diff --git a/scripts/Ateamclipper.py b/scripts/Ateamclipper.py
index 2227f92d830057ebe047563a768b11316ff5f01f..c7ba705c22edb4bbcba09cf378837553aed4f452 100755
--- a/scripts/Ateamclipper.py
+++ b/scripts/Ateamclipper.py
@@ -63,4 +63,4 @@ t.putcol('FLAG', flag)
t.close()
freq_tab.close()
-os.system('echo ' + str(freq[0]) + ' ' + str(output_flags_xx - input_flags_xx) + ' ' + str(output_flags_yy - input_flags_yy) + ' >> Ateamclipper.txt')
+os.system('echo ' + str(freq[0]) + ' ' + str(output_flags_xx - input_flags_xx) + ' ' + str(output_flags_yy - input_flags_yy) + ' >> Ateamclipper.txt')
\ No newline at end of file
diff --git a/scripts/PipelineStep_makeLosotoParset.py b/scripts/PipelineStep_makeLosotoParset.py
index 58137e0492e82f79053c4b7d6d84c50b9e424c30..a40ad412d7aa9d962b65d1fc5f79be01047e4e13 100755
--- a/scripts/PipelineStep_makeLosotoParset.py
+++ b/scripts/PipelineStep_makeLosotoParset.py
@@ -40,6 +40,4 @@ def plugin_main(args, **kwargs):
parset_file.close()
return 0
- pass
-
-
+ pass
\ No newline at end of file
diff --git a/scripts/TargetListToCoords.py b/scripts/TargetListToCoords.py
index 46654e2b54c0d781a2135cf6831a3f5ba9111b3b..b71aa0fd733b85dd3697596f9c81edcc8170b551 100644
--- a/scripts/TargetListToCoords.py
+++ b/scripts/TargetListToCoords.py
@@ -1,14 +1,9 @@
-import os
-import numpy as np
-import pyrap.tables, math
-from astropy import units as u
-from astropy.coordinates import SkyCoord
from astropy.table import Table
def plugin_main(**kwargs):
"""
Takes in a catalogue with a target and returns appropriate coordinates
-
+
Parameters
----------
filename: str
@@ -20,23 +15,32 @@ def plugin_main(**kwargs):
-------
result : dict
Output coordinates
-
"""
+
# parse the input
target_file = kwargs['target_file']
-
+ mode = kwargs['mode']
+
# read in the catalogue to get source_id, RA, and DEC
t = Table.read(target_file, format='csv')
- RA_val = t['RA'].data[0]
- DEC_val = t['DEC'].data[0]
- Source_id = t['Source_id'].data[0]
- if str(Source_id)[0:1] == 'I':
- pass
- elif str(Source_id)[0:1] == 'S':
- pass
- else:
- Source_id = 'S' + str(Source_id)
+ RA_val = t['RA'].data
+ DEC_val = t['DEC'].data
+ Source_id = t['Source_id'].data
+ if mode: # == 'single':
+ RA_val = [RA_val[0]]
+ DEC_val = [DEC_val[0]]
+ Source_id = Source_id[:1]
+ if str(Source_id[0])[0:1] == 'I':
+ pass
+ elif str(Source_id[0])[0:1] == 'S':
+ pass
+ else:
+ Source_id = ['S' + str(x) for x in Source_id[0]]
+
# make a string of coordinates for the NDPPP command
- ss = '["' + str(RA_val) + 'deg","' + str(DEC_val) + 'deg"]'
- result = {'name' : Source_id, 'coords' : ss}
+ ss = [ '[' + str(x) + 'deg,' + str(y) + 'deg]' for x, y in zip(RA_val, DEC_val) ]
+
+ result = {'name' : ",".join(Source_id),
+ 'coords' : ss[0] if len(ss) == 1 else "[" + ",".join(ss) + "]"}
+
return result
