutions/
+RUN ln -sf /opt/lofar/scripts/* /usr/local/bin/
RUN chmod +rx /usr/local/bin/*
ENV PYTHONPATH="/opt/lofar/scripts:${PYTHONPATH}"
ENTRYPOINT ["/home/lofaruser/.entrypoint"]
diff --git a/Docker/build_docker.sh b/Docker/build_docker.sh
index 58f6f1ae776d7c828c871fee958d87bb7cde738a..4e2638aa04f839a7e81c5fdfbe2374148f38f6f5 100755
--- a/Docker/build_docker.sh
+++ b/Docker/build_docker.sh
@@ -17,11 +17,9 @@ Prefactor_TAG=production
# FETCHES Prefactor
git_clone_or_pull https://github.com/lofar-astron/prefactor.git ${Prefactor_TAG} prefactor
-
SCRIPT_PATH=$(realpath ${BASH_SOURCE[0]})
DOCKER_PATH=$(dirname ${SCRIPT_PATH})
docker build ${DOCKER_PATH} -t lofareosc/prefactor
-
docker build ${DOCKER_PATH} -f ${DOCKER_PATH}/Dockerfile_ci -t lofareosc/prefactor-ci
diff --git a/lofar-cwl/steps/AOFlagger.cwl b/lofar-cwl/steps/AOFlagger.cwl
index b2e3eff72e50058b45bb05ee8f39fe290112cd8c..eac08767ec755c8c97fc141e931977f25cdaa72b 100644
--- a/lofar-cwl/steps/AOFlagger.cwl
+++ b/lofar-cwl/steps/AOFlagger.cwl
@@ -13,7 +13,7 @@ requirements:
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
baseCommand:
- aoflagger
diff --git a/lofar-cwl/steps/Ateamclipper.cwl b/lofar-cwl/steps/Ateamclipper.cwl
new file mode 100755
index 0000000000000000000000000000000000000000..0276008ef13c5626bf3edadb912c896eb9ed603e
--- /dev/null
+++ b/lofar-cwl/steps/Ateamclipper.cwl
@@ -0,0 +1,41 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: check_ateam_separation
+baseCommand:
+ - python3
+ - /usr/local/bin/Ateamclipper.py
+inputs:
+ - id: msin
+ type:
+ - Directory
+ - type: array
+ items: Directory
+ inputBinding:
+ position: 0
+ doc: Input measurement set
+outputs:
+ - id: msout
+ doc: Output MS
+ type: Directory
+ outputBinding:
+ glob: $(inputs.msin.basename)
+ - id: logfile
+ type: 'File[]'
+ outputBinding:
+ glob: Ateamclipper.log
+ - id: output
+ type: File
+ outputBinding:
+ glob: Ateamclipper.txt
+label: Ateamclipper
+hints:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+ - class: InlineJavascriptRequirement
+stdout: Ateamclipper.log
diff --git a/lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl b/lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
index 04e013599b67f0fa18b22afd81f889b0fcc888db..2850b977dcfc984b3bebf38f19d35166707e0b7d 100755
--- a/lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
@@ -14,7 +14,7 @@ inputs:
default: applycal
- id: parmdb
- type: string
+ type: File
doc: Path of parmdb in which the parameters are stored. This can also be an H5Parm file, in that case the filename has to end in '.h5'
- id: solset
type: string?
@@ -36,6 +36,10 @@ inputs:
- scalaramplitude
- rotationmeasure
- fulljones
+ - polalign
+ - bandpass
+ - RMextract
+ - phaseOrig
doc: |
Type of correction to perform, can be one of 'gain', 'tec', 'clock',
'(common)rotationangle' / 'rotation', '(common)scalarphase',
@@ -88,8 +92,6 @@ steps:
in:
- id: step_type
default: 'applycal'
- - id: output_files
- default: ["parmdb"]
- id: step_id
source: step_name
- id: steps
diff --git a/lofar-cwl/steps/DP3.AveragerStepGenerator.cwl b/lofar-cwl/steps/DP3.AveragerStepGenerator.cwl
index d5424919111a6c38f65053bfec5f2e299a98c076..47861182c3c60b1d24f5189334dabb7bb36f0e4d 100755
--- a/lofar-cwl/steps/DP3.AveragerStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.AveragerStepGenerator.cwl
@@ -41,7 +41,7 @@ inputs:
zero, it overrides <step>.timestep
default: 0
- id: freqresolution
- type: float
+ type: string
doc: >-
Target frequency resolution, in Hz (or append "MHz" or "kHz" to specify it
in those units). If this is given, and bigger than zero, it overrides
diff --git a/lofar-cwl/steps/DP3.Execute.cwl b/lofar-cwl/steps/DP3.Execute.cwl
index e1f3bbfd445ec81cfb820afd4fc8a52800d402be..a18021373b04553b9cde5e84ca8ab531ac14854a 100644
--- a/lofar-cwl/steps/DP3.Execute.cwl
+++ b/lofar-cwl/steps/DP3.Execute.cwl
@@ -41,6 +41,18 @@ outputs:
type: Directory
'sbg:x': 224.60113525390625
'sbg:y': 130
+ - id: logfile
+ outputSource:
+ - dppp/logfile
+ type: 'File[]'
+ 'sbg:x': 185.1875
+ 'sbg:y': 334.5
+ - id: parset
+ outputSource:
+ - generic_step/parset
+ type: File
+ 'sbg:x': 11.1875
+ 'sbg:y': -299.5
steps:
- id: generic_step
in:
diff --git a/lofar-cwl/steps/DP3.FilterStepGenerator.cwl b/lofar-cwl/steps/DP3.FilterStepGenerator.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..0a582b27c0d351d3b8a2f1fa2a2805094dc94ad3
--- /dev/null
+++ b/lofar-cwl/steps/DP3.FilterStepGenerator.cwl
@@ -0,0 +1,50 @@
+#!/usr/bin/env cwl-runner
+
+class: Workflow
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: dp3-filter-step-generator
+
+inputs:
+ - id: steps
+ type: Any[]?
+ default: []
+ - id: step_name
+ type: string
+ doc: unique name for the step
+ default: filter
+ - id: baseline
+ type: string
+ doc: baseline to keeps
+ - id: remove
+ type: boolean
+ doc: Remove or flag
+outputs:
+- id: augmented_steps
+ outputSource:
+ - DP3_GenericStep/augmented_steps
+ type: Any[]
+
+steps:
+ - id: DP3_GenericStep
+ in:
+ - id: steps
+ source: steps
+ - id: parameters
+ valueFrom: $(inputs)
+ - id: step_id
+ source: step_name
+ - id: step_type
+ default: 'filter'
+ - id: baseline
+ source: baseline
+ - id: remove
+ source: remove
+ out:
+ - augmented_steps
+ run: ../steps/DP3.GenericStep.cwl
+requirements:
+ - class: StepInputExpressionRequirement
+ - class: InlineJavascriptRequirement
+ - class: MultipleInputFeatureRequirement
\ No newline at end of file
diff --git a/lofar-cwl/steps/DP3.GenericStep.cwl b/lofar-cwl/steps/DP3.GenericStep.cwl
index 38829da42ed0deaac51bcf92c7c105e9139d4108..3c1a3031ced711121601e381e73ca08303a07a6f 100755
--- a/lofar-cwl/steps/DP3.GenericStep.cwl
+++ b/lofar-cwl/steps/DP3.GenericStep.cwl
@@ -39,7 +39,7 @@ expression: |-
delete inputs.parameters.steps;
delete inputs.parameters.parameters;
delete inputs.parameters.steps;
-
+ delete inputs.parameters.output_files;
var new_step = {'step_type': step_type,
'step_id': step_id,
diff --git a/lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl b/lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
index 03f6c11d6f16db4d72a38666e4a294a2f568fb28..64cd85154761c971cb2e86655fbcfe4355a19824 100755
--- a/lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
@@ -133,39 +133,31 @@ inputs:
31*nchan/32..nchan-1] to flag the first and last 2 or 8 channels
(depending on 64 or 256 channels in the observation).
- id: amplmin
- default: -1e+30
- type: float
+ type: float?
doc: >-
Correlation data with amplitude < amplmin will match. It can be given per
correlation. For example, amplmin=[100,,,100] matches data points with XX
or YY amplitude < 100. The non-specified amplitudes get the default value.
- id: amplmax
- default: 1e+30
- type: float
+ type: float?
doc: Correlation data with amplitude > amplmax will match.
- id: phasemin
- default: -1e+30
- type: float
+ type: float?
doc: Correlation data with phase < phasemin (in radians) will match.
- id: phasemax
- default: 1e+30
- type: float
+ type: float?
doc: Correlation data with phase > phasemax (in radians) will match.
- id: realmin
- default: -1e+30
- type: float
+ type: float?
doc: Correlation data with real complex part < realmin will match.
- id: realmax
- default: 1e+30
- type: float
+ type: float?
doc: Correlation data with real complex part > realmax will match.
- id: imagmin
- default: -1e+30
- type: float
+ type: float?
doc: Correlation data with imaginary complex part < imagmin will match.
- id: imagmax
- default: 1e+30
- type: float
+ type: float?
doc: Correlation data with imaginary complex part > imagmax will match.
outputs:
- id: augmented_steps
diff --git a/lofar-cwl/steps/DPPP.cwl b/lofar-cwl/steps/DPPP.cwl
index a756093a275e63decbec9ed6425628dfb5efedb9..8cd5a42291642598cd7fc2884a491b254246c476 100755
--- a/lofar-cwl/steps/DPPP.cwl
+++ b/lofar-cwl/steps/DPPP.cwl
@@ -17,7 +17,7 @@ inputs:
prefix: msin=
separate: false
doc: Input Measurement Set
- - default: out.MS
+ - default: "."
id: msout_name
type: string
inputBinding:
@@ -37,23 +37,61 @@ inputs:
- id: output_directory_names
type: Any
doc: Expected output file names
- - id: autoweight
+ - default: false
+ id: autoweight
type: boolean
- default: true
inputBinding:
- prefix: -msin.autoweight=True
- - id: baseline
+ position: 0
+ prefix: 'msin.autoweight=True'
+ - default: ''
+ id: baseline
type: string
- default: ""
inputBinding:
- prefix: -msin.baseline=
+ position: 0
+ prefix: 'msin.baseline='
+ separate: false
+ - default: DATA
+ id: output_column
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: 'msout.datacolumn='
+ separate: false
+ - default: DATA
+ id: input_column
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: 'msin.datacolumn='
separate: false
+ - id: writefullresflag
+ type: boolean
+ default: false
+ inputBinding:
+ prefix: msout.writefullresflag=True
+ - id: overwrite
+ type: boolean
+ default: false
+ inputBinding:
+ prefix: msout.overwrite=True
+ - id: storagemanager
+ type: string
+ default: ""
+ inputBinding:
+ prefix: msout.storagemanager=
+ separate: false
+ - id: databitrate
+ type: int
+ default: 0
+ inputBinding:
+ prefix: msout.storagemanager.databitrate=
+ separate: false
outputs:
- id: msout
doc: Output Measurement Set
type: Directory
outputBinding:
- glob: '$(inputs.msout_name=="."?inputs.msin:inputs.msout_name)'
+ glob: '$(inputs.msout_name=="." ? inputs.msin.basename : inputs.msout_name)'
- id: secondary_output_files
doc: Secondary output files
type: Any
@@ -89,12 +127,20 @@ outputs:
return output
}
- id: logfile
- type: File?
+ type: File[]
outputBinding:
- glob: DPPP.log
+ glob: 'DPPP*.log'
hints:
- class: DockerRequirement
- dockerPull: lofareosc/lofar-pipeline
+ dockerPull: lofareosc/prefactor:HBAcalibrator
stdout: DPPP.log
+stderr: DPPP_err.log
requirements:
- class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+ - entry: $(inputs.secondary_files)
+ - entry: $(inputs.secondary_directories)
+
diff --git a/lofar-cwl/steps/H5ParmCollector.cwl b/lofar-cwl/steps/H5ParmCollector.cwl
index 338109c750a0aab4ed2968134f2e58f798f35c7a..5b6a2dcdd0f11d241b367abbfd6465b8f8569c0f 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
@@ -24,10 +26,26 @@ inputs:
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: output.h5
id: outh5parmname
type: string
doc: Output h5parm name
+ inputBinding:
+ position: 0
+ prefix: '--outh5parm'
- id: squeeze
type: boolean
default: false
@@ -49,6 +67,7 @@ inputs:
position: 0
prefix: '-c'
doc: overwrite output
+
outputs:
- id: outh5parm
doc: Output h5parm
@@ -57,14 +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/lofar-pipeline-ci:latest'
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
stdout: $(inputs.outh5parmname)-parm_collector_output.log
+stderr: $(inputs.outh5parmname)-parm_collector_output_err.log
requirements:
- - class: InlineJavascriptRequirement
-
+ - 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 69ec253b41b480632695627d4280b966581a946d..4ce89e2b5da2f907508e68d757ebc5bfd9d0c178 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 867699dac1e0c2c43eef644a1ebced30aa34d104..d9cda24586263c8c703b2947ddd9da43327bda55 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.ClockTec.cwl b/lofar-cwl/steps/LoSoTo.ClockTec.cwl
index a328b6bef5d6e5fe25a636b50417220397c5f460..a02a92a0988dbde0e074d8f4ceaf89813bccbdab 100644
--- a/lofar-cwl/steps/LoSoTo.ClockTec.cwl
+++ b/lofar-cwl/steps/LoSoTo.ClockTec.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
@@ -52,14 +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.
@@ -67,11 +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.
@@ -91,5 +92,16 @@ outputs:
format: lofar:#H5Parm
outputBinding:
glob: $(inputs.input_h5parm.basename)
+ - id: parset
+ type: File
+ outputBinding:
+ glob: parset.config
+ - id: log
+ type: File[]
+ outputBinding:
+ glob: '$(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.Duplicate.cwl b/lofar-cwl/steps/LoSoTo.Duplicate.cwl
index 2219758c2eca17fc20d12b65453c3073bf5948e3..55208333d750c4e8354289712e076cb428ba5bbb 100644
--- a/lofar-cwl/steps/LoSoTo.Duplicate.cwl
+++ b/lofar-cwl/steps/LoSoTo.Duplicate.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
@@ -48,8 +49,13 @@ 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
+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 e3092536fcd656d83dabc303c343ed9900689e3e..c015e412fe54b1e5d17af3d33a33dabfcba58309 100644
--- a/lofar-cwl/steps/LoSoTo.Faraday.cwl
+++ b/lofar-cwl/steps/LoSoTo.Faraday.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
@@ -41,6 +42,9 @@ 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 +61,13 @@ 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
+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 30dbd1645e993d8cfebc2566629f68c2bc2910ed..302bc82554260d55d604b122dc5440c6fae7fcbf 100644
--- a/lofar-cwl/steps/LoSoTo.Flag.cwl
+++ b/lofar-cwl/steps/LoSoTo.Flag.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
@@ -101,5 +102,12 @@ 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
+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 1c67c12fa1fdeb7cd2e2cd3f9a16ebb6fc2a5a8b..be98dbb4dcfd3867838bffc81957a34345c5f5c8 100644
--- a/lofar-cwl/steps/LoSoTo.FlagStation.cwl
+++ b/lofar-cwl/steps/LoSoTo.FlagStation.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
@@ -76,7 +77,7 @@ inputs:
type: string?
doc: Specifies the telescope if mode = 'bandpass'.
- id: skipInternational
- type: string?
+ type: boolean?
doc: |
If True, skip flagging of international LOFAR stations (only used if
telescope = 'lofar')
@@ -100,5 +101,12 @@ 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
+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 330b2fb9b127c8f8e745d259e50bfbbed312e580..c64fae492a36b11aa871d0e77f11415db15af38a 100644
--- a/lofar-cwl/steps/LoSoTo.Flagextend.cwl
+++ b/lofar-cwl/steps/LoSoTo.Flagextend.cwl
@@ -28,12 +28,13 @@ 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
@@ -67,5 +68,12 @@ 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
+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 aa956ebff87c5e84f349fb1263432687346a13df..f2fee5dc730b44d34c6cdd90bb9ca2f9348ed489 100644
--- a/lofar-cwl/steps/LoSoTo.Interpolate.cwl
+++ b/lofar-cwl/steps/LoSoTo.Interpolate.cwl
@@ -29,12 +29,13 @@ 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
@@ -78,5 +79,12 @@ outputs:
format: lofar:#H5Parm
outputBinding:
glob: $(inputs.input_h5parm.basename)
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: '$(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 ce421868086c89c66db41c7ce23ce485bfbb3ac5..ffdc5dcc1db43c0c3ab15ae7ee5e3b87bdb95f43 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 e9cadbd666d9e2e9c65aabd3c0d757c5d4b04e99..f193e64cafc715019f6cd94294aebfbcb4290ce4 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 d3d077433b5262e300b6d837911c25ff53f3320a..abfc909b4dedeeb9a9a797290cbd3731364ab18f 100644
--- a/lofar-cwl/steps/LoSoTo.Plot.cwl
+++ b/lofar-cwl/steps/LoSoTo.Plot.cwl
@@ -15,29 +15,44 @@ 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: $(inputs.input_h5parm)
writable: true
+ - entryname: run_losoto_plot.sh
+ entry: |
+ #!/bin/bash
+ set -e
+
+ INPUT_H5PARM=$(inputs.input_h5parm.basename)
+ DO_PLOTS=$(inputs.execute)
+ if [ DO_PLOT ]; then
+ losoto --verbose $INPUT_H5PARM parset.config
+ else
+ echo Skipped plotting 3rd order tec solutions
+ fi
-baseCommand: "losoto"
+baseCommand: "bash"
arguments:
- - $(inputs.input_h5parm.basename)
- - parset.config
+ - run_losoto_plot.sh
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
type: File
format: lofar:#H5Parm
+ - id: execute
+ type: boolean?
+ default: true
- id: soltab
- type: string[]
+ type: string
doc: "Tabs to plot"
+
- id: axesInPlot
type: string[]?
@@ -78,6 +93,10 @@ inputs:
type: float[]?
doc: |
Min max value for the independent variable (0 means automatic).
+ - id: time.minmaxstep
+ type: float[]?
+ doc: |
+ Step size in time for subsequent plotting
- id: log
type: string?
doc: |
@@ -125,6 +144,17 @@ outputs:
type: File[]
outputBinding:
glob: "$(inputs.prefix)*.png"
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: '$(inputs.input_h5parm.basename)-losoto*.log'
+ - id: parset
+ type: File
+ outputBinding:
+ 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 a6a65068192cc1ce192f864364af6387dc44b453..fa4bfe34becb68bfc02c8acb0dd6f3e62a0288ce 100755
--- a/lofar-cwl/steps/LoSoTo.Polalign.cwl
+++ b/lofar-cwl/steps/LoSoTo.Polalign.cwl
@@ -43,12 +43,13 @@ 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
@@ -88,5 +89,10 @@ 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
+stderr: $(inputs.input_h5parm.basename)-losoto_err.log
diff --git a/lofar-cwl/steps/LoSoTo.PrefactorBandpass.cwl b/lofar-cwl/steps/LoSoTo.PrefactorBandpass.cwl
index c81efdab366125e0c818a211e7dd3c06dda39dec..021adf8b37dd3cb23b8c8d3f5feed7e44ef8434a 100644
--- a/lofar-cwl/steps/LoSoTo.PrefactorBandpass.cwl
+++ b/lofar-cwl/steps/LoSoTo.PrefactorBandpass.cwl
@@ -1,101 +1,131 @@
-#!/usr/bin/env cwl-runner
-
class: CommandLineTool
cwlVersion: v1.0
-id: losoto_prefactor_bandpass
-
$namespaces:
- lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
-doc: |
- This operation for LoSoTo implements the Prefactor bandpass operation
- WEIGHT: flag-only compliant, no need for weight
-
-
-requirements:
- InlineJavascriptRequirement:
- expressionLib:
- - { $include: utils.js}
- InitialWorkDirRequirement:
- listing:
- - entryname: 'parset.config'
- entry: $(get_losoto_config('PREFACTOR_BANDPASS').join('\n'))
-
- - entryname: $(inputs.input_h5parm.basename)
- entry: $(inputs.input_h5parm)
- writable: true
-
-baseCommand: "losoto"
-
-arguments:
- - $(inputs.input_h5parm.basename)
- - parset.config
-
-hints:
- DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
-
+ lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
+ sbg: 'https://www.sevenbridges.com/'
+id: losoto_prefactor_bandpass
+baseCommand:
+ - losoto
inputs:
- - id: input_h5parm
+ - format: 'lofar:#H5Parm'
+ id: input_h5parm
type: File
- format: lofar:#H5Parm
- id: soltab
type: string
- doc: "Solution table"
+ doc: Solution table
- id: chanWidth
type: string?
- doc: |
- the width of each channel in the data from which solutions were obtained. Can be
- either a string like "48kHz" or a float in Hz. If interpolate = True, chanWidth
- must be specified
+ doc: >
+ the width of each channel in the data from which solutions were obtained.
+ Can be
+
+ either a string like "48kHz" or a float in Hz. If interpolate = True,
+ chanWidth
+ must be specified
- id: BadSBList
type: string?
doc: a list of bad subbands that will be flagged
-
- id: outSoltabName
type: string?
- doc: |
- Name of the output bandpass soltab. An existing soltab with this name will be
+ doc: >
+ Name of the output bandpass soltab. An existing soltab with this name will
+ be
+
overwritten
- - id: interpolate
+ - default: false
+ id: interpolate
type: boolean?
- default: false
- doc: |
- If True, interpolate to a regular frequency grid and then smooth, ignoring bad
- subbands. If False, neither interpolation nor smoothing is done and the output
- frequency grid is the same as the input one. If interpolate = True, chanWidth
+ doc: >
+ If True, interpolate to a regular frequency grid and then smooth, ignoring
+ bad
+
+ subbands. If False, neither interpolation nor smoothing is done and the
+ output
+
+ frequency grid is the same as the input one. If interpolate = True,
+ chanWidth
+
must be specified
- id: removeTimeAxis
type: boolean?
- doc: |
- If True, the time axis of the output bandpass soltab is removed by doing a median
+ doc: >
+ If True, the time axis of the output bandpass soltab is removed by doing a
+ median
+
over time. If False, the output time grid is the same as the input one
- id: autoFlag
type: boolean?
- doc: If True, automatically flag bad frequencies and stations
-
+ doc: 'If True, automatically flag bad frequencies and stations'
- id: nSigma
type: float?
- doc: Number of sigma for autoFlagging. Amplitudes outside of nSigma*stddev are flagged
-
+ doc: >-
+ Number of sigma for autoFlagging. Amplitudes outside of nSigma*stddev are
+ flagged
- id: maxFlaggedFraction
type: float?
- doc: |
- Maximum allowable fraction of flagged frequencies for autoFlagging. Stations with
+ doc: >
+ Maximum allowable fraction of flagged frequencies for autoFlagging.
+ Stations with
+
higher fractions will be completely flagged
- id: maxStddev
type: float?
doc: Maximum allowable standard deviation for autoFlagging
-
- id: ncpu
type: int?
doc: Number of CPUs to use during autoFlagging (0 = all)
-
outputs:
- id: output_h5parm
type: File
- format: lofar:#H5Parm
outputBinding:
glob: $(inputs.input_h5parm.basename)
+ format: 'lofar:#H5Parm'
+doc: |
+ This operation for LoSoTo implements the Prefactor bandpass operation
+ WEIGHT: flag-only compliant, no need for weight
+arguments:
+ - $(inputs.input_h5parm.basename)
+ - parset.config
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: parset.config
+ entry: $(get_losoto_config('PREFACTOR_BANDPASS').join('\n'))
+ writable: false
+ - entryname: $(inputs.input_h5parm.basename)
+ entry: $(inputs.input_h5parm)
+ writable: true
+ - class: InlineJavascriptRequirement
+ expressionLib:
+ - |
+ function get_losoto_config(step_name) {
+ var par = ['soltab = ' + inputs.soltab]
+ if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);
+ console.log(inputs, par)
+ par.push("[" + step_name + "]")
+ par.push('operation=' + step_name)
+ for(var field_name in inputs){
+ if(field_name === 'input_h5parm' ||
+ field_name === 'soltab' ||
+ field_name === 'ncpu' ||
+ field_name === 'execute') continue;
+
+ if(inputs[field_name] === null ||
+ inputs[field_name] === 'null') continue;
+
+ if(inputs[field_name]["class"] !== undefined &&
+ (inputs[field_name]["class"] ==="Directory" ||
+ inputs[field_name]["class"] ==="File")){
+ par.push(field_name+'='+inputs[field_name].path)
+ } else {
+ par.push(field_name+'='+inputs[field_name])
+ }
+ }
+ return par
+ }
+hints:
+ - class: DockerRequirement
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
$schema:
- - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+ - 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
diff --git a/lofar-cwl/steps/LoSoTo.PrefactorXYoffset.cwl b/lofar-cwl/steps/LoSoTo.PrefactorXYoffset.cwl
index 49e072c3e00168540f0551dc35c4a183aa582a1d..2fd707f650e0f820db15c7dce9ce62d32ecc11a2 100644
--- a/lofar-cwl/steps/LoSoTo.PrefactorXYoffset.cwl
+++ b/lofar-cwl/steps/LoSoTo.PrefactorXYoffset.cwl
@@ -1,53 +1,73 @@
-#!/usr/bin/env cwl-runner
-
class: CommandLineTool
cwlVersion: v1.0
-id: losoto_prefactor_xyoffset
-
$namespaces:
- lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
-
-requirements:
- InlineJavascriptRequirement:
- expressionLib:
- - { $include: utils.js}
- InitialWorkDirRequirement:
- listing:
- - entryname: 'parset.config'
- entry: $(get_losoto_config('PREFACTOR_XYOFFSET').join('\n'))
-
- - entryname: $(inputs.input_h5parm.basename)
- entry: $(inputs.input_h5parm)
- writable: true
-
-baseCommand: "losoto"
-
-arguments:
- - $(inputs.input_h5parm.basename)
- - parset.config
-
-hints:
- DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
-
+ lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
+ sbg: 'https://www.sevenbridges.com/'
+id: losoto_prefactor_xyoffset
+baseCommand:
+ - losoto
inputs:
- - id: input_h5parm
+ - format: 'lofar:#H5Parm'
+ id: input_h5parm
type: File
- format: lofar:#H5Parm
- id: soltab
type: string
- doc: "Solution table"
+ doc: Solution table
- id: chanWidth
type: string
- doc: |
- the width of each channel in the data from which solutions were obtained. Can be
+ doc: >
+ the width of each channel in the data from which solutions were obtained.
+ Can be
+
either a string like "48kHz" or a float in Hz.
-
outputs:
- id: output_h5parm
type: File
- format: lofar:#H5Parm
outputBinding:
glob: $(inputs.input_h5parm.basename)
+ format: 'lofar:#H5Parm'
+arguments:
+ - $(inputs.input_h5parm.basename)
+ - parset.config
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: parset.config
+ entry: $(get_losoto_config('PREFACTOR_XYOFFSET').join('\n'))
+ writable: false
+ - entryname: $(inputs.input_h5parm.basename)
+ entry: $(inputs.input_h5parm)
+ writable: true
+ - class: InlineJavascriptRequirement
+ expressionLib:
+ - |
+ function get_losoto_config(step_name) {
+ var par = ['soltab = ' + inputs.soltab]
+ if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);
+ console.log(inputs, par)
+ par.push("[" + step_name + "]")
+ par.push('operation=' + step_name)
+ for(var field_name in inputs){
+ if(field_name === 'input_h5parm' ||
+ field_name === 'soltab' ||
+ field_name === 'ncpu' ||
+ field_name === 'execute') continue;
+
+ if(inputs[field_name] === null ||
+ inputs[field_name] === 'null') continue;
+
+ if(inputs[field_name]["class"] !== undefined &&
+ (inputs[field_name]["class"] ==="Directory" ||
+ inputs[field_name]["class"] ==="File")){
+ par.push(field_name+'='+inputs[field_name].path)
+ } else {
+ par.push(field_name+'='+inputs[field_name])
+ }
+ }
+ return par
+ }
+hints:
+ - class: DockerRequirement
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
$schema:
- - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+ - 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
diff --git a/lofar-cwl/steps/LoSoTo.Replicateonaxis.cwl b/lofar-cwl/steps/LoSoTo.Replicateonaxis.cwl
index f7512ea67e95e9d24eb11a0811e5fa593756afcd..3f953a16409b5b72b63dcc1e464ad5dbeb794c18 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 887b0b81b4bddd5e8c43962975924e56700ce93e..ea6e06cbee986d4ba62ff23ab1b1625c3f788bbd 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 9dd82a8a9cc3d57005c7c3d9093ee0711479fe7e..6642f7ec096493896668094eb5d4912b9a0806c9 100644
--- a/lofar-cwl/steps/LoSoTo.Residual.cwl
+++ b/lofar-cwl/steps/LoSoTo.Residual.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
@@ -49,9 +50,16 @@ 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
+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 abe16e2c611af5d5bd82cd9c56e03e9af6b0a486..e8f027619f73bfe800559ab70e45a5a4cd512562 100644
--- a/lofar-cwl/steps/LoSoTo.Reweight.cwl
+++ b/lofar-cwl/steps/LoSoTo.Reweight.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
@@ -77,5 +78,12 @@ 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
+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 cdf67851ae10b6274dbfe52f45c425f4b7c3ff34..7f0d07e3186b46075b2523f97a1b094d96cdc6d3 100644
--- a/lofar-cwl/steps/LoSoTo.Smooth.cwl
+++ b/lofar-cwl/steps/LoSoTo.Smooth.cwl
@@ -22,25 +22,38 @@ requirements:
listing:
- entryname: 'parset.config'
entry: $(get_losoto_config('SMOOTH').join('\n'))
-
- entryname: $(inputs.input_h5parm.basename)
entry: $(inputs.input_h5parm)
writable: true
+ - entryname: run_losoto_smooth.sh
+ entry: |
+ #!/bin/bash
+ set -e
+
+ INPUT_H5PARM=$(inputs.input_h5parm.basename)
+ DO_SMOOTH=$(inputs.execute)
+ if [ DO_SMOOTH ]; then
+ losoto --verbose $INPUT_H5PARM parset.config
+ else
+ echo Skipped smoothing.
+ fi
-baseCommand: "losoto"
+baseCommand: "bash"
arguments:
- - $(inputs.input_h5parm.basename)
- - parset.config
+ - run_losoto_smooth.sh
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
type: File
format: lofar:#H5Parm
+ - id: execute
+ type: boolean?
+ default: true
- id: soltab
type: string
doc: "Solution table"
@@ -82,5 +95,12 @@ outputs:
format: lofar:#H5Parm
outputBinding:
glob: $(inputs.input_h5parm.basename)
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: '$(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.Splitleak.cwl b/lofar-cwl/steps/LoSoTo.Splitleak.cwl
index 3405937529f95ab615be2ebdc6c572f3041bbbc9..c29e1da65f87a3918bf812746a5ba0f1c836e764 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 cdf29c2f61d88dfad58c78ed5c5ada0993ccb121..639a7e7da1695a70a0aff53486706d385848633d 100644
--- a/lofar-cwl/steps/LoSoTo.Structure.cwl
+++ b/lofar-cwl/steps/LoSoTo.Structure.cwl
@@ -27,12 +27,13 @@ requirements:
baseCommand: "losoto"
arguments:
+ - '--verbose'
- $(inputs.input_h5parm.basename)
- parset.config
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
inputs:
- id: input_h5parm
diff --git a/lofar-cwl/steps/applybeam.cwl b/lofar-cwl/steps/applybeam.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..00f3f3914b572778f869d3fbe96c662b05255a12
--- /dev/null
+++ b/lofar-cwl/steps/applybeam.cwl
@@ -0,0 +1,100 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: applycal
+baseCommand:
+ - DPPP
+inputs:
+ - id: msin
+ type: Directory
+ inputBinding:
+ position: 0
+ prefix: msin=
+ separate: false
+ doc: Input Measurement Set
+ - default: DATA
+ id: msin_datacolumn
+ type: string
+ inputBinding:
+ position: 0
+ prefix: msin.datacolumn=
+ separate: false
+ doc: Input data Column
+ - id: msout_datacolumn
+ type: string
+ inputBinding:
+ position: 0
+ prefix: msout.datacolumn=
+ separate: false
+ doc: Output data column
+ - default: applybeam
+ id: type
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: applybeam.type=
+ separate: false
+ doc: >
+ Type of correction to perform. When using H5Parm, this is for now the name
+ of the soltab; the type will be deduced from the metadata in that soltab,
+ except for full Jones, in which case correction should be 'fulljones'.
+ - id: storagemanager
+ type: string
+ default: ""
+ inputBinding:
+ prefix: msout.storagemanager=
+ - id: databitrate
+ type: int?
+ inputBinding:
+ prefix: msout.storagemanager.databitrate=
+ separate: false
+ - id: updateweights
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: applybeam.updateweights=
+ separate: false
+ - id: usechannelfreq
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: applybeam.usechannelfreq=
+ separate: false
+ - id: invert
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: applybeam.invert=
+ separate: false
+ - id: beammode
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: applybeam.beammode=
+ separate: false
+
+outputs:
+ - id: msout
+ doc: Output Measurement Set
+ type: Directory
+ outputBinding:
+ glob: $(inputs.msin.basename)
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: 'applycal_$(inputs.type)*.log'
+stdout: applycal_$(inputs.type).log
+stderr: applycal_$(inputs.type)_err.log
+arguments:
+ - 'steps=[applybeam]'
+ - msout=.
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+ - class: InlineJavascriptRequirement
+hints:
+ - class: DockerRequirement
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
diff --git a/lofar-cwl/steps/applycal.cwl b/lofar-cwl/steps/applycal.cwl
index 748029f85ade072e5bed2419133931070a17c6a6..49b2f718cf4eff4e31cc21f86f5cc019efb15608 100644
--- a/lofar-cwl/steps/applycal.cwl
+++ b/lofar-cwl/steps/applycal.cwl
@@ -48,17 +48,34 @@ inputs:
Type of correction to perform. When using H5Parm, this is for now the name
of the soltab; the type will be deduced from the metadata in that soltab,
except for full Jones, in which case correction should be 'fulljones'.
+ - id: storagemanager
+ type: string
+ default: ""
+ inputBinding:
+ prefix: msout.storagemanager=
+ - id: databitrate
+ type: int?
+ inputBinding:
+ prefix: msout.storagemanager.databitrate=
+ separate: false
- id: updateweights
- type: boolean?
+ type: string?
inputBinding:
position: 0
- prefix: applycal.updateweights=True
+ prefix: applycal.updateweights=
+ separate: false
outputs:
- id: msout
doc: Output Measurement Set
type: Directory
outputBinding:
glob: $(inputs.msin.basename)
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: 'applycal_$(inputs.correction)*.log'
+stdout: applycal_$(inputs.correction).log
+stderr: applycal_$(inputs.correction)_err.log
arguments:
- 'steps=[applycal]'
- msout=.
@@ -70,4 +87,4 @@ requirements:
- class: InlineJavascriptRequirement
hints:
- class: DockerRequirement
- dockerPull: 'lofareosc/lofar-pipeline-ci:latest'
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
diff --git a/lofar-cwl/steps/applytarget.cwl b/lofar-cwl/steps/applytarget.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..a079023d05e1ff8491a2444f8cb01b7e1f4ee85a
--- /dev/null
+++ b/lofar-cwl/steps/applytarget.cwl
@@ -0,0 +1,105 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: applytarget
+baseCommand:
+ - DPPP
+inputs:
+ - id: msin
+ type: Directory
+ inputBinding:
+ position: 0
+ prefix: msin=
+ separate: false
+ doc: Input Measurement Set
+ - id: msout_name
+ type: string
+ default: '.'
