diff --git a/lofar-cwl/steps/applytarget.cwl b/lofar-cwl/steps/applytarget.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..cb0f811446763fa75295a8d44b278878bc205e10
--- /dev/null
+++ b/lofar-cwl/steps/applytarget.cwl
@@ -0,0 +1,96 @@
+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
+ inputBinding:
+ position: 0
+ prefix: msout=msout_name
+ 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'.
+ - 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: 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]'
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+ - class: InlineJavascriptRequirement
+hints:
+ - class: DockerRequirement
+ dockerPull: 'lofareosc/prefactor:HBAcalibrator'
diff --git a/lofar-cwl/steps/dpppconcat.cwl b/lofar-cwl/steps/dpppconcat.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..47cd157076cb7194d07de76067efc9649007e964
--- /dev/null
+++ b/lofar-cwl/steps/dpppconcat.cwl
@@ -0,0 +1,118 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: dpppconcat
+baseCommand:
+ - DPPP
+inputs:
+ - id: msin
+ type: Directory[]
+ inputBinding:
+ position: 0
+ prefix: msin=
+ separate: false
+ doc: Input Measurement Set
+ - id: msout_name
+ type: string
+ inputBinding:
+ position: 0
+ prefix: msout=
+ separate: false
+ - default: DATA
+ id: msin_datacolumn
+ type: string
+ inputBinding:
+ position: 0
+ prefix: msin.datacolumn=
+ separate: false
+ doc: Input data Column
+ - default: DATA
+ id: msout_datacolumn
+ type: string
+ inputBinding:
+ position: 0
+ prefix: msout.datacolumn=
+ separate: false
+ - 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
+ - id: missingdata
+ type: boolean
+ inputBinding:
+ prefix: msout.missingdata=True
+ separate: false
+ - id: baseline
+ type: string?
+ default: '*'
+ inputBinding:
+ prefix: msin.baseline=
+ separate: false
+ - id: avg_timeresolution
+ type: int?
+ default: 1
+ inputBinding:
+ prefix: avg.timeresolution=
+ separate: false
+ - id: avg_freqresolution
+ type: string?
+ default: '12.205kHz'
+ inputBinding:
+ prefix: avg.freqresolution=
+ separate: false
+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'
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+ - class: InlineJavascriptRequirement
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: concat.log
+stderr: concat_err.log
\ No newline at end of file
diff --git a/lofar-cwl/steps/gaincal.cwl b/lofar-cwl/steps/gaincal.cwl
index 863583dfcf84d6defd8cb9e38d0748cea2518168..894068f51c465d3620cb64c1a7d527aeee70eae1 100644
--- a/lofar-cwl/steps/gaincal.cwl
+++ b/lofar-cwl/steps/gaincal.cwl
@@ -97,6 +97,14 @@ inputs:
prefix: msout=
separate: false
doc: Output Measurement Set
+ - default: true
+ id: propagatesolutions
+ type: boolean
+ inputBinding:
+ position: 0
+ prefix: propagatesolutions=True
+ separate: false
+ doc: Output Measurement Set
outputs:
- id: msout
doc: Output Measurement Set
@@ -109,8 +117,14 @@ outputs:
outputBinding:
glob: $(inputs.output_name_h5parm)
format: 'lofar:#H5Parm'
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: 'gaincal*.log'
+stdout: gaincal.log
+stderr: gaincal_err.log
arguments:
- - 'steps=[gaincal]'
+ - 'steps=[filter,gaincal]'
hints:
- class: DockerRequirement
dockerPull: 'lofareosc/prefactor:HBAcalibrator'
diff --git a/steps/add_missing_stations.cwl b/steps/add_missing_stations.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..ea4ecec182845c166e39e8a0f8e82576cb24eca4
--- /dev/null
+++ b/steps/add_missing_stations.cwl
@@ -0,0 +1,79 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ 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: '--refh5parm'
+ doc: External H5parm from which the full list of antennas is used from.
+ - id: solset
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--solset'
+ doc: Input calibration solutions
+ - id: refsolset
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--refsolset'
+ doc: Input calibration solutions of the reference h5parm file
+ - id: soltab_in
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--soltab_in'
+ doc: Input solution table
+ - id: soltab_out
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--soltab_out'
+ doc: Output solution table (has to be different from input solution table)
+ - id: filter
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--filter'
+ doc: Filter these antenna string from the processing
+ - id: bad_antennas
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--bad_antennas'
+ doc: Antenna string to be processed
+outputs:
+ - id: outh5parm
+ type: File
+ outputBinding:
+ glob: $(inputs.h5parm.basename)
+ - 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: $(inputs.h5parm)
+ writable: true
diff --git a/steps/filter_ms_group.cwl b/steps/filter_ms_group.cwl
index 5137406770592dbb1cc63578c94848a4fcf0d489..2d3b54179f9f809c1ac428bd7a0523116338c592 100644
--- a/steps/filter_ms_group.cwl
+++ b/steps/filter_ms_group.cwl
@@ -19,7 +19,7 @@ inputs:
position: 2
outputs:
- id: output
- type: 'Directory[]?'