diff --git a/scripts/check_Ateam_separation.py b/scripts/check_Ateam_separation.py
index d1549a8cd44bfbf8a38d007a1bb2a6eecadbc8e2..6e149f69bd36d4ade3f77ef2c4a5a0ec28438c50 100755
--- a/scripts/check_Ateam_separation.py
+++ b/scripts/check_Ateam_separation.py
@@ -175,5 +175,4 @@ if __name__ == '__main__':
args = parser.parse_args()
- main(args.MSfile, args.min_separation, args.outputimage)
-
+ main(args.MSfile, args.min_separation, args.outputimage)
\ No newline at end of file
diff --git a/scripts/generate_input.sh b/scripts/generate_input.sh
index 9e053603fb879ee0901e4c0a06a08ba40f99cc5d..9294e8d944fb8fdefe30b1342ecddb6c286157f0 100755
--- a/scripts/generate_input.sh
+++ b/scripts/generate_input.sh
@@ -88,4 +88,4 @@ EOF
# Close output file
exec 3>&-
-echo "Wrote output to '${YAML}'"
+echo "Wrote output to '${YAML}'"
\ No newline at end of file
diff --git a/scripts/make_summary.py b/scripts/make_summary.py
index 41a4d4a489b121400acb28d347f8c05fb90c7be3..2ca7ca3462857b33b978e19534e1cacc3708246c 100755
--- a/scripts/make_summary.py
+++ b/scripts/make_summary.py
@@ -247,4 +247,4 @@ if __name__=='__main__':
demix=args.demix, removed_bands=args.removed_bands,
min_unflagged=args.min_unflagged, refant=args.refant)
- sys.exit(0)
+ sys.exit(0)
\ No newline at end of file
diff --git a/steps/dp3_target_phaseup.cwl b/steps/dp3_target_phaseup.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..dfae68e24441a875562ce5d6ef0c6555acabe1b9
--- /dev/null
+++ b/steps/dp3_target_phaseup.cwl
@@ -0,0 +1,73 @@
+class: CommandLineTool
+cwlVersion: v1.2
+id: dp3_target_phaseup
+label: DP3 Target Phaseup
+doc: This tool applies the delay solutions to the target source and phase up to the various
+ target directions. It appends commands to a parset created in the previous step.
+
+
+baseCommand: DP3
+
+inputs:
+ - id: parset
+ type: File
+ doc: Input parset file.
+ default: dp3_explode.parset
+ inputBinding:
+ position: 0
+ - id: msin
+ type: Directory
+ doc: Input measurement set.
+ inputBinding:
+ position: 1
+ prefix: msin=
+ separate: false
+ shellQuote: false
+ - id: delay_solset
+ type: File
+ doc: Input delay solution set.
+ inputBinding:
+ position: 2
+ prefix: applycal.parmdb=
+ separate: false
+ shellQuote: false
+ - id: max_dp3_threads
+ type: int?
+ default: 8
+ doc: Maximum number of threads to use for DP3.
+ inputBinding:
+ position: 3
+ prefix: numthreads=
+ separate: false
+ shellQuote: false
+
+outputs:
+ - id: msout
+ type: Directory[]
+ outputBinding:
+ glob: "*.mstargetphaseup"
+ doc: Output measurement set which has been phaseshifted,
+ averaged and had solutions applied.
+ - id: logfile
+ type: File
+ outputBinding:
+ glob: dp3_target_phaseup.log
+ doc: DP3 processing log file.
+ - id: errorfile
+ type: File
+ outputBinding:
+ glob: dp3_target_phaseup_err.log
+ doc: DP3 processing error log file.