+ inputBinding:
+ position: 0
+ prefix: msout=
+ separate: false
+ doc: Name of output MS
+ - default: DATA
+ id: msin_datacolumn
+ type: string
+ inputBinding:
+ position: 0
+ prefix: msin.datacolumn=
+ separate: false
+ doc: Input data Column
+ - id: parmdb
+ type: File
+ inputBinding:
+ position: 0
+ prefix: applycal.parmdb=
+ separate: false
+ doc: >-
+ Path of parmdb in which the parameters are stored. This can also be an
+ H5Parm file, in that case the filename has to end in '.h5'
+ - id: msout_datacolumn
+ type: string
+ inputBinding:
+ position: 0
+ prefix: msout.datacolumn=
+ separate: false
+ doc: Output data column
+ - default: gain
+ id: correction
+ type: string
+ inputBinding:
+ position: 0
+ prefix: applycal.correction=
+ separate: false
+ doc: >
+ Type of correction to perform. When using H5Parm, this is for now the name
+ of the soltab; the type will be deduced from the metadata in that soltab,
+ except for full Jones, in which case correction should be 'fulljones'.
+ - default: 'sol000'
+ id: solset
+ type: string
+ inputBinding:
+ position: 0
+ prefix: applycal.solset=
+ separate: false
+ - id: storagemanager
+ type: string
+ default: ""
+ inputBinding:
+ prefix: msout.storagemanager=
+ separate: false
+ - id: databitrate
+ type: int?
+ inputBinding:
+ prefix: msout.storagemanager.databitrate=
+ separate: false
+ - id: updateweights
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: applycal.updateweights=
+ separate: false
+outputs:
+ - id: msout
+ doc: Output Measurement Set
+ type: Directory
+ outputBinding:
+ glob: '$(inputs.msout_name=="."?inputs.msin.basename:inputs.msout_name)'
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: 'applycal_$(inputs.correction).log'
+stdout: applycal_$(inputs.correction).log
+stderr: applycal_$(inputs.correction)_err.log
+arguments:
+ - 'steps=[applycal]'
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+ - class: InlineJavascriptRequirement
+hints:
+ - class: DockerRequirement
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
diff --git a/lofar-cwl/steps/calib_rot_diag.cwl b/lofar-cwl/steps/calib_rot_diag.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..f57c1a88952b2ea079fe83086359f145aaef9ba9
--- /dev/null
+++ b/lofar-cwl/steps/calib_rot_diag.cwl
@@ -0,0 +1,107 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
+ sbg: 'https://www.sevenbridges.com/'
+id: calib_rot_diag
+baseCommand:
+ - DPPP
+inputs:
+ - id: msin
+ type: Directory?
+ inputBinding:
+ position: 0
+ prefix: msin=
+ separate: false
+ doc: Input Measurement Set
+ - default: DATA
+ id: msin_datacolumn
+ type: string
+ inputBinding:
+ position: 0
+ prefix: msin.datacolumn=
+ separate: false
+ doc: Input data Column
+ - default: MODEL_DATA
+ id: msin_modelcolum
+ type: string
+ inputBinding:
+ position: 0
+ prefix: msin.modelcolumn=
+ separate: false
+ doc: Model data Column
+ - default: instrument.h5
+ id: output_name_h5parm
+ type: string
+ inputBinding:
+ position: 0
+ prefix: ddecal.h5parm=
+ separate: false
+ - default: out.MS
+ id: msout_name
+ type: string
+ inputBinding:
+ position: 0
+ prefix: msout=
+ separate: false
+ doc: Output Measurement Set
+ - default: true
+ id: propagate_solutions
+ type: boolean
+ inputBinding:
+ position: 0
+ prefix: propagatesolutions=True
+ - default: false
+ id: flagunconverged
+ type: boolean
+ inputBinding:
+ position: 0
+ prefix: flagdivergedonly=True
+ doc: |
+ Flag unconverged solutions (i.e., those from solves that did not converge
+ within maxiter iterations).
+ - default: false
+ id: flagdivergedonly
+ type: boolean
+ inputBinding:
+ position: 0
+ prefix: flagdivergedonly=True
+ doc: |
+ Flag only the unconverged solutions for which divergence was detected.
+ At the moment, this option is effective only for rotation+diagonal
+ solves, where divergence is detected when the amplitudes of any station
+ are found to be more than a factor of 5 from the mean amplitude over all
+ stations.
+ If divergence for any one station is detected, all stations are flagged
+ for that solution interval. Only effective when flagunconverged=true
+ and mode=rotation+diagonal.
+outputs:
+ - id: msout
+ doc: Output Measurement Set
+ type: Directory
+ outputBinding:
+ glob: '$(inputs.msout_name=="."?inputs.msin:inputs.msout_name)'
+ - id: h5parm
+ doc: Filename of output H5Parm (to be read by e.g. losoto)
+ type: File
+ outputBinding:
+ glob: $(inputs.output_name_h5parm)
+ format: 'lofar:#H5Parm'
+arguments:
+ - 'steps=[ddecal]'
+ - ddecal.mode=rotation+diagonal
+ - ddecal.uvlambdamin=300
+ - ddecal.maxiter=50
+ - ddecal.nchan=1
+ - ddecal.solint=1
+ - ddecal.propagateconvergedonly=True
+ - ddecal.flagdivergedonly=True
+ - ddecal.tolerance=1.e-3
+ - ddecal.usemodelcolumn=True
+hints:
+ - class: DockerRequirement
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
+requirements:
+ - class: InlineJavascriptRequirement
+$schema:
+ - 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
diff --git a/lofar-cwl/steps/check_ateam_separation.cwl b/lofar-cwl/steps/check_ateam_separation.cwl
index 1c383d46dc104cca27c070d63c0d3f076794197e..c8d801c94a6e32aac1ea6ba83a8d2687448baf22 100755
--- a/lofar-cwl/steps/check_ateam_separation.cwl
+++ b/lofar-cwl/steps/check_ateam_separation.cwl
@@ -1,7 +1,5 @@
class: CommandLineTool
cwlVersion: v1.0
-$namespaces:
- sbg: 'https://www.sevenbridges.com/'
id: check_ateam_separation
baseCommand:
- python3
@@ -39,6 +37,6 @@ outputs:
label: check_Ateam_separation
hints:
- class: DockerRequirement
- dockerPull: lofareosc/lofar-pipeline
+ dockerPull: lofareosc/prefactor:HBAcalibrator
- class: InlineJavascriptRequirement
stdout: Ateam_separation.log
diff --git a/lofar-cwl/steps/ddecal.cwl b/lofar-cwl/steps/ddecal.cwl
index cc54a6cda7892c991213dc11cbe3769fc8b55085..b0493198b5c1380b448c87442e422883786fd52a 100644
--- a/lofar-cwl/steps/ddecal.cwl
+++ b/lofar-cwl/steps/ddecal.cwl
@@ -7,10 +7,14 @@ baseCommand: [DPPP]
requirements:
InlineJavascriptRequirement: {}
+ InitialWorkDirRequirement:
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
hints:
DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
arguments:
- steps=[ddecal]
@@ -18,15 +22,14 @@ arguments:
- ddecal.maxiter=50
- ddecal.nchan=1
- ddecal.solint=1
- - ddecal.propagateconvergedonly=True
- - ddecal.flagdivergedonly=True
- ddecal.tolerance=1.e-3
- ddecal.usemodelcolumn=True
-
+ - ddecal.flagdivergedonly=True
+ - ddecal.propagateconvergedonly=True
inputs:
- id: msin
- type: Directory?
+ type: Directory
doc: Input Measurement Set
inputBinding:
prefix: msin=
@@ -57,7 +60,7 @@ inputs:
- id: msout_name
type: string
doc: Output Measurement Set
- default: out.MS
+ default: "OUT.MS"
inputBinding:
prefix: msout=
separate: false
@@ -67,7 +70,7 @@ inputs:
type: boolean
default: true
inputBinding:
- prefix: propagatesolutions=True
+ prefix: ddecal.propagatesolutions=True
- id: flagunconverged
type: boolean
default: false
@@ -75,7 +78,7 @@ inputs:
Flag unconverged solutions (i.e., those from solves that did not converge
within maxiter iterations).
inputBinding:
- prefix: flagdivergedonly=True
+ prefix: ddecal.flagdivergedonly=True
- id: flagdivergedonly
default: false
type: boolean
@@ -89,8 +92,13 @@ inputs:
for that solution interval. Only effective when flagunconverged=true
and mode=rotation+diagonal.
inputBinding:
- prefix: flagdivergedonly=True
-
+ prefix: ddecal.flagdivergedonly=True
+ - id: storagemanager
+ type: string
+ default: ""
+ inputBinding:
+ prefix: msout.storagemanager=
+ separate: false
- id: mode
type:
type: enum
@@ -116,15 +124,21 @@ outputs:
doc: Output Measurement Set
type: Directory
outputBinding:
- glob: $(inputs.msout_name=="."?inputs.msin:inputs.msout_name)
+ glob: $(inputs.msin.basename)
- id: h5parm
doc: Filename of output H5Parm (to be read by e.g. losoto)
type: File
- format: lofar:#H5Parm
+ format: 'lofar:#H5Parm'
outputBinding:
glob: $(inputs.output_name_h5parm)
-
+
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: 'ddecal*.log'
+stdout: ddecal.log
+stderr: ddecal_err.log
$namespaces:
lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
$schema:
diff --git a/lofar-cwl/steps/dpppconcat.cwl b/lofar-cwl/steps/dpppconcat.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..e4570f06b1db4bb7acb293e838ce4497d39ec9cf
--- /dev/null
+++ b/lofar-cwl/steps/dpppconcat.cwl
@@ -0,0 +1,141 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: dpppconcat
+baseCommand:
+ - DPPP
+inputs:
+ - id: msin
+ type: 'Directory[]'
+ inputBinding:
+ position: 0
+ prefix: msin=
+ separate: false
+ itemSeparator: ','
+ valueFrom: $(concatenate_path(self))
+ doc: Input Measurement Set
+ - id: msout_name
+ type: string
+ inputBinding:
+ prefix: msout=
+ separate: false
+ shellQuote: false
+ position: 0
+ - id: msin_datacolumn
+ type: string
+ inputBinding:
+ prefix: msin.datacolumn=
+ separate: false
+ shellQuote: false
+ position: 0
+ doc: Input data Column
+ default: DATA
+ - id: msout_datacolumn
+ type: string
+ inputBinding:
+ prefix: msout.datacolumn=
+ separate: false
+ shellQuote: false
+ position: 0
+ default: DATA
+ - id: filter_baselines
+ type: string
+ inputBinding:
+ prefix: filter.baseline=
+ separate: false
+ shellQuote: true
+ position: 0
+ valueFrom: $(self)
+ default: null
+ - id: filter_remove
+ type: boolean
+ inputBinding:
+ prefix: filter.remove=True
+ shellQuote: false
+ position: 0
+ default: false
+ - id: writefullresflag
+ type: boolean
+ inputBinding:
+ prefix: msout.writefullresflag=True
+ shellQuote: false
+ position: 0
+ default: false
+ - id: overwrite
+ type: boolean
+ inputBinding:
+ prefix: msout.overwrite=True
+ shellQuote: false
+ position: 0
+ default: false
+ - id: storagemanager
+ type: string
+ inputBinding:
+ prefix: msout.storagemanager=
+ separate: false
+ shellQuote: false
+ position: 0
+ default: ''
+ - id: databitrate
+ type: int?
+ inputBinding:
+ prefix: msout.storagemanager.databitrate=
+ separate: false
+ shellQuote: false
+ position: 0
+ - id: missingdata
+ type: boolean
+ inputBinding:
+ prefix: msout.missingdata=True
+ separate: false
+ shellQuote: false
+ position: 0
+ - id: baseline
+ type: string?
+ inputBinding:
+ prefix: msin.baseline=
+ separate: false
+ shellQuote: true
+ position: 0
+ default: '*'
+ - id: avg_timeresolution
+ type: int?
+ inputBinding:
+ prefix: avg.timeresolution=
+ separate: false
+ shellQuote: false
+ position: 0
+ default: 1
+ - id: avg_freqresolution
+ type: string?
+ inputBinding:
+ prefix: avg.freqresolution=
+ separate: false
+ shellQuote: false
+ position: 0
+ default: 12.205kHz
+outputs:
+ - id: msout
+ doc: Output Measurement Set
+ type: Directory
+ outputBinding:
+ glob: $(inputs.msout_name)
+ - id: logfile
+ type: 'File[]'
+ outputBinding:
+ glob: concat*.log
+arguments:
+ - 'steps=[filter,avg]'
+ - msout.orderms=False
+ - avg.type=average
+requirements:
+ - class: ShellCommandRequirement
+ - class: InlineJavascriptRequirement
+ expressionLib:
+ - { $include: 'utils.js' }
+hints:
+ - class: DockerRequirement
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
+stdout: concat.log
+stderr: concat_err.log
diff --git a/lofar-cwl/steps/filter_predict.cwl b/lofar-cwl/steps/filter_predict.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..35e182e29facec80f1313e2e824279a74008fa03
--- /dev/null
+++ b/lofar-cwl/steps/filter_predict.cwl
@@ -0,0 +1,118 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: predict
+baseCommand:
+ - DPPP
+inputs:
+ - id: msin
+ type: Directory
+ inputBinding:
+ position: 0
+ prefix: msin=
+ separate: false
+ doc: Input Measurement Set
+ - default: DATA
+ id: msin_datacolumn
+ type: string
+ inputBinding:
+ position: 0
+ prefix: msin.datacolumn=
+ separate: false
+ doc: Input data Column
+ - default: MODEL_DATA
+ id: msout_datacolumn
+ type: string
+ inputBinding:
+ position: 0
+ prefix: msout.datacolumn=
+ separate: false
+ - id: sources_db
+ type: File
+ inputBinding:
+ position: 0
+ prefix: predict.sourcedb=
+ separate: false
+ - default: null
+ id: sources
+ type: 'string[]'
+ inputBinding:
+ position: 0
+ prefix: predict.sources=
+ separate: false
+ itemSeparator: ','
+ valueFrom: "[$(self.join(','))]"
+ - default: false
+ id: usebeammodel
+ type: boolean
+ inputBinding:
+ position: 0
+ prefix: predict.usebeammodel=True
+ - default: false
+ id: onebeamperpatch
+ type: boolean
+ inputBinding:
+ position: 0
+ prefix: predict.onebeamperpatch=True
+ - default: null
+ id: filter_baselines
+ type: string
+ inputBinding:
+ position: 0
+ prefix: filter.baseline=
+ separate: false
+ valueFrom: '$(self)'
+ - default: false
+ id: filter_remove
+ type: boolean
+ inputBinding:
+ position: 0
+ prefix: filter.remove=True
+ - id: writefullresflag
+ type: boolean
+ default: false
+ inputBinding:
+ prefix: msout.writefullresflag=True
+ - id: overwrite
+ type: boolean
+ default: false
+ inputBinding:
+ prefix: msout.overwrite=True
+ - id: storagemanager
+ type: string
+ default: ""
+ inputBinding:
+ prefix: msout.storagemanager=
+ separate: false
+ - id: databitrate
+ type: int?
+ inputBinding:
+ prefix: msout.storagemanager.databitrate=
+ separate: false
+outputs:
+ - id: msout
+ doc: Output Measurement Set
+ type: Directory
+ outputBinding:
+ glob: $(inputs.msin.basename)
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: 'filter_predict*.log'
+arguments:
+ - 'steps=[filter,predict]'
+ - predict.beammode=array_factor
+ - predict.usechannelfreq=False
+ - msout=.
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+ - class: InlineJavascriptRequirement
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: filter_predict.log
+stderr: filter_predict_err.log
\ No newline at end of file
diff --git a/lofar-cwl/steps/gaincal.cwl b/lofar-cwl/steps/gaincal.cwl
index e017373e0bfe4a6ef68930d4f380dbfbc8cb65e7..3d668b023f5ed4f621d4aeecd4bd893cd311aa42 100644
--- a/lofar-cwl/steps/gaincal.cwl
+++ b/lofar-cwl/steps/gaincal.cwl
@@ -1,114 +1,181 @@
-#!/usr/bin/env cwl-runner
-
class: CommandLineTool
cwlVersion: v1.0
+$namespaces:
+ lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
+ sbg: 'https://www.sevenbridges.com/'
id: gaincal
-baseCommand: [DPPP]
-
-requirements:
- InlineJavascriptRequirement: {}
-
-hints:
- DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
-
-arguments:
- - steps=[gaincal]
-
-
+baseCommand:
+ - DPPP
inputs:
- id: msin
- type: Directory?
- doc: Input Measurement Set
+ type: Directory
inputBinding:
- prefix: msin=
- separate: false
+ position: 0
+ prefix: msin=
+ separate: false
+ doc: Input Measurement Set
- id: caltype
+ type:
+ type: enum
+ symbols:
+ - diagonal
+ - fulljones
+ - phaseonly
+ - scalarphase
+ - amplitude
+ - scalaramplitude
+ - tec
+ - tecandphase
+ name: caltype
+ inputBinding:
+ position: 0
+ prefix: gaincal.caltype=
+ separate: false
doc: |
The type of calibration that needs to be performed.
- type:
- type: enum
- symbols:
- - diagonal
- - fulljones
- - phaseonly
- - scalarphase
- - amplitude
- - scalaramplitude
- - tec
- - tecandphase
- inputBinding:
- prefix: gaincal.caltype=
- separate: false
- id: sourcedb
type: File
inputBinding:
- prefix: gaincal.sourcedb=
- separate: false
- - id: usebeammodel
+ position: 0
+ prefix: gaincal.sourcedb=
+ separate: false
+ - default: true
+ id: usebeammodel
type: boolean
- default: true
inputBinding:
- prefix: gaincal.usebeammodel=true
- separate: false
- - id: solint
+ position: 0
+ prefix: gaincal.usebeammodel=true
+ separate: false
+ - default: 1
+ id: solint
type: int
- default: 1
- doc: |
- Number of time slots on which a solution is assumed to be constant (same as CellSize.Time in BBS).
- 0 means all time slots. Note that for larger settings of solint, and specially for solint = 0,
- the memory usage of gaincal will be large (all visibilities for a solint should fit in memory).
- - id: msin_datacolumn
+ doc: >
+ Number of time slots on which a solution is assumed to be constant (same
+ as CellSize.Time in BBS).
+
+ 0 means all time slots. Note that for larger settings of solint, and
+ specially for solint = 0,
+
+ the memory usage of gaincal will be large (all visibilities for a solint
+ should fit in memory).
+ - default: DATA
+ id: msin_datacolumn
type: string?
- default: DATA
- doc: Input data Column
inputBinding:
- prefix: msin.datacolumn=
- separate: false
- - id: onebeamperpatch
- type: boolean
+ position: 0
+ prefix: msin.datacolumn=
+ separate: false
doc: Input data Column
- default: true
+ - default: false
+ id: onebeamperpatch
+ type: boolean
inputBinding:
- prefix: gaincal.onebeamperpatch=True
- separate: false
- - id: msin_modelcolum
+ position: 0
+ prefix: gaincal.onebeamperpatch=True
+ separate: false
+ doc: Input data Column
+ - default: MODEL_DATA
+ id: msin_modelcolum
type: string
- default: MODEL_DATA
- doc: Model data Column
inputBinding:
- prefix: msin.modelcolumn=
- separate: false
-
- - id: output_name_h5parm
+ position: 0
+ prefix: msin.modelcolumn=
+ separate: false
+ doc: Model data Column
+ - default: instrument.h5
+ id: output_name_h5parm
type: string
- default: instrument.h5
inputBinding:
- prefix: gaincal.parmdb=
- separate: false
- - id: msout_name
+ position: 0
+ prefix: gaincal.parmdb=
+ separate: false
+ - default: out.MS
+ id: msout_name
type: string
+ inputBinding:
+ position: 0
+ prefix: msout=
+ separate: false
doc: Output Measurement Set
- default: out.MS
+ - default: true
+ id: propagatesolutions
+ type: boolean
inputBinding:
- prefix: msout=
- separate: false
-
+ position: 0
+ prefix: gaincal.propagatesolutions=True
+ separate: false
+ - default: true
+ id: usechannelfreq
+ type: boolean
+ inputBinding:
+ position: 0
+ prefix: gaincal.usechannelfreq=True
+ separate: false
+ - default: array_factor
+ id: beammode
+ type: string
+ inputBinding:
+ position: 0
+ prefix: gaincal.beammode=
+ separate: false
+ - default: 0
+ id: nchan
+ type: int
+ inputBinding:
+ position: 0
+ prefix: gaincal.nchan=
+ separate: false
+ - default: 50
+ id: maxiter
+ type: int
+ inputBinding:
+ position: 0
+ prefix: gaincal.maxiter=
+ separate: false
+ - default: 1e-3
+ id: tolerance
+ type: float
+ inputBinding:
+ position: 0
+ prefix: gaincal.tolerance=
+ separate: false
+ - default: null
+ id: blrange
+ type: 'int[]'
+ inputBinding:
+ position: 0
+ prefix: filter.blrange=
+ separate: false
+ itemSeparator: ','
+ valueFrom: "[$(self.join(','))]"
outputs:
- id: msout
doc: Output Measurement Set
type: Directory
outputBinding:
- glob: $(inputs.msout_name=="."?inputs.msin:inputs.msout_name)
-
+ glob: '$(inputs.msout_name=="."?inputs.msin.basename:inputs.msout_name)'
- id: h5parm
doc: Filename of output H5Parm (to be read by e.g. losoto)
type: File
- format: lofar:#H5Parm
outputBinding:
glob: $(inputs.output_name_h5parm)
-
-$namespaces:
- lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+ format: 'lofar:#H5Parm'
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: 'gaincal*.log'
+stdout: gaincal.log
+stderr: gaincal_err.log
+arguments:
+ - 'steps=[filter,gaincal]'
+hints:
+ - class: DockerRequirement
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+ - class: InlineJavascriptRequirement
$schema:
- - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+ - 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
diff --git a/lofar-cwl/steps/interpolate_visibilities.cwl b/lofar-cwl/steps/interpolate_visibilities.cwl
index 7d7c97f932ab6fa0d122544332e6d870a385923f..f59288857c81a6935fba6464f40c6be170af1f47 100644
--- a/lofar-cwl/steps/interpolate_visibilities.cwl
+++ b/lofar-cwl/steps/interpolate_visibilities.cwl
@@ -3,50 +3,52 @@ cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: interpolate_visibilities
-
baseCommand:
- DPPP
-arguments:
- - msout.datacolumn=INTERP_DATA
- - msout=.
- - msin.datacolumn=DATA
- - steps=[interpolate]
inputs:
- id: msin
type: Directory
inputBinding:
- prefix: 'msin='
+ position: 0
+ prefix: msin=
separate: false
- - id: storage_manager
+ - default: Dysco
+ id: storage_manager
type: string
- default: Dysco
inputBinding:
+ position: 0
+ prefix: msout.storagemanager=
separate: false
- prefix: 'msout.storagemanager='
- - id: storage_manager_databitrate
+ - default: 0
+ id: storage_manager_databitrate
type: int
- default: 0
inputBinding:
- prefix: 'msout.storagemanager.databitrate='
+ position: 0
+ prefix: msout.storagemanager.databitrate=
separate: false
- id: window_size
type: int
inputBinding:
- prefix: 'interpolate.windowsize='
+ position: 0
+ prefix: interpolate.windowsize=
separate: false
-
outputs:
- id: msout
type: Directory
outputBinding:
glob: $(inputs.msin.basename)
label: interpolate_visibilities
-hints:
- - class: DockerRequirement
- dockerPull: lofareosc/lofar-pipeline-ci:latest
-
+arguments:
+ - msout.datacolumn=INTERP_DATA
+ - msout=.
+ - msin.datacolumn=DATA
+ - 'steps=[interpolate]'
requirements:
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.msin)
writable: true
+ - class: InlineJavascriptRequirement
+hints:
+ - class: DockerRequirement
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
diff --git a/lofar-cwl/steps/makesourcedb.cwl b/lofar-cwl/steps/makesourcedb.cwl
index fec1acf4708bbd8857e01b840a51cb93cd8fc60a..97b23e5f5e9cc7d16c11bec60c29dc9ff0ca32c1 100755
--- a/lofar-cwl/steps/makesourcedb.cwl
+++ b/lofar-cwl/steps/makesourcedb.cwl
@@ -10,6 +10,7 @@ inputs:
type:
- File
- string
+ default: '/data/skymodels/Ateam_LBA_CC.skymodel'
inputBinding:
position: 0
prefix: in=
@@ -21,7 +22,7 @@ inputs:
position: 1
prefix: out=
separate: false
- valueFrom: Ateam.sourcedb
+ valueFrom: $(inputs.output_file_name)
- default: blob
id: outtype
type: string?
@@ -36,6 +37,9 @@ inputs:
position: 3
prefix: format=
separate: false
+ - default: make_sourcedb.log
+ id: logname
+ type: string?
outputs:
- id: sourcedb
type:
@@ -46,11 +50,11 @@ outputs:
- id: log
type: File?
outputBinding:
- glob: make_sourcedb_ateam.log
+ glob: $(inputs.logname)
label: make_sourcedb_ateam
hints:
- class: DockerRequirement
- dockerPull: 'lofareosc/lofar-pipeline:latest'
-stdout: make_sourcedb_ateam.log
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
+stdout: $(inputs.logname)
requirements:
- class: InlineJavascriptRequirement
diff --git a/lofar-cwl/steps/ms_concat.cwl b/lofar-cwl/steps/ms_concat.cwl
index c374f67951bfc9d73f0e8049636bf29541edc8c6..e52cb633efc76310b182afbf2abbb44416f8ef36 100644
--- a/lofar-cwl/steps/ms_concat.cwl
+++ b/lofar-cwl/steps/ms_concat.cwl
@@ -3,14 +3,13 @@ cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: ms_concat
-
-
baseCommand:
- - concat_MS.py
+ - python3
+ - /usr/local/bin/concat_MS_CWL.py
inputs:
- - id: min_length
+ - default: 50
+ id: min_length
type: int?
- default: 50
inputBinding:
position: 0
prefix: '--min_length'
@@ -35,25 +34,25 @@ inputs:
position: 2
outputs:
- id: concat_meta_ms
- type: Directory[]
+ type: 'Directory[]'
outputBinding:
- glob: >
+ glob: |
$(inputs.msout)_[0-9*]
- id: concat_additional_ms
- type: Directory[]
+ type: 'Directory[]'
outputBinding:
glob: $(inputs.msout)_*_CONCAT
- id: ms_outs
- type: Directory[]
+ type: 'Directory[]'
outputBinding:
outputEval: $(inputs.msin)
label: ms_concat
requirements:
- class: ShellCommandRequirement
- class: DockerRequirement
- dockerPull: lofareosc/lofar-pipeline-ci:latest
- - class: InlineJavascriptRequirement
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.msin)
writable: true
+ - class: InlineJavascriptRequirement
diff --git a/lofar-cwl/steps/predict.cwl b/lofar-cwl/steps/predict.cwl
index d9facbb83d6430dcde76caf49490e711afe14952..dcd0781c256c0ed5c88d0a3ba41d7f80ece813af 100644
--- a/lofar-cwl/steps/predict.cwl
+++ b/lofar-cwl/steps/predict.cwl
@@ -49,12 +49,37 @@ inputs:
inputBinding:
position: 0
prefix: predict.usebeammodel=True
+ - id: writefullresflag
+ type: boolean
+ default: false
+ inputBinding:
+ prefix: msout.writefullresflag=True
+ - id: overwrite
+ type: boolean
+ default: false
+ inputBinding:
+ prefix: msout.overwrite=True
+ - id: storagemanager
+ type: string
+ default: ""
+ inputBinding:
+ prefix: msout.storagemanager=
+ separate: false
+ - id: databitrate
+ type: int?
+ inputBinding:
+ prefix: msout.storagemanager.databitrate=
+ separate: false
outputs:
- id: msout
doc: Output Measurement Set
type: Directory
outputBinding:
glob: $(inputs.msin.basename)
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: 'predict_cal*.log'
arguments:
- 'steps=[predict]'
- predict.beammode=array_factor
@@ -68,4 +93,6 @@ requirements:
- class: InlineJavascriptRequirement
hints:
- class: DockerRequirement
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: predict_cal.log
+stderr: predict_cal_err.log
\ No newline at end of file
diff --git a/lofar-cwl/steps/utils.js b/lofar-cwl/steps/utils.js
index 2077e7bab63619084d2d767fd3603f464f4c319b..711c00ab03dfc1af230f3e891dde819da5775431 100644
--- a/lofar-cwl/steps/utils.js
+++ b/lofar-cwl/steps/utils.js
@@ -1,13 +1,13 @@
function get_losoto_config(step_name) {
var par = ['soltab = ' + inputs.soltab]
if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);
- console.log(inputs, par)
par.push("[" + step_name + "]")
par.push('operation=' + step_name)
for(var field_name in inputs){
if(field_name === 'input_h5parm' ||
field_name === 'soltab' ||
- field_name === 'ncpu') continue;
+ field_name === 'ncpu' ||
+ field_name === 'execute') continue;
if(inputs[field_name] === null ||
inputs[field_name] === 'null') continue;
@@ -22,3 +22,9 @@ function get_losoto_config(step_name) {
}
return par
}
+
+function concatenate_path(object_list){
+ object_list.forEach(function (x, index, arr) {arr[index] = x.path;});
+ return '[' + object_list.join(',') + ']'
+
+}
\ No newline at end of file
diff --git a/lofar-cwl/steps/wsclean.cwl b/lofar-cwl/steps/wsclean.cwl
index b1ab1734c56bf7af9f1efb30a6a94c9e77dd3ad4..08d1e3d6596529d97a9ff5f718a983676afd748c 100644
--- a/lofar-cwl/steps/wsclean.cwl
+++ b/lofar-cwl/steps/wsclean.cwl
@@ -1,42 +1,47 @@
class: CommandLineTool
cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
id: wsclean
baseCommand:
- wsclean
inputs:
- - id: image_size
- type: int[]
- default: [1000, 1000]
+ - default:
+ - 1000
+ - 1000
+ id: image_size
+ type: 'int[]'
inputBinding:
position: 1
- prefix: -size
- - id: image_scale
+ prefix: '-size'
+ - default: 0.01
+ id: image_scale
type: float
- default: 0.01
inputBinding:
position: 1
- prefix: -scale
+ prefix: '-scale'
valueFrom: $(self)deg
- - id: image_name
- default: image
+ - default: image
+ id: image_name
type: string
inputBinding:
position: 1
- prefix: -name
+ prefix: '-name'
- id: msin
type: Directory
inputBinding:
position: 2
outputs:
- dirty_image:
+ - id: dirty_image
type: File
outputBinding:
glob: $(inputs.image_name)-dirty.fits
- image:
+ - id: image
type: File
outputBinding:
glob: $(inputs.image_name)-image.fits
label: WSClean
requirements:
- class: DockerRequirement
- dockerPull: lofareosc/lofar-pipeline-ci:latest
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
+ - class: InlineJavascriptRequirement
diff --git a/steps/add_missing_stations.cwl b/steps/add_missing_stations.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..d2258e1771c70c2055aaf01b9b0ead31285cc0ae
--- /dev/null
+++ b/steps/add_missing_stations.cwl
@@ -0,0 +1,89 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
+ sbg: 'https://www.sevenbridges.com/'
+id: add_missing_stations
+baseCommand:
+ - python3
+ - /usr/local/bin/add_missing_stations.py
+inputs:
+ - default: output.h5
+ id: h5parm
+ type: File
+ inputBinding:
+ position: 1
+ doc: H5parm to which this action should be performed.
+ - id: refh5parm
+ type: File
+ inputBinding:
+ position: 0
+ prefix: '--refh5'
+ doc: External H5parm from which the full list of antennas is used from.
+ - id: solset
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--solset'
+ default: 'sol000'
+ doc: Input calibration solutions
+ - id: refsolset
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--refsolset'
+ doc: Input calibration solutions of the reference h5parm file
+ default: 'sol000'
+ - id: soltab_in
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--soltab_in'
+ doc: Input solution table
+ default: 'phase000'
+ - id: soltab_out
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--soltab_out'
+ doc: Output solution table (has to be different from input solution table)
+ default: 'GSMphase'
+ - id: filter
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--filter'
+ doc: Filter these antenna string from the processing
+ default: '[CR]S*&'
+ - id: bad_antennas
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--bad_antennas'
+ doc: Antenna string to be processed
+ default: '[CR]S*&'
+outputs:
+ - id: outh5parm
+ type: File
+ outputBinding:
+ glob: $(inputs.h5parm.basename)
+ format: 'lofar:#H5Parm'
+ - id: log
+ type: File[]
+ outputBinding:
+ glob: 'add_missing_stations*.log'
+
+stdout: add_missing_stations.log
+stderr: add_missing_stations_err.log
+label: add_missing_stations
+hints:
+ - class: DockerRequirement
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.h5parm)
+ writable: true
+$schema:
+ - 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
diff --git a/steps/blsmooth.cwl b/steps/blsmooth.cwl
index ccce108ee515d21d5c22202ea074d63d564fde93..47d6c59a1af6a835f6ff6e3bb0d1c467f31e1ce3 100644
--- a/steps/blsmooth.cwl
+++ b/steps/blsmooth.cwl
@@ -22,8 +22,9 @@ inputs:
type: boolean
doc: 'If true performs smoothing'
inputBinding:
- prefix: '--smooth=SMOOTH'
-
+ prefix: -S
+ valueFrom: "$(self ? 'True': 'False')"
+ separate: true
- default: 0.5
id: bscalefactor
type: float
@@ -81,12 +82,17 @@ outputs:
type: Directory
outputBinding:
glob: $(inputs.msin.basename)
+ - id: logfile
+ type: File
+ outputBinding:
+ glob: BLsmooth.log
hints:
- class: DockerRequirement
- dockerPull: lofareosc/prefactor-ci:master
+ dockerPull: lofareosc/prefactor:HBAcalibrator
requirements:
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.msin)
writable: true
- class: InlineJavascriptRequirement
+stderr: BLsmooth.log
diff --git a/steps/bulk_rename.cwl b/steps/bulk_rename.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..9102a16c2b80e11c577082a1b0f2498319eb2779
--- /dev/null
+++ b/steps/bulk_rename.cwl
@@ -0,0 +1,39 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: bulk_rename
+baseCommand:
+ - bash
+ - bulk_rename.sh
+inputs:
+ - id: file_list
+ type: 'File[]'
+ inputBinding:
+ position: 0
+ - id: file_prefix
+ type: string
+ - id: file_suffix
+ type: string?
+outputs:
+ - id: output
+ type: 'File[]'
+ outputBinding:
+ glob: "tmp/$(inputs.file_prefix)*"
+label: bulk_rename
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: bulk_rename.sh
+ entry: |
+ #!/bin/bash
+ set -e
+ FILE_LIST=("\${@}")
+ FILE_PREFIX=$(inputs.file_prefix)
+ FILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)
+ mkdir tmp
+ for i in "\${!FILE_LIST[@]}"; do
+ cp "\${FILE_LIST[\$i]}" "tmp/\${FILE_PREFIX}_\${i}\${FILE_SUFFIX}"
+ done
+ writable: false
+ - class: InlineJavascriptRequirement
\ No newline at end of file
diff --git a/steps/check_ateam_separation.cwl b/steps/check_ateam_separation.cwl
old mode 100755
new mode 100644
index 977d9f86e63f3b003833aee677d330f1f188253d..516beb6100f9e73b06cef498a05fc64ae74bd101
--- a/steps/check_ateam_separation.cwl
+++ b/steps/check_ateam_separation.cwl
@@ -39,6 +39,6 @@ outputs:
label: check_Ateam_separation
hints:
- class: DockerRequirement
- dockerPull: lofareosc/prefactor
+ dockerPull: lofareosc/prefactor:HBAcalibrator
- class: InlineJavascriptRequirement
stdout: Ateam_separation.log
diff --git a/steps/check_unflagged_fraction.cwl b/steps/check_unflagged_fraction.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..0a42b9ff12519530c2abf7c49d1479d8be50ec95
--- /dev/null
+++ b/steps/check_unflagged_fraction.cwl
@@ -0,0 +1,74 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: check_unflagged_fraction
+baseCommand:
+ - python3
+inputs:
+ - id: msin
+ type: Directory
+ doc: MS to check
+ inputBinding:
+ position: 0
+ - id: min_fraction
+ type: float?