+ type: Directory[]
outputBinding:
loadContents: true
glob: selected_ms.json
diff --git a/steps/find_skymodel_target.cwl b/steps/find_skymodel_target.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..d6efc014bf32d3252666009c208f0937ac4b9050
--- /dev/null
+++ b/steps/find_skymodel_target.cwl
@@ -0,0 +1,77 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$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
+ null = None
+
+ from download_skymodel_target import main as download_skymodel_target
+
+ mss = sys.argv[1:]
+
+ SkymodelPath = $(inputs.skymodels)
+ if SkymodelPath is None:
+ SkymodelPath = "target.skymodel"
+ else:
+ SkymodelPath = SkymodelPath["path"]
+
+ Radius = $(inputs.Radius)
+ Source = $(inputs.Source)
+ DoDownload = "$(inputs.DoDownload)"
+
+ output = {}
+ if DoDownload != 'null':
+ output = download_skymodel_target(mss, SkymodelPath, Radius, DoDownload="True", Source)
+ else:
+ output = download_skymodel_target(mss, SkymodelPath, Radius, DoDownload="False", Source)
+
+ if SkymodelPath != "target.skymodel":
+ 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/h5parmcat.cwl b/steps/h5parmcat.cwl
index 76f8ae83013bd5123d8695cd43b068cf24470be9..f14f7e38892ff91bf78c80ada21c9d5b3b713fa7 100644
--- a/steps/h5parmcat.cwl
+++ b/steps/h5parmcat.cwl
@@ -58,6 +58,13 @@ inputs:
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
@@ -68,7 +75,7 @@ outputs:
- id: log
type: File[]
outputBinding:
- glob: 'parm_collector_output*.log'
+ glob: 'h5parm_collector_output*.log'
label: h5parm_cat
arguments:
- position: 0
diff --git a/steps/sort_times_into_freqGroups.cwl b/steps/sort_times_into_freqGroups.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..ed27af576713f4177cb1cffb7eb6b716cb15e896
--- /dev/null
+++ b/steps/sort_times_into_freqGroups.cwl
@@ -0,0 +1,99 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: sort_times_into_freqGroups
+baseCommand:
+ - python3
+inputs:
+ - id: msin
+ type: Directory[]
+ doc: MS to sort
+ inputBinding:
+ position: 0
+ - id: numbands
+ type: int?
+ default: 10
+ doc: Number of how many files should be grouped together in frequency.
+ - id: NDPPPfill
+ type: boolean?
+ default: True
+ doc: Add dummy file-names for missing frequencies, so that NDPPP can fill the data with flagged dummy data.
+ - id: stepname
+ type: string?
+ default: null
+ doc: Add this step-name into the file-names of the output files.
+ - id: firstSB
+ type: int?
+ default: null
+ doc: If set, then reference the grouping of files to this station-subband. As if a file with this station-subband would be included in the input files.
+ - id: mergeLastGroup
+ type: boolean?
+ default: False
+ doc: Add dummy file-names for missing frequencies, so that NDPPP can fill the data with flagged dummy data.
+ - id: truncateLastSBs
+ type: boolean?
+ default: True
+ doc: Add dummy file-names for missing frequencies, so that NDPPP can fill the data with flagged dummy data.
+
+label: sort_times_into_freqGroups.py
+arguments:
+ - '-c'
+ - |
+ import sys
+ import json
+ from sort_times_into_freqGroups_CWL import main as sort_times_into_freqGroups
+
+ mss = sys.argv[1:]
+ numbands = int($(inputs.numbands))
+ stepname = $(inputs.stepname)
+ mergeLastGroup = $(inputs.mergeLastGroup)
+ truncateLastSBs = $(inputs.truncateLastSBs)
+ firstSB = int($(inputs.firstSB))
+
+ output = sort_times_into_freqGroups(mss, numbands, NDPPPfill, stepname, mergeLastGroup, truncateLastSBs, firstSB)
+
+ filenames = output['filenames']
+ groupnames = output['groupnames']
+
+ #cwl_output = {}
+ #filelists = []
+ #for groupname in groupnames:
+ # filelist = []
+ # for filename in filenames[groupname]:
+ # filelist.append({'class': 'Dictionary', 'path': filename})
+ # filelists.append(filelist)
+
+ 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)
+
+ return(0)
+
+outputs:
+ - id: filenames
+ type: File
+ outputBinding:
+ glob: 'filenames.json'
+ - id: groupnames
+ type: string[]
+ outputBinding:
+ loadContents: true
+ glob: 'out.json'
+ outputEval: $(JSON.parse(self[0].contents).groupnames)
+ - id: logfile
+ type: File?