+
+
+
+hints:
+ - class: DockerRequirement
+ dockerPull: vlbi-cwl
+ - class: ResourceRequirement
+ coresMax: $(inputs.max_dp3_threads)
+ coresMin: 2
+
+
+stdout: dp3_target_phaseup.log
+stderr: dp3_target_phaseup_err.log
\ No newline at end of file
diff --git a/steps/flatten.cwl b/steps/flatten.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..e42538ee0f5889f1e443fdbe32107cba0e44af93
--- /dev/null
+++ b/steps/flatten.cwl
@@ -0,0 +1,31 @@
+cwlVersion: v1.2
+class: ExpressionTool
+id: flatten_array
+label: Flatten Array
+doc: "Flatten a nested array of 'Any' type into an array. Taken from https://github.com/common-workflow-library/cwl-patterns/tree/main"
+requirements:
+ InlineJavascriptRequirement: {}
+inputs:
+ nestedarray:
+ type:
+ type: array
+ items:
+ type: array
+ items: ["null", Any]
+outputs:
+ flattenedarray:
+ type:
+ type: array
+ items: Any
+expression: |
+ ${
+ var flattenedarray = [];
+ for (var i = 0; i < inputs.nestedarray.length; i++) {
+ for (var j = 0; j < inputs.nestedarray[i].length; j++) {
+ if (inputs.nestedarray[i][j] != null) {
+ flattenedarray.push(inputs.nestedarray[i][j]);
+ }
+ }
+ }
+ return {"flattenedarray": flattenedarray};
+ }
\ No newline at end of file
diff --git a/steps/generate_filenames.cwl b/steps/generate_filenames.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..fdf437118f871bbe81ed7b24f5b1dfc10f8deb38
--- /dev/null
+++ b/steps/generate_filenames.cwl
@@ -0,0 +1,45 @@
+cwlVersion: v1.2
+class: CommandLineTool
+id: generate_filenames
+label: Generate direction filenames
+doc: |
+ Take a MeasurementSet and a list of target sources, and
+ creates a list of strings where the MeasurementSet name
+ and target names are concatenated.
+
+baseCommand: [python3, concatenate.py]
+
+inputs:
+ - id: msin
+ type: Directory
+ doc: A MeasurementSet to extract the name from.
+
+ - id: source_ids
+ type: string
+ doc: A string containing a list of target source IDs.
+
+outputs:
+ - id: msout_names
+ type: string
+ doc: |
+ a string containing the names for the MeasurementSets
+ for each direction.
+ outputBinding:
+ loadContents: true
+ glob: out.json
+ outputEval: $(JSON.parse(self[0].contents).filenames)
+
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: concatenate.py
+ entry: |
+ import json
+
+ msin = "$(inputs.msin.basename)".split(".")[0]
+ source_ids = "$(inputs.source_ids)".split(",")
+ list = [ msin + x + ".mstargetphase" for x in source_ids]
+ result = {'filenames' : "[" + ",".join(list) + "]"}
+ with open('./out.json', 'w') as fp:
+ json.dump(result, fp)
diff --git a/steps/generate_parset_split.cwl b/steps/generate_parset_split.cwl
new file mode 100755
index 0000000000000000000000000000000000000000..63a15856a611af4fb89af40ae0bd2ce3a18d4abe
--- /dev/null
+++ b/steps/generate_parset_split.cwl
@@ -0,0 +1,82 @@
+cwlVersion: v1.2
+class: CommandLineTool
+id: generate_parset_split_directions
+label: Generate DP3 parset for split directions
+doc: |
+ Generates a DP3 parameterset to split off
+ directions from a given MeasurementSet.
+
+baseCommand: [cat, input.parset]
+
+stdout: dp3_explode.parset
+
+inputs:
+ - id: msout_names
+ type: string
+ doc: |
+ A string of names, one for each direction to image.
+
+ - id: phase_centers
+ type: string
+ doc: |
+ A string of pairs of right ascension and declination
+ coordinates, one for each direction to image.
+
+ - id: frequency_resolution
+ type: string?
+ default: '390.56kHz'
+ doc: |
+ Frequency resolution for the third averaging.
+
+ - id: time_resolution
+ type: string?
+ default: '32.'
+ doc: |
+ Time resolution in seconds for the third averaging.
+
+outputs:
+ - id: parset
+ type: File
+ doc: A DP3 parameterset file.