+ default: 0.5
+ doc: Fraction of flagged data in a MS to be acceptable
+
+label: check_unflagged_fraction
+arguments:
+ - '-c'
+ - |
+ import sys
+ import json
+ import shutil
+ import os
+
+ from check_unflagged_fraction import main as check_unflagged_fraction
+
+ ms = sys.argv[1]
+ min_fraction = float($(inputs.min_fraction))
+
+ output = check_unflagged_fraction(ms, min_fraction=min_fraction, print_fraction=True)
+
+ filename = os.path.basename(output['flagged'])
+ unflagged_fraction = output['unflagged_fraction']
+
+ if filename != 'None':
+ shutil.move(filename, filename.lstrip('out_'))
+
+ cwl_output = {}
+ cwl_output['unflagged_fraction'] = unflagged_fraction
+
+ with open('./out.json', 'w') as fp:
+ json.dump(cwl_output, fp)
+
+outputs:
+ - id: msout
+ type: Directory[]
+ outputBinding:
+ glob: 'L*.dpppconcat'
+ - id: unflagged_fraction
+ type: float
+ outputBinding:
+ loadContents: true
+ glob: 'out.json'
+ outputEval: $(JSON.parse(self[0].contents).unflagged_fraction)
+ - id: logfile
+ type: File[]?
+ outputBinding:
+ glob: 'check_unflagged_fraction*.log'
+
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: check_unflagged_fraction.log
+stderr: check_unflagged_fraction_err.log
\ No newline at end of file
diff --git a/steps/collectlog.cwl b/steps/collectlog.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..ab5987b158461486c26fd1c3f6066c54c4136ffa
--- /dev/null
+++ b/steps/collectlog.cwl
@@ -0,0 +1,49 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: collectlog
+baseCommand:
+ - bash
+ - collect_logs.sh
+inputs:
+ - id: start_directory
+ type: Directory?
+ - id: log_files
+ type:
+ - File
+ - type: array
+ items:
+ - File
+ - Directory
+ inputBinding:
+ position: 0
+ - id: sub_directory_name
+ type: string
+outputs:
+ - id: log_dir
+ type: Directory
+ outputBinding:
+ glob: |
+ $(inputs.start_directory === null ? inputs.sub_directory_name: inputs.start_directory.basename)
+label: CollectLog
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: collect_logs.sh
+ entry: |
+ #!/bin/bash
+ set -e
+ BASE_DIR="$(inputs.start_directory === null ? "" : inputs.start_directory.basename)"
+ SUB_DIR="$(inputs.sub_directory_name)"
+ if [ -z "$BASE_DIR" ]
+ then
+ OUTPUT_PATH=$SUB_DIR
+ else
+ OUTPUT_PATH=$BASE_DIR/$SUB_DIR
+ fi
+ echo $OUTPUT_PATH
+ mkdir -p $OUTPUT_PATH
+ cp -rL $* $OUTPUT_PATH
+ writable: false
+ - class: InlineJavascriptRequirement
diff --git a/steps/compare_station_list.cwl b/steps/compare_station_list.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..21e18c5f8aeec2430e1ebbd850a297d69575c5c0
--- /dev/null
+++ b/steps/compare_station_list.cwl
@@ -0,0 +1,65 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: compare_station_list
+baseCommand:
+ - python3
+inputs:
+ - id: msin
+ type: Directory[]
+ doc: MS to compare with
+ inputBinding:
+ position: 0
+ - id: h5parmdb
+ type: File
+ doc: H5parm database to compare with
+ - id: solset_name
+ type: string?
+ doc: Name of the H5parm solset
+ default: 'sol000'
+ - id: filter
+ type: string?
+ default: '*&'
+ doc: Filter these baselines for the comparison
+
+label: compareStationList.py
+arguments:
+ - '-c'
+ - |
+ import sys
+ import json
+ from compareStationList import main as compareStationList
+
+ mss = sys.argv[1:]
+ h5parmdb = $(inputs.h5parmdb)['path']
+ solset_name = '$(inputs.solset_name)'
+ filter = '$(inputs.filter)'
+
+ output = compareStationList(mss, h5parmdb, solset_name, filter)
+
+ filter_out = output['filter']
+ cwl_output = {"filter_out": filter_out}
+
+ with open('./out.json', 'w') as fp:
+ json.dump(cwl_output, fp)
+outputs:
+ - id: filter_out
+ type: string
+ outputBinding:
+ loadContents: true
+ glob: 'out.json'
+ outputEval: $(JSON.parse(self[0].contents).filter_out)
+ - id: logfile
+ type: File[]?
+ outputBinding:
+ glob: 'compareStationList*.log'
+
+requirements:
+ - class: InlineJavascriptRequirement
+
+hints:
+ DockerRequirement:
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: compareStationList.log
+stderr: compareStationList_err.log
\ No newline at end of file
diff --git a/steps/concatenate_files.cwl b/steps/concatenate_files.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..e3f5bdac0a5e03c744726b23699baf0c3834a212
--- /dev/null
+++ b/steps/concatenate_files.cwl
@@ -0,0 +1,37 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: concatfiles
+baseCommand:
+ - bash
+ - bulk_rename.sh
+inputs:
+ - id: file_list
+ type: 'File[]'
+ inputBinding:
+ position: 0
+ - id: file_prefix
+ type: string
+ - id: file_suffix
+ type: string?
+ default: log
+outputs:
+ - id: output
+ type: File
+ outputBinding:
+ glob: "$(inputs.file_prefix).$(inputs.file_suffix)"
+label: concatfiles
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: bulk_rename.sh
+ entry: |
+ #!/bin/bash
+ set -e
+ FILE_LIST=("\${@}")
+ FILE_PREFIX=$(inputs.file_prefix)
+ FILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)
+ cat "\${FILE_LIST[@]}" > $FILE_PREFIX.$FILE_SUFFIX
+ writable: false
+ - class: InlineJavascriptRequirement
diff --git a/steps/createRMh5parm.cwl b/steps/createRMh5parm.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..d79ceaa783f93cf1dee382d2c398319b5f5ed019
--- /dev/null
+++ b/steps/createRMh5parm.cwl
@@ -0,0 +1,123 @@
+class: CommandLineTool
+cwlVersion: v1.0
+id: createRMh5parm
+label: createRMh5parm
+baseCommand:
+ - python3
+ - /usr/local/bin/createRMh5parm.py
+inputs:
+ - id: msin
+ type:
+ - Directory
+ - type: array
+ items: Directory
+ inputBinding:
+ position: 1
+ doc: Input measurement set
+ - id: h5parm
+ type: File
+ inputBinding:
+ position: 2
+ doc: Input h5parm solutions file
+ - id: ionex_server
+ type: string
+ doc: IONEX Server path
+ default: 'ftp://ftp.aiub.unibe.ch/CODE/'
+ inputBinding:
+ prefix: '--server'
+ position: 0
+ - id: ionex_prefix
+ type: string
+ doc: IONEX Prefix
+ default: 'CODG'
+ inputBinding:
+ prefix: '--prefix'
+ position: 0
+ - id: ionex_path
+ type: string
+ doc: IONEX path
+ default: './'
+ inputBinding:
+ prefix: '--path'
+ position: 0
+ - id: solset
+ type: string
+ doc: solset in which IONEX solution are put
+ default: 'sol000'
+ inputBinding:
+ prefix: '--solsetName'
+ position: 0
+ - id: timestep
+ type: float
+ doc: timestep in seconds
+ default: 300.
+ inputBinding:
+ prefix: '-t'
+ position: 0
+ - id: smart_interpol
+ type: float
+ doc: float parameter describing how much of Earth rotation is taken in to account in interpolation of the IONEX files. 1.0 means time interpolation assumes ionosphere rotates in opposite direction of the Earth
+ default: 0.
+ inputBinding:
+ prefix: '-e'
+ position: 0
+ - id: proxyserver
+ type: string
+ doc: Specify proxy server if necessary
+ default: null
+ inputBinding:
+ prefix: '--proxyserver'
+ position: 0
+ - id: proxyport
+ type: int
+ doc: Specify proxy port if necessary
+ default: null
+ inputBinding:
+ prefix: '--proxyport'
+ position: 0
+ - id: proxytype
+ type: string
+ doc: Specify proxy type if necessary
+ default: null
+ inputBinding:
+ prefix: '--proxytype'
+ position: 0
+ - id: proxyuser
+ type: string
+ doc: Specify proxy user name if necessary
+ default: null
+ inputBinding:
+ prefix: '--proxyuser'
+ position: 0
+ - id: proxypass
+ type: string
+ doc: Specify proxy server password if necessary
+ default: null
+ inputBinding:
+ prefix: '--proxypass'
+ position: 0
+outputs:
+ - id: h5parmout
+ doc: h5parm output
+ type: File
+ format: 'lofar:#H5Parm'
+ outputBinding:
+ glob: $(inputs.h5parm.basename)
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: 'createh5parm*.log'
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.h5parm)
+ writable: true
+
+stdout: createh5parm.log
+stderr: createh5parm_err.log
+$namespaces:
+ lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+$schema:
+ - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
diff --git a/steps/create_workflow_input.cwl b/steps/create_workflow_input.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..505eecf6aa537f5e59391e59a1e3d46f7deaec71
--- /dev/null
+++ b/steps/create_workflow_input.cwl
@@ -0,0 +1,42 @@
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: create_workflow_input
+label: create_workflow_input
+class: CommandLineTool
+cwlVersion: v1.0
+inputs:
+ - id: msin
+ type: Directory[]
+ inputBinding:
+ position: 0
+
+outputs:
+ - id: output
+ type: File
+ outputBinding:
+ glob: workflow_input.json
+
+baseCommand:
+ - python3
+ - script.py
+doc: ''
+requirements:
+ InitialWorkDirRequirement:
+ listing:
+ - entryname: script.py
+ entry: |
+ #!/usr/bin/env python3
+
+ import sys
+ import json
+ import os
+ dir_list = sys.argv[1:]
+ rendered_leafs = []
+
+ for dir in dir_list:
+ file_name = dir.split(os.path.sep)[-1]
+ rendered_leaf = {'class': 'Directory', 'path': file_name}
+ rendered_leafs.append(rendered_leaf)
+
+ with open('workflow_input.json', 'w') as fp:
+ json.dump({'msin': rendered_leafs}, fp, indent=4)
\ No newline at end of file
diff --git a/steps/filter_ms_group.cwl b/steps/filter_ms_group.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..d51dcf695a9e51a0b748b14c56842b4e76d64284
--- /dev/null
+++ b/steps/filter_ms_group.cwl
@@ -0,0 +1,58 @@
+class: CommandLineTool
+cwlVersion: v1.0
+id: filter_ms_group
+baseCommand:
+ - python3
+arguments:
+ - position: 0
+ valueFrom: script.py
+inputs:
+ - id: group_id
+ type: string
+ - id: groups_specification
+ type: File
+ inputBinding:
+ position: 1
+ - id: measurement_sets
+ type: 'Directory[]'
+ inputBinding:
+ position: 2
+outputs:
+ - id: output
+ type: Directory[]
+ outputBinding:
+ loadContents: true
+ glob: selected_ms.json
+ outputEval: '$(JSON.parse(self[0].contents))'
+label: filter_ms_group
+
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: script.py
+ entry: |
+ import sys
+ import json
+ import os
+
+ group_id = "$(inputs.group_id)"
+ json_file = sys.argv[1]
+ ms_list = sys.argv[2:]
+
+ ms_by_name = { ms.split(os.path.sep)[-1]:
+ {'class':'Directory', 'path': ms} for ms in ms_list}
+
+ output_file = 'selected_ms.json'
+
+ with open(json_file, 'r') as f_stream:
+ selected_ms = json.load(f_stream)[group_id]
+ print(selected_ms, ms_by_name)
+ selected_ms = [ms_by_name[os.path.basename(ms_name)] for ms_name in selected_ms]
+
+
+ with open(output_file, 'w') as f_stream:
+ json.dump(selected_ms, f_stream)
+
+
+
diff --git a/steps/findRefAnt.cwl b/steps/findRefAnt.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..e6562e0f61183e65d7046c146915940877264a61
--- /dev/null
+++ b/steps/findRefAnt.cwl
@@ -0,0 +1,54 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: findRefAnt
+baseCommand:
+ - python3
+inputs:
+ - id: msin
+ type: Directory
+ doc: MS to compare with
+ inputBinding:
+ position: 0
+
+label: findRefAnt.py
+arguments:
+ - '-c'
+ - |
+ import sys
+ import json
+ from findRefAnt import main as findRefAnt
+
+ ms = sys.argv[1]
+
+ flagged_fraction_dict = str(findRefAnt(ms))
+
+ cwl_output = {"flagged_fraction_dict": flagged_fraction_dict}
+
+ with open('./out.json', 'w') as fp:
+ json.dump(cwl_output, fp)
+
+outputs:
+ - id: flagged_fraction_dict
+ type: string
+ outputBinding:
+ loadContents: true
+ glob: 'out.json'
+ outputEval: $(JSON.parse(self[0].contents).flagged_fraction_dict)
+ - id: logfile
+ type: File?
+ outputBinding:
+ glob: findRefAnt.log
+
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: findRefAnt.log
+stderr: findRefAnt_err.log
\ No newline at end of file
diff --git a/steps/findRefAnt_join.cwl b/steps/findRefAnt_join.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..11636573f7705c50ca1e783ec862e133cc2dfb11
--- /dev/null
+++ b/steps/findRefAnt_join.cwl
@@ -0,0 +1,80 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: findRefAnt_join
+baseCommand:
+ - python3
+inputs:
+ - id: flagged_fraction_dict
+ type: string[]?
+ default: []
+ doc: list of flagged antennas per MS
+ - id: filter_station
+ type: string?
+ default: '*&'
+ doc: Filter these baselines for the comparison
+
+label: findRefAnt_join
+arguments:
+ - '-c'
+ - |
+
+ import sys
+ import json
+ import re
+ import ast
+
+ flagged_fraction_dict_list = $(inputs.flagged_fraction_dict)
+ filter_station = '$(inputs.filter_station)'
+
+ flagged_fraction_data = {}
+ for flagged_fraction_dict in flagged_fraction_dict_list:
+ entry = ast.literal_eval(flagged_fraction_dict)
+ antennas = entry.keys()
+ selected_stations = [ station_name for station_name in antennas if re.match(filter_station, station_name) ]
+ if len(selected_stations) == 0:
+ raiseError('No stations left after filtering.')
+ for antenna in selected_stations:
+ try:
+ flagged_fraction_data[antenna].append(float(entry[antenna]))
+ except KeyError:
+ flagged_fraction_data[antenna] = [float(entry[antenna])]
+
+ flagged_fraction_list = []
+ sorted_stations = sorted(flagged_fraction_data.keys())
+
+ for antenna in sorted_stations:
+ flagged_fraction = sum(flagged_fraction_data[antenna]) / len(flagged_fraction_data[antenna])
+ flagged_fraction_list.append(flagged_fraction)
+ try:
+ flagged_fraction_data[flagged_fraction].append(antenna)
+ except KeyError:
+ flagged_fraction_data[flagged_fraction] = [antenna]
+
+ min_flagged_fraction = min(flagged_fraction_list)
+ refant = flagged_fraction_data[min_flagged_fraction][0]
+ print('Selected station ' + str(refant) + ' as reference antenna. Fraction of flagged data is ' + '{:>3}'.format('{:.1f}'.format(min_flagged_fraction) + '%'))
+
+ cwl_output = {'refant': str(refant)}
+
+ with open('./out.json', 'w') as fp:
+ json.dump(cwl_output, fp)
+
+outputs:
+ - id: refant
+ type: string
+ outputBinding:
+ loadContents: true
+ glob: 'out.json'
+ outputEval: $(JSON.parse(self[0].contents).refant)
+ - id: logfile
+ type: File?
+ outputBinding:
+ glob: findRefAnt.log
+
+requirements:
+ - class: InlineJavascriptRequirement
+
+stdout: findRefAnt.log
+stderr: findRefAnt_err.log
\ No newline at end of file
diff --git a/steps/find_skymodel_cal.cwl b/steps/find_skymodel_cal.cwl
index 4bfe9b81deb56d97c324a10c4d156a08bd63bee4..4d0956951eda01b2d626f12344c73209f97de776 100644
--- a/steps/find_skymodel_cal.cwl
+++ b/steps/find_skymodel_cal.cwl
@@ -7,53 +7,90 @@ baseCommand:
- python3
inputs:
- id: msin
- type: Directory
+ type:
+ - Directory
+ - Directory[]
doc: MS containing the calibrator
inputBinding:
position: 0
- id: skymodels
- type: Directory
- doc: Directory containing the sky models
+ type:
+ - Directory?
+ - File?
+ doc: Directory or file containing the sky models
- id: skymodels_extension
type: string?
doc: path extension of the sky models
+ - id: max_separation_arcmin
+ type: float?
+ doc: max separation in arc minutes
label: find_skymodel_cal.py
arguments:
- - '-c'
- - |
- import sys
-
- from unittest.mock import MagicMock
- sys.modules['lofarpipe.support.data_map'] = MagicMock()
-
-
- from find_skymodel_cal import main as find_skymodel
- import json
- mss = sys.argv[1:]
- skymodels = "$(inputs.skymodels.path)"
-
- extension = "$(inputs.skymodels_extension)"
- output = {}
- if extension != 'null':
- output = find_skymodel(mss, skymodels, extension)
- else:
- output = find_skymodel(mss, skymodels )
-
- cwl_output = {'class': 'File', 'path': output['SkymodelCal']}
- with open('./out.json', 'w') as fp:
- json.dump(cwl_output, fp)
+ - find_sky.py
outputs:
- id: output_models
type: File
outputBinding:
loadContents: true
glob: 'out.json'
- outputEval: $(JSON.parse(self[0].contents))
+ outputEval: $(JSON.parse(self[0].contents).file)
+ - id: model_name
+ type: string
+ outputBinding:
+ loadContents: true
+ glob: 'out.json'
+ outputEval: $(JSON.parse(self[0].contents).skymodel_name)
+ - id: logfile
+ type: File?
+ outputBinding:
+ glob: find_skymodel_cal.log
+
requirements:
- class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: 'find_sky.py'
+ entry: |
+ import sys
+ import os
+ import shutil
+ null = None
+
+ from unittest.mock import MagicMock
+ sys.modules['lofarpipe.support.data_map'] = MagicMock()
+
+
+ from find_skymodel_cal import main as find_skymodel
+ import json
+ mss = sys.argv[1:]
+
+ skymodels = $(inputs.skymodels)
+ max_separation_arcmin = $(inputs.max_separation_arcmin)
+ max_separation_arcmin = 1.0 if max_separation_arcmin else max_separation_arcmin
+ extension = "$(inputs.skymodels_extension)"
+ if skymodels is None:
+ skymodels = "/data/skymodels"
+ else:
+ skymodels = skymodels["path"]
+ output = {}
+ if extension != 'null':
+ output = find_skymodel(mss, skymodels, extension, max_separation_arcmin=max_separation_arcmin)
+ else:
+ output = find_skymodel(mss, skymodels, max_separation_arcmin=max_separation_arcmin)
+
+ skymodel_path = output['SkymodelCal']
+ skymodel_name = output['SkymodelName']
+ skymodel_path = shutil.copy(skymodel_path, os.getcwd())
+ cwl_output = {"file":{'class': 'File', 'path': skymodel_path},
+ "skymodel_name": skymodel_name}
+
+ with open('./out.json', 'w') as fp:
+ json.dump(cwl_output, fp)
+
hints:
DockerRequirement:
- dockerPull: lofareosc/prefactor-ci:master
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: find_skymodel_cal.log
diff --git a/steps/find_skymodel_target.cwl b/steps/find_skymodel_target.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..36191f1c6d89c1fa6240eb81698c211f4c8f481b
--- /dev/null
+++ b/steps/find_skymodel_target.cwl
@@ -0,0 +1,74 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: find_skymodel_target_py
+baseCommand:
+ - python3
+inputs:
+ - id: msin
+ type: Directory[]
+ doc: MS containing the target
+ inputBinding:
+ position: 0
+ - id: SkymodelPath
+ type: File?
+ doc: File containing or putting the skymodel
+ - id: Radius
+ type: float?
+ doc: Radius of the skymodel
+ default: 5.0
+ - id: Source
+ type: string?
+ doc: Source of the skymodel
+ default: 'TGSS'
+ - id: DoDownload
+ type: boolean?
+ doc: Download a new skymodel if given path is empty
+ default: true
+
+label: find_skymodel_target.py
+arguments:
+ - '-c'
+ - |
+ import sys
+ import shutil
+ import os
+ null = None
+
+ from download_skymodel_target import main as download_skymodel_target
+
+ mss = sys.argv[1:]
+
+ SkymodelPath = $(inputs.SkymodelPath)
+ if SkymodelPath is None:
+ SkymodelPath = os.getcwd() + "/target.skymodel"
+ else:
+ SkymodelPath = SkymodelPath["path"]
+
+ Radius = $(inputs.Radius)
+ Source = "$(inputs.Source)"
+ DoDownload = "$(inputs.DoDownload)"
+
+ output = download_skymodel_target(mss, SkymodelPath, Radius, DoDownload, Source)
+
+ if "target.skymodel" not in SkymodelPath:
+ shutil.copyfile(SkymodelPath, "target.skymodel")
+
+outputs:
+ - id: skymodel
+ type: File?
+ outputBinding:
+ glob: target.skymodel
+ - id: logfile
+ type: File?
+ outputBinding:
+ glob: find_skymodel_target.log
+
+requirements:
+ - class: InlineJavascriptRequirement
+
+hints:
+ DockerRequirement:
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: find_skymodel_target.log
\ No newline at end of file
diff --git a/steps/get_targetname.cwl b/steps/get_targetname.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..9c999be81045fae929190a57bcb4ce20ebb009ae
--- /dev/null
+++ b/steps/get_targetname.cwl
@@ -0,0 +1,55 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
+ sbg: 'https://www.sevenbridges.com/'
+id: get_targetname
+baseCommand:
+ - python3
+inputs:
+ - id: msin
+ type: Directory[]
+ doc: MS to compare with
+ inputBinding:
+ position: 0
+
+arguments:
+ - '-c'
+ - |
+ import sys
+ import json
+ from getTargetName import main as getTargetName
+
+ mss = sys.argv[1:]
+
+ output = getTargetName(mss)
+
+ targetName = output['targetName']
+ cwl_output = {"targetName": targetName}
+
+ with open('./out.json', 'w') as fp:
+ json.dump(cwl_output, fp)
+
+outputs:
+ - id: targetname
+ type: string
+ outputBinding:
+ loadContents: true
+ glob: 'out.json'
+ outputEval: $(JSON.parse(self[0].contents).targetName)
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: 'get_targetname*.log'
+
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: get_targetname.log
+stderr: get_targetname_err.log
diff --git a/steps/h5parm_pointingname.cwl b/steps/h5parm_pointingname.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..30ecb0cf1940c57d0b9fae3167980bf646a68f96
--- /dev/null
+++ b/steps/h5parm_pointingname.cwl
@@ -0,0 +1,55 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
+ sbg: 'https://www.sevenbridges.com/'
+id: h5parm_pointingname
+baseCommand:
+ - python3
+ - /usr/local/bin/h5parm_pointingname.py
+inputs:
+ - format: 'lofar:#H5Parm'
+ id: h5parmFile
+ type: File
+ inputBinding:
+ position: 0
+ doc: List of h5parm files
+ - default: 'target'
+ id: solsetName
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--solsetName'
+ doc: Input solset name
+ - default: 'POINTING'
+ id: pointing
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--pointing'
+ doc: Name of the pointing
+outputs:
+ - id: outh5parm
+ doc: Output h5parm
+ type: File
+ outputBinding:
+ glob: $(inputs.h5parmFile.basename)
+ format: lofar:#H5Parm
+ - id: log
+ type: File[]
+ outputBinding:
+ glob: 'h5parm_pointingname*.log'
+label: h5parm_pointingname
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.h5parmFile)
+ writable: true
+ - class: InlineJavascriptRequirement
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: h5parm_pointingname.log
+stderr: h5parm_pointingname_err.log
+$schema:
+ - 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
diff --git a/steps/h5parmcat.cwl b/steps/h5parmcat.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..2770fc827f22878db2d626da6f0ff81fa6189535
--- /dev/null
+++ b/steps/h5parmcat.cwl
@@ -0,0 +1,96 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
+ sbg: 'https://www.sevenbridges.com/'
+id: h5parm_cat
+baseCommand:
+ - H5parm_collector.py
+inputs:
+ - format: 'lofar:#H5Parm'
+ id: h5parmFile
+ type: File
+ 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: output.h5
+ id: input_file
+ type: File
+ doc: Output h5parm name
+ - default: false
+ id: squeeze
+ type: boolean
+ 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: false
+ id: clobber
+ type: boolean
+ inputBinding:
+ position: 0
+ prefix: '-c'
+ doc: overwrite output
+ - default: false
+ id: history
+ type: boolean
+ inputBinding:
+ position: 0
+ prefix: '-H'
+ doc: Keep history of the export soltabs
+outputs:
+ - id: outh5parm
+ doc: Output h5parm
+ type: File
+ outputBinding:
+ glob: $(inputs.input_file.basename)
+ format: lofar:#H5Parm
+ - id: log
+ type: File[]
+ outputBinding:
+ glob: 'h5parm_collector_output*.log'
+label: h5parm_cat
+arguments:
+ - position: 0
+ prefix: '-o'
+ valueFrom: $(inputs.input_file.basename)
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.input_file)
+ writable: true
+ - class: InlineJavascriptRequirement
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: h5parm_collector_output.log
+stderr: h5parm_collector_output_err.log
+$schema:
+ - 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
diff --git a/steps/identify_bad_antennas.cwl b/steps/identify_bad_antennas.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..0fa09ff11bd4a10d481a196c4fd3441d37ca8b6e
--- /dev/null
+++ b/steps/identify_bad_antennas.cwl
@@ -0,0 +1,55 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: identify_bad_antennas
+baseCommand:
+ - python3
+inputs:
+ - id: msin
+ type: Directory
+ doc: MS to compare with
+ inputBinding:
+ position: 0
+
+label: identifyBadAntennas.py
+arguments:
+ - '-c'
+ - |
+ import sys
+ import json
+ from identifyBadAntennas_CWL import main as identifyBadAntennas
+
+ ms = sys.argv[1]
+
+ output = identifyBadAntennas(ms)
+
+ flaggedants = output['flaggedants']
+ cwl_output = {"flaggedants": flaggedants}
+
+ with open('./out.json', 'w') as fp:
+ json.dump(cwl_output, fp)
+
+outputs:
+ - id: flaggedants
+ type: string
+ outputBinding:
+ loadContents: true
+ glob: 'out.json'
+ outputEval: $(JSON.parse(self[0].contents).flaggedants)
+ - id: logfile
+ type: File?
+ outputBinding:
+ glob: identifyBadAntennas.log
+
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: identifyBadAntennas.log
+stderr: identifyBadAntennas_err.log
\ No newline at end of file
diff --git a/steps/identify_bad_antennas_join.cwl b/steps/identify_bad_antennas_join.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..03a3c2e5b9b6548c9325bbd9eaf18fcd96b5c514
--- /dev/null
+++ b/steps/identify_bad_antennas_join.cwl
@@ -0,0 +1,57 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: identify_bad_antennas_join
+baseCommand:
+ - python3
+inputs:
+ - id: flaggedants
+ type: string[]?
+ default: []
+ doc: list of flagged antennas
+ - id: filter
+ type: string?
+ default: '*&'
+ doc: Filter these baselines for the comparison
+
+label: identifyBadAntennas_join
+arguments:
+ - '-c'
+ - |
+
+ import sys
+ import json
+
+ flaggedants = $(inputs.flaggedants)
+ filter = '$(inputs.filter)'
+
+
+ flaggedants_list = [ flaggedant.split(',') for flaggedant in flaggedants ]
+ flagged_antenna_list = set.intersection(*map(set, flaggedants_list))
+
+ for flagged_antenna in flagged_antenna_list:
+ filter += ';!' + flagged_antenna + '*&&*'
+
+ cwl_output = {"filter": filter}
+
+ with open('./out.json', 'w') as fp:
+ json.dump(cwl_output, fp)
+
+outputs:
+ - id: filter_out
+ type: string
+ outputBinding:
+ loadContents: true
+ glob: 'out.json'
+ outputEval: $(JSON.parse(self[0].contents).filter)
+ - id: logfile
+ type: File?
+ outputBinding:
+ glob: identifyBadAntennas.log
+
+requirements:
+ - class: InlineJavascriptRequirement
+
+stdout: identifyBadAntennas.log
+stderr: identifyBadAntennas_err.log
\ No newline at end of file
diff --git a/steps/merge_array.cwl b/steps/merge_array.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..7d8fef0a75749789ad62c9fdd4840fc9ce17a986
--- /dev/null
+++ b/steps/merge_array.cwl
@@ -0,0 +1,31 @@
+id: merge_array
+label: merge_array
+class: ExpressionTool
+
+cwlVersion: v1.0
+inputs:
+ - id: input
+ type:
+ - type: array
+ items:
+ - type: array
+ items: Directory
+outputs:
+ - id: output
+ type: Directory[]
+
+expression: |
+ ${
+ var out_dir = []
+ for(var i=0; i<inputs.input.length; i++){
+ var item = inputs.input[i]
+ if(item != null){
+ out_dir = out_dir.concat(item)
+ }
+ }
+ return {'output': out_dir}
+ }
+
+
+requirements:
+ - class: InlineJavascriptRequirement
\ No newline at end of file
diff --git a/steps/merge_array_files.cwl b/steps/merge_array_files.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..c4c5c6122e03f690e2bcf14307ec052f4d846f86
--- /dev/null
+++ b/steps/merge_array_files.cwl
@@ -0,0 +1,31 @@
+id: merge_array_files
+label: merge_array_files
+class: ExpressionTool
+
+cwlVersion: v1.0
+inputs:
+ - id: input
+ type:
+ - type: array
+ items:
+ - type: array
+ items: File
+outputs:
+ - id: output
+ type: File[]
+
+expression: |
+ ${
+ var out_file = []
+ for(var i=0; i<inputs.input.length; i++){
+ var item = inputs.input[i]
+ if(item != null){
+ out_file = out_file.concat(item)
+ }
+ }
+ return {'output': out_file}
+ }
+
+
+requirements:
+ - class: InlineJavascriptRequirement
\ No newline at end of file
diff --git a/steps/plot_Ateamclipper.cwl b/steps/plot_Ateamclipper.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..6d5f88253ec404b3418b2e5934ce7b3240d8be7b
--- /dev/null
+++ b/steps/plot_Ateamclipper.cwl
@@ -0,0 +1,28 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: plot_Ateamclipper
+baseCommand:
+ - python3
+ - /usr/local/bin/plot_Ateamclipper.py
+inputs:
+ - id: clipper_output
+ type: File
+ inputBinding:
+ position: 1
+ - id: outputimage
+ type: string?
+ default: Ateamclipper.png
+ inputBinding:
+ position: 2
+outputs:
+ - id: output_imag
+ doc: Output image
+ type: File
+ outputBinding:
+ glob: $(inputs.outputimage)
+label: plot_Ateamclipper
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor:HBAcalibrator
diff --git a/steps/plot_unflagged.cwl b/steps/plot_unflagged.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..290636c556f95452422d22151eee4620996094dc
--- /dev/null
+++ b/steps/plot_unflagged.cwl
@@ -0,0 +1,52 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: plot_unflagged
+baseCommand:
+ - python3
+inputs:
+ - id: msin
+ type: 'Directory[]'
+ inputBinding:
+ position: 1
+ - id: unflagged_fraction
+ type: float[]
+ inputBinding:
+ position: 2
+
+label: plot_unflagged
+arguments:
+ - '-c'
+ - |
+ import sys
+ import os
+
+ from plot_unflagged_fraction import main as plot_unflagged_fraction
+
+ center = int((len(sys.argv) - 1) / 2 + 1)
+
+ mss = sys.argv[1:center]
+ unflagged_fraction = sys.argv[center:]
+
+ output = plot_unflagged_fraction(ms_list = mss, frac_list = unflagged_fraction, outfile = os.getcwd() + '/unflagged_fraction.png')
+
+outputs:
+ - id: output_imag
+ doc: Output image
+ type: File
+ outputBinding:
+ glob: 'unflagged_fraction.png'
+ - id: logfile
+ type: File[]?
+ outputBinding:
+ glob: 'plot_unflagged_fraction*.log'
+
+
+hints:
+ - class: DockerRequirement
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
+requirements:
+ - class: InlineJavascriptRequirement
+stdout: plot_unflagged_fraction.log
+stderr: plot_unflagged_fraction_err.log
\ No newline at end of file
diff --git a/steps/read_surl_list.cwl b/steps/read_surl_list.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..b1527d08845a46d2bc037dc98084d4fb8b7a85b3
--- /dev/null
+++ b/steps/read_surl_list.cwl
@@ -0,0 +1,23 @@
+class: ExpressionTool
+cwlVersion: v1.0
+id: read_surl_file
+inputs:
+ - id: surl_list
+ type: File
+ doc: input surl file
+ inputBinding:
+ loadContents: True
+outputs:
+ - id: surls
+ type: string[]
+
+expression: |
+ ${
+ var surl_list = inputs.surl_list.contents.split("\n");
+ surl_list = surl_list.filter(function (el) { return el != ''; } );
+ return {'surls': surl_list}
+ }
+label: ReadSurlList
+
+requirements:
+ - class: InlineJavascriptRequirement
diff --git a/steps/selectfirstdirectory.cwl b/steps/selectfirstdirectory.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..c4ecb01874588d841d2080a853e0ee6f8d716619
--- /dev/null
+++ b/steps/selectfirstdirectory.cwl
@@ -0,0 +1,25 @@
+id: selectfirstdirectory
+label: selectfirstdirectory
+class: ExpressionTool
+
+cwlVersion: v1.0
+inputs:
+ - id: input
+ type: Directory[]
+outputs:
+ - id: output
+ type: Directory
+
+requirements:
+
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - $(inputs.input)
+
+
+expression: |
+ ${
+ return {'output': inputs.input[0]}
+ }
+
diff --git a/steps/selectfirstfile.cwl b/steps/selectfirstfile.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..b928a3ffdc95e6ded6dfa0bd9f11db36500900bd
--- /dev/null
+++ b/steps/selectfirstfile.cwl
@@ -0,0 +1,19 @@
+class: ExpressionTool
+cwlVersion: v1.0
+id: select_first_file
+inputs:
+ - id: inputs
+ type: File[]
+ doc: input files
+outputs:
+ - id: output
+ type: File
+
+expression: |
+ ${
+ return {'output': inputs.inputs[0]}
+ }
+label: FileSelector
+
+requirements:
+ - class: InlineJavascriptRequirement
diff --git a/steps/separate_results_directory.cwl b/steps/separate_results_directory.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..a5e1389e9b7498126e78973a4f8637e41eecf55b
--- /dev/null
+++ b/steps/separate_results_directory.cwl
@@ -0,0 +1,31 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: separate_results_directory
+baseCommand:
+ - echo "exploding directory"
+inputs:
+ - id: input
+ type: Directory
+ inputBinding:
+ shellQuote: false
+ position: 0
+outputs:
+ - id: quality_plots
+ type: 'File[]'
+ outputBinding:
+ glob: $(inputs.input)/inspections/*
+ - id: calibrated_ms
+ type: 'Directory[]'
+ outputBinding:
+ glob: $(inputs.input)/out_*
+ - id: calibrator_solutions
+ type: File
+ outputBinding:
+ glob: |
+ $(inputs.input)/cal_values/*
+label: separate_results_directory
+requirements:
+ - class: ShellCommandRequirement
+ - class: InlineJavascriptRequirement
diff --git a/steps/sort_times_into_freqGroups.cwl b/steps/sort_times_into_freqGroups.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..c2dffe021efe70adbb703250dba0c80a6130e48f
--- /dev/null
+++ b/steps/sort_times_into_freqGroups.cwl
@@ -0,0 +1,94 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: sort_times_into_freqGroups
+baseCommand:
+ - python3
+inputs:
+ - id: msin
+ type: Directory[]
+ doc: MS to sort
+ inputBinding:
+ position: 0
+ - id: numbands
+ type: int?
+ default: 10
+ doc: Number of how many files should be grouped together in frequency.
+ - id: NDPPPfill
+ type: boolean?