+ outputBinding:
+ glob: sort_times_into_freqGroups.log
+
+requirements:
+ - class: InlineJavascriptRequirement
+
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: sort_times_into_freqGroups.log
\ No newline at end of file
diff --git a/subworkflow/concat_calibrate.cwl b/subworkflow/concat_calibrate.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..225dbc4067e946fb6e94ea26d9f61dd3582264bd
--- /dev/null
+++ b/subworkflow/concat_calibrate.cwl
@@ -0,0 +1,206 @@
+class: Workflow
+cwlVersion: v1.0
+id: concat_calibrate
+label: concat_calibrate
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: msin
+ type: Directory[]
+ 'sbg:x': -1000
+ 'sbg:y': -100
+ - id: group_id
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: groups_specification
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': 100
+ - id: filter_baselines
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': 200
+ - id: avg_timeresolution_concat
+ type: int
+ 'sbg:x': -1000
+ 'sbg:y': 300
+ - id: avg_freqresolution_concat
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': 400
+ - id: skymodel
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': 500
+ - id: do_smooth
+ type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': 600
+ - id: propagatesolutions
+ type: boolean
+ 'sbg:x': -1000
+ 'sbg:y': 700
+outputs:
+ - id: msout
+ outputSource:
+ - dpppconcat/msout
+ type: Directory
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: dpppconcat.log
+ outputSource:
+ - concat_logfiles_dpppconcat/output
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': -300
+ - 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': 200
+ - id: outh5parm
+ outputSource:
+ - calib_targ/h5parm
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 400
+
+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: baseline
+ source: filter_baselines
+ - id: filter_baselines
+ source: filter_baselines
+ - id: filter_remove
+ default: true
+ - id: overwrite
+ default: false
+ - id: missingdata
+ default: True
+ - id: storagemanager
+ default: "Dysco"
+ - id: databitrate
+ default: 0
+ - 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: BLsmooth
+ in:
+ - id: msin
+ source: dpppconcat/msout
+ - 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': 100
+ 'sbg:y': 0
+ - id: calib_targ
+ in:
+ - id: msin
+ source: BLsmooth/msout
+ - id: msin_datacolumn
+ default: SMOOTHED_DATA
+ - id: sourcedb
+ source: skymodel
+ - id: parmdb
+ default: 'instrument.h5'
+ - id: caltype
+ default: 'phaseonly'
+ - 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': 400
+ '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_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: []
\ No newline at end of file
diff --git a/workflows/HBA_target.cwl b/workflows/HBA_target.cwl
index c3d15abe8a9a6c80e3eae44a183476e30a470368..2d9971500760179813ea5f17a0dc841c0071810a 100644
--- a/workflows/HBA_target.cwl
+++ b/workflows/HBA_target.cwl
@@ -174,8 +174,8 @@ inputs:
'sbg:x': -1000
'sbg:y': 1600
- id: avg_timeresolution
- type: float?
- default: 4.
+ type: int?
+ default: 4
'sbg:x': -1000
'sbg:y': 1700
- id: avg_freqresolution
@@ -184,8 +184,8 @@ inputs:
'sbg:x': -1000
'sbg:y': 1800
- id: avg_timeresolution_concat
- type: float?
- default: 8.
+ type: int?
+ default: 8
'sbg:x': -1000
'sbg:y': 1900
- id: avg_freqresolution_concat
@@ -199,10 +199,8 @@ inputs:
'sbg:x': -1000
'sbg:y': 2100
- id: reference_stationSB
- type:
- - int?
- - string?
- default: ''
+ type: int?
+ default: null
'sbg:x': -1000
'sbg:y': 2200
- id: ionex_server
diff --git a/workflows/prefactor_target.cwl b/workflows/prefactor_target.cwl
index e6d97096708490ebce16cba309bdeaac75aab245..90b1bec1723aaa499f792a46e957364ee0b41f5a 100644
--- a/workflows/prefactor_target.cwl
+++ b/workflows/prefactor_target.cwl
@@ -170,7 +170,7 @@ inputs:
'sbg:y': 1500
- id: skymodel_source
type: string?