+ outputBinding:
+ glob: dp3_explode.parset
+
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: input.parset
+ entry: |+
+ steps = [split]
+
+ split.replaceparms = [phaseshift.phasecenter, applybeam.direction, msout.name]
+ split.steps = [phaseshift, averager1, applybeam, averager2, applycal, averager3, msout]
+
+ phaseshift.type = phaseshift
+ phaseshift.phasecenter = $(inputs.phase_centers)
+
+ averager1.type = averager
+ averager1.freqresolution = 48.82kHz
+ averager1.timeresolution = 4.
+
+ applybeam.type = applybeam
+ applybeam.direction = $(inputs.phase_centers)
+ applybeam.beammode = full
+
+ averager2.type = averager
+ averager2.freqresolution = 390.56kHz
+ averager2.timeresolution = 32
+
+ # Apply solutions and more average_target
+
+ applycal.type = applycal
+ applycal.correction = fulljones
+ applycal.soltab = [amplitude000, phase000]
+
+ averager3.type = averager
+ averager3.freqresolution = $(inputs.frequency_resolution)
+ averager3.timeresolution = $(inputs.time_resolution)
+
+ msout.storagemanager = dysco
+ msout.name = $(inputs.msout_names)
+ msout.overwrite = True
diff --git a/steps/order_by_direction.cwl b/steps/order_by_direction.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..08b2491865c0d97bbc83beba45695ada675f4e68
--- /dev/null
+++ b/steps/order_by_direction.cwl
@@ -0,0 +1,65 @@
+class: CommandLineTool
+cwlVersion: v1.1
+id: order_by_direction
+label: Order by Direction
+doc: |
+ This tool takes an array of arrays of directories containing MeasurementSet files which are in groups of frequency.
+ It re-orders them such that they are in groups of direction ready to be concatenated.
+
+baseCommand:
+ - python3
+ - order_by_direction.py
+
+inputs:
+ - id: msin
+ type:
+ type: array
+ items:
+ type: array
+ items: Directory
+ inputBinding:
+ position: 0
+ doc: Array of arrays of directories containing the MeasurementSet files to be ordered
+
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: order_by_direction.py
+ entry: |
+ import sys
+ import numpy as np
+ import json
+
+ mss = $(inputs)['msin']
+ print(mss)
+
+ #The line below does the re-ordering. It performs the transpose of a list.
+ output = list(map(list, zip(*mss)))
+
+ cwl_output = {}
+
+ cwl_output['msout'] = output
+
+ print(cwl_output)
+
+ with open('./out.json', 'w') as fp:
+ json.dump(cwl_output, fp)
+
+
+
+outputs:
+ - id: msout
+ type:
+ type: array
+ items:
+ type: array
+ items: Directory
+ outputBinding:
+ loadContents: true
+ glob: out.json
+ outputEval: $(JSON.parse(self[0].contents).msout)
+ doc: Array of arrays of directories containing the MeasurementSet
+ files ordered by direction.
+
+
diff --git a/steps/prep_delay.cwl b/steps/prep_delay.cwl
index da56b4bb92e3e4cdd7b7ad062a4ce776bdbe7563..9c18409818b9a690c3baf3eed77e7fc40205e497 100644
--- a/steps/prep_delay.cwl
+++ b/steps/prep_delay.cwl
@@ -11,6 +11,9 @@ inputs:
- id: delay_calibrator
type: File
doc: file containing target info.
+ - id: extract_single
+ type: boolean?