+ default: True
+ doc: Add dummy file-names for missing frequencies, so that NDPPP can fill the data with flagged dummy data.
+ - id: stepname
+ type: string?
+ default: '.ms'
+ doc: Add this step-name into the file-names of the output files.
+ - id: firstSB
+ type: int?
+ default: null
+ doc: If set, then reference the grouping of files to this station-subband. As if a file with this station-subband would be included in the input files.
+ - id: mergeLastGroup
+ type: boolean?
+ default: False
+ doc: Add dummy file-names for missing frequencies, so that NDPPP can fill the data with flagged dummy data.
+ - id: truncateLastSBs
+ type: boolean?
+ default: True
+ doc: Add dummy file-names for missing frequencies, so that NDPPP can fill the data with flagged dummy data.
+
+label: sort_times_into_freqGroups.py
+arguments:
+ - '-c'
+ - |
+ import sys
+ import json
+ from sort_times_into_freqGroups_CWL import main as sort_times_into_freqGroups
+ null = None
+ false = False
+ true = True
+
+ mss = sys.argv[1:]
+ numbands = int($(inputs.numbands))
+ stepname = "$(inputs.stepname)"
+ NDPPPfill = $(inputs.NDPPPfill)
+ mergeLastGroup = $(inputs.mergeLastGroup)
+ truncateLastSBs = $(inputs.truncateLastSBs)
+ firstSB = $(inputs.firstSB)
+
+ output = sort_times_into_freqGroups(mss, numbands, NDPPPfill, stepname, mergeLastGroup, truncateLastSBs, firstSB)
+
+ filenames = output['filenames']
+ groupnames = output['groupnames']
+
+ cwl_output = {}
+ cwl_output['groupnames'] = groupnames
+
+ with open('./filenames.json', 'w') as fp:
+ json.dump(filenames, fp)
+
+ with open('./out.json', 'w') as fp:
+ json.dump(cwl_output, fp)
+
+outputs:
+ - id: filenames
+ type: File
+ outputBinding:
+ glob: 'filenames.json'
+ - id: groupnames
+ type: string[]
+ outputBinding:
+ loadContents: true
+ glob: 'out.json'
+ outputEval: $(JSON.parse(self[0].contents).groupnames)
+ - id: logfile
+ type: File?
+ outputBinding:
+ glob: sort_times_into_freqGroups.log
+
+requirements:
+ - class: InlineJavascriptRequirement
+
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: sort_times_into_freqGroups.log
\ No newline at end of file
diff --git a/steps/stage.cwl b/steps/stage.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..0cc4266af5f67fb477e425d90e9055525473b2e4
--- /dev/null
+++ b/steps/stage.cwl
@@ -0,0 +1,21 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: stage
+baseCommand:
+ - gfal-legacy-bringonline
+inputs:
+ - id: input
+ type: string
+ inputBinding:
+ shellQuote: false
+ position: 0
+outputs:
+ - id: output
+ type: string
+ outputBinding:
+ outputEval: $(inputs.input)
+label: stage
+requirements:
+ - class: InlineJavascriptRequirement
diff --git a/steps/structure_function.cwl b/steps/structure_function.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..434d75f0513a3a4b421f9624bb0c4078382728e3
--- /dev/null
+++ b/steps/structure_function.cwl
@@ -0,0 +1,62 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
+ sbg: 'https://www.sevenbridges.com/'
+id: structure_function
+baseCommand:
+ - python3
+ - /usr/local/bin/getStructure_from_phases.py
+inputs:
+ - format: 'lofar:#H5Parm'
+ id: h5parmFile
+ type: File
+ inputBinding:
+ position: 0
+ doc: List of h5parm files
+ - default: 'target'
+ id: solset
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--solset'
+ doc: Input solset name
+ - default: 'phase000'
+ id: soltab
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--soltab'
+ doc: Name of the soltab
+ - default: 'POINTING'
+ id: outbasename
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--outbasename'
+ doc: Namebase of the output files
+outputs:
+ - id: structure_plot
+ doc: Output plot
+ type: File
+ outputBinding:
+ glob: $(inputs.outbasename+'_structure.png')
+ - id: structure_txt
+ doc: Output text
+ type: File
+ outputBinding:
+ glob: $(inputs.outbasename+'_structure.txt')
+ - id: log
+ type: File[]
+ outputBinding:
+ glob: 'structure_function*.log'
+label: structure_function
+requirements:
+ - class: InlineJavascriptRequirement
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: structure_function.log
+stderr: structure_function_err.log
+$schema:
+ - 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
diff --git a/steps/surl_copy.cwl b/steps/surl_copy.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..08bd4527548054a827a951a02f5948ce596598fa
--- /dev/null
+++ b/steps/surl_copy.cwl
@@ -0,0 +1,23 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: surl_copy
+baseCommand:
+ - gfal-copy
+inputs:
+ - id: surl
+ type: string
+ inputBinding:
+ position: -1
+outputs:
+ - id: output
+ type: File
+ outputBinding:
+ glob: '*'
+doc: Download a file give a surl
+label: surl_copy
+arguments:
+ - .
+temporaryFailCodes:
+ - 70
diff --git a/steps/transfer_solutions.cwl b/steps/transfer_solutions.cwl
index 9f0ac4510bb0da8908f037d6085a8aecfa19b409..e92ba2e468cc0cd4d35da32b24009cc0a0428122 100644
--- a/steps/transfer_solutions.cwl
+++ b/steps/transfer_solutions.cwl
@@ -4,16 +4,20 @@ $namespaces:
sbg: 'https://www.sevenbridges.com/'
id: transfer_solutions
baseCommand:
- - transfer_solutions.py
+ - python3
+ - /usr/local/bin/transfer_solutions.py
inputs:
- - 'sbg:toolDefaultValue': output.h5
- id: h5parm_name
- type: string?
+ - default: output.h5
+ id: h5parm
+ type: File
inputBinding:
position: 1
doc: H5parm to which the solutions should be transferred.
- id: refh5parm
- type: File
+ type:
+ - File?
+ - string?
+ default: '/data/solutions/3C48.h5'
inputBinding:
position: 0
prefix: '--refh5parm'
@@ -48,14 +52,53 @@ inputs:
position: 0
prefix: '--antenna'
doc: Regular expression of antenna solutions to be transferred
-outputs:
- - id: output
+ - id: do_transfer
+ type: boolean?
+ inputBinding:
+ position: 0
+ prefix: '--do_transfer True'
+ doc: Enable/disable the task
+ - id: trusted
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--trusted'
+ doc: Comma-separated list of sources to be trusted
+ - id: max_separation_arcmin
+ type: float?
+ inputBinding:
+ position: 0
+ prefix: '--max_separation_arcmin'
+ doc: define the maximum seperation between pointing and model direction in arcmin
+ - 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: $(inputs.h5parm_name)
+ glob: "*.png"
+
+stdout: transfer_solutions.log
+stderr: transfer_solutions_err.log
label: transfer_solutions
hints:
- class: DockerRequirement
- dockerPull: 'lofareosc/prefactor:latest'
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
requirements:
- class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.h5parm)
+ writable: true
diff --git a/steps/untar.cwl b/steps/untar.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..55d02a9d7e4d3b154312c21c7ef6980d6410ccb8
--- /dev/null
+++ b/steps/untar.cwl
@@ -0,0 +1,30 @@
+id: untar
+label: untar
+class: CommandLineTool
+cwlVersion: v1.0
+inputs:
+ - id: tar_file
+ type: File
+ inputBinding:
+ position: 0
+
+outputs:
+ - id: uncompressed
+ type: Directory
+ outputBinding:
+ glob: 'out/*'
+baseCommand:
+ - 'bash'
+ - 'untar.sh'
+doc: 'Untar a compressed file'
+requirements:
+ InitialWorkDirRequirement:
+ listing:
+ - entryname: 'untar.sh'
+ entry: |
+ #!/bin/bash
+ mkdir out
+ cd out
+ tar -xvf $1
+
+
diff --git a/subworkflow/apply_calibrate_bp.cwl b/subworkflow/apply_calibrate_bp.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..5aca7b54f7212a8ba60306f9ed9514ed6e167016
--- /dev/null
+++ b/subworkflow/apply_calibrate_bp.cwl
@@ -0,0 +1,279 @@
+class: Workflow
+cwlVersion: v1.0
+id: apply_calibrate
+label: apply_calibrate
+$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: apply_fr.log
+ outputSource:
+ - concat_logfiles_applyFR/output
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': -300
+ - 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:
+ - concat_logfiles_applyBP/output
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: calib_cal.log
+ outputSource:
+ - concat_logfiles_calib_cal/output
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 100
+ - id: outh5parm
+ outputSource:
+ - calib_cal/h5parm
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 200
+ - id: apply_pa.log
+ outputSource:
+ - concat_logfiles_applyPA/output
+ 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:
+ - id: msin
+ source: msin
+ - id: msin_datacolumn
+ default: DATA
+ - id: parmdb
+ source: input_h5parm
+ - id: msout_datacolumn
+ default: CORRECTED_DATA
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
+ - id: correction
+ default: polalign
+ out:
+ - id: msout
+ - id: logfile
+ run: ../lofar-cwl/steps/applycal.cwl
+ label: applyPA
+ 'sbg:x': -400
+ 'sbg:y': 0
+ - id: applyBP
+ in:
+ - id: msin
+ source: applyPA/msout
+ - id: msin_datacolumn
+ default: CORRECTED_DATA
+ - id: parmdb
+ source: input_h5parm
+ - id: msout_datacolumn
+ default: CORRECTED_DATA
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
+ - id: correction
+ default: bandpass
+ - id: updateweights
+ default: 'True'
+ out:
+ - id: msout
+ - id: logfile
+ run: ../lofar-cwl/steps/applycal.cwl
+ label: applyBP
+ 'sbg:x': -200
+ 'sbg:y': 0
+ - id: applybeam
+ in:
+ - id: msin
+ source: applyBP/msout
+ - id: msin_datacolumn
+ default: CORRECTED_DATA
+ - id: msout_datacolumn
+ default: CORRECTED_DATA
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
+ - id: type
+ default: applybeam
+ - id: updateweights
+ default: 'true'
+ - id: usechannelfreq
+ default: 'false'
+ - id: invert
+ default: 'true'
+ - id: beammode
+ default: element
+ out:
+ - id: msout
+ - id: logfile
+ run: ../lofar-cwl/steps/applybeam.cwl
+ label: applybeam
+ 'sbg:x': 0
+ 'sbg:y': 0
+ - id: applyFR
+ in:
+ - id: msin
+ source: applybeam/msout
+ - id: msin_datacolumn
+ default: CORRECTED_DATA
+ - id: parmdb
+ source: input_h5parm
+ - id: msout_datacolumn
+ default: CORRECTED_DATA
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
+ - id: correction
+ default: faraday
+ out:
+ - id: msout
+ - id: logfile
+ run: ../lofar-cwl/steps/applycal.cwl
+ label: applyFR
+ 'sbg:x': 200
+ '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': 400
+ '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: propagate_solutions
+ source: propagatesolutions
+ - id: flagunconverged
+ source: flagunconverged
+ - id: mode
+ default: diagonal
+ out:
+ - id: msout
+ - id: h5parm
+ - id: logfile
+ run: ../lofar-cwl/steps/ddecal.cwl
+ 'sbg:x': 600
+ 'sbg:y': 0
+ - id: concat_logfiles_calib_cal
+ in:
+ - id: file_list
+ source:
+ - calib_cal/logfile
+ - id: file_prefix
+ default: calib_cal
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_calib_cal
+ 'sbg:x': 700
+ 'sbg:y': 200
+ - id: concat_logfiles_applyFR
+ in:
+ - id: file_list
+ source:
+ - applyFR/logfile
+ - id: file_prefix
+ default: applycal
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_applyFR
+ 'sbg:x': 400
+ 'sbg:y': 200
+ - id: concat_logfiles_applybeam
+ in:
+ - id: file_list
+ source:
+ - applybeam/logfile
+ - id: file_prefix
+ default: applybeam
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_applybeam
+ 'sbg:x': 200
+ 'sbg:y': 200
+ - id: concat_logfiles_applyBP
+ in:
+ - id: file_list
+ source:
+ - applyBP/logfile
+ - id: file_prefix
+ default: applycal
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_applyBP
+ 'sbg:x': 0
+ 'sbg:y': 200
+ - id: concat_logfiles_applyPA
+ in:
+ - id: file_list
+ source:
+ - applyPA/logfile
+ - id: file_prefix
+ default: applycal
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_applyPA
+ 'sbg:x': -200
+ 'sbg:y': 200
+requirements: []
diff --git a/subworkflow/apply_calibrate_fr.cwl b/subworkflow/apply_calibrate_fr.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..3c20638a5f7dfa43e0c60c18ab97eb6a1f193898
--- /dev/null
+++ b/subworkflow/apply_calibrate_fr.cwl
@@ -0,0 +1,145 @@
+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:
+ - concat_logfiles_applycal/output
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: calib_cal.log
+ outputSource:
+ - concat_logfiles_calib_cal/output
+ 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: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
+ - 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
+ - id: concat_logfiles_calib_cal
+ in:
+ - id: file_list
+ source:
+ - calib_cal/logfile
+ - id: file_prefix
+ default: calib_cal
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_calib_cal
+ 'sbg:x': 700
+ 'sbg:y': 200
+ - id: concat_logfiles_applycal
+ in:
+ - id: file_list
+ source:
+ - applyFR/logfile
+ - id: file_prefix
+ default: applycal
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_applycal
+ 'sbg:x': -200
+ 'sbg:y': 200
+requirements: []
diff --git a/subworkflow/apply_calibrate_pa.cwl b/subworkflow/apply_calibrate_pa.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..c8f1ea5cf33df4b2e381e0357129676db82147db
--- /dev/null
+++ b/subworkflow/apply_calibrate_pa.cwl
@@ -0,0 +1,193 @@
+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:
+ - concat_logfiles_applycal/output
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: calib_cal.log
+ outputSource:
+ - concat_logfiles_calib_cal/output
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 100
+ - id: outh5parm
+ outputSource:
+ - calib_cal/h5parm
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 200
+ - id: applybeam.log
+ outputSource:
+ - concat_logfiles_applybeam/output
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 300
+steps:
+ - id: applyPA
+ in:
+ - id: msin
+ source: msin
+ - id: msin_datacolumn
+ default: DATA
+ - id: parmdb
+ source: input_h5parm
+ - id: msout_datacolumn
+ default: CORRECTED_DATA
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
+ - id: correction
+ default: polalign
+ out:
+ - id: msout
+ - id: logfile
+ run: ../lofar-cwl/steps/applycal.cwl
+ label: applyPA
+ 'sbg:x': -400
+ 'sbg:y': 0
+ - id: applybeam
+ in:
+ - id: msin_datacolumn
+ default: CORRECTED_DATA
+ - id: msout_datacolumn
+ default: CORRECTED_DATA
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
+ - id: updateweights
+ default: 'true'
+ - id: invert
+ default: 'true'
+ - id: beammode
+ default: element
+ - id: usechannelfreq
+ default: 'false'
+ - id: msin
+ source: applyPA/msout
+ - id: type
+ default: applybeam
+ out:
+ - id: msout
+ - id: logfile
+ run: ../lofar-cwl/steps/applybeam.cwl
+ label: applybeam
+ 'sbg:x': -200
+ 'sbg:y': 0
+ - id: BLsmooth
+ in:
+ - id: msin
+ source: applybeam/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: rotation+diagonal
+ out:
+ - id: msout
+ - id: h5parm
+ - id: logfile
+ run: ../lofar-cwl/steps/ddecal.cwl
+ 'sbg:x': 500
+ 'sbg:y': 0
+ - id: concat_logfiles_calib_cal
+ in:
+ - id: file_list
+ source:
+ - calib_cal/logfile
+ - id: file_prefix
+ default: calib_cal
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_calib_cal
+ 'sbg:x': 700
+ 'sbg:y': 200
+ - id: concat_logfiles_applybeam
+ in:
+ - id: file_list
+ source:
+ - applybeam/logfile
+ - id: file_prefix
+ default: applybeam
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_applybeam
+ 'sbg:x': 0
+ 'sbg:y': 200
+ - id: concat_logfiles_applycal
+ in:
+ - id: file_list
+ source:
+ - applyPA/logfile
+ - id: file_prefix
+ default: applycal
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_applycal
+ 'sbg:x': -200
+ 'sbg:y': 200
+requirements: []
diff --git a/subworkflow/bandpass.cwl b/subworkflow/bandpass.cwl
index 0d73a6263d3ebe36efc8bd1af192dac894a87346..63f7dc6355cfdbe1cbf68ffe531c192b9eaf637b 100644
--- a/subworkflow/bandpass.cwl
+++ b/subworkflow/bandpass.cwl
@@ -1,134 +1,265 @@
class: Workflow
cwlVersion: v1.0
-id: bandpass
-label: bandpass
+id: losoto_bandpass
+label: losoto_bandpass
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
+ - id: ampRange
+ type: 'float[]?'
+ 'sbg:x': 397.4866943359375
+ 'sbg:y': 73.48989868164062
- id: skipInternational
- type: string?
- 'sbg:x': 600.0303344726562
- 'sbg:y': -411.65814208984375
+ type: boolean?
+ 'sbg:x': 401.4047546386719
+ 'sbg:y': -185.20863342285156
+ - id: input_h5parm
+ type: File
+ 'sbg:x': 395.389404296875
+ 'sbg:y': -51.39104080200195
- id: max2interpolate
type: int?
- 'sbg:x': 472.91082763671875
- 'sbg:y': -275.4460144042969
+ 'sbg:x': 398.02581787109375
+ 'sbg:y': -311.48223876953125
- id: bandpass_freqresolution
type: string
- 'sbg:x': 479.5017395019531
- 'sbg:y': 199.0994415283203
+ 'sbg:x': 404.9237365722656
+ 'sbg:y': -440.521484375
- id: avg_freqresolution
type: string?
- 'sbg:x': 527.5851440429688
- 'sbg:y': 368.7982482910156
- - id: ampRange
- type: 'float[]?'
- 'sbg:x': 721.8663330078125
- 'sbg:y': 423.6078186035156
- - id: outh5parmname
- type: string?
- 'sbg:x': 805.8613891601562
- 'sbg:y': -296.09796142578125
- - id: antenna_to_transfer
- type: string?
- 'sbg:x': 985.4193725585938
- 'sbg:y': 183.84898376464844
+ 'sbg:x': 401.60693359375
+ 'sbg:y': 198.58273315429688
outputs:
- - id: output
+ - id: output_h5parm
+ outputSource:
+ - smoothb/output_h5parm
+ type: File
+ 'sbg:x': 2315
+ 'sbg:y': -50
+ - id: logfiles
outputSource:
- - transfer_solutions/output
- type: File?
- 'sbg:x': 1310.1014404296875
- 'sbg:y': -65.6321029663086
+ - duplicateAbkp/log
+ - losoto_flag/log
+ - flagbp/log
+ - flagextend/log
+ - merge/log
+ - duplicateAbkp2/log
+ - smooth/logfile
+ - bandpass/logfile
+ - interp/logfile
+ - smoothb/logfile
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 2315.6181640625
+ 'sbg:y': 352.22503662109375
steps:
- - id: h5imp_cal_bandpass
+ - id: duplicateAbkp
in:
- - id: insolset
- default: bandpass
- - id: squeeze
- default: true
- - id: verbose
- default: true
- - id: clobber
- default: true
+ - id: input_h5parm
+ source: input_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: soltabOut
+ default: amplitudeOrig000
out:
- - id: outh5parm
+ - id: output_h5parm
- id: log
- run: ../lofar-cwl/steps/H5ParmCollector.cwl
- label: h5imp_cal_bandpass
- scatter:
- - h5parmFiles
- 'sbg:x': 553.6541748046875
- 'sbg:y': -29.645381927490234
- - id: h5exp_cal_bandpass
+ run: ../lofar-cwl/steps/LoSoTo.Duplicate.cwl
+ 'sbg:x': 600
+ 'sbg:y': -50
+ - id: losoto_flag
in:
- - id: h5parmFiles
- source:
- - losoto_bandpass/output_h5parm
- - id: insolset
- default: bandpass
- - id: outh5parmname
- default: cal_solutions.h5
- source: outh5parmname
- - id: verbose
- default: true
- - id: clobber
- default: true
+ - id: input_h5parm
+ source: duplicateAbkp/output_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: axesToFlag
+ default:
+ - time
+ - freq
+ - id: order
+ default:
+ - 100
+ - 40
+ - id: maxCycles
+ default: 1
+ - id: maxRms
+ default: 5
+ - id: mode
+ default: smooth
+ - id: preflagzeros
+ default: false
+ - id: replace
+ default: false
out:
- - id: outh5parm
+ - id: output_h5parm
- id: log
- run: ../lofar-cwl/steps/H5ParmCollector.cwl
- label: h5exp_cal_bandpass
- 'sbg:x': 943
- 'sbg:y': -45
- - id: transfer_solutions
+ run: ../lofar-cwl/steps/LoSoTo.Flag.cwl
+ label: flag
+ 'sbg:x': 750
+ 'sbg:y': -50
+ - id: flagbp
in:
- - id: refh5parm
- source: h5exp_cal_bandpass/outh5parm
- - id: insolset
- default: calibrator
- - id: outsolset
- default: calibrator
- - id: insoltab
- default: bandpass
- - id: outsoltab
+ - id: input_h5parm
+ source: losoto_flag/output_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: mode
default: bandpass
- - id: antenna
- source: antenna_to_transfer
- out:
- - id: output
- run: ../steps/transfer_solutions.cwl
- label: transfer_solutions
- 'sbg:x': 1132
- 'sbg:y': -62
- - id: losoto_bandpass
- in:
- id: ampRange
- default:
- - 0
- - 0
source:
- ampRange
- id: skipInternational
- default: 'True'
source: skipInternational
+ out:
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.FlagStation.cwl
+ 'sbg:x': 900
+ 'sbg:y': -50
+ - id: flagextend
+ in:
- id: input_h5parm
- source: h5imp_cal_bandpass/outh5parm
- - id: max2interpolate
- default: 30
- source: max2interpolate
- - id: bandpass_freqresolution
- default: 195.3125kHz
+ source: flagbp/output_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: axesToExt
+ default:
+ - time
+ - freq
+ - id: size
+ default:
+ - 200
+ - 80
+ - id: percent
+ default: 50
+ - id: maxCycles
+ default: 2
+ out:
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.Flagextend.cwl
+ 'sbg:x': 1050
+ 'sbg:y': -50
+ - id: merge
+ in:
+ - id: input_h5parm
+ source: flagextend/output_h5parm
+ - id: soltab
+ default: sol000/phase000
+ - id: mode
+ default: copy
+ - id: soltabImport
+ default: amplitude000
+ out:
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.Reweight.cwl
+ 'sbg:x': 1200
+ 'sbg:y': -50
+ - id: duplicateAbkp2
+ in:
+ - id: input_h5parm
+ source: merge/output_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: soltabOut
+ default: amplitudeOrig001
+ out:
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.Duplicate.cwl
+ 'sbg:x': 1350
+ 'sbg:y': -50
+ - id: smooth
+ in:
+ - id: input_h5parm
+ source: duplicateAbkp2/output_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: axesToSmooth
+ default:
+ - time
+ - id: mode
+ default: median
+ - id: log
+ default: true
+ - id: replace
+ default: false
+ out:
+ - id: output_h5parm
+ - id: logfile
+ run: ../lofar-cwl/steps/LoSoTo.Smooth.cwl
+ 'sbg:x': 1500
+ 'sbg:y': -50
+ - id: bandpass
+ in:
+ - id: input_h5parm
+ source: smooth/output_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: axesToSmooth
+ default:
+ - freq
+ - id: size
+ default:
+ - 17
+ - id: mode
+ default: savitzky-golay
+ - id: degree
+ default: 2
+ - id: log
+ default: true
+ out:
+ - id: output_h5parm
+ - id: logfile
+ run: ../lofar-cwl/steps/LoSoTo.Smooth.cwl
+ 'sbg:x': 1650
+ 'sbg:y': -50
+ - id: interp
+ in:
+ - id: input_h5parm
+ source: bandpass/output_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: axisToRegrid
+ default: freq
+ - id: outSoltab
+ default: bandpass
+ - id: newdelta
source: bandpass_freqresolution
- - id: avg_freqresolution
- default: 48.82kHz
+ - id: delta
source: avg_freqresolution
+ - id: maxFlaggedWidth
+ source: max2interpolate
+ - id: log
+ default: true
+ out:
+ - id: output_h5parm
+ - id: logfile
+ run: ../lofar-cwl/steps/LoSoTo.Interpolate.cwl
+ 'sbg:x': 1800
+ 'sbg:y': -50
+ - id: smoothb
+ in:
+ - id: input_h5parm
+ source: interp/output_h5parm
+ - id: soltab
+ default: sol000/bandpass
+ - id: axesToSmooth
+ default:
+ - time
+ - id: mode
+ default: median
+ - id: replace
+ default: true
+ - id: log
+ default: true
out:
- id: output_h5parm
- run: ./losoto_bandpass.cwl
- label: losoto_bandpass
- 'sbg:x': 747.5215454101562
- 'sbg:y': -46.37216567993164
-requirements:
- - class: SubworkflowFeatureRequirement
- - class: ScatterFeatureRequirement
+ - id: logfile
+ run: ../lofar-cwl/steps/LoSoTo.Smooth.cwl
+ label: smoothb
+ 'sbg:x': 1950
+ 'sbg:y': -50
+requirements: []
diff --git a/subworkflow/calib_cal.cwl b/subworkflow/calib_cal.cwl
index 1857e5bc044f162234b0bf3e12c0b744002c577a..1fceb82d5f227d8243c7b89d8d4d05a291cea5da 100644
--- a/subworkflow/calib_cal.cwl
+++ b/subworkflow/calib_cal.cwl
@@ -1,45 +1,37 @@
class: Workflow
cwlVersion: v1.0
-id: calib_cal
-label: calib_cal
+id: calibrate_calibrator
+label: calibrate_calibrator
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: msin
type: Directory
- 'sbg:x': -752
- 'sbg:y': -23
- - id: skymodels
- type: Directory
- 'sbg:x': -626
- 'sbg:y': -302
- - id: flagunconverged
- type: boolean
- 'sbg:x': 41
- 'sbg:y': 100
- - id: propagate_solutions
- type: boolean
- 'sbg:x': 77.1015625
- 'sbg:y': -259
+ 'sbg:x': -1000
+ 'sbg:y': -100
- id: do_smooth
type: boolean
- 'sbg:x': -604
- 'sbg:y': 123
-outputs:
- - id: h5parm
- outputSource:
- - calib_rot_diag/h5parm
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: sourcedb
type: File
- 'sbg:x': 429
- 'sbg:y': -52
+ 'sbg:x': -1000
+ 'sbg:y': 100
+outputs:
- id: msout
outputSource:
- - calib_rot_diag/msout
+ - predict/msout
type: Directory
- 'sbg:x': 404
- 'sbg:y': -227
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: BLsmooth.log
+ outputSource:
+ - BLsmooth/logfile
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 100
steps:
- - id: blsmooth
+ - id: BLsmooth
in:
- id: msin
source: msin
@@ -47,58 +39,23 @@ steps:
source: do_smooth
out:
- id: msout
+ - id: logfile
run: ../steps/blsmooth.cwl
label: BLsmooth
- 'sbg:x': -420
- 'sbg:y': -26
+ 'sbg:x': -500
+ 'sbg:y': 0
- id: predict
in:
- id: msin
- source: blsmooth/msout
+ source: BLsmooth/msout
+ - id: msout_datacolumn
+ default: MODEL_DATA
- id: sources_db
- source: make_sourcedb/sourcedb
+ source: sourcedb
out:
- id: msout
run: ../lofar-cwl/steps/predict.cwl
- 'sbg:x': -1
- 'sbg:y': -71
- - id: find_skymodel_cal_py
- in:
- - id: msin
- source: msin
- - id: skymodels
- source: skymodels
- out:
- - id: output_models
- run: ../steps/find_skymodel_cal.cwl
- label: find_skymodel_cal.py
- 'sbg:x': -416
- 'sbg:y': -209
- - id: make_sourcedb
- in:
- - id: sky_model
- source: find_skymodel_cal_py/output_models
- out:
- - id: sourcedb
- - id: log
- run: ../lofar-cwl/steps/makesourcedb.cwl
- label: make_sourcedb
- 'sbg:x': -221
- 'sbg:y': -217
- - id: calib_rot_diag
- in:
- - id: msin
- source: predict/msout
- - id: msin_datacolumn
- default: SMOOTHED_DATA
- - id: propagate_solutions
- source: propagate_solutions
- - id: flagunconverged
- source: flagunconverged
- out:
- - id: msout
- - id: h5parm
- run: ../lofar-cwl/steps/ddecal.cwl
- 'sbg:x': 222
- 'sbg:y': -89
-requirements: []
+ 'sbg:x': 0
+ 'sbg:y': 0
+requirements:
+ - class: ScatterFeatureRequirement
diff --git a/subworkflow/calib_targ.cwl b/subworkflow/calib_targ.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..5ff661bbd13c4c1894795283e94696a697af4a15
--- /dev/null
+++ b/subworkflow/calib_targ.cwl
@@ -0,0 +1,122 @@
+class: Workflow
+cwlVersion: v1.0
+id: calibrate_target
+label: calibrate_target
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: msin
+ type: Directory
+ 'sbg:x': -1000
+ 'sbg:y': -200
+ - id: skymodel
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': -100
+ - id: do_smooth
+ type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: propagatesolutions
+ type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': 100
+outputs:
+ - id: msout
+ outputSource:
+ - calib_targ/msout
+ type: Directory
+ 'sbg:x': 1000
+ 'sbg:y': -200
+ - id: BLsmooth.log
+ outputSource:
+ - BLsmooth/logfile
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': -100
+ - id: gaincal.log
+ outputSource:
+ - concat_logfiles_gaincal/output
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: outh5parm
+ outputSource:
+ - calib_targ/h5parm
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 100
+steps:
+ - id: BLsmooth
+ in:
+ - id: msin
+ source: msin
+ - id: do_smooth
+ source: do_smooth
+ - id: in_column_name
+ default: DATA
+ - id: restore
+ default: true
+ out:
+ - id: msout
+ - id: logfile
+ run: ../steps/blsmooth.cwl
+ label: BLsmooth
+ 'sbg:x': -500
+ 'sbg:y': 0
+ - id: calib_targ
+ in:
+ - id: msin
+ source: BLsmooth/msout
+ - id: msin_datacolumn
+ default: SMOOTHED_DATA
+ - id: msout_name
+ default: .
+ - id: blrange
+ default:
+ - 150
+ - 9999999
+ - id: caltype
+ default: phaseonly
+ - id: sourcedb
+ source: skymodel
+ - id: maxiter
+ default: 50
+ - id: solint
+ default: 1
+ - id: nchan
+ default: 0
+ - id: tolerance
+ default: 1e-3
+ - id: propagatesolutions
+ source: propagatesolutions
+ - id: usebeammodel
+ default: true
+ - id: usechannelfreq
+ default: true
+ - id: beammode
+ default: array_factor
+ - id: onebeamperpatch
+ default: false
+ out:
+ - id: msout
+ - id: h5parm
+ - id: logfile
+ run: ../lofar-cwl/steps/gaincal.cwl
+ 'sbg:x': 0
+ 'sbg:y': 0
+ - id: concat_logfiles_gaincal
+ in:
+ - id: file_list
+ source:
+ - calib_targ/logfile
+ - id: file_prefix
+ default: gaincal
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_gaincal
+ 'sbg:x': 600
+ 'sbg:y': 400
+requirements:
+ - class: MultipleInputFeatureRequirement
diff --git a/subworkflow/clocktec.cwl b/subworkflow/clocktec.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..77eb284a40ef5119df515ae8ce5602c3dfafbec2
--- /dev/null
+++ b/subworkflow/clocktec.cwl
@@ -0,0 +1,260 @@
+class: Workflow
+cwlVersion: v1.0
+id: losoto_ion
+label: losoto_ion
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: input_h5parm
+ type: File
+ 'sbg:x': -700
+ 'sbg:y': -400
+ - id: fit3rdorder
+ type: boolean?
+ 'sbg:x': -700
+ 'sbg:y': -200
+ - id: refAnt
+ type: string?
+ 'sbg:x': -700
+ 'sbg:y': 0
+ - id: maxStddev
+ type: float?
+ 'sbg:x': -700
+ 'sbg:y': 200
+ - id: clock_smooth
+ type: boolean?