- default: TGSS
+ default: "TGSS"
'sbg:x': -1000
'sbg:y': 1600
- id: avg_timeresolution
@@ -184,13 +184,13 @@ inputs:
'sbg:x': -1000
'sbg:y': 1800
- id: avg_timeresolution_concat
- type: float?
+ type: int?
default: 8
'sbg:x': -1000
'sbg:y': 1900
- id: avg_freqresolution_concat
type: string?
- default: 97.64kHz
+ default: '97.64kHz'
'sbg:x': -1000
'sbg:y': 2000
- id: num_SBs_per_group
@@ -199,45 +199,45 @@ inputs:
'sbg:x': -1000
'sbg:y': 2100
- id: reference_stationSB
- type: string?
- default: ''
+ type: int?
+ default: null
'sbg:x': -1000
- 'sbg:y': 1800
+ 'sbg:y': 2200
- id: ionex_server
type: string?
default: 'ftp://ftp.aiub.unibe.ch/CODE/'
'sbg:x': -1000
- 'sbg:y': 1900
+ 'sbg:y': 2300
- id: ionex_prefix
type: string?
default: CODG
'sbg:x': -1000
- 'sbg:y': 2000
+ 'sbg:y': 2400
- id: proxy_server
type: string?
default: null
'sbg:x': -1000
- 'sbg:y': 2100
+ 'sbg:y': 2500
- id: proxy_port
type: string?
default: null
'sbg:x': -1000
- 'sbg:y': 2200
+ 'sbg:y': 2600
- id: proxy_type
type: string?
default: null
'sbg:x': -1000
- 'sbg:y': 2300
+ 'sbg:y': 2700
- id: proxy_user
type: string?
default: null
'sbg:x': -1000
- 'sbg:y': 2400
+ 'sbg:y': 2800
- id: proxy_pass
type: string?
default: null
'sbg:x': -1000
- 'sbg:y': 2500
+ 'sbg:y': 2900
outputs:
- id: inspection
outputSource:
@@ -248,20 +248,21 @@ outputs:
'sbg:y': -600
- id: solutions
outputSource:
- - prep/outh5parm
+ - finalize/solutions
type: File
'sbg:x': 2000
'sbg:y': -500
- id: msout
outputSource:
- - concat/msout
+ - finalize/msout
type: 'Directory[]'
'sbg:x': 2000
'sbg:y': 0
- id: logfiles
outputSource:
- prep/logfiles
- - concat/logfiles
+ - gsmcal/logfiles
+ - finalize/logfiles
type: 'File[]'
linkMerge: merge_flattened
'sbg:x': 2000
@@ -345,19 +346,66 @@ steps:
label: prep
'sbg:x': 0
'sbg:y': 0
- - id: concat
+ - 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
out:
- id: msout
+ - id: outh5parm
+ - id: bad_antennas
+ - id: outh5parm_logfile
- id: logfiles
- run: ./prefactor_target/concat.cwl
- label: concat
+ run: ./prefactor_target/gsmcal.cwl
+ label: gsmcal
'sbg:x': 500
'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
+ out:
+ - id: msout
+ - id: solutions
+ - id: logfiles
+ run: ./prefactor_target/finalize.cwl
+ label: finalize
+ 'sbg:x': 800
+ 'sbg:y': 0
requirements:
- class: SubworkflowFeatureRequirement
diff --git a/workflows/prefactor_target/concat.cwl b/workflows/prefactor_target/concat.cwl
deleted file mode 100644
index d8978090f678cdbbadbddce4a8d9ad22185bb7c2..0000000000000000000000000000000000000000
--- a/workflows/prefactor_target/concat.cwl
+++ /dev/null
@@ -1,47 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-id: concat
-label: concat
-$namespaces:
- sbg: 'https://www.sevenbridges.com/'
-inputs:
- - id: msin
- type: 'Directory[]'
- 'sbg:x': -1000
- 'sbg:y': -900
- - id: filter_baselines
- type: string
- 'sbg:x': -1000
- 'sbg:y': -800
-outputs:
- - id: msout
- outputSource:
- - msin
- type: 'Directory[]'
- 'sbg:x': 1000
- 'sbg:y': 0
- - id: logfiles
- linkMerge: merge_flattened
- outputSource:
- - identifybadantennas/logfile
- type: 'File[]'
- 'sbg:x': 1000
- 'sbg:y': 800
-steps:
- - id: identifybadantennas
- in:
- - id: msin
- source:
- - msin
- - id: filter
- source: filter_baselines
- out:
- - id: filter_out
- - id: logfile
- run: ../../steps/identify_bad_antennas.cwl
- label: identifybadantennas