+ default: false
requirements:
- class: InlineJavascriptRequirement
@@ -25,8 +28,9 @@ requirements:
inputs = json.loads(r"""$(inputs)""")
target_file = inputs['delay_calibrator']['path']
+ mode = inputs['extract_single']
- output = targetListToCoords(target_file=target_file)
+ output = targetListToCoords(target_file=target_file, mode=mode)
coords = output['coords']
name = output['name']
diff --git a/steps/sort_concatmap.cwl b/steps/sort_concatmap.cwl
index 48f6f52ab08c9232a9362d583917e988353de8e7..cc9e2a7fb7e17fea01ce4da45f15f81a27ffe77d 100755
--- a/steps/sort_concatmap.cwl
+++ b/steps/sort_concatmap.cwl
@@ -1,7 +1,7 @@
class: CommandLineTool
cwlVersion: v1.2
id: sort_concatmap
-label: sort_concatmap
+label: Sort Concatmap
baseCommand:
- python3
@@ -50,6 +50,7 @@ requirements:
from sort_times_into_freqGroups import main as sort_times_into_freqGroups
mss = sys.argv[1:]
+
inputs = json.loads(r"""$(inputs)""")
numbands = inputs['numbands']
@@ -59,8 +60,10 @@ requirements:
truncateLastSBs = inputs['truncateLastSBs']
firstSB = inputs['firstSB']
- output = sort_times_into_freqGroups(mss, numbands, NDPPPfill, stepname, mergeLastGroup, truncateLastSBs, firstSB)
+ print(mss, numbands, NDPPPfill, stepname, mergeLastGroup, truncateLastSBs, firstSB)
+ output = sort_times_into_freqGroups(mss, numbands, NDPPPfill, stepname, mergeLastGroup, truncateLastSBs, firstSB)
+ print(output)
filenames = output['filenames']
groupnames = output['groupnames']
total_bandwidth = output['total_bandwidth']
diff --git a/steps/target_solve.cwl b/steps/target_solve.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..f1f16c55bf6706a1cb2cf91796e1e7450623c490
--- /dev/null
+++ b/steps/target_solve.cwl
@@ -0,0 +1,74 @@
+cwlVersion: v1.2
+class: CommandLineTool
+id: target_solve
+label: Target Solve
+doc: |
+ This tool performs selfcalibration on the target source.
+ It uses the facetselfcal.py script from the LOFAR helper scripts with the --auto setting.
+
+baseCommand:
+ - python3
+ - delay_solve.py
+
+inputs:
+ - id: msin
+ type: Directory
+ doc: Delay calibrator measurement set.
+ - id: configfile
+ type: File
+ doc: Configuration options for self-calibration.
+ - id: selfcal
+ type: Directory
+ doc: External self-calibration script.
+ - id: h5merger
+ type: Directory
+ doc: External LOFAR helper scripts for merging h5 files.
+
+outputs:
+ - id: images
+ type: File[]
+ outputBinding:
+ glob: '*.png'
+ - id: fits_images
+ type: File[]
+ outputBinding:
+ glob: '*MFS-image.fits'
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: target_solve*.log
+
+requirements:
+ - class: ShellCommandRequirement
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.configfile)
+ - entry: $(inputs.msin)
+ - entry: $(inputs.h5merger)
+ - entryname: delay_solve.py
+ entry: |
+ import subprocess
+ import sys
+ import json
+
+ inputs = json.loads(r"""$(inputs)""")
+
+ msin = inputs['msin']['basename']
+ configfile = inputs['configfile']['path']
+ selfcal = inputs['selfcal']['path']
+ h5merge = inputs['h5merger']['path']
+
+ imagename = msin.split('.copy')[0]
+
+ subprocess.run(f'python3 {selfcal}/facetselfcal.py {msin} --helperscriptspath {selfcal}
+ --helperscriptspathh5merge {h5merge} --weightspectrum-clipvalue 30.0 --auto --imagename {imagename}', shell = True)
+
+hints:
+ - class: DockerRequirement
+ dockerPull: vlbi-cwl
+ - class: ResourceRequirement
+ coresMin: 6
+
+stdout: target_solve.log
+stderr: target_solve_err.log
diff --git a/target_selfcal_config.txt b/target_selfcal_config.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef0e1c7ccd9de55e6205897edd9af827dc5a94d6
--- /dev/null
+++ b/target_selfcal_config.txt
@@ -0,0 +1,3 @@
+imsize = 1600
+pixelscale = 0.075
+auto = True
\ No newline at end of file
diff --git a/workflows/phaseup-concat.cwl b/workflows/phaseup-concat.cwl
index 6c7b5c7254ea9f63049d02655c19be39af52439c..eb45b9a8f5f258079ea74f986547d0244e0ba3ba 100644
--- a/workflows/phaseup-concat.cwl
+++ b/workflows/phaseup-concat.cwl
@@ -72,6 +72,8 @@ steps:
in:
- id: delay_calibrator
source: delay_calibrator
+ - id: extract_single
+ default: true
out:
- id: source_id
- id: coordinates
diff --git a/workflows/split-directions.cwl b/workflows/split-directions.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..55fff245506eebb3688debf99290fabdfdfc12bd
--- /dev/null
+++ b/workflows/split-directions.cwl
@@ -0,0 +1,194 @@
+class: Workflow
+cwlVersion: v1.2
+id: split-directions
+label: Split Directions
+doc: |
+ This is a workflow for the LOFAR-VLBI pipeline that
+ splits a LOFAR MeasurementSet into various target directions, applies delay calibrator solutions and then optionally performs
+ self-calibration on the target directions.