+ 'sbg:x': -700
+ 'sbg:y': 400
+outputs:
+ - id: output_h5parm
+ outputSource:
+ - losoto_flagstation/output_h5parm
+ type: File
+ 'sbg:x': 1500
+ 'sbg:y': 0
+ - id: logfiles
+ outputSource:
+ - duplicateAbkp/log
+ - flag/log
+ - flagextend/log
+ - merge/log
+ - duplicatePbkp/log
+ - losoto_clocktec/log
+ - losoto_residual/log
+ - duplicateCbkp/log
+ - smooth/logfile
+ - losoto_flagstation/log
+ type: 'File[]'
+ linkMerge: merge_flattened
+ '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:
+ - id: input_h5parm
+ source: input_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: soltabOut
+ default: amplitudeOrig
+ out:
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.Duplicate.cwl
+ 'sbg:x': -500
+ 'sbg:y': 0
+ - id: flag
+ in:
+ - id: input_h5parm
+ source: duplicateAbkp/output_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: axesToFlag
+ default:
+ - time
+ - freq
+ - id: order
+ default:
+ - 100
+ - 40
+ - id: maxCycles
+ 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': -300
+ 'sbg:y': 0
+ - id: flagextend
+ in:
+ - id: input_h5parm
+ source: flag/output_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: axesToExt
+ default:
+ - time
+ - freq
+ - id: size
+ default:
+ - 200
+ - 80
+ - id: percent
+ default: 50
+ - id: maxCycles
+ default: 2
+ out:
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.Flagextend.cwl
+ 'sbg:x': -100
+ 'sbg:y': 0
+ - id: merge
+ in:
+ - id: input_h5parm
+ source: flagextend/output_h5parm
+ - id: soltab
+ default: sol000/phase000
+ - id: mode
+ default: copy
+ - id: soltabImport
+ default: amplitude000
+ out:
+ - id: output_h5parm
+ - id: log
+ run: ../lofar-cwl/steps/LoSoTo.Reweight.cwl
+ 'sbg:x': 100
+ 'sbg:y': 0
+ - id: duplicatePbkp
+ in:
+ - id: input_h5parm
+ source: merge/output_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': 300
+ 'sbg:y': 0
+ - id: losoto_clocktec
+ in:
+ - id: input_h5parm
+ source: duplicatePbkp/output_h5parm
+ - id: soltab
+ default: sol000/phase000
+ - id: clocksoltabOut
+ default: clock
+ - id: tecsoltabOut
+ default: tec
+ - id: offsetsoltabOut
+ default: phase_offset
+ - id: tec3rdsoltabOut
+ default: tec3rd
+ - id: FlagBadChannels
+ default: false
+ - id: CombinePol
+ default: true
+ - 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': 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
+ default: sol000/clock
+ - id: axesToSmooth
+ default:
+ - time
+ - id: mode
+ default: median
+ - id: replace
+ default: true
+ - id: log
+ default: false
+ out:
+ - id: output_h5parm
+ - id: logfile
+ run: ../lofar-cwl/steps/LoSoTo.Smooth.cwl
+ 'sbg:x': 1100
+ 'sbg:y': 0
+ - id: losoto_flagstation
+ in:
+ - id: input_h5parm
+ source: smooth/output_h5parm
+ - id: soltab
+ default: sol000/phase000
+ - 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.FlagStation.cwl
+ 'sbg:x': 1300
+ 'sbg:y': 0
+requirements:
+ - class: StepInputExpressionRequirement
+ - class: InlineJavascriptRequirement
diff --git a/subworkflow/concat.cwl b/subworkflow/concat.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..c7337131d8d95a0985d1e6b3ae62c1214edaa79c
--- /dev/null
+++ b/subworkflow/concat.cwl
@@ -0,0 +1,159 @@
+class: Workflow
+cwlVersion: v1.0
+id: concat
+label: concat
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: msin
+ type: 'Directory[]'
+ 'sbg:x': -1000
+ 'sbg:y': -300
+ - id: group_id
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': -200
+ - id: groups_specification
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': -100
+ - id: filter_baselines
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: avg_timeresolution_concat
+ type: int
+ 'sbg:x': -1000
+ 'sbg:y': 100
+ - id: avg_freqresolution_concat
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': 200
+ - id: min_unflagged_fraction
+ type: float
+ 'sbg:x': -1000
+ 'sbg:y': 300
+outputs:
+ - id: msout_old
+ outputSource:
+ - dpppconcat/msout
+ type: Directory
+ 'sbg:x': 1000
+ 'sbg:y': -200
+ - id: unflagged_fraction
+ outputSource:
+ - check_unflagged_fraction/unflagged_fraction
+ type: float
+ 'sbg:x': 1000
+ 'sbg:y': -100
+ - id: msout
+ outputSource:
+ - check_unflagged_fraction/msout
+ type: 'Directory[]'
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: dpppconcat.log
+ outputSource:
+ - concat_logfiles_dpppconcat/output
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 100
+ - id: check_unflagged_fraction.log
+ outputSource:
+ - concat_logfiles_unflagged/output
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 200
+steps:
+ - id: filter_ms_group
+ in:
+ - id: group_id
+ source: group_id
+ - id: groups_specification
+ source: groups_specification
+ - id: measurement_sets
+ source:
+ - msin
+ out:
+ - id: output
+ run: ../steps/filter_ms_group.cwl
+ label: filter_ms_group
+ 'sbg:x': -500
+ 'sbg:y': 0
+ - id: dpppconcat
+ in:
+ - id: msin
+ source:
+ - filter_ms_group/output
+ - id: msout_name
+ source: group_id
+ - id: msin_datacolumn
+ default: DATA
+ - id: msout_datacolumn
+ default: DATA
+ - id: filter_baselines
+ source: filter_baselines
+ - id: filter_remove
+ default: true
+ - id: overwrite
+ default: false
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
+ - id: missingdata
+ default: true
+ - id: baseline
+ source: filter_baselines
+ - id: avg_timeresolution
+ source: avg_timeresolution_concat
+ - id: avg_freqresolution
+ source: avg_freqresolution_concat
+ out:
+ - id: msout
+ - id: logfile
+ run: ../lofar-cwl/steps/dpppconcat.cwl
+ label: dpppconcat
+ 'sbg:x': -200
+ 'sbg:y': 0
+ - id: check_unflagged_fraction
+ in:
+ - id: msin
+ source: dpppconcat/msout
+ - id: min_fraction
+ source: min_unflagged_fraction
+ out:
+ - id: msout
+ - id: unflagged_fraction
+ - id: logfile
+ run: ../steps/check_unflagged_fraction.cwl
+ label: check_unflagged_fraction
+ 'sbg:x': 100
+ 'sbg:y': 0
+ - id: concat_logfiles_dpppconcat
+ in:
+ - id: file_list
+ source:
+ - dpppconcat/logfile
+ - id: file_prefix
+ default: dpppconcat
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_dpppconcat
+ 'sbg:x': 600
+ 'sbg:y': 200
+ - id: concat_logfiles_unflagged
+ in:
+ - id: file_list
+ source:
+ - check_unflagged_fraction/logfile
+ - id: file_prefix
+ default: check_unflagged_fraction
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_unflagged
+ 'sbg:x': 600
+ 'sbg:y': 400
+requirements: []
diff --git a/subworkflow/faraday_rotation.cwl b/subworkflow/faraday_rotation.cwl
index ab6edc0ca862b312c625ac4d7d479ec56a81c297..7afd26b6adc4e93c0c2c385554bf3b653465ab21 100644
--- a/subworkflow/faraday_rotation.cwl
+++ b/subworkflow/faraday_rotation.cwl
@@ -3,95 +3,66 @@ cwlVersion: v1.0
id: faraday_rotation
label: faraday_rotation
$namespaces:
+ lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
inputs:
- - id: msin
- type: 'Directory[]'
- 'sbg:x': -1017.7406616210938
- 'sbg:y': -230.76498413085938
- 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_faraday/output_h5parm
+ type: File
+ format: 'lofar:#H5Parm'
+ 'sbg:x': 152.59103393554688
+ 'sbg:y': -289.2899169921875
+ - id: logfiles
+ outputSource:
+ - losoto_duplicate/log
+ - losoto_faraday/log
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 300.5910339355469
+ 'sbg:y': 0
steps:
- - id: h5imp_cal_FR
+ - id: losoto_duplicate
in:
- - id: h5parmFiles
- linkMerge: merge_flattened
- - 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
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
- 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
- out:
- - id: outh5parm
- - 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: msout_datacolumn
- default: CORRECTED_DATA
- - 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
+requirements: []
+$schema:
+ - 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
diff --git a/subworkflow/ndppp_prep_cal.cwl b/subworkflow/ndppp_prep_cal.cwl
index 633a06d3dffd5d1be757d3783cea09905679fa8e..6bcdf446b3a632500708dabb251e23deb0820aa6 100644
--- a/subworkflow/ndppp_prep_cal.cwl
+++ b/subworkflow/ndppp_prep_cal.cwl
@@ -33,18 +33,46 @@ inputs:
type: Directory?
'sbg:x': 2306.83056640625
'sbg:y': 318.2810363769531
+ - id: msin_baseline
+ type: string?
+ 'sbg:x': 2273.798583984375
+ 'sbg:y': 182.7539825439453
- id: skymodel
type: File
- 'sbg:x': 1428.3411865234375
- 'sbg:y': 273.64007568359375
+ 'sbg:x': 1335.2567138671875
+ 'sbg:y': 148.68453979492188
- id: timeresolution
type: float
'sbg:x': 2021.81787109375
'sbg:y': -352.4759216308594
- id: freqresolution
- type: float
+ type: string
'sbg:x': 1999.5889892578125
'sbg:y': 170.7563934326172
+ - id: demix_timestep
+ type: int
+ 'sbg:x': 1371.962646484375
+ 'sbg:y': 307.4278259277344
+ - id: demix_freqstep
+ type: int
+ 'sbg:x': 1465.0855712890625
+ 'sbg:y': 450.8930358886719
+ - id: demix_baseline
+ type: string
+ 'sbg:x': 1585.496826171875
+ 'sbg:y': 588.0062866210938
+ - id: target_source
+ type: string
+ 'sbg:x': 1439.47314453125
+ 'sbg:y': -325.6144104003906
+ - id: ntimechunk
+ type: int
+ 'sbg:x': 1149.4033203125
+ 'sbg:y': 349.2409362792969
+ - id: subtract_sources
+ type: 'string[]?'
+ 'sbg:x': 1257.9327392578125
+ 'sbg:y': -290.095703125
outputs:
- id: msout
outputSource:
@@ -54,8 +82,8 @@ outputs:
'sbg:y': 53.67763900756836
- id: logfile
outputSource:
- - dppp/logfile
- type: File?
+ - concat_logfiles_dppp/output
+ type: File
'sbg:x': 2857.9423828125
'sbg:y': 253.50680541992188
- id: parset
@@ -175,8 +203,21 @@ steps:
- flagamp/augmented_steps
- id: step_name
default: demixer
+ - id: baseline
+ source: demix_baseline
+ - id: demixtimestep
+ source: demix_timestep
+ - id: demixfreqstep
+ source: demix_freqstep
+ - id: ntimechunk
+ source: ntimechunk
- id: skymodel
source: skymodel
+ - id: subtractsources
+ source:
+ - subtract_sources
+ - id: targetsource
+ source: target_source
out:
- id: augmented_steps
run: ../lofar-cwl/steps/DP3.DemixerStepGenerator.cwl
@@ -215,6 +256,16 @@ steps:
source: parsetgenerator/output_file_names
- id: output_directory_names
source: parsetgenerator/output_directory_names
+ - id: autoweight
+ source: raw_data
+ - id: baseline
+ source: msin_baseline
+ - id: writefullresflag
+ default: false
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
out:
- id: msout
- id: secondary_output_files
@@ -234,11 +285,26 @@ steps:
source: timeresolution
- id: freqresolution
source: freqresolution
+ - id: minpoints
+ default: 1
out:
- id: augmented_steps
run: ../lofar-cwl/steps/DP3.AveragerStepGenerator.cwl
'sbg:x': 2158.297119140625
'sbg:y': -55.93873977661133
+ - id: concat_logfiles_dppp
+ in:
+ - id: file_list
+ source:
+ - dppp/logfile
+ - id: file_prefix
+ default: dppp
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_dppp
+ 'sbg:x': 2759.2265625
+ 'sbg:y': 140.91714477539062
requirements:
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
diff --git a/subworkflow/ndppp_prep_targ.cwl b/subworkflow/ndppp_prep_targ.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..45d923d9430a8745aa6aace52a5759d98ee54cf8
--- /dev/null
+++ b/subworkflow/ndppp_prep_targ.cwl
@@ -0,0 +1,475 @@
+class: Workflow
+cwlVersion: v1.0
+id: ndppp_prep_targ
+label: ndppp_prep_targ
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: baselines_to_flag
+ type: 'string[]'
+ 'sbg:x': 732.2234497070312
+ 'sbg:y': 79.11939239501953
+ - id: elevation_to_flag
+ type: string
+ 'sbg:x': 815.8416137695312
+ 'sbg:y': -281.40777587890625
+ - id: min_amplitude_to_flag
+ type: float
+ 'sbg:x': 964.3058471679688
+ 'sbg:y': 191.110595703125
+ - id: memoryperc
+ type: int
+ 'sbg:x': 136.78256225585938
+ 'sbg:y': -341.9549560546875
+ - id: raw_data
+ type: boolean
+ 'sbg:x': 464.3541259765625
+ 'sbg:y': -200.52120971679688
+ - id: demix
+ type: boolean
+ 'sbg:x': 1647.1820068359375
+ 'sbg:y': -314.6533508300781
+ - id: msin
+ type: Directory?
+ 'sbg:x': 3819.599853515625
+ 'sbg:y': 423.25006103515625
+ - id: skymodel
+ type: File
+ 'sbg:x': 1335.2567138671875
+ 'sbg:y': 148.68453979492188
+ - id: timeresolution
+ type: float
+ 'sbg:x': 3344.8515625
+ 'sbg:y': -733.585693359375
+ - id: freqresolution
+ type: string
+ 'sbg:x': 3358.795654296875
+ 'sbg:y': 298.08917236328125
+ - id: demix_timestep
+ type: int
+ 'sbg:x': 1371.962646484375
+ 'sbg:y': 307.4278259277344
+ - id: demix_freqstep
+ type: int
+ 'sbg:x': 1465.0855712890625
+ 'sbg:y': 450.8930358886719
+ - id: process_baselines_target
+ type: string
+ 'sbg:x': 1585.496826171875
+ 'sbg:y': 588.0062866210938
+ - id: target_source
+ type: string
+ 'sbg:x': 1439.47314453125
+ 'sbg:y': -325.6144104003906
+ - id: ntimechunk
+ type: int
+ 'sbg:x': 1149.4033203125
+ 'sbg:y': 349.2409362792969
+ - id: subtract_sources
+ type: 'string[]?'
+ 'sbg:x': 1257.9327392578125
+ 'sbg:y': -290.095703125
+ - id: parmdb
+ type: File
+ 'sbg:x': 1930.5469970703125
+ 'sbg:y': 298.99664306640625
+ - id: apply_tec_correction
+ type: boolean
+ 'sbg:x': 2310.848876953125
+ 'sbg:y': 446.3658752441406
+ - id: apply_rm_correction
+ type: boolean
+ 'sbg:x': 2461.30224609375
+ 'sbg:y': 719.8994140625
+ - id: apply_phase_correction
+ type: boolean
+ 'sbg:x': 2544.00341796875
+ 'sbg:y': 844.8623657226562
+ - id: apply_clock_correction
+ type: boolean
+ 'sbg:x': 2238.046630859375
+ 'sbg:y': 327.0130920410156
+ - id: apply_beam_correction
+ type: boolean
+ 'sbg:x': 2391.738037109375
+ 'sbg:y': 585.3051147460938
+ - id: filter_baselines
+ type: string
+ 'sbg:x': 1880
+ 'sbg:y': -380
+ - id: updateweights
+ type: boolean
+ 'sbg:x': 2234.90185546875
+ 'sbg:y': -393.8929748535156
+outputs:
+ - id: prep_logfile
+ outputSource:
+ - concat_logfiles_dppp/output
+ type: File?
+ 'sbg:x': 5500
+ 'sbg:y': 100
+ - id: predict_logfile
+ outputSource:
+ - concat_logfiles_predict/output
+ type: File?
+ 'sbg:x': 5500
+ 'sbg:y': 0
+ - id: clipper_logfile
+ outputSource:
+ - concat_logfiles_clipper/output
+ type: File?
+ 'sbg:x': 5500
+ 'sbg:y': -100
+ - id: msout
+ outputSource:
+ - predict/msout
+ type: Directory
+ 'sbg:x': 5502.318359375
+ 'sbg:y': -279.49835205078125
+ - id: clipper_output
+ outputSource:
+ - Ateamclipper/output
+ type: File
+ 'sbg:x': 5502.318359375
+ 'sbg:y': -500
+ - id: parset
+ outputSource:
+ - dp3_execute/parset
+ type: File
+ 'sbg:x': 5427.662109375
+ 'sbg:y': -765.5377197265625
+steps:
+ - id: flagbaseline
+ in:
+ - id: steps
+ source:
+ - process_raw_data_select/selected_steps
+ - id: step_name
+ default: flagbaseline
+ - id: baseline
+ source:
+ - baselines_to_flag
+ out:
+ - id: augmented_steps
+ run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
+ 'sbg:x': 955.2450561523438
+ 'sbg:y': -75.71149444580078
+ - id: flagelev
+ in:
+ - id: steps
+ source:
+ - flagbaseline/augmented_steps
+ - id: step_name
+ default: flagelev
+ - id: elevation
+ source: elevation_to_flag
+ out:
+ - id: augmented_steps
+ run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
+ 'sbg:x': 1187.4771728515625
+ 'sbg:y': -83
+ - id: process_raw_data_select
+ in:
+ - id: select_a
+ source: raw_data
+ - id: a_steps
+ source:
+ - aoflag/augmented_steps
+ - id: b_steps
+ default: []
+ out:
+ - id: selected_steps
+ run: ../lofar-cwl/steps/DP3.Selector.cwl
+ label: Selector
+ 'sbg:x': 621.4892578125
+ 'sbg:y': -71.31844329833984
+ - id: flagamp
+ in:
+ - id: steps
+ source:
+ - flagelev/augmented_steps
+ - id: step_name
+ default: flagamp
+ - id: amplmin
+ source: min_amplitude_to_flag
+ out:
+ - id: augmented_steps
+ run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
+ 'sbg:x': 1385.993408203125
+ 'sbg:y': -42.28850555419922
+ - id: flagedge
+ in:
+ - id: steps
+ default: []
+ - id: step_name
+ default: flagedge
+ - id: chan
+ default: '[0..nchan/32-1,31*nchan/32..nchan-1]'
+ out:
+ - id: augmented_steps
+ run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
+ 'sbg:x': 122.25408935546875
+ 'sbg:y': -54.06163024902344
+ - id: aoflag
+ in:
+ - id: steps
+ source:
+ - flagedge/augmented_steps
+ - id: step_name
+ default: aoflag
+ - id: memoryperc
+ source: memoryperc
+ - id: keepstatistics
+ default: false
+ out:
+ - id: augmented_steps
+ run: ../lofar-cwl/steps/DP3.AOFlaggerStepGenerator.cwl
+ 'sbg:x': 369.9876708984375
+ 'sbg:y': -38.086280822753906
+ - id: demix_select
+ in:
+ - id: select_a
+ source: demix
+ - id: a_steps
+ source:
+ - demixstepgenerator/augmented_steps
+ - id: b_steps
+ source:
+ - flagamp/augmented_steps
+ out:
+ - id: selected_steps
+ run: ../lofar-cwl/steps/DP3.Selector.cwl
+ label: demix?
+ 'sbg:x': 1888.8828125
+ 'sbg:y': -24.5985050201416
+ - id: demixstepgenerator
+ in:
+ - id: steps
+ source:
+ - flagamp/augmented_steps
+ - id: step_name
+ default: demixer
+ - id: baseline
+ source: process_baselines_target
+ - id: demixtimestep
+ source: demix_timestep
+ - id: demixfreqstep
+ source: demix_freqstep
+ - id: ntimechunk
+ source: ntimechunk
+ - id: skymodel
+ source: skymodel
+ - id: subtractsources
+ source:
+ - subtract_sources
+ - id: targetsource
+ source: target_source
+ out:
+ - id: augmented_steps
+ run: ../lofar-cwl/steps/DP3.DemixerStepGenerator.cwl
+ 'sbg:x': 1676.6593017578125
+ 'sbg:y': 90.7158203125
+ - id: average_step_generator
+ in:
+ - id: steps
+ source:
+ - prep_target_applycal/selected_steps
+ - id: step_name
+ default: averager
+ - id: minpoints
+ default: 1
+ - id: timeresolution
+ source: timeresolution
+ - id: freqresolution
+ source: freqresolution
+ out:
+ - id: augmented_steps
+ run: ../lofar-cwl/steps/DP3.AveragerStepGenerator.cwl
+ 'sbg:x': 3743.862060546875
+ 'sbg:y': -426.2447814941406
+ - id: concat_logfiles_dppp
+ in:
+ - id: file_list
+ source:
+ - dp3_execute/logfile
+ - id: file_prefix
+ default: dppp
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_dppp
+ 'sbg:x': 4543.36376953125
+ 'sbg:y': -6.564670085906982
+ - id: concat_logfiles_predict
+ in:
+ - id: file_list
+ source:
+ - predict/logfile
+ - id: file_prefix
+ default: predict_targ
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_predict
+ 'sbg:x': 4700
+ 'sbg:y': -6.564670085906982
+ - id: concat_logfiles_clipper
+ in:
+ - id: file_list
+ source:
+ - Ateamclipper/logfile
+ - id: file_prefix
+ default: Ateamclipper
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_clipper
+ 'sbg:x': 4900
+ 'sbg:y': -6.564670085906982
+ - id: dp3_execute
+ in:
+ - id: msout_name
+ source: msin
+ valueFrom: $("out_"+self.basename)
+ - id: msin
+ source: msin
+ - id: steps
+ source:
+ - average_step_generator/augmented_steps
+ - id: autoweight
+ default: false
+ source: raw_data
+ out:
+ - id: secondary_output_files
+ - id: secondary_output_directories
+ - id: msout
+ - id: logfile
+ - id: parset
+ run: ../lofar-cwl/steps/DP3.Execute.cwl
+ label: DP3.Execute
+ 'sbg:x': 4154.9287109375
+ 'sbg:y': -344.5472106933594
+ - id: filter
+ in:
+ - id: steps
+ source:
+ - demix_select/selected_steps
+ - id: step_name
+ default: filter
+ - id: baseline
+ source: filter_baselines
+ - id: remove
+ default: true
+ out:
+ - id: augmented_steps
+ run: ../lofar-cwl/steps/DP3.FilterStepGenerator.cwl
+ 'sbg:x': 2049.48486328125
+ 'sbg:y': -18.005611419677734
+ - id: applyPA
+ in:
+ - id: steps
+ source:
+ - filter/augmented_steps
+ - id: step_name
+ default: apply_pa_1
+ - id: parmdb
+ source: parmdb
+ - id: solset
+ default: calibrator
+ - id: correction
+ default: polalign
+ out:
+ - id: augmented_steps
+ run: ../lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
+ 'sbg:x': 2205.820068359375
+ 'sbg:y': 7.381086349487305
+ - id: applyBandpass
+ in:
+ - id: steps
+ source:
+ - applyPA/augmented_steps
+ - id: step_name
+ default: apply_bandpass_1
+ - id: parmdb
+ source: parmdb
+ - id: solset
+ default: calibrator
+ - id: correction
+ default: bandpass
+ out:
+ - id: augmented_steps
+ run: ../lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
+ 'sbg:x': 2420.382568359375
+ 'sbg:y': -149.9799346923828
+ - id: prep_target_applycal
+ in:
+ - id: steps
+ source:
+ - applyBandpass/augmented_steps
+ - id: apply_clock_correction
+ source: apply_clock_correction
+ - id: apply_tec_correction
+ source: apply_tec_correction
+ - id: apply_rm_correction
+ source: apply_rm_correction
+ - id: apply_beam_correction
+ source: apply_beam_correction
+ - id: apply_phase_correction
+ source: apply_phase_correction
+ - id: parmdb
+ source: parmdb
+ - id: updateweights
+ source: updateweights
+ out:
+ - id: selected_steps
+ run: ./prep_target_applycal.cwl
+ label: prep_target_applycal
+ 'sbg:x': 2728.697998046875
+ 'sbg:y': -18.151018142700195
+ - id: predict
+ in:
+ - id: msin
+ source: dp3_execute/msout
+ - id: msin_datacolumn
+ default: DATA
+ - id: msout_datacolumn
+ default: MODEL_DATA
+ - id: sources_db
+ source: skymodel
+ - id: sources
+ default:
+ - VirA_4_patch
+ - CygAGG
+ - CasA_4_patch
+ - TauAGG
+ - id: usebeammodel
+ default: true
+ - id: onebeamperpatch
+ default: true
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
+ out:
+ - id: msout
+ - id: logfile
+ run: ../lofar-cwl/steps/filter_predict.cwl
+ 'sbg:x': 4500
+ 'sbg:y': -344.5472106933594
+ - id: Ateamclipper
+ in:
+ - id: msin
+ source:
+ - predict/msout
+ out:
+ - id: msout
+ - id: logfile
+ - id: output
+ run: ../lofar-cwl/steps/Ateamclipper.cwl
+ label: Ateamclipper
+ 'sbg:x': 4700
+ 'sbg:y': -344.5472106933594
+requirements:
+ - class: SubworkflowFeatureRequirement
+ - class: InlineJavascriptRequirement
+ - class: StepInputExpressionRequirement
diff --git a/subworkflow/pol_align.cwl b/subworkflow/pol_align.cwl
index 91666c3f84f2a439e81d3306ac2784d3e44b5732..808e4fa193fdf98be78c1067f6f12b7c7ffa4dc0 100644
--- a/subworkflow/pol_align.cwl
+++ b/subworkflow/pol_align.cwl
@@ -14,13 +14,26 @@ inputs:
type: File
'sbg:x': -743.1871948242188
'sbg:y': -316.5615234375
+ - id: fit_offset_PA
+ type: boolean?
+ 'sbg:x': -743.1871948242188
+ 'sbg:y': -316.5615234375
outputs:
- id: output_h5parm
outputSource:
- losoto_residual/output_h5parm
type: File
+ 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: losoto_duplicate
in:
@@ -32,6 +45,7 @@ steps:
default: phaseOrig
out:
- id: output_h5parm
+ - id: log
run: ../lofar-cwl/steps/LoSoTo.Duplicate.cwl
'sbg:x': -423.6229248046875
'sbg:y': -287.8958435058594
@@ -47,10 +61,15 @@ steps:
default: true
- id: replace
default: true
+ - id: maxResidual
+ default: 1.0
+ - id: fitOffset
+ source: fit_offset_PA
- id: refAnt
source: refAnt
out:
- id: output_h5parm
+ - id: log
run: ../lofar-cwl/steps/LoSoTo.Polalign.cwl
'sbg:x': -203.663818359375
'sbg:y': -292.61700439453125
@@ -65,6 +84,7 @@ steps:
- polalign
out:
- id: output_h5parm
+ - id: log
run: ../lofar-cwl/steps/LoSoTo.Residual.cwl
'sbg:x': -0.012040258385241032
'sbg:y': -287.7294006347656
diff --git a/subworkflow/predict_calibrate.cwl b/subworkflow/predict_calibrate.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..4186dd11968ae6f8bb8e95aa1bf9f54f4b133562
--- /dev/null
+++ b/subworkflow/predict_calibrate.cwl
@@ -0,0 +1,140 @@
+class: Workflow
+cwlVersion: v1.0
+id: predict_calibrate
+label: predict_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: sourcedb
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: flagunconverged
+ type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': 100
+ - id: propagatesolutions
+ type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': 200
+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: predict_cal.log
+ outputSource:
+ - concat_logfiles_predict/output
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: calib_cal.log
+ outputSource:
+ - concat_logfiles_calib_cal/output
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 100
+ - id: outh5parm
+ outputSource:
+ - calib_cal/h5parm
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 200
+steps:
+ - id: BLsmooth
+ in:
+ - id: msin
+ source: msin
+ - id: do_smooth
+ source: do_smooth
+ out:
+ - id: msout
+ - id: logfile
+ run: ../steps/blsmooth.cwl
+ label: BLsmooth
+ 'sbg:x': -500
+ 'sbg:y': 0
+ - id: predict
+ in:
+ - id: msin
+ source: BLsmooth/msout
+ - id: msin_datacolumn
+ default: SMOOTHED_DATA
+ - id: msout_datacolumn
+ default: MODEL_DATA
+ - id: sources_db
+ source: sourcedb
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
+ out:
+ - id: msout
+ - id: logfile
+ run: ../lofar-cwl/steps/predict.cwl
+ 'sbg:x': 0
+ 'sbg:y': 0
+ - id: calib_cal
+ in:
+ - id: msin
+ source: predict/msout
+ - id: msin_datacolumn
+ default: SMOOTHED_DATA
+ - id: msin_modelcolum
+ default: MODEL_DATA
+ - id: propagate_solutions
+ source: propagatesolutions
+ - id: flagunconverged
+ source: flagunconverged
+ - id: mode
+ default: rotation+diagonal
+ out:
+ - id: msout
+ - id: h5parm
+ - id: logfile
+ run: ../lofar-cwl/steps/ddecal.cwl
+ 'sbg:x': 500
+ 'sbg:y': 0
+ - id: concat_logfiles_predict
+ in:
+ - id: file_list
+ source:
+ - predict/logfile
+ - id: file_prefix
+ default: predict
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_predict
+ 'sbg:x': 500
+ 'sbg:y': 200
+ - id: concat_logfiles_calib_cal
+ in:
+ - id: file_list
+ source:
+ - calib_cal/logfile
+ - id: file_prefix
+ default: calib_cal
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_calib_cal
+ 'sbg:x': 700
+ 'sbg:y': 200
+requirements: []
diff --git a/subworkflow/prep_target_applycal.cwl b/subworkflow/prep_target_applycal.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..e3968609efdafd6e652bf9da367a96a29e02267f
--- /dev/null
+++ b/subworkflow/prep_target_applycal.cwl
@@ -0,0 +1,226 @@
+class: Workflow
+cwlVersion: v1.0
+id: prep_target_applycal
+label: prep_target_applycal
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: steps
+ type: 'Any[]?'
+ 'sbg:x': 1566.9437255859375
+ 'sbg:y': 173.2586669921875
+ - id: apply_clock_correction
+ type: boolean
+ 'sbg:x': 1622.751953125
+ 'sbg:y': -235.5788116455078
+ - id: apply_tec_correction
+ type: boolean
+ 'sbg:x': 1990.8035888671875
+ 'sbg:y': -230.75811767578125
+ - id: apply_rm_correction
+ type: boolean
+ 'sbg:x': 2502.2421875
+ 'sbg:y': -225.68701171875
+ - id: apply_beam_correction
+ type: boolean
+ 'sbg:x': 2273.170166015625
+ 'sbg:y': -251.86672973632812
+ - id: apply_phase_correction
+ type: boolean
+ 'sbg:x': 2750.948974609375
+ 'sbg:y': -241.39480590820312
+ - id: parmdb
+ type: File
+ 'sbg:x': 2007.115234375
+ 'sbg:y': 685.0719604492188
+ - id: updateweights
+ type: boolean
+ 'sbg:x': 2167.219970703125
+ 'sbg:y': 422.6792297363281
+outputs:
+ - id: selected_steps
+ outputSource:
+ - apply_phase/selected_steps
+ type: Any
+ 'sbg:x': 3129.244873046875
+ 'sbg:y': 165.6987762451172
+steps:
+ - id: applyClock
+ in:
+ - id: steps
+ source:
+ - steps
+ - id: step_name
+ default: apply_clock
+ - id: parmdb
+ source: parmdb
+ - id: solset
+ default: calibrator
+ - id: correction
+ default: clock
+ out:
+ - id: augmented_steps
+ run: ../lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
+ 'sbg:x': 1747.8311767578125
+ 'sbg:y': 285.2012634277344
+ - id: applyTec
+ in:
+ - id: steps
+ source:
+ - apply_clock/selected_steps
+ - id: step_name
+ default: apply_tec
+ - id: parmdb
+ source: parmdb
+ - id: solset
+ default: calibrator
+ - id: correction
+ default: tec
+ out:
+ - id: augmented_steps
+ run: ../lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
+ 'sbg:x': 2056.49462890625
+ 'sbg:y': 277.8923034667969
+ - id: applyPhase
+ in:
+ - id: steps
+ source:
+ - apply_rm/selected_steps
+ - id: step_name
+ default: apply_phase
+ - id: parmdb
+ source: parmdb
+ - id: solset
+ default: calibrator
+ - id: correction
+ default: phaseOrig
+ out:
+ - id: augmented_steps
+ run: ../lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
+ 'sbg:x': 2805.44873046875
+ 'sbg:y': 299.8974304199219
+ - id: applyRM
+ in:
+ - id: steps
+ source:
+ - apply_beam/selected_steps
+ - id: step_name
+ default: apply_rm
+ - id: parmdb
+ source: parmdb
+ - id: solset
+ default: target
+ - id: correction
+ default: RMextract
+ out:
+ - id: augmented_steps
+ run: ../lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
+ 'sbg:x': 2545.4775390625
+ 'sbg:y': 291.2240295410156
+ - id: applybeam
+ in:
+ - id: steps
+ source:
+ - apply_tec/selected_steps
+ - id: step_name
+ default: apply_beam
+ - id: usechannelfreq
+ default: true
+ - id: updateweights
+ source: updateweights
+ - id: invert
+ default: true
+ - id: beammode
+ default: default
+ out:
+ - id: augmented_steps
+ run: ../lofar-cwl/steps/DP3.ApplyBeamStepGenerator.cwl
+ 'sbg:x': 2321
+ 'sbg:y': 285.3694763183594
+ - id: apply_beam
+ in:
+ - id: select_a
+ source: apply_beam_correction
+ - id: a_steps
+ source:
+ - applybeam/augmented_steps
+ - id: b_steps
+ default: []
+ source:
+ - apply_tec/selected_steps
+ out:
+ - id: selected_steps
+ run: ../lofar-cwl/steps/DP3.Selector.cwl
+ label: apply_beam
+ 'sbg:x': 2441.14599609375
+ 'sbg:y': 167.0730438232422
+ - id: apply_rm
+ in:
+ - id: select_a
+ source: apply_rm_correction
+ - id: a_steps
+ source:
+ - applyRM/augmented_steps
+ - id: b_steps
+ default: []
+ source:
+ - apply_beam/selected_steps
+ out:
+ - id: selected_steps
+ run: ../lofar-cwl/steps/DP3.Selector.cwl
+ label: apply_rm?
+ 'sbg:x': 2648.432373046875
+ 'sbg:y': 167.062255859375
+ - id: apply_clock
+ in:
+ - id: select_a
+ source: apply_clock_correction
+ - id: a_steps
+ source:
+ - applyClock/augmented_steps
+ - id: b_steps
+ default: []
+ source:
+ - steps
+ out:
+ - id: selected_steps
+ run: ../lofar-cwl/steps/DP3.Selector.cwl
+ label: apply_clock?
+ 'sbg:x': 1909.072998046875
+ 'sbg:y': 167.82034301757812
+ - id: apply_tec
+ in:
+ - id: select_a
+ source: apply_tec_correction
+ - id: a_steps
+ source:
+ - applyTec/augmented_steps
+ - id: b_steps
+ default: []
+ source:
+ - apply_clock/selected_steps
+ out:
+ - id: selected_steps
+ run: ../lofar-cwl/steps/DP3.Selector.cwl
+ label: apply_tec?
+ 'sbg:x': 2192.246826171875
+ 'sbg:y': 166.15206909179688
+ - id: apply_phase
+ in:
+ - id: select_a
+ source: apply_phase_correction
+ - id: a_steps
+ source:
+ - applyPhase/augmented_steps
+ - id: b_steps
+ default: []
+ source:
+ - apply_rm/selected_steps
+ out:
+ - id: selected_steps
+ run: ../lofar-cwl/steps/DP3.Selector.cwl
+ label: apply_phase
+ 'sbg:x': 2927.22412109375
+ 'sbg:y': 162.4778289794922
+requirements:
+ - class: SubworkflowFeatureRequirement
diff --git a/test_workflow/empty_dirs/ms1/README b/test_workflow/empty_dirs/ms1/README
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/test_workflow/empty_dirs/ms2/README b/test_workflow/empty_dirs/ms2/README
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/test_workflow/empty_dirs/ms3/README b/test_workflow/empty_dirs/ms3/README
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/test_workflow/empty_dirs/ms5/README b/test_workflow/empty_dirs/ms5/README
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/test_workflow/filter_ms_group.json b/test_workflow/filter_ms_group.json
new file mode 100644
index 0000000000000000000000000000000000000000..dbdcc34733a9aa358d6d7bd9a2d4769b7e80bf5e
--- /dev/null
+++ b/test_workflow/filter_ms_group.json
@@ -0,0 +1,9 @@
+{
+"group_id": "1",
+"groups_specification": {"class": "File", "path": "groups_spec.json"},
+"measurement_sets": [
+ {"class": "Directory", "path": "empty_dirs/ms1"},
+ {"class": "Directory", "path": "empty_dirs/ms2"},
+ {"class": "Directory", "path": "empty_dirs/ms3"},
+ {"class": "Directory", "path": "empty_dirs/ms5"}]
+}
diff --git a/test_workflow/groups_spec.json b/test_workflow/groups_spec.json
new file mode 100644
index 0000000000000000000000000000000000000000..89e56a1ffbd550d4ed4f48841a01cc2feaa47578
--- /dev/null
+++ b/test_workflow/groups_spec.json
@@ -0,0 +1,4 @@
+{
+ "1": ["ms1", "ms2"],
+ "2": ["ms3", "ms5"]
+}
diff --git a/workflows/HBA_calibrator.cwl b/workflows/HBA_calibrator.cwl
index 101392e71b433db42dcba5d45c3a6bf993211d55..664c6dda2b7a1ed1556b528ff4a21ec04c39fa6d 100644
--- a/workflows/HBA_calibrator.cwl
+++ b/workflows/HBA_calibrator.cwl
@@ -1,117 +1,126 @@
class: Workflow
cwlVersion: v1.0
-id: _h_b_a
-label: HBA.cwl
+id: HBA_calibrator
+label: HBA_calibrator
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: msin
type: 'Directory[]'
'sbg:x': -1000
- 'sbg:y': -1700
+ 'sbg:y': -1900
- id: refant
type: string?
- default: CS001HBA0
+ default: 'CS00.*'
'sbg:x': -1000
- 'sbg:y': -1600
+ 'sbg:y': -1800
- id: flag_baselines
type: 'string[]?'
default: []
'sbg:x': -1000
- 'sbg:y': -1500
+ 'sbg:y': -1700
- id: process_baselines_cal
type: string?
default: '*&'
'sbg:x': -1000
- 'sbg:y': -1400
+ 'sbg:y': -1600
- id: filter_baselines
type: string?
default: '*&'
'sbg:x': -1000
- 'sbg:y': -1300
+ 'sbg:y': -1500
+ - id: fit_offset_PA
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -1400
- id: do_smooth
type: boolean?
default: false
'sbg:x': -1000
- 'sbg:y': -1200
+ 'sbg:y': -1300
- id: rfistrategy
type: string?
default: HBAdefault.rfis
'sbg:x': -1000
- 'sbg:y': -1100
+ 'sbg:y': -1200
- id: max2interpolate
type: int?
default: 30
'sbg:x': -1000
- 'sbg:y': -1000
+ 'sbg:y': -1100
- id: ampRange
- type: 'int[]?'