- 'sbg:x': 0
- 'sbg:y': -300
-requirements:
- - class: SubworkflowFeatureRequirement
- - class: ScatterFeatureRequirement
diff --git a/workflows/prefactor_target/finalize.cwl b/workflows/prefactor_target/finalize.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..7864e5663bb8168241526a2a70bb2f69bbf75f8f
--- /dev/null
+++ b/workflows/prefactor_target/finalize.cwl
@@ -0,0 +1,173 @@
+class: Workflow
+cwlVersion: v1.0
+id: finalize
+label: finalize
+$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': -200
+ - id: process_baselines_target
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': -100
+ - id: bad_antennas
+ type: string
+ 'sbg:x': -1000
+ 'sbg:y': 0
+ - id: insolutions
+ type: File
+ 'sbg:x': -1000
+ 'sbg:y': 100
+ - id: compression_bitrate
+ type: int
+ 'sbg:x': -1000
+ 'sbg:y': 200
+
+outputs:
+ - id: msout
+ outputSource:
+ - apply_gsmcal/msout
+ type: 'Directory[]'
+ 'sbg:x': 1000
+ 'sbg:y': 0
+ - id: solutions
+ outputSource:
+ - write_solutions/outh5parm
+ type: File
+ 'sbg:x': 1000
+ 'sbg:y': 200
+ - id: logfiles
+ outputSource:
+ - concat_logfiles_applygsm/output
+ - concat_logfiles_solutions/output
+ type: 'File[]'
+ linkMerge: merge_flattened
+ 'sbg:x': 1000
+ 'sbg:y': 800
+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
+ - id: soltab_out
+ default: 'TGSSphase'
+ - 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: parmdb
+ source: write_solutions/outh5parm
+ - id: msout_datacolumn
+ default: DATA
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ source: compression_bitrate
+ - id: correction
+ default: 'TGSSphase'
+ - id: solset
+ default: 'target'
+ - id: msout_name
+ source: msin
+ valueFrom: $(self.basename+'_prep.ms')
+ out:
+ - id: msout
+ - id: logfile
+ run: ../../lofar-cwl/steps/applytarget.cwl
+ label: apply_gsmcal
+ scatter:
+ - msin
+ 'sbg:x': 400
+ 'sbg:y': 0
+ - id: write_solutions
+ in:
+ - id: h5parmFile
+ source: add_missing_stations/outh5parm
+ - id: outsolset
+ default: target
+ - id: insoltab
+ default: 'TGSSphase'
+ - 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: concat_logfiles_applygsm
+ in:
+ - id: file_list
+ source:
+ - apply_gsmcal/logfile
+ - 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
+ - id: file_prefix
+ default: losoto_gsmcal
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_solutions
+ 'sbg:x': 500
+ 'sbg:y': 500
+requirements:
+ - class: SubworkflowFeatureRequirement
+ - class: ScatterFeatureRequirement
diff --git a/workflows/prefactor_target/gsmcal.cwl b/workflows/prefactor_target/gsmcal.cwl
index 3faf8dbb4f11839314fe40720c4f8e39031317bb..a4ed1749c5ca980e682defb2062e9e672f827029 100644
--- a/workflows/prefactor_target/gsmcal.cwl
+++ b/workflows/prefactor_target/gsmcal.cwl
@@ -1,142 +1,71 @@
class: Workflow
cwlVersion: v1.0
-id: prep
-label: prep
+id: gsmcal
+label: gsmcal
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: msin
type: 'Directory[]'
'sbg:x': -1000
- 'sbg:y': -900
+ 'sbg:y': -400
- id: filter_baselines
type: string
'sbg:x': -1000
- 'sbg:y': -800
- - id: raw_data
- type: boolean
- 'sbg:x': -1000
- 'sbg:y': -700
- - id: propagatesolutions
- type: boolean
- 'sbg:x': -1000
- 'sbg:y': -600
- - id: flagunconverged
- type: boolean
- 'sbg:x': -1000
- 'sbg:y': -500
- - id: demix
- type: boolean
- 'sbg:x': -1000
- 'sbg:y': -400
- - id: max_dppp_threads
- type: int?