+
+ This step should be run after the delay calibration workflow.
+
+
+requirements:
+ - class: SubworkflowFeatureRequirement
+ - class: MultipleInputFeatureRequirement
+ - class: ScatterFeatureRequirement
+
+inputs:
+ - id: msin
+ type: Directory[]
+ doc: The input MS. This should have coverage of the target directions.
+ - id: delay_solset
+ type: File
+ doc: The solution tables generated by the VLBI delay calibration workflow in an HDF5 format.
+ - id: image_cat
+ type: File
+ doc: The image catalogue (in CSV format) containing the target directions.
+ default: lotss_catalogue.csv
+ - id: max_dp3_threads
+ type: int?
+ default: 4
+ doc: Number of cores to use per job for
+ tasks with high I/O or memory.
+ - id: numbands
+ type: int?
+ default: -1
+ doc: The number of bands to group. -1 means all bands.
+ - id: do_flagging
+ type: boolean?
+ default: false
+ doc: Whether to flag the data before splitting.
+ - id: truncateLastSBs
+ type: boolean?
+ default: true
+ doc: Whether to truncate the last subbands of the
+ MSs to the same length.
+ - id: do_selfcal
+ type: boolean?
+ default: false
+ doc: Whether to do selfcal on the direction concat MSs.
+ - id: configfile
+ type: File
+ doc: The configuration file to be used to run
+ facetselfcal.py during the target_solve step.
+ - id: h5merger
+ type: Directory
+ doc: The h5merger directory.
+ - id: selfcal
+ type: Directory
+ doc: The selfcal directory.
+
+
+steps:
+ - id: target_phaseup
+ label: Target Phaseup
+ in:
+ - id: msin
+ source: msin
+ - id: image_cat
+ source: image_cat
+ out:
+ - id: parset
+ run: ./subworkflows/split_parset.cwl
+ scatter: msin
+
+ - id: dp3_target_phaseup
+ label: DP3 Target Phaseup
+ in:
+ - id: msin
+ source: msin
+ - id: parset
+ source: target_phaseup/parset
+ linkMerge: merge_flattened
+ - id: delay_solset
+ source: delay_solset
+ - id: max_dp3_threads
+ source: max_dp3_threads
+ out:
+ - id: msout
+ run: ../steps/dp3_target_phaseup.cwl
+ scatter: [msin, parset]
+ scatterMethod: dotproduct
+
+ - id: order_by_direction
+ label: Order by Direction
+ in:
+ - id: msin
+ source: dp3_target_phaseup/msout
+ out:
+ - id: msout
+ run: ../steps/order_by_direction.cwl
+
+ - id: sort_concatmap
+ label: Sort Concatmap
+ in:
+ - id: msin
+ source: order_by_direction/msout
+ - id: numbands
+ source: numbands
+ - id: truncateLastSBs
+ source: truncateLastSBs
+ out:
+ - id: filenames
+ - id: groupnames
+ run: ../steps/sort_concatmap.cwl
+ scatter: msin
+
+ - id: flatten_groupnames
+ label: Flatten Groupnames
+ in:
+ - id: nestedarray
+ source: sort_concatmap/groupnames
+ out:
+ - id: flattenedarray
+ run: ../steps/flatten.cwl
+
+
+ - id: concatenation
+ label: concatenation
+ in:
+ - id: msin
+ source: order_by_direction/msout
+ - id: groups_specification
+ source: sort_concatmap/filenames
+ - id: group_id
+ source: flatten_groupnames/flattenedarray