+ type: 'float[]?'
default:
- 0
- 0
'sbg:x': -1000
- 'sbg:y': -900
+ 'sbg:y': -1000
- id: skip_international
type: boolean?
default: true
'sbg:x': -1000
- 'sbg:y': -800
+ 'sbg:y': -900
- id: raw_data
type: boolean?
default: false
'sbg:x': -1000
- 'sbg:y': -700
+ 'sbg:y': -800
- id: propagatesolutions
type: boolean?
default: true
'sbg:x': -1000
- 'sbg:y': -600
+ 'sbg:y': -700
- id: flagunconverged
type: boolean?
default: false
'sbg:x': -1000
- 'sbg:y': -500
+ 'sbg:y': -600
- id: maxStddev
type: float?
default: -1.0
'sbg:x': -1000
- 'sbg:y': -400
+ 'sbg:y': -500
- id: solutions2transfer
type: File?
- default: /data/solutions/3C48.h5
'sbg:x': -1000
- 'sbg:y': -300
+ 'sbg:y': -400
- id: antennas2transfer
- type: File?
+ type: string?
default: '[FUSPID].*'
'sbg:x': -1000
+ 'sbg:y': -300
+ - id: do_transfer
+ type: boolean
+ default: false
+ 'sbg:x': -1000
'sbg:y': -200
+ - id: trusted_sources
+ type: string
+ default: '3C48,3C147,3C196,3C295'
+ 'sbg:x': -1000
+ 'sbg:y': -100
- id: demix_sources
type: 'string[]?'
default:
- CasA
- CygA
'sbg:x': -1000
- 'sbg:y': -100
+ 'sbg:y': 0
- id: demix_target
type: string?
default: ''
'sbg:x': -1000
- 'sbg:y': 0
+ 'sbg:y': 100
- id: demix_freqstep
type: int?
default: 16
'sbg:x': -1000
- 'sbg:y': 100
+ 'sbg:y': 200
- id: demix_timestep
type: int?
default: 10
'sbg:x': -1000
- 'sbg:y': 200
- - id: raw_data
- type: boolean?
- default: false
- 'sbg:x': -1000
'sbg:y': 300
- id: demix
type: boolean?
@@ -138,44 +147,42 @@ inputs:
default: false
'sbg:x': -1000
'sbg:y': 800
+ - id: max_dppp_threads
+ type: int?
+ default: 10
+ 'sbg:x': -1000
+ 'sbg:y': 900
- id: memoryperc
type: int?
default: 20
'sbg:x': -1000
- 'sbg:y': 900
+ 'sbg:y': 1000
- id: min_length
type: int?
default: 50
'sbg:x': -1000
- 'sbg:y': 1000
+ 'sbg:y': 1100
- id: overhead
type: float?
default: 0.8
'sbg:x': -1000
- 'sbg:y': 1100
+ 'sbg:y': 1200
- id: min_separation
type: int?
default: 30
'sbg:x': -1000
- 'sbg:y': 1200
+ 'sbg:y': 1300
- id: max_separation_arcmin
type: float?
- default: 1
+ default: 1.0
'sbg:x': -1000
- 'sbg:y': 1300
+ 'sbg:y': 1400
- id: calibrator_path_skymodel
type: Directory?
- default: /data/skymodels
- 'sbg:x': -1000
- 'sbg:y': 1400
- - id: A-Team_sky_model
- type: File?
- default: /data/skymodels/Ateam_LBA_CC.skymodel
'sbg:x': -1000
'sbg:y': 1500
- - id: cal_solutions
- type: string?
- default: cal_solutions.h5
+ - id: A-Team_skymodel
+ type: File?
'sbg:x': -1000
'sbg:y': 1600
- id: avg_timeresolution
@@ -194,55 +201,35 @@ inputs:
'sbg:x': -1000
'sbg:y': 1900
outputs:
- - id: msout
- outputSource:
- - prefactor/msout
- type: 'Directory[]'
- 'sbg:x': 289.5600891113281
- 'sbg:y': -144.01869201660156
- - id: make_sourcedb_ateam.log
- outputSource:
- - prefactor/make_sourcedb_ateam.log
- type: File?
- 'sbg:x': 317.4496154785156
- 'sbg:y': 9.373631477355957
- - id: logfile_prep_cal
+ - id: logs
outputSource:
- - prefactor/logfile_prep_cal
- type: 'File[]?'
- 'sbg:x': 315.0741882324219
- 'sbg:y': 180.26284790039062
- - id: check_Ateam_separation.png
- outputSource:
- - prefactor/check_Ateam_separation.png
- type: 'File[]?'
- 'sbg:x': 287.6455078125
- 'sbg:y': 344.1313171386719
- - id: check_Ateam_separation.log
- outputSource:
- - prefactor/check_Ateam_separation.log
- type: 'File[]?'
- 'sbg:x': 315.5941467285156
- 'sbg:y': 494.9656982421875
- - id: parset
+ - save_logfiles/log_dir
+ type: Directory
+ 'sbg:x': 1500
+ 'sbg:y': -100
+ - id: results
outputSource:
- - prefactor/parset
- type: 'File[]'
- 'sbg:x': 293.33331298828125
- 'sbg:y': -305.4627990722656
+ - save_results/log_dir
+ type: Directory
+ 'sbg:x': 1500
+ 'sbg:y': 0
steps:
- id: prefactor
in:
- id: msin
- source: msin
+ source:
+ - msin
- id: refant
source: refant
- id: flag_baselines
- source: flag_baselines
+ source:
+ - flag_baselines
- id: process_baselines_cal
source: process_baselines_cal
- id: filter_baselines
source: filter_baselines
+ - id: fit_offset_PA
+ source: fit_offset_PA
- id: do_smooth
source: do_smooth
- id: rfistrategy
@@ -250,7 +237,8 @@ steps:
- id: max2interpolate
source: max2interpolate
- id: ampRange
- source: ampRange
+ source:
+ - ampRange
- id: skip_international
source: skip_international
- id: raw_data
@@ -265,8 +253,13 @@ steps:
source: solutions2transfer
- id: antennas2transfer
source: antennas2transfer
+ - id: do_transfer
+ source: do_transfer
+ - id: trusted_sources
+ source: trusted_sources
- id: demix_sources
- source: demix_sources
+ source:
+ - demix_sources
- id: demix_target
source: demix_target
- id: demix_freqstep
@@ -283,6 +276,8 @@ steps:
source: tables2export
- id: final_apply
source: final_apply
+ - id: max_dppp_threads
+ source: max_dppp_threads
- id: memoryperc
source: memoryperc
- id: min_length
@@ -295,10 +290,8 @@ steps:
source: max_separation_arcmin
- id: calibrator_path_skymodel
source: calibrator_path_skymodel
- - id: A-Team_sky_model
- source: Team_sky_model
- - id: cal_solutions
- source: cal_solutions
+ - id: A-Team_skymodel
+ source: A-Team_skymodel
- id: avg_timeresolution
source: avg_timeresolution
- id: avg_freqresolution
@@ -306,15 +299,73 @@ 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
- run: ./prefactor_calibrator_test.cwl
+ - id: solutions
+ - id: inspection
+ run: ./prefactor_calibrator.cwl
label: prefactor_calibrator
'sbg:x': 0
'sbg:y': 0
+ - id: save_logfiles
+ in:
+ - id: log_files
+ linkMerge: merge_flattened
+ source:
+ - prefactor/logfiles
+ - id: sub_directory_name
+ default: logs
+ out:
+ - id: log_dir
+ run: ./../steps/collectlog.cwl
+ label: save_logfiles
+ 'sbg:x': 1000
+ 'sbg:y': -200
+ - id: save_inspection
+ in:
+ - id: log_files
+ linkMerge: merge_flattened
+ source:
+ - prefactor/inspection
+ - id: sub_directory_name
+ default: inspection
+ out:
+ - id: log_dir
+ run: ./../steps/collectlog.cwl
+ label: save_inspection
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: save_solutions
+ in:
+ - id: log_files
+ source:
+ - prefactor/solutions
+ - id: sub_directory_name
+ default: cal_values
+ out:
+ - id: log_dir
+ run: ./../steps/collectlog.cwl
+ label: save_solutions
+ 'sbg:x': 1000
+ 'sbg:y': 200
+ - id: save_results
+ in:
+ - id: log_files
+ linkMerge: merge_flattened
+ source:
+ - save_solutions/log_dir
+ - save_inspection/log_dir
+ - prefactor/msout
+ - id: sub_directory_name
+ default: results
+ out:
+ - id: log_dir
+ run: ./../steps/collectlog.cwl
+ label: save_results
+ 'sbg:x': 1200
+ 'sbg:y': 0
requirements:
- class: SubworkflowFeatureRequirement
+ - class: MultipleInputFeatureRequirement
+
diff --git a/workflows/HBA_target.cwl b/workflows/HBA_target.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..a42768111708e306c360753e9d9489adb16f995a
--- /dev/null
+++ b/workflows/HBA_target.cwl
@@ -0,0 +1,415 @@
+class: Workflow
+cwlVersion: v1.0
+id: HBA_target
+label: HBA_target
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: msin
+ type: 'Directory[]'
+ 'sbg:x': -1000
+ 'sbg:y': -1700
+ - id: cal_solutions
+ type: 'File'
+ 'sbg:x': -1000
+ 'sbg:y': -1600
+ - id: refant
+ type: string?
+ default: 'CS00.*'
+ 'sbg:x': -1000
+ 'sbg:y': -1500
+ - id: flag_baselines
+ type: 'string[]?'
+ default: []
+ 'sbg:x': -1000
+ 'sbg:y': -1400
+ - id: process_baselines_target
+ type: string?
+ default: '[CR]S*&'
+ 'sbg:x': -1000
+ 'sbg:y': -1300
+ - id: filter_baselines
+ type: string?
+ default: '[CR]S*&'
+ 'sbg:x': -1000
+ 'sbg:y': -1200
+ - id: do_smooth
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -1100
+ - id: rfistrategy
+ type: string?
+ default: HBAdefault.rfis
+ 'sbg:x': -1000
+ 'sbg:y': -1000
+ - id: min_unflagged_fraction
+ type: float?
+ default: 0.5
+ 'sbg:x': -1000
+ 'sbg:y': -900
+ - id: compression_bitrate
+ type: int?
+ default: 16
+ 'sbg:x': -1000
+ 'sbg:y': -800
+ - id: raw_data
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -700
+ - id: propagatesolutions
+ type: boolean?
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': -600
+ - id: demix_sources
+ type: 'string[]?'
+ default:
+ - CasA
+ - CygA
+ 'sbg:x': -1000
+ 'sbg:y': -500
+ - id: demix_target
+ type: string?
+ default: ''
+ 'sbg:x': -1000
+ 'sbg:y': -400
+ - id: demix_freqstep
+ type: int?
+ default: 16
+ 'sbg:x': -1000
+ 'sbg:y': -300
+ - id: demix_timestep
+ type: int?
+ default: 10
+ 'sbg:x': -1000
+ 'sbg:y': -200
+ - id: demix
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -100
+ - id: apply_tec
+ type: boolean
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: apply_clock
+ type: boolean
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 100
+ - id: apply_phase
+ type: boolean
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': 200
+ - id: apply_RM
+ type: boolean
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 300
+ - id: apply_beam
+ type: boolean
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 400
+ - id: clipATeam
+ type: boolean?
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 500
+ - id: gsmcal_step
+ type: string?
+ default: 'phase'
+ 'sbg:x': -1000
+ 'sbg:y': 600
+ - id: updateweights
+ type: boolean?
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 700
+ - id: max_dppp_threads
+ type: int?
+ default: 10
+ 'sbg:x': -1000
+ 'sbg:y': 800
+ - id: memoryperc
+ type: int?
+ default: 20
+ 'sbg:x': -1000
+ 'sbg:y': 900
+ - id: min_length
+ type: int?
+ default: 5
+ 'sbg:x': -1000
+ 'sbg:y': 1000
+ - id: overhead
+ type: float?
+ default: 0.7
+ 'sbg:x': -1000
+ 'sbg:y': 1100
+ - id: min_separation
+ type: int?
+ default: 30
+ 'sbg:x': -1000
+ 'sbg:y': 1200
+ - id: A-Team_skymodel
+ type: File?
+ 'sbg:x': -1000
+ 'sbg:y': 1300
+ - id: target_skymodel
+ type: File?
+ 'sbg:x': -1000
+ 'sbg:y': 1400
+ - id: use_target
+ type: boolean?
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 1500
+ - id: skymodel_source
+ type: string?
+ default: 'TGSS'
+ 'sbg:x': -1000
+ 'sbg:y': 1600
+ - id: avg_timeresolution
+ type: int?
+ default: 4
+ 'sbg:x': -1000
+ 'sbg:y': 1700
+ - id: avg_freqresolution
+ type: string?
+ default: 48.82kHz
+ 'sbg:x': -1000
+ 'sbg:y': 1800
+ - id: avg_timeresolution_concat
+ type: int?
+ default: 8
+ 'sbg:x': -1000
+ 'sbg:y': 1900
+ - id: avg_freqresolution_concat
+ type: string?
+ default: 97.64kHz
+ 'sbg:x': -1000
+ 'sbg:y': 2000
+ - id: num_SBs_per_group
+ type: int?
+ default: 10
+ 'sbg:x': -1000
+ 'sbg:y': 2100
+ - id: reference_stationSB
+ type: int?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 2200
+ - id: ionex_server
+ type: string?
+ default: 'ftp://ftp.aiub.unibe.ch/CODE/'
+ 'sbg:x': -1000
+ 'sbg:y': 2300
+ - id: ionex_prefix
+ type: string?
+ default: 'CODG'
+ 'sbg:x': -1000
+ 'sbg:y': 2400
+ - id: proxy_server
+ type: string?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 2500
+ - id: proxy_port
+ type: string?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 2600
+ - id: proxy_type
+ type: string?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 2700
+ - id: proxy_user
+ type: string?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 2800
+ - id: proxy_pass
+ type: string?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 2900
+outputs:
+ - id: results
+ outputSource:
+ - save_results/log_dir
+ type: Directory
+ 'sbg:x': 1500
+ 'sbg:y': 0
+steps:
+ - id: prefactor
+ in:
+ - id: msin
+ source:
+ - msin
+ - id: cal_solutions
+ source: cal_solutions
+ - id: refant
+ source: refant
+ - id: flag_baselines
+ source:
+ - flag_baselines
+ - id: process_baselines_target
+ source: process_baselines_target
+ - id: filter_baselines
+ source: filter_baselines
+ - id: do_smooth
+ source: do_smooth
+ - id: rfistrategy
+ source: rfistrategy
+ - id: min_unflagged_fraction
+ source: min_unflagged_fraction
+ - id: compression_bitrate
+ source: compression_bitrate
+ - id: raw_data
+ source: raw_data
+ - id: propagatesolutions
+ source: propagatesolutions
+ - id: apply_tec
+ source: apply_tec
+ - id: apply_clock
+ source: apply_clock
+ - id: apply_phase
+ source: apply_phase
+ - id: apply_RM
+ source: apply_RM
+ - id: apply_beam
+ source: apply_beam
+ - id: demix_sources
+ source:
+ - demix_sources
+ - id: demix_target
+ source: demix_target
+ - id: demix_freqstep
+ source: demix_freqstep
+ - id: demix_timestep
+ source: demix_timestep
+ - id: demix
+ source: demix
+ - id: clipATeam
+ source: clipATeam
+ - id: updateweights
+ source: updateweights
+ - id: max_dppp_threads
+ source: max_dppp_threads
+ - id: memoryperc
+ source: memoryperc
+ - id: min_length
+ source: min_length
+ - id: overhead
+ source: overhead
+ - id: min_separation
+ source: min_separation
+ - id: A-Team_skymodel
+ source: A-Team_skymodel
+ - id: target_skymodel
+ source: target_skymodel
+ - id: use_target
+ source: use_target
+ - id: skymodel_source
+ source: skymodel_source
+ - id: avg_timeresolution
+ source: avg_timeresolution
+ - id: avg_freqresolution
+ source: avg_freqresolution
+ - id: avg_timeresolution_concat
+ source: avg_timeresolution_concat
+ - id: avg_freqresolution_concat
+ source: avg_freqresolution_concat
+ - id: num_SBs_per_group
+ source: num_SBs_per_group
+ - id: reference_stationSB
+ source: reference_stationSB
+ - id: ionex_server
+ source: ionex_server
+ - id: ionex_prefix
+ source: ionex_prefix
+ - id: proxy_server
+ source: proxy_server
+ - id: proxy_port
+ source: proxy_port
+ - id: proxy_type
+ source: proxy_type
+ - id: proxy_user
+ source: proxy_user
+ - id: proxy_pass
+ source: proxy_pass
+ out:
+ - id: logfiles
+ - id: msout
+ - id: solutions
+ - id: inspection
+ run: ./prefactor_target.cwl
+ label: prefactor_target
+ 'sbg:x': 0
+ 'sbg:y': 0
+ - id: save_logfiles
+ in:
+ - id: log_files
+ linkMerge: merge_flattened
+ source:
+ - prefactor/logfiles
+ - id: sub_directory_name
+ default: logs
+ out:
+ - id: log_dir
+ run: ./../steps/collectlog.cwl
+ label: save_logfiles
+ 'sbg:x': 1000
+ 'sbg:y': -200
+ - id: save_inspection
+ in:
+ - id: log_files
+ linkMerge: merge_flattened
+ source:
+ - prefactor/inspection
+ - id: sub_directory_name
+ default: inspection
+ out:
+ - id: log_dir
+ run: ./../steps/collectlog.cwl
+ label: save_inspection
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: save_solutions
+ in:
+ - id: log_files
+ source:
+ - prefactor/solutions
+ - id: sub_directory_name
+ default: cal_values
+ out:
+ - id: log_dir
+ run: ./../steps/collectlog.cwl
+ label: save_solutions
+ 'sbg:x': 1000
+ 'sbg:y': 200
+ - id: save_results
+ in:
+ - id: log_files
+ linkMerge: merge_flattened
+ source:
+ - save_solutions/log_dir
+ - save_inspection/log_dir
+ - save_logfiles/log_dir
+ - prefactor/msout
+ - id: sub_directory_name
+ default: results
+ out:
+ - id: log_dir
+ run: ./../steps/collectlog.cwl
+ label: save_results
+ 'sbg:x': 1200
+ 'sbg:y': 0
+requirements:
+ - class: SubworkflowFeatureRequirement
+ - class: MultipleInputFeatureRequirement
diff --git a/workflows/dowload_surl_and_create_input_file-json.cwl b/workflows/dowload_surl_and_create_input_file-json.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..328385f3b8dc90e93f9bdf58a94950ec09671fc4
--- /dev/null
+++ b/workflows/dowload_surl_and_create_input_file-json.cwl
@@ -0,0 +1,71 @@
+class: Workflow
+cwlVersion: v1.0
+id: dowload_surl_and_create_input_file_json
+label: dowload_surl_and_create_input_file.json
+
+inputs:
+ - id: surl_list
+ type: File
+outputs:
+ - id: results
+ outputSource:
+ - _h_b_a_calibrator/results
+ type: Directory
+ - id: logs
+ outputSource:
+ - _h_b_a_calibrator/logs
+ type: Directory
+steps:
+ - id: read_surl_list
+ in:
+ - id: surl_list
+ source: surl_list
+ out:
+ - id: surls
+ run: ../steps/read_surl_list.cwl
+ label: ReadSurlList
+ - id: surl_copy
+ in:
+ - id: surl
+ source: stage/output
+ out:
+ - id: output
+ run: ../steps/surl_copy.cwl
+ label: surl_copy
+ scatter:
+ - surl
+ - id: untar
+ in:
+ - id: tar_file
+ source: surl_copy/output
+ out:
+ - id: uncompressed
+ run: ../steps/untar.cwl
+ label: untar
+ scatter:
+ - tar_file
+ - id: stage
+ in:
+ - id: input
+ source: read_surl_list/surls
+ out:
+ - id: output
+ run: ../steps/stage.cwl
+ label: stage
+ scatter:
+ - input
+ - id: _h_b_a_calibrator
+ in:
+ - id: msin
+ source:
+ - untar/uncompressed
+ out:
+ - id: logs
+ - id: results
+ run: ./HBA_calibrator.cwl
+ label: HBA_calibrator
+requirements:
+ - class: SubworkflowFeatureRequirement
+ - class: ScatterFeatureRequirement
+ - class: InlineJavascriptRequirement
+ - class: StepInputExpressionRequirement
diff --git a/workflows/prefactor_calibrator.cwl b/workflows/prefactor_calibrator.cwl
index 5eeb2026640386bb2ccc842f6d67a26a69ede115..00fa893a16f765d2c33e4865c8c18d28711deb58 100644
--- a/workflows/prefactor_calibrator.cwl
+++ b/workflows/prefactor_calibrator.cwl
@@ -5,211 +5,498 @@ label: prefactor_calibrator
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- - id: raw_data
- type: boolean
- 'sbg:x': -634
- 'sbg:y': -688
- - id: demix
- type: boolean
- 'sbg:x': -639.3313598632812
- 'sbg:y': -271
- id: msin
type: 'Directory[]'
- 'sbg:x': -635
- 'sbg:y': -543
- - id: skymodels
- type: Directory
- 'sbg:x': -123
- 'sbg:y': -850
- - id: memoryperc
- type: int
- default: 20
- 'sbg:x': -634
- 'sbg:y': -411
- - id: baselines_to_flag
- type: 'string[]'
+ 'sbg:x': -1000
+ 'sbg:y': -1900
+ - id: refant
+ type: string?
+ default: 'CS00.*'
+ 'sbg:x': -1000
+ 'sbg:y': -1800
+ - id: flag_baselines
+ type: 'string[]?'
default: []
- 'sbg:x': -635.8651123046875
- 'sbg:y': -148
- - id: uvw
- type: File?
- 'sbg:x': -356.9723205566406
- 'sbg:y': -804.0709838867188
- - id: strategy
- type: File?
- 'sbg:x': -352
- 'sbg:y': -713
- - id: propagate_solutions
- type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': -1700
+ - id: process_baselines_cal
+ type: string?
+ default: '*&'
+ 'sbg:x': -1000
+ 'sbg:y': -1600
+ - id: filter_baselines
+ type: string?
+ default: '*&'
+ 'sbg:x': -1000
+ 'sbg:y': -1500
+ - id: fit_offset_PA
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -1400
+ - id: do_smooth
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -1300
+ - id: rfistrategy
+ type: string?
+ default: HBAdefault.rfis
+ 'sbg:x': -1000
+ 'sbg:y': -1200
+ - id: max2interpolate
+ type: int?
+ default: 30
+ 'sbg:x': -1000
+ 'sbg:y': -1100
+ - id: ampRange
+ type: 'float[]?'
+ default:
+ - 0
+ - 0
+ 'sbg:x': -1000
+ 'sbg:y': -1000
+ - id: skip_international
+ type: boolean?
default: true
- 'sbg:x': -112
- 'sbg:y': -737
- - id: flagunconverged
- type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': -900
+ - id: raw_data
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -800
+ - id: propagatesolutions
+ type: boolean?
default: true
- 'sbg:x': -92
+ 'sbg:x': -1000
+ 'sbg:y': -700
+ - id: flagunconverged
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -600
+ - id: maxStddev
+ type: float?
+ default: -1
+ 'sbg:x': -1000
+ 'sbg:y': -500
+ - id: solutions2transfer
+ type: File?
+ 'sbg:x': -1000
'sbg:y': -400
- - id: do_smooth
- type: boolean
+ - id: antennas2transfer
+ type: string?
+ default: '[FUSPID].*'
+ 'sbg:x': -1000
+ 'sbg:y': -300
+ - id: do_transfer
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -200
+ - id: trusted_sources
+ type: string
+ default: '3C48,3C147,3C196,3C295'
+ 'sbg:x': -1000
+ 'sbg:y': -100
+ - id: demix_sources
+ type: 'string[]?'
+ default:
+ - CasA
+ - CygA
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: demix_target
+ type: string?
+ default: ''
+ 'sbg:x': -1000
+ 'sbg:y': 100
+ - id: demix_freqstep
+ type: int?
+ default: 16
+ 'sbg:x': -1000
+ 'sbg:y': 200
+ - id: demix_timestep
+ type: int?
+ default: 10
+ 'sbg:x': -1000
+ 'sbg:y': 300
+ - id: demix
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': 400
+ - id: ion_3rd
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': 500
+ - id: clock_smooth
+ type: boolean?
default: true
- 'sbg:x': -89
- 'sbg:y': -276
- - id: min_separation
- type: int
+ 'sbg:x': -1000
+ 'sbg:y': 600
+ - id: tables2export
+ type: string?
+ default: clock
+ 'sbg:x': -1000
+ 'sbg:y': 700
+ - id: final_apply
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': 800
+ - id: max_dppp_threads
+ type: int?
+ default: 10
+ 'sbg:x': -1000
+ 'sbg:y': 900
+ - id: memoryperc
+ type: int?
default: 20
- 'sbg:x': -638.4987182617188
- 'sbg:y': 31.238996505737305
- - id: A-Team_sky_model
- type: string
- 'sbg:x': -889.9927978515625
- 'sbg:y': -845.9927978515625
+ 'sbg:x': -1000
+ 'sbg:y': 1000
+ - id: min_length
+ type: int?
+ default: 50
+ 'sbg:x': -1000
+ 'sbg:y': 1100
+ - id: overhead
+ type: float?
+ default: 0.8
+ 'sbg:x': -1000
+ 'sbg:y': 1200
+ - id: min_separation
+ type: int?
+ default: 30
+ 'sbg:x': -1000
+ 'sbg:y': 1300
+ - id: max_separation_arcmin
+ type: float?
+ default: 1
+ 'sbg:x': -1000
+ 'sbg:y': 1400
+ - id: calibrator_path_skymodel
+ type: Directory?
+ 'sbg:x': -1000
+ 'sbg:y': 1500
+ - id: A-Team_skymodel
+ type: File?
+ 'sbg:x': -1000
+ 'sbg:y': 1600
+ - id: avg_timeresolution
+ type: float?
+ default: 4
+ 'sbg:x': -1000
+ 'sbg:y': 1700
+ - id: avg_freqresolution
+ type: string?
+ default: 48.82kHz
+ 'sbg:x': -1000
+ 'sbg:y': 1800
+ - id: bandpass_freqresolution
+ type: string?
+ default: 195.3125kHz
+ 'sbg:x': -1000
+ 'sbg:y': 1900
outputs:
- - id: outh5parm
+ - id: inspection
+ linkMerge: merge_flattened
outputSource:
- - h5parm_collector/outh5parm
- type: File
- 'sbg:x': 477
- 'sbg:y': -546.076171875
- - id: log
+ - prep/check_Ateam_separation.png
+ - pa/inspection
+ - fr/inspection
+ - bp/inspection
+ - ion/inspection
+ type: File[]
+ 'sbg:x': 2000
+ 'sbg:y': -600
+ - id: solutions
outputSource:
- - h5parm_collector/log
+ - ion/outsolutions
type: File
- 'sbg:x': 481.1239318847656
- 'sbg:y': -368.0228576660156
- - id: output_imag
+ 'sbg:x': 2000
+ 'sbg:y': -500
+ - id: msout
outputSource:
- - check_ateam_separation/output_imag
- type: File?
- 'sbg:x': 486.94464111328125
- 'sbg:y': -5.156437873840332
- - id: logfile
+ - bp/msout
+ type: 'Directory[]'
+ 'sbg:x': 2000
+ 'sbg:y': 0
+ - id: parset
outputSource:
- - check_ateam_separation/logfile
- type: File?
- 'sbg:x': 492.1335754394531
- 'sbg:y': 133
- - id: log_1
+ - ion/parsets
+ type: 'File[]'
+ 'sbg:x': 2000
+ 'sbg:y': 200
+ - id: logfiles
outputSource:
- - make_sourcedb/log
- type: File?
- 'sbg:x': 495.6245422363281
- 'sbg:y': -1257.4857177734375
+ - prep/logfiles
+ - concat_logfiles_RefAnt/output
+ - pa/logfiles
+ - fr/logfiles
+ - bp/logfiles
+ - ion/logfiles
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 2000
+ 'sbg:y': 600
steps:
- - id: ndppp_prep_cal
+ - id: prep
in:
- - id: baselines_to_flag
- default: []
+ - id: msin
source:
- - baselines_to_flag
- - id: elevation_to_flag
- default: 0deg..20deg
- - id: min_amplitude_to_flag
- default: 1.e-30
- - id: memoryperc
- default: 20
- source: memoryperc
+ - msin
+ - id: filter_baselines
+ source: filter_baselines
- id: raw_data
source: raw_data
+ - id: propagatesolutions
+ source: propagatesolutions
+ - id: flagunconverged
+ source: flagunconverged
- id: demix
source: demix
- - id: msin
- linkMerge: merge_flattened
+ - id: max_dppp_threads
+ source: max_dppp_threads
+ - id: memoryperc
+ source: memoryperc
+ - id: flag_baselines
source:
- - msin
- - id: skymodel
- source: make_sourcedb/sourcedb
- - id: timeresolution
- default: 1
- - id: freqresolution
- default: 1
+ - flag_baselines
+ - id: avg_timeresolution
+ source: avg_timeresolution
+ - id: avg_freqresolution
+ source: avg_freqresolution
+ - id: process_baselines_cal
+ source: process_baselines_cal
+ - id: demix_timestep
+ source: demix_timestep
+ - id: demix_freqstep
+ source: demix_freqstep
+ - id: demix_target
+ source: demix_target
+ - id: demix_sources
+ source:
+ - demix_sources
+ - id: min_length
+ source: min_length
+ - id: overhead
+ 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
+ - id: calibrator_path_skymodel
+ source: calibrator_path_skymodel
out:
+ - id: outh5parm
+ - id: logfiles
+ - id: outh5parm_logfile
+ - id: check_Ateam_separation.png
- id: msout
- run: ../subworkflow/ndppp_prep_cal.cwl
- label: ndppp_prep_cal
+ - id: parset
+ - id: calibrator_name
+ run: ./prefactor_calibrator/prep.cwl
+ label: prep
+ 'sbg:x': 0
+ 'sbg:y': 0
+ - id: findRefAnt
+ in:
+ - id: msin
+ source: prep/msout
+ out:
+ - id: flagged_fraction_dict
+ - id: logfile
+ run: ./../steps/findRefAnt.cwl
+ label: findRefAnt
scatter:
- msin
- 'sbg:x': -359
- 'sbg:y': -519
- - id: aoflagger
+ 'sbg:x': 300
+ 'sbg:y': 0
+ - id: findRefAnt_join
in:
- - id: msin
+ - id: flagged_fraction_dict
+ source: findRefAnt/flagged_fraction_dict
+ - id: filter_station
+ source: refant
+ out:
+ - id: refant
+ - id: logfile
+ run: ./../steps/findRefAnt_join.cwl
+ label: findRefAnt_join
+ 'sbg:x': 500
+ 'sbg:y': 0
+ - id: concat_logfiles_RefAnt
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
source:
- - ndppp_prep_cal/msout
- - id: strategy
- source: strategy
- - id: uvw
- source: uvw
+ - findRefAnt/logfile
+ - findRefAnt_join/logfile
+ - id: file_prefix
+ default: findRefAnt
out:
- - id: output_ms
- run: ../lofar-cwl/steps/AOFlagger.cwl
- label: AOFlagger
- scatterMethod: flat_crossproduct
- 'sbg:x': -164
- 'sbg:y': -565
- - id: calib_cal
+ - id: output
+ run: ./../steps/concatenate_files.cwl
+ label: concat_logfiles_RefAnt
+ 'sbg:x': 700
+ 'sbg:y': 300
+
+ - id: pa
in:
- id: msin
- source: aoflagger/output_ms
- - id: skymodels
- source: skymodels
+ source:
+ - prep/msout
+ - id: h5parm
+ source:
+ - prep/outh5parm
+ - id: refant
+ source: findRefAnt_join/refant
+ - id: inh5parm_logfile
+ source:
+ - prep/outh5parm_logfile
- id: flagunconverged
source: flagunconverged
- - id: propagate_solutions
- source: propagate_solutions
+ - id: propagatesolutions
+ source: propagatesolutions
- id: do_smooth
source: do_smooth
+ - id: fit_offset_PA
+ source: fit_offset_PA
out:
- - id: h5parm
- id: msout
- run: ../subworkflow/calib_cal.cwl
- label: calib_cal
- scatter:
- - msin
- 'sbg:x': 47
- 'sbg:y': -583
- - id: h5parm_collector
+ - id: outsolutions
+ - id: inspection
+ - id: logfiles
+ - id: outh5parm
+ - id: outh5parm_logfile
+ run: ./prefactor_calibrator/pa.cwl
+ label: PA
+ 'sbg:x': 700
+ 'sbg:y': 0
+ - id: fr
in:
- - id: h5parmFiles
+ - id: msin
+ source:
+ - pa/msout
+ - id: h5parm
source:
- - calib_cal/h5parm
- - id: squeeze
- default: true
- - id: verbose
- default: true
- - id: clobber
- default: true
+ - pa/outh5parm
+ - id: refant
+ source: findRefAnt_join/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: log
- run: ../lofar-cwl/steps/H5ParmCollector.cwl
- label: H5parm_collector
- 'sbg:x': 292.1979675292969
- 'sbg:y': -543.7208251953125
- - id: check_ateam_separation
+ - id: outh5parm_logfile
+ run: ./prefactor_calibrator/fr.cwl
+ label: FR
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: bp
in:
- - id: ms
+ - id: msin
source:
- - msin
- - id: min_separation
- source: min_separation
+ - fr/msout
+ - id: h5parm
+ source:
+ - fr/outh5parm
+ - id: refant
+ source: findRefAnt_join/refant
+ - id: inh5parm_logfile
+ source:
+ - fr/outh5parm_logfile
+ - id: flagunconverged
+ source: flagunconverged
+ - id: propagatesolutions
+ source: propagatesolutions
+ - id: ampRange
+ source: ampRange
+ - id: skipInternational
+ source: skip_international
+ - id: max2interpolate
+ source: max2interpolate
+ - id: bandpass_freqresolution
+ source: bandpass_freqresolution
+ - id: avg_freqresolution
+ source: avg_freqresolution
+ - id: do_smooth
+ source: do_smooth
+ - id: insolutions
+ source: fr/outsolutions
+ - id: solutions2transfer
+ source: solutions2transfer
+ - id: antennas2transfer
+ source: antennas2transfer
+ - id: do_transfer
+ source: do_transfer
+ - id: trusted_sources
+ source: trusted_sources
+ - id: max_separation_arcmin
+ source: max_separation_arcmin
+ - id: calibrator_name
+ source: prep/calibrator_name
out:
- - id: output_imag
- - id: logfile
- run: ../lofar-cwl/steps/check_ateam_separation.cwl
- label: check_Ateam_separation
- 'sbg:x': -331.452392578125
- 'sbg:y': 23.596216201782227
- - id: make_sourcedb
+ - id: msout
+ - id: outsolutions
+ - id: inspection
+ - id: logfiles
+ - id: outh5parm
+ - id: outh5parm_logfile
+ run: ./prefactor_calibrator/bp.cwl
+ label: BP
+ 'sbg:x': 1300
+ 'sbg:y': 0
+ - id: ion
in:
- - id: sky_model
- source: A-Team_sky_model
+ - id: h5parm
+ source:
+ - bp/outh5parm
+ - id: refant
+ source: findRefAnt_join/refant
+ - id: inh5parm_logfile
+ source:
+ - bp/outh5parm_logfile
+ - id: insolutions
+ source: bp/outsolutions
+ - id: maxStddev
+ source: maxStddev
+ - id: ion_3rd
+ source: ion_3rd
+ - id: tables2export
+ source: tables2export
+ - id: clock_smooth
+ source: clock_smooth
+ - id: calibrator_name
+ source: prep/calibrator_name
out:
- - id: sourcedb
- - id: log
- run: ../lofar-cwl/steps/makesourcedb.cwl
- label: make_sourcedb_ateam
- 'sbg:x': -628.7400512695312
- 'sbg:y': -847.117919921875
+ - id: outsolutions
+ - id: inspection
+ - id: logfiles
+ - id: parsets
+ run: ./prefactor_calibrator/ion.cwl
+ label: ion
+ 'sbg:x': 1600
+ 'sbg:y': 0
requirements:
- class: SubworkflowFeatureRequirement
- - class: ScatterFeatureRequirement
+ - class: ScatterFeatureRequirement
\ No newline at end of file
diff --git a/workflows/prefactor_calibrator/bp.cwl b/workflows/prefactor_calibrator/bp.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..e65eb63938c33a7f8c1e6762090cffdca896f7a9
--- /dev/null
+++ b/workflows/prefactor_calibrator/bp.cwl
@@ -0,0 +1,593 @@
+class: Workflow
+cwlVersion: v1.0
+id: bp
+label: BP
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: max_separation_arcmin
+ type: float
+ 'sbg:x': -1000
+ 'sbg:y': -800
+ - id: calibrator_name
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': -700
+ - id: ampRange
+ type: 'float[]?'