- default: 10
- 'sbg:x': -1000
'sbg:y': -300
- - id: memoryperc
+ - id: num_SBs_per_group
type: int
'sbg:x': -1000
'sbg:y': -200
- - id: flag_baselines
- type: 'string[]'
+ - id: reference_stationSB
+ type: int
+ default: null
'sbg:x': -1000
'sbg:y': -100
- - id: avg_timeresolution
- type: float
+ - id: use_target
+ type: boolean
'sbg:x': -1000
'sbg:y': 0
- - id: avg_freqresolution
- type: string
+ - id: target_skymodel
+ type: File?
'sbg:x': -1000
'sbg:y': 100
- - id: process_baselines_cal
+ - id: skymodel_source
type: string
'sbg:x': -1000
'sbg:y': 200
- - id: demix_timestep
- type: int
+ - id: do_smooth
+ type: boolean
'sbg:x': -1000
'sbg:y': 300
- - id: demix_freqstep
- type: int
+ - id: propagatesolutions
+ type: boolean
'sbg:x': -1000
'sbg:y': 400
- - id: demix_target
- type: string
+ - id: avg_timeresolution_concat
+ type: int
'sbg:x': -1000
'sbg:y': 500
- - id: demix_sources
- type: 'string[]'
- 'sbg:x': -1000
- 'sbg:y': 600
- - id: min_length
- type: int?
- 'sbg:x': -1000
- 'sbg:y': 700
- - id: overhead
- type: float?
- 'sbg:x': -1000
- 'sbg:y': 800
- - id: min_separation
- type: int?
- 'sbg:x': -1000
- 'sbg:y': 900
- - id: do_smooth
- type: boolean?
- default: false
- 'sbg:x': -1000
- 'sbg:y': 1000
- - id: max_separation_arcmin
- type: float?
- 'sbg:x': -1000
- 'sbg:y': 1100
- - id: calibrator_path_skymodel
- type: Directory?
- 'sbg:x': -1000
- 'sbg:y': 1200
- - id: A-Team_skymodel
- type: File?
- 'sbg:x': -1000
- 'sbg:y': 1300
- - id: elevation
+ - id: avg_freqresolution_concat
type: string
- default: 0deg..20deg
'sbg:x': -1000
- 'sbg:y': 1400
- - id: amplmin
- type: float
- default: 1.e-30
- 'sbg:x': -1000
- 'sbg:y': 1500
+ 'sbg:y': 600
outputs:
- - id: outh5parm
- outputSource:
- - h5parm_collector/outh5parm
- type: File
- 'sbg:x': 1000
- 'sbg:y': -500
- - id: check_Ateam_separation.png
- outputSource:
- - check_ateam_separation/output_imag
- type: File
- 'sbg:x': 1000
- 'sbg:y': -300
- id: msout
outputSource:
- - predict_calibrate/msout
+ - concat_calibrate/msout
type: 'Directory[]'
'sbg:x': 1000
'sbg:y': 0
- - id: parset
+ - id: outh5parm
outputSource:
- - ndppp_prep_cal/parset
- type: 'File[]'
+ - h5parm_collector/outh5parm
+ type: File
'sbg:x': 1000
'sbg:y': 200
- - id: calibrator_name
+ - id: bad_antennas
outputSource:
- - find_skymodel_cal/model_name
+ - identifybadantennas/filter_out
type: string
'sbg:x': 1000
'sbg:y': 400
@@ -145,224 +74,169 @@ outputs:
- h5parm_collector/log
type: File[]
'sbg:x': 1000
- 'sbg:y': 650
+ 'sbg:y': 600
- id: logfiles
- linkMerge: merge_flattened
outputSource:
+ - identifybadantennas/logfile
+ - sort_times_into_freqGroups/logfile
+ - find_skymodel_target/logfile
+ - make_sourcedb_target/log
- concat_logfiles_calib/output
- - concat_logfiles_predict/output
+ - concat_logfiles_dpppconcat/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': 1000
'sbg:y': 800
+
steps:
- - id: ndppp_prep_cal
+ - id: identifybadantennas
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: '*'
+ - id: filter
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: filter_out
- id: logfile
- - id: parset
- run: ../../subworkflow/ndppp_prep_cal.cwl
- label: ndppp_prep_cal
- scatter:
- - msin
- 'sbg:x': 0
- 'sbg:y': 0
- - id: predict_calibrate
+ run: ../../steps/identify_bad_antennas.cwl
+ label: identifybadantennas
+ 'sbg:x': -200
+ 'sbg:y': -300
+ - id: sort_times_into_freqGroups
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': 500
- 'sbg:y': 0
- - id: check_ateam_separation
- in:
- - id: ms
source:
- msin
- - id: min_separation
- source: min_separation
+ - 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: output_imag
+ - id: filenames
+ - id: groupnames
- id: logfile
- run: ../../lofar-cwl/steps/check_ateam_separation.cwl
- label: check_Ateam_separation
- 'sbg:x': 0
- 'sbg:y': -300
- - 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: find_skymodel_cal