+ - id: do_flagging
+ source: do_flagging
+ out:
+ - id: msout
+ run: ./subworkflows/concatenation.cwl
+ scatter: [msin, groups_specification, group_id]
+ scatterMethod: dotproduct
+
+
+ - id: target_selfcal
+ label: Target Selfcal
+ in:
+ - id: msin
+ source: concatenation/msout
+ - id: configfile
+ source: configfile
+ - id: h5merger
+ source: h5merger
+ - id: selfcal
+ source: selfcal
+ - id: do_selfcal
+ source: do_selfcal
+ out:
+ - id: images
+ - id: fits_images
+ when: $(inputs.do_selfcal)
+ run: ../steps/target_solve.cwl
+ scatter: msin
+
+outputs:
+ - id: msout_phaseup
+ type:
+ type: array
+ items:
+ type: array
+ items: Directory
+ outputSource: dp3_target_phaseup/msout
+ - id: msout_concat
+ type: Directory[]
+ outputSource: concatenation/msout
+ - id: images
+ type:
+ type: array
+ items:
+ type: array
+ items: File
+ outputSource:
+ - target_selfcal/images
+ pickValue: all_non_null
+ - id: fits_images
+ type:
+ type: array
+ items:
+ type: array
+ items: File
+ outputSource:
+ - target_selfcal/fits_images
+ pickValue: all_non_null
diff --git a/workflows/subworkflows/split_parset.cwl b/workflows/subworkflows/split_parset.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..d0d3df30ca09f52a87cb291a670e3ac08d6887fc
--- /dev/null
+++ b/workflows/subworkflows/split_parset.cwl
@@ -0,0 +1,65 @@
+cwlVersion: v1.2
+class: Workflow
+id: split_parset
+label: Create parset split directions
+doc: |
+ This workflow does the following:
+
+ * It creates a list of target direction coordinates (RA, Dec).
+ * For each direction it creates a name for the MeasurementSet
+ * It creates a parameter set file for DP3 to phase shift the
+ target data to each direction, and to store that phase-shifted
+ data in a MeasurementSet with the name generated before.
+
+ The output is a DP3 parameter set file.
+
+inputs:
+ - id: msin
+ type: Directory
+ doc: The input data in MeasurementSet format.
+
+ - id: image_cat
+ type: File
+ doc: |
+ The image catalogue in CSV format,
+ containing the target directions.
+
+outputs:
+ - id: parset
+ type: File
+ doc: The parameterset file for DP3.
+ outputSource: generate_parset/parset
+
+steps:
+ - id: get_coordinates
+ label: Get target ID and coordinates
+ in:
+ - id: delay_calibrator
+ source: image_cat
+ out:
+ - id: source_id
+ - id: coordinates
+ - id: logfile
+ run: ../../steps/prep_delay.cwl
+
+ - id: generate_filenames
+ label: Generate MeasurementSet output names
+ in:
+ - id: msin
+ source: msin
+ - id: source_ids
+ source: get_coordinates/source_id
+ out:
+ - id: msout_names
+ run: ../../steps/generate_filenames.cwl
+
+ - id: generate_parset
+ label: Generate direction parset.
+ in:
+ - id: msout_names
+ source: generate_filenames/msout_names
+ - id: phase_centers
+ source: get_coordinates/coordinates
+ out:
+ - id: parset
+ run: ../../steps/generate_parset_split.cwl