+ 'sbg:x': -1000
+ 'sbg:y': -600
+ - id: skipInternational
+ type: boolean?
+ 'sbg:x': -1000
+ 'sbg:y': -500
+ - id: max2interpolate
+ type: int?
+ 'sbg:x': -1000
+ 'sbg:y': -400
+ - id: bandpass_freqresolution
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': -300
+ - id: avg_freqresolution
+ type: string?
+ 'sbg:x': -1000
+ 'sbg:y': -200
+ - id: flagunconverged
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -100
+ - id: propagatesolutions
+ type: boolean?
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: msin
+ type: 'Directory[]'
+ 'sbg:x': -1000
+ 'sbg:y': 100
+ - id: h5parm
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': 200
+ - id: solutions2transfer
+ type: File?
+ 'sbg:x': -1000
+ 'sbg:y': 300
+ - id: inh5parm_logfile
+ type: File[]
+ 'sbg:x': -1000
+ 'sbg:y': 400
+ - id: do_smooth
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': 500
+ - id: insolutions
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': 600
+ - id: antennas2transfer
+ type: string?
+ 'sbg:x': -1000
+ 'sbg:y': 700
+ - id: do_transfer
+ type: boolean?
+ 'sbg:x': -1000
+ 'sbg:y': 800
+ - id: trusted_sources
+ type: string?
+ 'sbg:x': -1000
+ 'sbg:y': 900
+outputs:
+ - id: outh5parm
+ outputSource:
+ - h5parm_collector/outh5parm
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': -200
+ - id: msout
+ outputSource:
+ - apply_calibrate_bp/msout
+ type: 'Directory[]'
+ 'sbg:x': 1000
+ 'sbg:y': -100
+ - id: inspection
+ outputSource:
+ - losoto_plot_A1/output_plots
+ - losoto_plot_A2/output_plots
+ - losoto_plot_B1/output_plots
+ - losoto_plot_B2/output_plots
+ - losoto_plot_B3/output_plots
+ - transfer_solutions/plots
+ type: 'File[]?'
+ linkMerge: merge_flattened
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: outsolutions
+ outputSource:
+ - transfer_solutions/outh5parm
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 100
+ - id: logfiles
+ outputSource:
+ - concat_logfiles_bp/output
+ - concat_logfiles_calib/output
+ - concat_logfiles_blsmooth/output
+ - 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
+ 'sbg:y': 200
+ - id: outh5parm_logfile
+ outputSource:
+ - h5parm_collector/log
+ type: File[]
+ 'sbg:x': 1000
+ 'sbg:y': 300
+steps:
+ - id: bandpass
+ in:
+ - id: ampRange
+ source: ampRange
+ - id: input_h5parm
+ source: h5parm
+ - id: skipInternational
+ source: skipInternational
+ - id: max2interpolate
+ source: max2interpolate
+ - id: bandpass_freqresolution
+ source: bandpass_freqresolution
+ - id: avg_freqresolution
+ source: avg_freqresolution
+ out:
+ - id: output_h5parm
+ - id: logfiles
+ run: ../../subworkflow/bandpass.cwl
+ label: bandpass
+ 'sbg:x': -500
+ 'sbg:y': 0
+ - id: losoto_plot_A1
+ in:
+ - id: input_h5parm
+ source: bandpass/output_h5parm
+ - id: soltab
+ default: sol000/amplitudeOrig000
+ - id: axesInPlot
+ default:
+ - time
+ - freq
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: true
+ - id: prefix
+ default: ampBFlag_
+ out:
+ - id: output_plots
+ - id: logfile
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_A1
+ 'sbg:x': -200
+ 'sbg:y': -200
+ - id: losoto_plot_A2
+ in:
+ - id: input_h5parm
+ source: bandpass/output_h5parm
+ - id: soltab
+ default: sol000/amplitudeOrig001
+ - id: axesInPlot
+ default:
+ - time
+ - freq
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: true
+ - id: prefix
+ default: ampAFlag_
+ out:
+ - id: output_plots
+ - id: logfile
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_A2
+ 'sbg:x': -200
+ 'sbg:y': -100
+ - id: losoto_plot_B1
+ 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_
+ out:
+ - id: output_plots
+ - id: logfile
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_B1
+ 'sbg:x': -200
+ 'sbg:y': 0
+ - id: losoto_plot_B2
+ 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_
+ out:
+ - id: output_plots
+ - id: logfile
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_B2
+ 'sbg:x': -200
+ 'sbg:y': 100
+ - id: losoto_plot_B3
+ 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: bandpass_
+ out:
+ - id: output_plots
+ - id: logfile
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_B3
+ '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
+ linkMerge: merge_flattened
+ source:
+ - inh5parm_logfile
+ - bandpass/logfiles
+ - losoto_plot_A1/logfile
+ - losoto_plot_A2/logfile
+ - losoto_plot_B1/logfile
+ - losoto_plot_B2/logfile
+ - losoto_plot_B3/logfile
+ - write_solutions/log
+ - h5parm_pointingname/log
+ - transfer_solutions/log
+ - id: file_prefix
+ default: losoto_bandpass
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_bp
+ 'sbg:x': 500
+ 'sbg:y': 500
+ - id: write_solutions
+ in:
+ - id: h5parmFile
+ source: bandpass/output_h5parm
+ - id: input_file
+ source: insolutions
+ - id: outsolset
+ default: calibrator
+ - id: insoltab
+ default: bandpass
+ - 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': -200
+ 'sbg:y': 700
+ - id: apply_calibrate_bp
+ in:
+ - id: msin
+ source: msin
+ - id: do_smooth
+ source: do_smooth
+ - id: flagunconverged
+ source: flagunconverged
+ - id: propagatesolutions
+ source: propagatesolutions
+ - id: input_h5parm
+ source: transfer_solutions/outh5parm
+ out:
+ - id: msout
+ - id: BLsmooth.log
+ - id: apply_cal.log
+ - 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
+ scatter:
+ - msin
+ 'sbg:x': 500
+ 'sbg:y': 0
+ - id: concat_logfiles_blsmooth
+ in:
+ - id: file_list
+ source:
+ - apply_calibrate_bp/BLsmooth.log
+ - id: file_prefix
+ default: blsmooth_bandpass
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_blsmooth
+ 'sbg:x': 750
+ 'sbg:y': 300
+ - id: concat_logfiles_apply_pa
+ in:
+ - id: file_list
+ source:
+ - apply_calibrate_bp/apply_pa.log
+ - id: file_prefix
+ default: apply_pa_bandpass
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_apply_pa
+ 'sbg:x': 750
+ 'sbg:y': 400
+ - id: concat_logfiles_apply_fr
+ in:
+ - id: file_list
+ source:
+ - apply_calibrate_bp/apply_fr.log
+ - id: file_prefix
+ default: apply_fr_bandpass
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_apply_fr
+ 'sbg:x': 750
+ 'sbg:y': 500
+ - id: concat_logfiles_apply
+ in:
+ - id: file_list
+ source:
+ - apply_calibrate_bp/apply_cal.log
+ - id: file_prefix
+ default: apply_cal_bandpass
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ 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_bandpass
+ 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
+ source:
+ - apply_calibrate_bp/calib_cal.log
+ - id: file_prefix
+ default: calib_cal_bandpass
+ 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_bp/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
+ - id: h5parm_pointingname
+ in:
+ - id: h5parmFile
+ 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: do_transfer
+ source: do_transfer
+ - id: trusted
+ source: trusted_sources
+ - id: max_separation_arcmin
+ source: max_separation_arcmin
+ - 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
+ - class: MultipleInputFeatureRequirement
diff --git a/workflows/prefactor_calibrator/fr.cwl b/workflows/prefactor_calibrator/fr.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..dbb17414c51f0b76454133888aaf30a6fef212ef
--- /dev/null
+++ b/workflows/prefactor_calibrator/fr.cwl
@@ -0,0 +1,365 @@
+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
+ 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
+ - id: parset
+ 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
+ - id: parset
+ 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
+ - id: parset
+ 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
+ - id: parset
+ 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
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_fr
+ 'sbg:x': 0
+ 'sbg:y': 200
+ - 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
+ - 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: outsolset
+ default: calibrator
+ - id: insoltab
+ default: faraday
+ - id: input_file
+ source: insolutions
+ - 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/ion.cwl b/workflows/prefactor_calibrator/ion.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..e567ef2eb019c79aa3c0d17635c91ba741a02490
--- /dev/null
+++ b/workflows/prefactor_calibrator/ion.cwl
@@ -0,0 +1,412 @@
+class: Workflow
+cwlVersion: v1.0
+id: ion
+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
+ 'sbg:y': -100
+ - id: ion_3rd
+ type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: refant
+ type: string?
+ 'sbg:x': -1000
+ 'sbg:y': 100
+ - id: h5parm
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': 200
+ - id: tables2export
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': 300
+ - id: inh5parm_logfile
+ type: 'File[]'
+ 'sbg:x': -1000
+ 'sbg:y': 400
+ - id: maxStddev
+ type: float
+ 'sbg:x': -1000
+ 'sbg:y': 500
+ - id: insolutions
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': 600
+outputs:
+ - id: inspection
+ outputSource:
+ - losoto_plot_A1/output_plots
+ - losoto_plot_A2/output_plots
+ - losoto_plot_P3/output_plots
+ - losoto_plot_Pd/output_plots
+ - losoto_plot_tec/output_plots
+ - losoto_plot_tec3rd/output_plots
+ - losoto_plot_clock/output_plots
+ - losoto_plot_Pr/output_plots
+ - losoto_plot_Pr3/output_plots
+ type: 'File[]?'
+ linkMerge: merge_flattened
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: outsolutions
+ outputSource:
+ - h5parm_pointingname/outh5parm
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 100
+ - id: logfiles
+ outputSource:
+ - concat_logfiles_ion/output
+ type: 'File[]'
+ 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:
+ - id: input_h5parm
+ source: h5parm
+ - id: maxStddev
+ source: maxStddev
+ - id: fit3rdorder
+ source: ion_3rd
+ - id: clock_smooth
+ source: clock_smooth
+ out:
+ - id: output_h5parm
+ - id: logfiles
+ - id: parset
+ run: ../../subworkflow/clocktec.cwl
+ label: clocktec
+ 'sbg:x': -500
+ 'sbg:y': 0
+ - id: losoto_plot_A1
+ in:
+ - id: input_h5parm
+ source: clocktec/output_h5parm
+ - id: soltab
+ default: sol000/amplitudeOrig
+ - id: axesInPlot
+ default:
+ - time
+ - freq
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: true
+ - id: prefix
+ default: ion_ampBFlag_
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_A1
+ 'sbg:x': 0
+ 'sbg:y': -400
+ - id: losoto_plot_A2
+ in:
+ - id: input_h5parm
+ source: clocktec/output_h5parm
+ - id: soltab
+ default: sol000/amplitude000
+ - id: axesInPlot
+ default:
+ - time
+ - freq
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: true
+ - id: prefix
+ default: ion_ampAFlag_
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_A2
+ 'sbg:x': 0
+ 'sbg:y': -300
+ - id: losoto_plot_P3
+ in:
+ - id: input_h5parm
+ source: clocktec/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: ion_ph_
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ 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: clocktec/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: ion_ph_poldif
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_Pd
+ 'sbg:x': 0
+ 'sbg:y': -100
+ - id: losoto_plot_tec
+ in:
+ - id: input_h5parm
+ source: clocktec/output_h5parm
+ - id: soltab
+ default: sol000/tec
+ - id: axesInPlot
+ default:
+ - time
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: false
+ - id: refAnt
+ source: refant
+ - id: prefix
+ default: tec
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_tec
+ 'sbg:x': 0
+ 'sbg:y': 0
+ - id: losoto_plot_tec3rd
+ in:
+ - id: input_h5parm
+ source: clocktec/output_h5parm
+ - id: soltab
+ default: 'sol000/tec3rd'
+ - id: axesInPlot
+ default:
+ - time
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: false
+ - id: refAnt
+ source: refant
+ - id: prefix
+ default: tec3rd
+ - id: execute
+ source: ion_3rd
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_tec3rd
+ 'sbg:x': 0
+ 'sbg:y': 100
+ - id: losoto_plot_clock
+ in:
+ - id: input_h5parm
+ source: clocktec/output_h5parm
+ - id: soltab
+ default: sol000/clockOrig
+ - id: axesInPlot
+ default:
+ - time
+ - id: axisInTable
+ default: ant
+ - id: plotFlag
+ default: false
+ - id: refAnt
+ source: refant
+ - id: prefix
+ default: clock
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_clock
+ 'sbg:x': 0
+ 'sbg:y': 200
+ - id: losoto_plot_Pr
+ in:
+ - id: input_h5parm
+ source: clocktec/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: ion_ph-res_poldif
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_Pr
+ 'sbg:x': 0
+ 'sbg:y': 300
+ - id: losoto_plot_Pr3
+ in:
+ - id: input_h5parm
+ source: clocktec/output_h5parm
+ - id: soltab
+ default: sol000/phase000
+ - 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: ion_ph-res_
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_Pr3
+ 'sbg:x': 0
+ 'sbg:y': 400
+ - id: concat_logfiles_ion
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - inh5parm_logfile
+ - clocktec/logfiles
+ - losoto_plot_A1/logfile
+ - losoto_plot_A2/logfile
+ - losoto_plot_P3/logfile
+ - losoto_plot_Pd/logfile
+ - losoto_plot_tec/logfile
+ - losoto_plot_tec3rd/logfile
+ - losoto_plot_clock/logfile
+ - losoto_plot_Pr/logfile
+ - losoto_plot_Pr3/logfile
+ - write_solutions/log
+ - h5parm_pointingname/log
+ - id: file_prefix
+ default: losoto_ion
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_ion
+ 'sbg:x': 500
+ 'sbg:y': 500
+ - id: write_solutions
+ in:
+ - id: h5parmFile
+ source: clocktec/output_h5parm
+ - id: outsolset
+ default: calibrator
+ - id: insoltab
+ source: tables2export
+ - id: input_file
+ source: insolutions
+ - id: squeeze
+ default: true
+ - id: verbose
+ default: true
+ out:
+ - id: outh5parm
+ - id: log
+ run: ../../steps/h5parmcat.cwl
+ label: write_solutions
+ 'sbg:x': -200
+ 'sbg:y': 700
+ - id: h5parm_pointingname
+ in:
+ - id: h5parmFile
+ 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
diff --git a/workflows/prefactor_calibrator/pa.cwl b/workflows/prefactor_calibrator/pa.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..fa1d3eabf48540a8a42147a76573a587eebee5b3
--- /dev/null
+++ b/workflows/prefactor_calibrator/pa.cwl
@@ -0,0 +1,461 @@
+class: Workflow
+cwlVersion: v1.0
+id: pa
+label: PA
+$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: fit_offset_PA
+ type: boolean?
+ default: false
+ '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_pa/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_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: outsolutions
+ outputSource:
+ - write_solutions/outh5parm
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 100
+ - id: logfiles
+ outputSource:
+ - concat_logfiles_pa/output
+ - concat_logfiles_calib/output
+ - concat_logfiles_blsmooth/output
+ - concat_logfiles_beam/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: pol_align
+ in:
+ - id: refAnt
+ default: CS001HBA0
+ source: refant
+ - id: input_h5parm
+ source: h5parm
+ - id: fit_offset_PA
+ source: fit_offset_PA
+ 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
+ - id: parset
+ 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
+ - id: parset
+ 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
+ - id: parset
+ 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
+ - id: parset
+ 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
+ - id: parset
+ 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
+ - id: parset
+ 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
+ - id: parset
+ 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:
+ - inh5parm_logfile
+ - 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: outsolset
+ default: calibrator
+ - id: insoltab
+ default: polalign
+ - id: outh5parmname
+ default: cal_solutions.h5
+ - id: squeeze
+ default: true
+ - id: verbose
+ default: true
+ out:
+ - id: outh5parm
+ - id: log
+ run: ../../lofar-cwl/steps/H5ParmCollector.cwl
+ label: write_solutions
+ 'sbg:x': 0
+ 'sbg:y': 500
+ - id: apply_calibrate_pa
+ 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
+ - id: applybeam.log
+ run: ../../subworkflow/apply_calibrate_pa.cwl
+ label: apply_calibrate_pa
+ scatter:
+ - msin
+ 'sbg:x': 500
+ 'sbg:y': 0
+ - id: concat_logfiles_blsmooth
+ in:
+ - id: file_list
+ source:
+ - apply_calibrate_pa/BLsmooth.log
+ - id: file_prefix
+ default: blsmooth_PA
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_blsmooth
+ 'sbg:x': 750
+ 'sbg:y': 300
+ - id: concat_logfiles_beam
+ in:
+ - id: file_list
+ source:
+ - apply_calibrate_pa/applybeam.log
+ - id: file_prefix
+ default: applybeam_PA
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_beam
+ 'sbg:x': 750
+ 'sbg:y': 400
+ - id: concat_logfiles_apply
+ in:
+ - id: file_list
+ source:
+ - apply_calibrate_pa/apply_cal.log
+ - id: file_prefix
+ default: apply_cal_PA
+ 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_pa/calib_cal.log
+ - id: file_prefix
+ default: calib_cal_PA
+ 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_pa/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/prep.cwl b/workflows/prefactor_calibrator/prep.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..dba3a8e3f7d667076b2613fd74cc2b0ebb2cbbfe
--- /dev/null
+++ b/workflows/prefactor_calibrator/prep.cwl
@@ -0,0 +1,395 @@
+class: Workflow
+cwlVersion: v1.0
+id: prep
+label: prep
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: msin
+ type: 'Directory[]'
+ 'sbg:x': -515.1839599609375
+ 'sbg:y': 330.674560546875
+ - id: filter_baselines
+ type: string
+ 'sbg:x': 254.234375
+ 'sbg:y': 684
+ - id: raw_data
+ type: boolean
+ 'sbg:x': 0
+ 'sbg:y': 563
+ - id: propagatesolutions
+ type: boolean
+ 'sbg:x': 0
+ 'sbg:y': 670
+ - id: flagunconverged
+ type: boolean
+ 'sbg:x': 559.319091796875
+ 'sbg:y': 837.5
+ - id: demix
+ type: boolean
+ 'sbg:x': 254.234375
+ 'sbg:y': 1326
+ - id: max_dppp_threads
+ type: int?
+ default: 10
+ 'sbg:x': 254.234375
+ 'sbg:y': 214
+ - id: memoryperc
+ type: int
+ 'sbg:x': 254.234375
+ 'sbg:y': 107
+ - id: flag_baselines
+ type: 'string[]'
+ 'sbg:x': 254.234375
+ 'sbg:y': 442
+ - id: avg_timeresolution
+ type: float
+ 'sbg:x': 254.234375
+ 'sbg:y': 1554
+ - id: avg_freqresolution
+ type: string
+ 'sbg:x': 254.234375
+ 'sbg:y': 1661
+ - id: process_baselines_cal
+ type: string
+ 'sbg:x': 0
+ 'sbg:y': 777
+ - id: demix_timestep
+ type: int
+ 'sbg:x': 254.234375
+ 'sbg:y': 898
+ - id: demix_freqstep
+ type: int
+ 'sbg:x': 254.234375
+ 'sbg:y': 1219
+ - id: demix_target
+ type: string
+ 'sbg:x': 254.234375
+ 'sbg:y': 1005
+ - id: demix_sources
+ type: 'string[]'
+ 'sbg:x': 254.234375
+ 'sbg:y': 1112
+ - id: min_length
+ type: int?
+ 'sbg:x': 360
+ 'sbg:y': 1919.42626953125
+ - id: overhead
+ type: float?
+ 'sbg:x': 180
+ 'sbg:y': 1903.963134765625
+ - id: min_separation
+ type: int?
+ 'sbg:x': 0
+ 'sbg:y': 884
+ - id: do_smooth
+ type: boolean?
+ default: false
+ 'sbg:x': 559.319091796875
+ 'sbg:y': 944.5
+ - id: max_separation_arcmin
+ type: float?
+ 'sbg:x': 0
+ 'sbg:y': 991
+ - id: calibrator_path_skymodel
+ type: Directory?
+ 'sbg:x': 0
+ 'sbg:y': 1098
+ - id: A-Team_skymodel
+ type: File?
+ 'sbg:x': 0
+ 'sbg:y': 1205
+ - id: elevation
+ type: string
+ default: 0deg..20deg
+ 'sbg:x': 254.234375
+ 'sbg:y': 791
+ - id: amplmin
+ type: float
+ default: 1.e-30
+ 'sbg:x': 254.234375
+ 'sbg:y': 1768
+outputs:
+ - id: outh5parm
+ outputSource:
+ - h5parm_collector/outh5parm
+ type: File
+ 'sbg:x': 1554.5106201171875
+ 'sbg:y': 884
+ - id: check_Ateam_separation.png
+ outputSource:
+ - check_ateam_separation/output_imag
+ type: File
+ 'sbg:x': 559.319091796875
+ 'sbg:y': 1051.5
+ - id: msout
+ outputSource:
+ - predict_calibrate/msout
+ type: 'Directory[]'
+ 'sbg:x': 1329.937255859375
+ 'sbg:y': 663
+ - id: parset
+ outputSource:
+ - ndppp_prep_cal/parset
+ type: 'File[]'
+ 'sbg:x': 1027.490966796875
+ 'sbg:y': 884
+ - id: calibrator_name
+ outputSource:
+ - find_skymodel_cal/model_name
+ type: string
+ 'sbg:x': 559.319091796875
+ 'sbg:y': 1158.5
+ - id: outh5parm_logfile
+ outputSource:
+ - h5parm_collector/log
+ type: 'File[]'
+ 'sbg:x': 1554.5106201171875
+ 'sbg:y': 777
+ - id: logfiles
+ outputSource:
+ - concat_logfiles_calib/output
+ - 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
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 1554.5106201171875
+ 'sbg:y': 991
+steps:
+ - id: select
+ in:
+ - id: input
+ source:
+ - msin
+ out:
+ - id: output
+ run: ../../steps/selectfirstdirectory.cwl
+ label: select_ony_first
+ 'sbg:x': -303.7861022949219
+ 'sbg:y': 542.37646484375
+ - id: ndppp_prep_cal
+ in:
+ - id: baselines_to_flag
+ default: []
+ source:
+ - flag_baselines
+ - id: elevation_to_flag
+ source: elevation
+ - id: min_amplitude_to_flag
+ source: amplmin
+ - id: memoryperc
+ default: 20
+ source: memoryperc
+ - id: raw_data
+ default: false
+ source: raw_data
+ - id: demix
+ default: false
+ source: demix
+ - id: msin
+ linkMerge: merge_flattened
+ source:
+ - msin
+ - id: msin_baseline
+ default: '*'
+ source: filter_baselines
+ - id: skymodel
+ source: make_sourcedb_ateam/sourcedb
+ - id: timeresolution
+ default: 1
+ source: avg_timeresolution
+ - id: freqresolution
+ default: 12.21kHz
+ source: avg_freqresolution
+ - id: demix_timestep
+ default: 1
+ source: demix_timestep
+ - id: demix_freqstep
+ default: 1
+ source: demix_freqstep
+ - id: demix_baseline
+ default: '*'
+ source: process_baselines_cal
+ - id: target_source
+ source: demix_target
+ - id: ntimechunk
+ default: 10
+ source: max_dppp_threads
+ - id: subtract_sources
+ source:
+ - demix_sources
+ out:
+ - id: msout
+ - id: logfile
+ - id: parset
+ run: ../../subworkflow/ndppp_prep_cal.cwl
+ label: ndppp_prep_cal
+ scatter:
+ - msin
+ 'sbg:x': 559.319091796875
+ 'sbg:y': 497.5
+ - id: predict_calibrate
+ in:
+ - id: msin
+ linkMerge: merge_flattened
+ source:
+ - ndppp_prep_cal/msout
+ - id: do_smooth
+ source: do_smooth
+ - id: sourcedb
+ source: make_sourcedb/sourcedb
+ - id: flagunconverged
+ source: flagunconverged
+ - id: propagatesolutions
+ source: propagatesolutions
+ out:
+ - id: msout
+ - id: BLsmooth.log
+ - id: predict_cal.log
+ - id: calib_cal.log
+ - id: outh5parm
+ run: ../../subworkflow/predict_calibrate.cwl
+ label: predict_calibrate
+ scatter:
+ - msin
+ 'sbg:x': 1027.490966796875
+ 'sbg:y': 749
+ - id: check_ateam_separation
+ in:
+ - id: ms
+ source:
+ - select/output
+ - id: min_separation
+ source: min_separation
+ out:
+ - id: output_imag
+ - id: logfile
+ run: ../../lofar-cwl/steps/check_ateam_separation.cwl
+ label: check_Ateam_separation
+ 'sbg:x': 254.234375
+ 'sbg:y': 1440
+ - id: make_sourcedb_ateam
+ in:
+ - id: sky_model
+ source: A-Team_skymodel
+ - id: logname
+ default: make_sourcedb_ateam.log
+ out:
+ - id: sourcedb
+ - id: log
+ run: ../../lofar-cwl/steps/makesourcedb.cwl
+ label: make_sourcedb_ateam
+ 'sbg:x': 254.234375
+ 'sbg:y': 328
+ - id: find_skymodel_cal
+ in:
+ - id: msin
+ source:
+ - select/output
+ - id: skymodels
+ source: calibrator_path_skymodel
+ - id: max_separation_arcmin
+ source: max_separation_arcmin
+ out:
+ - id: output_models
+ - id: model_name
+ - id: logfile
+ run: ../../steps/find_skymodel_cal.cwl
+ label: find_skymodel_cal
+ 'sbg:x': 254.234375
+ 'sbg:y': 563
+ - id: make_sourcedb
+ in:
+ - id: sky_model
+ source: find_skymodel_cal/output_models
+ - id: output_file_name
+ default: calibrator.sourcedb
+ out:
+ - id: sourcedb
+ - id: log
+ run: ../../lofar-cwl/steps/makesourcedb.cwl
+ label: make_sourcedb
+ 'sbg:x': 559.319091796875
+ 'sbg:y': 723.5
+ - id: concat_logfiles_prep_cal
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - ndppp_prep_cal/logfile
+ - id: file_prefix
+ default: ndppp_prep_cal
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_prep_cal
+ 'sbg:x': 1027.490966796875
+ 'sbg:y': 991
+ - id: concat_logfiles_blsmooth
+ in:
+ - id: file_list
+ source:
+ - predict_calibrate/BLsmooth.log
+ - id: file_prefix
+ default: blsmooth_prep
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_blsmooth
+ 'sbg:x': 1329.937255859375
+ 'sbg:y': 1105
+ - id: concat_logfiles_predict
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - predict_calibrate/predict_cal.log
+ - id: file_prefix
+ default: predict_cal
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_predict
+ 'sbg:x': 1329.937255859375
+ 'sbg:y': 891
+ - id: concat_logfiles_calib
+ in:
+ - id: file_list
+ source:
+ - predict_calibrate/calib_cal.log
+ - id: file_prefix
+ default: calib_cal_prep
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_calib
+ 'sbg:x': 1329.937255859375
+ 'sbg:y': 998
+ - id: h5parm_collector
+ in:
+ - id: h5parmFiles
+ source:
+ - predict_calibrate/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': 1329.937255859375
+ 'sbg:y': 777
+requirements:
+ - class: SubworkflowFeatureRequirement
+ - class: ScatterFeatureRequirement
+ - class: InlineJavascriptRequirement
+ - class: StepInputExpressionRequirement
diff --git a/workflows/prefactor_calibrator_test.cwl b/workflows/prefactor_calibrator_test.cwl
deleted file mode 100644
index aa2db155ed3737bf1ca408c3a0b8e1810058b5c7..0000000000000000000000000000000000000000
--- a/workflows/prefactor_calibrator_test.cwl
+++ /dev/null
@@ -1,149 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-id: prefactor_calibrator
-label: prefactor_calibrator
-$namespaces:
- sbg: 'https://www.sevenbridges.com/'
-inputs:
- - id: raw_data
- type: boolean
- 'sbg:x': -634
- 'sbg:y': -688
- - id: demix
- type: boolean
- 'sbg:x': -639
- 'sbg:y': -206.68032836914062
- - id: msin
- type: 'Directory[]'
- 'sbg:x': -635
- 'sbg:y': -543
- - id: memoryperc
- type: int
- 'sbg:x': -634
- 'sbg:y': -411
- - id: baselines_to_flag
- type: 'string[]'
- 'sbg:x': -635
- 'sbg:y': -100.83224487304688
- - id: min_separation
- type: float?
- 'sbg:x': -638.4987182617188
- 'sbg:y': 31.238996505737305
- - id: A-Team_sky_model
- default: /data/skymodels/Ateam_LBA_CC.skymodel
- type:
- - string?
- - File?
- 'sbg:x': -889
- 'sbg:y': -983.5078735351562
- - id: timeresolution
- type: float
- 'sbg:x': -634.4667358398438
- 'sbg:y': -817.0217895507812
- - id: freqresolution
- type: string
- 'sbg:x': -641.6406860351562
- 'sbg:y': -298.1281433105469
-outputs:
- - id: check_Ateam_separation.png
- outputSource:
- - check_ateam_separation/output_imag
- type: 'File[]?'
- 'sbg:x': 68.06497955322266
- 'sbg:y': -3.1985559463500977
- - id: check_Ateam_separation.log
- outputSource:
- - check_ateam_separation/logfile
- type: 'File[]?'
- 'sbg:x': 83.07220458984375
- 'sbg:y': 136.60289001464844
- - id: make_sourcedb_ateam.log
- outputSource:
- - make_sourcedb/log
- type: File?
- 'sbg:x': 71.66065216064453
- 'sbg:y': -880.4981689453125
- - id: msout
- outputSource:
- - ndppp_prep_cal/msout
- type: 'Directory[]'
- 'sbg:x': 52.33274459838867
- 'sbg:y': -546.0951538085938
- - id: logfile_prep_cal
- outputSource:
- - ndppp_prep_cal/logfile
- type: 'File[]?'
- 'sbg:x': 43.325523376464844
- 'sbg:y': -371.35504150390625
- - id: parset
- outputSource:
- - ndppp_prep_cal/parset
- type: 'File[]'
- 'sbg:x': 49.54720687866211
- 'sbg:y': -680.8679809570312
-steps:
- - id: ndppp_prep_cal
- in:
- - id: baselines_to_flag
- default: []
- source:
- - baselines_to_flag
- - id: elevation_to_flag
- default: 0deg..20deg
- - id: min_amplitude_to_flag
- default: 1.e-30
- - id: memoryperc
- default: 20
- source: memoryperc
- - id: raw_data
- source: raw_data
- - id: demix
- source: demix
- - id: msin
- linkMerge: merge_flattened
- source:
- - msin
- - id: skymodel
- source: make_sourcedb/sourcedb
- - id: timeresolution
- source: timeresolution
- - id: freqresolution
- source: freqresolution
- out:
- - id: msout
- - id: logfile
- - id: parset
- run: ../subworkflow/ndppp_prep_cal.cwl
- label: ndppp_prep_cal
- scatter:
- - msin
- 'sbg:x': -359
- 'sbg:y': -519
- - id: check_ateam_separation
- in:
- - id: ms
- source:
- - msin
- - id: min_separation
- source: min_separation
- out:
- - id: output_imag
- - id: logfile
- run: ../lofar-cwl/steps/check_ateam_separation.cwl
- label: check_Ateam_separation
- 'sbg:x': -331.452392578125
- 'sbg:y': 23.596216201782227
- - id: make_sourcedb
- in:
- - id: sky_model
- source: A-Team_sky_model
- out:
- - id: sourcedb
- - id: log
- run: ../lofar-cwl/steps/makesourcedb.cwl
- label: make_sourcedb_ateam
- 'sbg:x': -647.0108642578125
- 'sbg:y': -981.3153076171875
-requirements:
- - class: SubworkflowFeatureRequirement
- - class: ScatterFeatureRequirement
diff --git a/workflows/prefactor_target.cwl b/workflows/prefactor_target.cwl
index 7986942f49eb71cf1f3161c65ee7bd01d75f49f0..6e624e973e2d8592d95c548fe578a90a6908f950 100644
--- a/workflows/prefactor_target.cwl
+++ b/workflows/prefactor_target.cwl
@@ -5,17 +5,463 @@ label: prefactor_target
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
+ - id: msin
+ type: 'Directory[]'
+ 'sbg:x': -1000
+ 'sbg:y': -1700
- id: cal_solutions
type: File
- 'sbg:x': -327
- 'sbg:y': -42
+ 'sbg:x': -1000
+ 'sbg:y': -1600
+ - id: refant
+ type: string?
+ default: CS00.*
+ 'sbg:x': -1000
+ 'sbg:y': -1500
+ - id: flag_baselines
+ type: 'string[]?'
+ default: []
+ 'sbg:x': -1000
+ 'sbg:y': -1400
+ - id: process_baselines_target
+ type: string?
+ default: '[CR]S*&'
+ 'sbg:x': -1000
+ 'sbg:y': -1300
+ - id: filter_baselines
+ type: string?
+ default: '[CR]S*&'
+ 'sbg:x': -1000
+ 'sbg:y': -1200
+ - id: do_smooth
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -1100
+ - id: rfistrategy
+ type: string?
+ default: HBAdefault.rfis
+ 'sbg:x': -1000
+ 'sbg:y': -1000
+ - id: min_unflagged_fraction
+ type: float?
+ default: 0.5
+ 'sbg:x': -1000
+ 'sbg:y': -900
+ - id: compression_bitrate
+ type: int?
+ default: 16
+ 'sbg:x': -1000
+ 'sbg:y': -800
+ - id: raw_data
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -700
+ - id: propagatesolutions
+ type: boolean?
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': -600
+ - id: demix_sources
+ type: 'string[]?'
+ default:
+ - CasA
+ - CygA
+ 'sbg:x': -1000
+ 'sbg:y': -500
+ - id: demix_target
+ type: string?
+ default: ''
+ 'sbg:x': -1000
+ 'sbg:y': -400
+ - id: demix_freqstep
+ type: int?
+ default: 16
+ 'sbg:x': -1000
+ 'sbg:y': -300
+ - id: demix_timestep
+ type: int?
+ default: 10
+ 'sbg:x': -1000
+ 'sbg:y': -200
+ - id: demix
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -100
+ - id: apply_tec
+ type: boolean
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: apply_clock
+ type: boolean
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 100
+ - id: apply_phase
+ type: boolean
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': 200
+ - id: apply_RM
+ type: boolean
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 300
+ - id: apply_beam
+ type: boolean
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 400
+ - id: clipATeam
+ type: boolean?
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 500
+ - id: gsmcal_step
+ type: string?
+ default: phase
+ 'sbg:x': -1000
+ 'sbg:y': 600
+ - id: updateweights
+ type: boolean?
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 700
+ - id: max_dppp_threads
+ type: int?
+ default: 10
+ 'sbg:x': -1000
+ 'sbg:y': 800
+ - id: memoryperc
+ type: int?
+ default: 20
+ 'sbg:x': -1000
+ 'sbg:y': 900
+ - id: min_length
+ type: int?
+ default: 5
+ 'sbg:x': -1000
+ 'sbg:y': 1000
+ - id: overhead
+ type: float?
+ default: 0.7
+ 'sbg:x': -1000
+ 'sbg:y': 1100
+ - id: min_separation
+ type: int?
+ default: 30
+ 'sbg:x': -1000
+ 'sbg:y': 1200
+ - id: A-Team_skymodel
+ type: File?