+ 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: skymodels
- source: calibrator_path_skymodel
- - id: max_separation_arcmin
- source: max_separation_arcmin
+ - id: SkymodelPath
+ source: target_skymodel
+ - id: Radius
+ default: 5
+ - id: Source
+ source: skymodel_source
+ - id: DoDownload
+ source: use_target
out:
- - id: output_models
- - id: model_name
+ - id: skymodel
- id: logfile
- run: ../../steps/find_skymodel_cal.cwl
- label: find_skymodel_cal
- 'sbg:x': -500
- 'sbg:y': 500
- - id: make_sourcedb
+ 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_cal/output_models
- - id: output_file_name
- default: calibrator.sourcedb
+ source: find_skymodel_target/skymodel
+ - id: logname
+ default: make_sourcedb_target.log
out:
- id: sourcedb
- id: log
run: ../../lofar-cwl/steps/makesourcedb.cwl
- label: make_sourcedb
+ label: make_sourcedb_target
'sbg:x': 0
- 'sbg:y': 500
- - id: concat_logfiles_prep_cal
+ 'sbg:y': -500
+ - id: concat_logfiles_dpppconcat
in:
- id: file_list
- linkMerge: merge_flattened
- source: ndppp_prep_cal/logfile
+ source:
+ - concat_calibrate/dpppconcat.log
- id: file_prefix
- default: ndppp_prep_cal
+ default: dpppconcat
out:
- id: output
run: ../../steps/concatenate_files.cwl
- label: concat_logfiles_prep_cal
- 'sbg:x': 250
- 'sbg:y': 300
+ label: concat_logfiles_dpppconcat
+ 'sbg:x': 750
+ 'sbg:y': 100
- id: concat_logfiles_blsmooth
in:
- id: file_list
source:
- - predict_calibrate/BLsmooth.log
+ - concat_calibrate/BLsmooth.log
- id: file_prefix
- default: blsmooth_prep
+ default: blsmooth_target
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_blsmooth
'sbg:x': 750
'sbg:y': 300
- - id: concat_logfiles_predict
+ - id: concat_logfiles_calib
in:
- id: file_list
- linkMerge: merge_flattened
source:
- - predict_calibrate/predict_cal.log
+ - concat_calibrate/gaincal.log
- id: file_prefix
- default: predict_cal
+ default: gaincal
out:
- id: output
run: ../../steps/concatenate_files.cwl
- label: concat_logfiles_predict
+ label: concat_logfiles_calib
'sbg:x': 750
'sbg:y': 500
- - id: concat_logfiles_calib
+ - id: concat_calibrate
in:
- - id: file_list
+ - id: msin
source:
- - predict_calibrate/calib_cal.log
- - id: file_prefix
- default: calib_cal_prep
+ - msin
+ - id: group_id
+ source: sort_times_into_freqGroups/groupnames
+ - id: groups_specification
+ source: sort_times_into_freqGroups/filenames
+ - id: filter_baselines
+ source: identifybadantennas/filter_out
+ - id: skymodel
+ source: make_sourcedb_target/sourcedb
+ - 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
out:
- - id: output
- run: ../../steps/concatenate_files.cwl
- label: concat_logfiles_calib
- 'sbg:x': 750
- 'sbg:y': 800
+ - id: msout
+ - id: dpppconcat.log
+ - id: BLsmooth.log
+ - id: gaincal.log
+ - id: outh5parm
+ run: ../../subworkflow/concat_calibrate.cwl
+ label: concat_calibrate
+ scatter:
+ - group_id
+ 'sbg:x': 200
+ 'sbg:y': 0
- id: h5parm_collector
in:
- id: h5parmFiles
source:
- - predict_calibrate/outh5parm
+ - concat_calibrate/outh5parm
- id: squeeze
default: true
- id: verbose
diff --git a/workflows/prefactor_target/prep_gsmcal.cwl b/workflows/prefactor_target/prep_gsmcal.cwl
deleted file mode 100644
index 3faf8dbb4f11839314fe40720c4f8e39031317bb..0000000000000000000000000000000000000000
--- a/workflows/prefactor_target/prep_gsmcal.cwl
+++ /dev/null
@@ -1,381 +0,0 @@
-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': -900
- - id: filter_baselines
- type: string
- 'sbg:x': -1000
- 'sbg:y': -800
- - id: raw_data
- type: boolean
- 'sbg:x': -1000
- 'sbg:y': -700
- - id: propagatesolutions
- type: boolean
- 'sbg:x': -1000
- 'sbg:y': -600
- - id: flagunconverged
- type: boolean
- 'sbg:x': -1000
- 'sbg:y': -500
- - id: demix
- type: boolean
- 'sbg:x': -1000
- 'sbg:y': -400
- - id: max_dppp_threads
- type: int?
- default: 10
- 'sbg:x': -1000
- 'sbg:y': -300
- - id: memoryperc
- type: int
- 'sbg:x': -1000
- 'sbg:y': -200
- - id: flag_baselines
- type: 'string[]'
- 'sbg:x': -1000
- 'sbg:y': -100
- - id: avg_timeresolution
- type: float
- 'sbg:x': -1000
- 'sbg:y': 0
- - id: avg_freqresolution
- type: string
- 'sbg:x': -1000
- 'sbg:y': 100
- - id: process_baselines_cal
- type: string
- 'sbg:x': -1000
- 'sbg:y': 200
- - id: demix_timestep
- type: int
- 'sbg:x': -1000
- 'sbg:y': 300
- - id: demix_freqstep
- type: int
- 'sbg:x': -1000
- 'sbg:y': 400
- - id: demix_target
- type: string
- 'sbg:x': -1000
- 'sbg:y': 500
- - id: demix_sources
- type: 'string[]'
- 'sbg:x': -1000
- 'sbg:y': 600
- - id: min_length
- type: int?
- 'sbg:x': -1000
- 'sbg:y': 700
- - id: overhead
- type: float?
- 'sbg:x': -1000
- 'sbg:y': 800
- - id: min_separation
- type: int?
- 'sbg:x': -1000
- 'sbg:y': 900
- - id: do_smooth
- type: boolean?
- default: false
- 'sbg:x': -1000
- 'sbg:y': 1000
- - id: max_separation_arcmin
- type: float?
- 'sbg:x': -1000
- 'sbg:y': 1100
- - id: calibrator_path_skymodel
- type: Directory?
- 'sbg:x': -1000
- 'sbg:y': 1200
- - id: A-Team_skymodel
- type: File?
- 'sbg:x': -1000
- 'sbg:y': 1300
- - id: elevation
- type: string
- default: 0deg..20deg
- 'sbg:x': -1000
- 'sbg:y': 1400
- - id: amplmin
- type: float
- default: 1.e-30
- 'sbg:x': -1000
- 'sbg:y': 1500
-outputs:
- - id: outh5parm
- outputSource:
- - h5parm_collector/outh5parm
- type: File
- 'sbg:x': 1000
- 'sbg:y': -500
- - id: check_Ateam_separation.png
- outputSource:
- - check_ateam_separation/output_imag
- type: File
- 'sbg:x': 1000
- 'sbg:y': -300
- - id: msout
- outputSource:
- - predict_calibrate/msout
- type: 'Directory[]'
- 'sbg:x': 1000
- 'sbg:y': 0
- - id: parset
- outputSource:
- - ndppp_prep_cal/parset
- type: 'File[]'
- 'sbg:x': 1000
- 'sbg:y': 200
- - id: calibrator_name
- outputSource:
- - find_skymodel_cal/model_name
- type: string
- 'sbg:x': 1000
- 'sbg:y': 400
- - id: outh5parm_logfile
- outputSource:
- - h5parm_collector/log
- type: File[]
- 'sbg:x': 1000
- 'sbg:y': 650
- - id: logfiles
- linkMerge: merge_flattened
- 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[]'
- 'sbg:x': 1000
- 'sbg:y': 800
-steps:
- - 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': 0
- 'sbg:y': 0
- - 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': 500
- 'sbg:y': 0
- - 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': 0
- 'sbg:y': -300
- - 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: find_skymodel_cal
- in:
- - id: msin
- source:
- - msin
- - 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': -500
- 'sbg:y': 500
- - 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': 0
- 'sbg:y': 500
- - 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': 250
- 'sbg:y': 300
- - 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': 750
- 'sbg:y': 300
- - 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': 750
- 'sbg:y': 500
- - 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': 750
- 'sbg:y': 800
- - 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': 750
- 'sbg:y': -300
-requirements:
- - class: SubworkflowFeatureRequirement
- - class: ScatterFeatureRequirement