+ 'sbg:x': -1000
+ 'sbg:y': 1300
+ - id: target_skymodel
+ type: File?
+ 'sbg:x': -1000
+ 'sbg:y': 1400
+ - id: use_target
+ type: boolean?
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 1500
+ - id: skymodel_source
+ type: string?
+ default: TGSS
+ 'sbg:x': -1000
+ 'sbg:y': 1600
+ - id: avg_timeresolution
+ type: float?
+ default: 4
+ 'sbg:x': -1000
+ 'sbg:y': 1700
+ - id: avg_freqresolution
+ type: string?
+ default: 48.82kHz
+ 'sbg:x': -1000
+ 'sbg:y': 1800
+ - id: avg_timeresolution_concat
+ type: int?
+ default: 8
+ 'sbg:x': -1000
+ 'sbg:y': 1900
+ - id: avg_freqresolution_concat
+ type: string?
+ default: 97.64kHz
+ 'sbg:x': -1000
+ 'sbg:y': 2000
+ - id: num_SBs_per_group
+ type: int?
+ default: 10
+ 'sbg:x': -1000
+ 'sbg:y': 2100
+ - id: reference_stationSB
+ type: int?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 2200
+ - id: ionex_server
+ type: string?
+ default: 'ftp://ftp.aiub.unibe.ch/CODE/'
+ 'sbg:x': -1000
+ 'sbg:y': 2300
+ - id: ionex_prefix
+ type: string?
+ default: CODG
+ 'sbg:x': -1000
+ 'sbg:y': 2400
+ - id: proxy_server
+ type: string?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 2500
+ - id: proxy_port
+ type: string?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 2600
+ - id: proxy_type
+ type: string?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 2700
+ - id: proxy_user
+ type: string?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 2800
+ - id: proxy_pass
+ type: string?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 2900
outputs:
+ - id: inspection
+ outputSource:
+ - prep/inspection
+ - gsmcal/inspection
+ - finalize/inspection
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 2000
+ 'sbg:y': -600
- id: solutions
outputSource:
- - cal_solutions
+ - finalize/solutions
type: File
- 'sbg:x': -58
- 'sbg:y': -43
- source: input.cal_solutions
-steps: []
-requirements: []
+ 'sbg:x': 2000
+ 'sbg:y': -500
+ - id: msout
+ outputSource:
+ - finalize/msout
+ type: 'Directory[]'
+ 'sbg:x': 2000
+ 'sbg:y': 0
+ - id: logfiles
+ outputSource:
+ - prep/logfiles
+ - concat_logfiles_RefAnt/output
+ - gsmcal/logfiles
+ - finalize/logfiles
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 2000
+ 'sbg:y': 600
+steps:
+ - id: prep
+ in:
+ - id: msin
+ source:
+ - msin
+ - id: cal_solutions
+ source: cal_solutions
+ - id: flag_baselines
+ source:
+ - flag_baselines
+ - id: process_baselines_target
+ source: process_baselines_target
+ - id: filter_baselines
+ source: filter_baselines
+ - id: raw_data
+ source: raw_data
+ - id: propagatesolutions
+ source: propagatesolutions
+ - id: demix_sources
+ source:
+ - demix_sources
+ - id: demix_target
+ source: demix_target
+ - id: demix_freqstep
+ source: demix_freqstep
+ - id: demix_timestep
+ source: demix_timestep
+ - id: demix
+ source: demix
+ - id: apply_tec
+ source: apply_tec
+ - id: apply_clock
+ source: apply_clock
+ - id: apply_phase
+ source: apply_phase
+ - id: apply_RM
+ source: apply_RM
+ - id: apply_beam
+ source: apply_beam
+ - id: clipATeam
+ source: clipATeam
+ - id: updateweights
+ source: updateweights
+ - id: max_dppp_threads
+ source: max_dppp_threads
+ - id: memoryperc
+ source: memoryperc
+ - id: min_separation
+ source: min_separation
+ - id: A-Team_skymodel
+ source: A-Team_skymodel
+ - id: avg_timeresolution
+ source: avg_timeresolution
+ - id: avg_freqresolution
+ source: avg_freqresolution
+ - id: ionex_server
+ source: ionex_server
+ - id: ionex_prefix
+ source: ionex_prefix
+ - id: proxy_server
+ source: proxy_server
+ - id: proxy_port
+ source: proxy_port
+ - id: proxy_type
+ source: proxy_type
+ - id: proxy_user
+ source: proxy_user
+ - id: proxy_pass
+ source: proxy_pass
+ out:
+ - id: outh5parm
+ - id: inspection
+ - id: msout
+ - id: logfiles
+ run: ./prefactor_target/prep.cwl
+ label: prep
+ 'sbg:x': 0
+ 'sbg:y': 0
+ - id: findRefAnt
+ in:
+ - id: msin
+ source: prep/msout
+ out:
+ - id: flagged_fraction_dict
+ - id: logfile
+ run: ./../steps/findRefAnt.cwl
+ label: findRefAnt
+ scatter:
+ - msin
+ 'sbg:x': 400
+ 'sbg:y': 0
+ - id: findRefAnt_join
+ in:
+ - id: flagged_fraction_dict
+ source:
+ - findRefAnt/flagged_fraction_dict
+ - id: filter_station
+ source: refant
+ out:
+ - id: refant
+ - id: logfile
+ run: ./../steps/findRefAnt_join.cwl
+ label: findRefAnt_join
+ 'sbg:x': 600
+ 'sbg:y': 0
+ - id: concat_logfiles_RefAnt
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - findRefAnt/logfile
+ - findRefAnt_join/logfile
+ - id: file_prefix
+ default: findRefAnt
+ out:
+ - id: output
+ run: ./../steps/concatenate_files.cwl
+ label: concat_logfiles_RefAnt
+ 'sbg:x': 800
+ 'sbg:y': 300
+ - id: gsmcal
+ in:
+ - id: msin
+ source:
+ - prep/msout
+ - id: filter_baselines
+ source: process_baselines_target
+ - id: num_SBs_per_group
+ source: num_SBs_per_group
+ - id: reference_stationSB
+ source: reference_stationSB
+ - id: use_target
+ source: use_target
+ - id: target_skymodel
+ source: target_skymodel
+ - id: skymodel_source
+ source: skymodel_source
+ - id: do_smooth
+ source: do_smooth
+ - id: propagatesolutions
+ source: propagatesolutions
+ - id: avg_timeresolution_concat
+ source: avg_timeresolution_concat
+ - id: avg_freqresolution_concat
+ source: avg_freqresolution_concat
+ - id: min_unflagged_fraction
+ source: min_unflagged_fraction
+ - id: refant
+ source: findRefAnt_join/refant
+ out:
+ - id: msout
+ - id: outh5parm
+ - id: bad_antennas
+ - id: outh5parm_logfile
+ - id: inspection
+ - id: logfiles
+ run: ./prefactor_target/gsmcal.cwl
+ label: gsmcal
+ 'sbg:x': 900
+ 'sbg:y': 0
+ - id: finalize
+ in:
+ - id: msin
+ source:
+ - gsmcal/msout
+ - id: input_h5parm
+ source: gsmcal/outh5parm
+ - id: inh5parm_logfile
+ source: gsmcal/outh5parm_logfile
+ - id: gsmcal_step
+ source: gsmcal_step
+ - id: process_baselines_target
+ source: process_baselines_target
+ - id: bad_antennas
+ source: gsmcal/bad_antennas
+ - id: insolutions
+ source: prep/outh5parm
+ - id: compression_bitrate
+ source: compression_bitrate
+ - id: skymodel_source
+ source: skymodel_source
+ out:
+ - id: msout
+ - id: solutions
+ - id: logfiles
+ - id: inspection
+ run: ./prefactor_target/finalize.cwl
+ label: finalize
+ 'sbg:x': 1200
+ 'sbg:y': 0
+requirements:
+ - class: SubworkflowFeatureRequirement
+ - class: ScatterFeatureRequirement
+ - class: MultipleInputFeatureRequirement
diff --git a/workflows/prefactor_target/finalize.cwl b/workflows/prefactor_target/finalize.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..93346d0285251d714b0db13f4035d71f1edcb1e0
--- /dev/null
+++ b/workflows/prefactor_target/finalize.cwl
@@ -0,0 +1,279 @@
+class: Workflow
+cwlVersion: v1.0
+id: finalize
+label: finalize
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: msin
+ type: 'Directory[]'
+ 'sbg:x': -1000
+ 'sbg:y': -400
+ - id: input_h5parm
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': -300
+ - id: inh5parm_logfile
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': -200
+ - id: gsmcal_step
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': -100
+ - id: process_baselines_target
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: bad_antennas
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': 100
+ - id: insolutions
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': 200
+ - id: compression_bitrate
+ type: int
+ 'sbg:x': -1000
+ 'sbg:y': 300
+ - id: skymodel_source
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': 400
+outputs:
+ - id: msout
+ outputSource:
+ - apply_gsmcal/msout
+ type: 'Directory[]'
+ 'sbg:x': 1300
+ 'sbg:y': 0
+ - id: solutions
+ outputSource:
+ - h5parm_pointingname/outh5parm
+ type: File
+ 'sbg:x': 1300
+ 'sbg:y': 200
+ - id: logfiles
+ outputSource:
+ - concat_logfiles_applygsm/output
+ - concat_logfiles_solutions/output
+ - concat_logfiles_structure/output
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 1300
+ 'sbg:y': 800
+ - id: inspection
+ outputSource:
+ - structure_function/structure_plot
+ type: 'File[]?'
+ linkMerge: merge_flattened
+ 'sbg:x': 1300
+ 'sbg:y': 500
+steps:
+ - id: add_missing_stations
+ in:
+ - id: h5parm
+ source: input_h5parm
+ - id: solset
+ default: 'sol000'
+ - id: refsolset
+ default: 'target'
+ - id: refh5parm
+ source: insolutions
+ - id: soltab_in
+ source: gsmcal_step
+ valueFrom: $(self+'000')
+ - id: soltab_out
+ source:
+ - skymodel_source
+ - gsmcal_step
+ valueFrom: $(self.join(''))
+ - id: filter
+ source: process_baselines_target
+ - id: bad_antennas
+ source: bad_antennas
+ out:
+ - id: outh5parm
+ - id: log
+ run: ../../steps/add_missing_stations.cwl
+ label: add_missing_stations
+ 'sbg:x': -200
+ 'sbg:y': -300
+
+ - id: apply_gsmcal
+ in:
+ - id: msin
+ source: msin
+ - id: msin_datacolumn
+ default: DATA
+ - id: msout_name
+ source: msin
+ valueFrom: $(self.nameroot+'_pre-cal.ms')
+ linkMerge: merge_flattened
+ - id: parmdb
+ source: write_solutions/outh5parm
+ - id: msout_datacolumn
+ default: DATA
+ - id: storagemanager
+ default: "Dysco"
+ - id: databitrate
+ source: compression_bitrate
+ - id: correction
+ source:
+ - skymodel_source
+ - gsmcal_step
+ valueFrom: $(self.join(''))
+ - id: solset
+ default: 'target'
+ out:
+ - id: msout
+ - id: logfile
+ run: ../../lofar-cwl/steps/applytarget.cwl
+ label: apply_gsmcal
+ scatter:
+ - msin
+ - msout_name
+ scatterMethod: flat_crossproduct
+ 'sbg:x': 400
+ 'sbg:y': 0
+ - id: merge_array_files
+ in:
+ - id: input
+ source:
+ - apply_gsmcal/logfile
+ out:
+ - id: output
+ run: ../../steps/merge_array_files.cwl
+ label: merge_array_files
+ 'sbg:x': 600
+ 'sbg:y': 0
+
+ - id: write_solutions
+ in:
+ - id: h5parmFile
+ source: add_missing_stations/outh5parm
+ - id: outsolset
+ default: target
+ - id: insoltab
+ source:
+ - skymodel_source
+ - gsmcal_step
+ valueFrom: $(self.join(''))
+ - id: input_file
+ source: insolutions
+ - id: squeeze
+ default: true
+ - id: verbose
+ default: true
+ - id: history
+ default: true
+ out:
+ - id: outh5parm
+ - id: log
+ run: ../../steps/h5parmcat.cwl
+ label: write_solutions
+ 'sbg:x': 200
+ 'sbg:y': 500
+ - id: h5parm_pointingname
+ in:
+ - id: h5parmFile
+ source: write_solutions/outh5parm
+ - id: outsolset
+ default: 'target'
+ - id: solsetName
+ default: 'target'
+ - id: pointing
+ source: get_targetname/targetname
+ out:
+ - id: outh5parm
+ - id: log
+ run: ../../steps/h5parm_pointingname.cwl
+ label: h5parm_pointingname
+ 'sbg:x': 400
+ 'sbg:y': 200
+ - id: structure_function
+ in:
+ - id: h5parmFile
+ source: write_solutions/outh5parm
+ - id: solset
+ default: 'target'
+ - id: soltab
+ source:
+ - skymodel_source
+ - gsmcal_step
+ valueFrom: $(self.join(''))
+ - id: outbasename
+ source: get_targetname/targetname
+ out:
+ - id: structure_plot
+ - id: structure_txt
+ - id: log
+ run: ../../steps/structure_function.cwl
+ label: structure_function
+ 'sbg:x': 500
+ 'sbg:y': 300
+ - id: concat_logfiles_applygsm
+ in:
+ - id: file_list
+ source:
+ - merge_array_files/output
+ - id: file_prefix
+ default: apply_gsmcal
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_applygsm
+ 'sbg:x': 750
+ 'sbg:y': 500
+ - id: concat_logfiles_solutions
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - inh5parm_logfile
+ - add_missing_stations/log
+ - write_solutions/log
+ - get_targetname/logfile
+ - h5parm_pointingname/log
+ - id: file_prefix
+ default: losoto_gsmcal
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_solutions
+ 'sbg:x': 500
+ 'sbg:y': 500
+ - id: concat_logfiles_structure
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - structure_function/log
+ - structure_function/structure_txt
+ - id: file_prefix
+ source: get_targetname/targetname
+ valueFrom: $(self+'_structure')
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_structure
+ 'sbg:x': 950
+ 'sbg:y': 500
+ - id: get_targetname
+ in:
+ - id: msin
+ linkMerge: merge_flattened
+ source: msin
+ out:
+ - id: targetname
+ - id: logfile
+ run: ../../steps/get_targetname.cwl
+ label: get_targetname
+ 'sbg:x': 200
+ 'sbg:y': 200
+requirements:
+ - class: SubworkflowFeatureRequirement
+ - class: ScatterFeatureRequirement
+ - class: StepInputExpressionRequirement
+ - class: InlineJavascriptRequirement
\ No newline at end of file
diff --git a/workflows/prefactor_target/gsmcal.cwl b/workflows/prefactor_target/gsmcal.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..a94c5e97938b0f2e88f32287674bba73ea140c83
--- /dev/null
+++ b/workflows/prefactor_target/gsmcal.cwl
@@ -0,0 +1,506 @@
+class: Workflow
+cwlVersion: v1.0
+id: gsmcal
+label: gsmcal
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: msin
+ type: 'Directory[]'
+ 'sbg:x': -1000
+ 'sbg:y': -400
+ - id: filter_baselines
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': -300
+ - id: num_SBs_per_group
+ type: int
+ 'sbg:x': -1000
+ 'sbg:y': -200
+ - id: reference_stationSB
+ type: int
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': -100
+ - id: use_target
+ type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: target_skymodel
+ type: File?
+ 'sbg:x': -1000
+ 'sbg:y': 100
+ - id: skymodel_source
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': 200
+ - id: do_smooth
+ type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': 300
+ - id: propagatesolutions
+ type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': 400
+ - id: avg_timeresolution_concat
+ type: int
+ 'sbg:x': -1000
+ 'sbg:y': 500
+ - id: avg_freqresolution_concat
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': 600
+ - id: min_unflagged_fraction
+ type: float
+ 'sbg:x': -1000
+ 'sbg:y': 700
+ - id: refant
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': 800
+outputs:
+ - id: msout
+ outputSource:
+ - calibrate_target/msout
+ type: 'Directory[]'
+ 'sbg:x': 1500
+ 'sbg:y': 0
+ - id: outh5parm
+ outputSource:
+ - h5parm_collector/outh5parm
+ type: File
+ 'sbg:x': 1500
+ 'sbg:y': 200
+ - id: bad_antennas
+ outputSource:
+ - identifybadantennas_join/filter_out
+ type: string
+ 'sbg:x': 1500
+ 'sbg:y': 400
+ - id: outh5parm_logfile
+ outputSource:
+ - concat_logfiles_losoto/output
+ type: File
+ 'sbg:x': 1500
+ 'sbg:y': 600
+ - id: inspection
+ outputSource:
+ - losoto_plot_P/output_plots
+ - losoto_plot_P2/output_plots
+ - losoto_plot_Pd/output_plots
+ - losoto_plot_Pd2/output_plots
+ - plot_unflagged/output_imag
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 1500
+ 'sbg:y': 800
+ - id: logfiles
+ outputSource:
+ - concat_logfiles_identify/output
+ - sort_times_into_freqGroups/logfile
+ - find_skymodel_target/logfile
+ - make_sourcedb_target/log
+ - concat_logfiles_calib/output
+ - concat_logfiles_dpppconcat/output
+ - concat_logfiles_blsmooth/output
+ - concat_logfiles_unflagged/output
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 1500
+ 'sbg:y': 1000
+steps:
+ - id: identifybadantennas
+ in:
+ - id: msin
+ source: msin
+ out:
+ - id: flaggedants
+ - id: logfile
+ run: ../../steps/identify_bad_antennas.cwl
+ label: identifybadantennas
+ scatter:
+ - msin
+ 'sbg:x': -200
+ 'sbg:y': -300
+ - id: identifybadantennas_join
+ in:
+ - id: flaggedants
+ source: identifybadantennas/flaggedants
+ - id: filter
+ source: filter_baselines
+ out:
+ - id: filter_out
+ - id: logfile
+ run: ../../steps/identify_bad_antennas_join.cwl
+ label: identifybadantennas_join
+ 'sbg:x': 0
+ 'sbg:y': -300
+ - id: sort_times_into_freqGroups
+ in:
+ - id: msin
+ source:
+ - msin
+ - id: numbands
+ source: num_SBs_per_group
+ - id: NDPPPfill
+ default: true
+ - id: stepname
+ default: .dpppconcat
+ - id: firstSB
+ source: reference_stationSB
+ - id: truncateLastSBs
+ default: false
+ out:
+ - id: filenames
+ - id: groupnames
+ - id: logfile
+ run: ../../steps/sort_times_into_freqGroups.cwl
+ label: sorttimesintofreqGroups
+ 'sbg:x': -200
+ 'sbg:y': 0
+ - id: find_skymodel_target
+ in:
+ - id: msin
+ source:
+ - msin
+ - id: SkymodelPath
+ source: target_skymodel
+ - id: Radius
+ default: 5
+ - id: Source
+ source: skymodel_source
+ - id: DoDownload
+ source: use_target
+ out:
+ - id: skymodel
+ - id: logfile
+ run: ../../steps/find_skymodel_target.cwl
+ label: find_skymodel_target
+ 'sbg:x': -200
+ 'sbg:y': -500
+ - id: make_sourcedb_target
+ in:
+ - id: sky_model
+ source: find_skymodel_target/skymodel
+ - id: output_file_name
+ default: target.sourcedb
+ - id: logname
+ default: make_sourcedb_target.log
+ out:
+ - id: sourcedb
+ - id: log
+ run: ../../lofar-cwl/steps/makesourcedb.cwl
+ label: make_sourcedb_target
+ 'sbg:x': 0
+ 'sbg:y': -500
+ - id: concat_logfiles_dpppconcat
+ in:
+ - id: file_list
+ source:
+ - concat/dpppconcat.log
+ - id: file_prefix
+ default: dpppconcat
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_dpppconcat
+ 'sbg:x': 1200
+ 'sbg:y': 100
+ - id: concat_logfiles_blsmooth
+ in:
+ - id: file_list
+ source:
+ - calibrate_target/BLsmooth.log
+ - id: file_prefix
+ default: blsmooth_target
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_blsmooth
+ 'sbg:x': 1200
+ 'sbg:y': 300
+ - id: concat_logfiles_calib
+ in:
+ - id: file_list
+ source:
+ - calibrate_target/gaincal.log
+ - id: file_prefix
+ default: gaincal
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_calib
+ 'sbg:x': 1200
+ 'sbg:y': 500
+ - id: concat_logfiles_losoto
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - h5parm_collector/log
+ - losoto_plot_P/logfile
+ - losoto_plot_P2/logfile
+ - losoto_plot_Pd/logfile
+ - losoto_plot_Pd2/logfile
+ - id: file_prefix
+ default: losoto_gsmcal
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_losoto
+ 'sbg:x': 1200
+ 'sbg:y': 700
+ - id: concat_logfiles_unflagged
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - concat/check_unflagged_fraction.log
+ - plot_unflagged/logfile
+ - id: file_prefix
+ default: check_unflagged_fraction
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_unflagged
+ 'sbg:x': 1200
+ 'sbg:y': 900
+ - id: concat_logfiles_identify
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - identifybadantennas/logfile
+ - identifybadantennas_join/logfile
+ - id: file_prefix
+ default: identifyBadAntennas
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_identify
+ 'sbg:x': 1200
+ 'sbg:y': -100
+ - id: concat
+ in:
+ - id: msin
+ source:
+ - msin
+ - id: group_id
+ source: sort_times_into_freqGroups/groupnames
+ - id: groups_specification
+ source: sort_times_into_freqGroups/filenames
+ - id: filter_baselines
+ source: identifybadantennas_join/filter_out
+ - id: avg_timeresolution_concat
+ source: avg_timeresolution_concat
+ - id: avg_freqresolution_concat
+ source: avg_freqresolution_concat
+ - id: min_unflagged_fraction
+ source: min_unflagged_fraction
+ out:
+ - id: msout_old
+ - id: unflagged_fraction
+ - id: msout
+ - id: dpppconcat.log
+ - id: check_unflagged_fraction.log
+ run: ../../subworkflow/concat.cwl
+ label: concat
+ scatter:
+ - group_id
+ 'sbg:x': 200
+ 'sbg:y': 0
+ - id: merge_array
+ in:
+ - id: input
+ source:
+ - concat/msout
+ out:
+ - id: output
+ run: ../../steps/merge_array.cwl
+ label: merge_array
+ 'sbg:x': 400
+ 'sbg:y': 0
+ - id: calibrate_target
+ in:
+ - id: msin
+ source: merge_array/output
+ - id: skymodel
+ source: make_sourcedb_target/sourcedb
+ - id: do_smooth
+ source: do_smooth
+ - id: propagatesolutions
+ source: propagatesolutions
+ out:
+ - id: msout
+ - id: BLsmooth.log
+ - id: gaincal.log
+ - id: outh5parm
+ run: ../../subworkflow/calib_targ.cwl
+ label: calibrate_target
+ scatter:
+ - msin
+ 'sbg:x': 600
+ 'sbg:y': 0
+ - id: h5parm_collector
+ in:
+ - id: h5parmFiles
+ source:
+ - calibrate_target/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
+ - id: plot_unflagged
+ in:
+ - id: msin
+ source:
+ - concat/msout_old
+ - id: unflagged_fraction
+ source:
+ - concat/unflagged_fraction
+ out:
+ - id: output_imag
+ - id: logfile
+ run: ../../steps/plot_unflagged.cwl
+ label: plot_unflagged
+ 'sbg:x': 500
+ 'sbg:y': -200
+ - id: losoto_plot_P
+ in:
+ - id: input_h5parm
+ source: h5parm_collector/outh5parm
+ - id: soltab
+ default: sol000/phase000
+ - 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: ph_
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_P
+ 'sbg:x': 1000
+ 'sbg:y': 200
+ - id: losoto_plot_P2
+ in:
+ - id: input_h5parm
+ source: h5parm_collector/outh5parm
+ - id: soltab
+ default: sol000/phase000
+ - id: axesInPlot
+ default:
+ - time
+ - 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: ph_
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_P2
+ 'sbg:x': 1000
+ 'sbg:y': 50
+ - id: losoto_plot_Pd
+ in:
+ - id: input_h5parm
+ source: h5parm_collector/outh5parm
+ - 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: ph_poldif_
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_Pd
+ 'sbg:x': 1000
+ 'sbg:y': -100
+ - id: losoto_plot_Pd2
+ in:
+ - id: input_h5parm
+ source: h5parm_collector/outh5parm
+ - id: soltab
+ default: sol000/phase000
+ - id: axesInPlot
+ default:
+ - time
+ - 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: ph_poldif_
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_Pd2
+ 'sbg:x': 1000
+ 'sbg:y': -250
+requirements:
+ - class: StepInputExpressionRequirement
+ - class: InlineJavascriptRequirement
+ - class: SubworkflowFeatureRequirement
+ - class: ScatterFeatureRequirement
+ - class: MultipleInputFeatureRequirement
diff --git a/workflows/prefactor_target/prep.cwl b/workflows/prefactor_target/prep.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..1e1ebb52fb6326cd33b18425db8a6112b8a510e1
--- /dev/null
+++ b/workflows/prefactor_target/prep.cwl
@@ -0,0 +1,491 @@
+class: Workflow
+cwlVersion: v1.0
+id: prep
+label: prep
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: msin
+ type: 'Directory[]'
+ 'sbg:x': -1000
+ 'sbg:y': -1700
+ - id: cal_solutions
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': -1600
+ - id: flag_baselines
+ type: 'string[]?'
+ default: []
+ 'sbg:x': -1000
+ 'sbg:y': -1500
+ - id: process_baselines_target
+ type: string?
+ default: '[CR]S*&'
+ 'sbg:x': -1000
+ 'sbg:y': -1400
+ - id: filter_baselines
+ type: string?
+ default: '[CR]S*&'
+ 'sbg:x': -1000
+ 'sbg:y': -1300
+ - id: rfistrategy
+ type: string?
+ default: HBAdefault.rfis
+ 'sbg:x': -1000
+ 'sbg:y': -1200
+ - id: raw_data
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -1100
+ - id: propagatesolutions
+ type: boolean?
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': -1000
+ - id: demix_sources
+ type: 'string[]?'
+ default:
+ - CasA
+ - CygA
+ 'sbg:x': -1000
+ 'sbg:y': -900
+ - id: demix_target
+ type: string?
+ default: ''
+ 'sbg:x': -1000
+ 'sbg:y': -800
+ - id: demix_freqstep
+ type: int?
+ default: 16
+ 'sbg:x': -1000
+ 'sbg:y': -700
+ - id: demix_timestep
+ type: int?
+ default: 10
+ 'sbg:x': -1000
+ 'sbg:y': -600
+ - id: demix
+ type: boolean?
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -500
+ - id: apply_tec
+ type: boolean
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -400
+ - id: apply_clock
+ type: boolean
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': -300
+ - id: apply_phase
+ type: boolean
+ default: false
+ 'sbg:x': -1000
+ 'sbg:y': -200
+ - id: apply_RM
+ type: boolean
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': -100
+ - id: apply_beam
+ type: boolean
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: clipATeam
+ type: boolean?
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 100
+ - id: updateweights
+ type: boolean?
+ default: true
+ 'sbg:x': -1000
+ 'sbg:y': 200
+ - id: max_dppp_threads
+ type: int?
+ default: 10
+ 'sbg:x': -1000
+ 'sbg:y': 300
+ - id: memoryperc
+ type: int?
+ default: 20
+ 'sbg:x': -1000
+ 'sbg:y': 400
+ - id: min_separation
+ type: int?
+ default: 30
+ 'sbg:x': -1000
+ 'sbg:y': 500
+ - id: A-Team_skymodel
+ type: File?
+ 'sbg:x': -1000
+ 'sbg:y': 600
+ - id: avg_timeresolution
+ type: float?
+ default: 4
+ 'sbg:x': -1000
+ 'sbg:y': 700
+ - id: avg_freqresolution
+ type: string?
+ default: 48.82kHz
+ 'sbg:x': -1000
+ 'sbg:y': 800
+ - id: ionex_server
+ type: string?
+ default: 'ftp://ftp.aiub.unibe.ch/CODE/'
+ 'sbg:x': -1000
+ 'sbg:y': 900
+ - id: ionex_prefix
+ type: string?
+ default: CODG
+ 'sbg:x': -1000
+ 'sbg:y': 1000
+ - id: proxy_server
+ type: string?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 1100
+ - id: proxy_port
+ type: int?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 1200
+ - id: proxy_type
+ type: string?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 1300
+ - id: proxy_user
+ type: string?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 1400
+ - id: proxy_pass
+ type: string?
+ default: null
+ 'sbg:x': -1000
+ 'sbg:y': 1500
+ - id: elevation
+ type: string
+ default: 0deg..20deg
+ 'sbg:x': -1000
+ 'sbg:y': 1600
+ - id: amplmin
+ type: float
+ default: 1.e-30
+ 'sbg:x': -1000
+ 'sbg:y': 1700
+outputs:
+ - id: outh5parm
+ outputSource:
+ - createRMh5parm/h5parmout
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': -500
+ - id: inspection
+ outputSource:
+ - check_ateam_separation/output_imag
+ - losoto_plot_RM/output_plots
+ - plot_Ateamclipper/output_imag
+ type: 'File[]?'
+ linkMerge: merge_flattened
+ 'sbg:x': 1000
+ 'sbg:y': -300
+ - id: msout
+ outputSource:
+ - dppp_prep_target/msout
+ type: 'Directory[]'
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: logfiles
+ outputSource:
+ - make_sourcedb_ateam/log
+ - check_ateam_separation/logfile
+ - concat_logfiles_stationlist/output
+ - concat_logfiles_RMextract/output
+ - concat_logfiles_prep_targ/output
+ - concat_logfiles_predict_targ/output
+ - concat_logfiles_clipper_targ/output
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 1000
+ 'sbg:y': 800
+steps:
+ - id: check_ateam_separation
+ in:
+ - id: ms
+ source:
+ - msin
+ - id: min_separation
+ source: min_separation
+ out:
+ - id: output_imag
+ - id: logfile
+ run: ../../lofar-cwl/steps/check_ateam_separation.cwl
+ label: check_Ateam_separation
+ 'sbg:x': -500
+ 'sbg:y': -300
+ - id: compare_station_list
+ in:
+ - id: msin
+ source:
+ - msin
+ - id: h5parmdb
+ source: cal_solutions
+ - id: solset_name
+ default: 'calibrator'
+ - id: filter
+ source: filter_baselines
+ out:
+ - id: filter_out
+ - id: logfile
+ run: ../../steps/compare_station_list.cwl
+ label: compare_station_list
+ 'sbg:x': -500
+ 'sbg:y': -500
+ - id: make_sourcedb_ateam
+ in:
+ - id: sky_model
+ source: A-Team_skymodel
+ - id: logname
+ default: make_sourcedb_ateam.log
+ out:
+ - id: sourcedb
+ - id: log
+ run: ../../lofar-cwl/steps/makesourcedb.cwl
+ label: make_sourcedb_ateam
+ 'sbg:x': -500
+ 'sbg:y': 300
+ - id: createRMh5parm
+ in:
+ - id: msin
+ source:
+ - msin
+ - id: h5parm
+ source: cal_solutions
+ - id: ionex_server
+ source: ionex_server
+ - id: ionex_prefix
+ source: ionex_prefix
+ - id: solset
+ default: target
+ - id: proxyserver
+ source: proxy_server
+ - id: proxyport
+ source: proxy_port
+ - id: proxytype
+ source: proxy_type
+ - id: proxyuser
+ source: proxy_user
+ - id: proxypass
+ source: proxy_pass
+ out:
+ - id: h5parmout
+ - id: logfile
+ run: ../../steps/createRMh5parm.cwl
+ label: createRMh5parm
+ 'sbg:x': -500
+ 'sbg:y': 0
+ - id: losoto_plot_RM
+ in:
+ - id: input_h5parm
+ source: createRMh5parm/h5parmout
+ - id: soltab
+ default: target/RMextract
+ - id: axesInPlot
+ default:
+ - time
+ - id: axisInTable
+ default: ant
+ - id: prefix
+ default: RMextract
+ out:
+ - id: output_plots
+ - id: logfile
+ - id: parset
+ run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
+ label: losoto_plot_RM
+ 'sbg:x': 0
+ 'sbg:y': -300
+ - id: dppp_prep_target
+ in:
+ - id: msin
+ linkMerge: merge_flattened
+ source:
+ - msin
+ - id: msin_baseline
+ default: '*'
+ source: compare_station_list/filter_out
+ - id: baselines_to_flag
+ source: flag_baselines
+ - id: elevation_to_flag
+ source: elevation
+ - id: min_amplitude_to_flag
+ source: amplmin
+ - id: memoryperc
+ default: 20
+ source: memoryperc
+ - id: raw_data
+ default: false
+ source: raw_data
+ - id: demix
+ default: false
+ source: demix
+ - id: skymodel
+ source: make_sourcedb_ateam/sourcedb
+ - id: timeresolution
+ default: 1
+ source: avg_timeresolution
+ - id: freqresolution
+ default: 12.21kHz
+ source: avg_freqresolution
+ - id: demix_timestep
+ default: 1
+ source: demix_timestep
+ - id: demix_freqstep
+ default: 1
+ source: demix_freqstep
+ - id: process_baselines_target
+ default: '*'
+ source: process_baselines_target
+ - id: target_source
+ source: demix_target
+ - id: ntimechunk
+ default: 10
+ source: max_dppp_threads
+ - id: subtract_sources
+ source:
+ - demix_sources
+ - id: parmdb
+ source: createRMh5parm/h5parmout
+ - id: apply_tec_correction
+ source: apply_tec
+ default: false
+ - id: apply_rm_correction
+ source: apply_RM
+ default: true
+ - id: apply_phase_correction
+ source: apply_phase
+ default: false
+ - id: apply_clock_correction
+ source: apply_clock
+ default: true
+ - id: apply_beam_correction
+ source: apply_beam
+ default: true
+ - id: filter_baselines
+ source: compare_station_list/filter_out
+ - id: updateweights
+ source: updateweights
+ out:
+ - id: msout
+ - id: prep_logfile
+ - id: predict_logfile
+ - id: clipper_logfile
+ - id: clipper_output
+ - id: parset
+ run: ../../subworkflow/ndppp_prep_targ.cwl
+ label: ndppp_prep_target
+ scatter:
+ - msin
+ 'sbg:x': 0
+ 'sbg:y': 0
+ - id: plot_Ateamclipper
+ in:
+ - id: clipper_output
+ source: concat_logfiles_clipper_output/output
+ out:
+ - id: output_imag
+ run: ../../steps/plot_Ateamclipper.cwl
+ label: concat_logfiles_clipper_output
+ 'sbg:x': 600
+ 'sbg:y': 200
+ - id: concat_logfiles_clipper_output
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source: dppp_prep_target/clipper_output
+ - id: file_prefix
+ default: Ateamclipper
+ - id: file_suffix
+ default: txt
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_clipper_output
+ 'sbg:x': 400
+ 'sbg:y': 200
+ - id: concat_logfiles_prep_targ
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source: dppp_prep_target/prep_logfile
+ - id: file_prefix
+ default: ndppp_prep_targ
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_prep_target
+ 'sbg:x': 400
+ 'sbg:y': 300
+ - id: concat_logfiles_predict_targ
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source: dppp_prep_target/predict_logfile
+ - id: file_prefix
+ default: predict_targ
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_predict_targ
+ 'sbg:x': 400
+ 'sbg:y': 400
+ - id: concat_logfiles_clipper_targ
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source: dppp_prep_target/clipper_logfile
+ - id: file_prefix
+ default: Ateamclipper
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_clipper_targ
+ 'sbg:x': 400
+ 'sbg:y': 500
+ - id: concat_logfiles_RMextract
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - createRMh5parm/logfile
+ - losoto_plot_RM/logfile
+ - id: file_prefix
+ default: RMextract
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_RMextract
+ 'sbg:x': 400
+ 'sbg:y': 600
+ - id: concat_logfiles_stationlist
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - compare_station_list/logfile
+ - id: file_prefix
+ default: compareStationList
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_stationlist
+ 'sbg:x': 400
+ 'sbg:y': 700
+requirements:
+ - class: ScatterFeatureRequirement
\ No newline at end of file