@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix rdf: .
@prefix ScatterMethod: .
@prefix Dirent: .
@prefix cwl: .
@prefix ResourceRequirement: .
a cwl:CommandLineTool ;
rdfs:comment "This step splits a multi-facet region file into individual facet region files." ;
rdfs:label "Split Polygon Facets" ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( "$(inputs.lofar_helpers.path)/ds9_helpers/split_polygon_facets.py" "--extra_boundary=0.0" ) ;
cwl:baseCommand ( "python3" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "vlbi-cwl"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1
] ;
cwl:inputs , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "$(inputs.h5parm)" ] ;
cwl:listing [ cwl:entry "$(inputs.facet_regions)" ]
] ;
cwl:stderr "split_polygons_err.log" ;
cwl:stdout "split_polygons.log" .
a cwl:Workflow ;
rdfs:comment "Use WSClean to predict and subtract model data, to split all facets into separate MeasurementSets." ;
rdfs:label "Facet subtraction" ;
ns1:original_cwlVersion "v1.2" ;
Workflow:steps , , , , , , ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , , , , , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] .
rdfs:comment "Directory containing 1.2\" (or optionally other resolution) model images." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--model_image_folder"
] ;
sld:type cwl:Directory .
a cwl:CommandLineTool ;
rdfs:comment "Generates DS9 facet layout for direction-dependent facet imaging." ;
rdfs:label "DS9 Facet Generator" ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( "$( inputs.facetselfcal.path + '/submods/ds9facetgenerator.py' )" ) ;
cwl:baseCommand ( "python3" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "vlbi-cwl"
] ;
cwl:inputs , , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "$(inputs.msin)" ] ;
cwl:listing [ cwl:entry "$(inputs.h5parm)" ]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stderr "get_facet_layout_err.log" ;
cwl:stdout "get_facet_layout.log" .
cwl:source .
cwl:source .
cwl:source .
cwl:source .
rdfs:comment "Number of cores to use during the subtract." ;
sld:default 16 ;
sld:type xsd:int , sld:null .
rdfs:comment "facetselfcal directory." ;
sld:type cwl:Directory .
rdfs:label "Predict a polygon back in empty MS" ;
cwl:in , , , , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:flat_crossproduct .
rdfs:comment "Folder with 1.2\" model images." ;
sld:type cwl:Directory .
a cwl:CommandLineTool ;
rdfs:comment "Generate direction concatenation parsets\n" ;
rdfs:label "Make concat parsets" ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( "$( inputs.lofar_helpers.path + '/ms_helpers/concat_with_dummies.py' )" "--make_only_parset" "--only_basename" ) ;
cwl:baseCommand ( "python3" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "vlbi-cwl"
] ;
cwl:inputs , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ Dirent:writable false ;
cwl:entry "$(inputs.msin)"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stderr "python_concat_err.log" ;
cwl:stdout "python_concat.log" .
rdfs:label "Make concat parsets" ;
cwl:in , , ;
cwl:out ;
cwl:run .
rdfs:label "Run DP3 parsets" ;
cwl:in , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) .
rdfs:label "Subtract complete FoV" ;
cwl:in , , , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) .
rdfs:comment "Log files from current step." ;
cwl:outputBinding [ CommandOutputBinding:glob
"predict_facet*.log" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:comment "This step uses WSClean to subtract visibilities corresponding to model images." ;
rdfs:label "Subtract with WSClean" ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( "$( inputs.lofar_helpers.path + '/subtract/subtract_with_wsclean.py' )" ) ;
cwl:baseCommand ( "python3" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "vlbi-cwl"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(inputs.ncpu)"
] ;
cwl:inputs , , , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "${\n // Set 'writable' on the \"msin\" entry only if copy_to_local_scratch is true.\n let stagedListing = [\n { entry: inputs.msin },\n { entry: inputs.model_image_folder },\n { entry: inputs.facet_regions },\n { entry: inputs.h5parm }\n ];\n if (!inputs.copy_to_local_scratch) {\n stagedListing[0].writable = true;\n }\n return stagedListing;\n}\n"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stderr "subtract_fov_err.log" ;
cwl:stdout "subtract_fov.log" .
rdfs:comment "MeasurementSet" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--ms"
] ;
sld:type cwl:Directory .
rdfs:comment "Log files from current step." ;
cwl:outputBinding [ CommandOutputBinding:glob
"split_polygons*.log" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:comment "Uses WSClean to predict sources within a facet and adds the predicted visibilities to the input data." ;
rdfs:label "Predict with WSClean" ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( "$( inputs.lofar_helpers.path + '/subtract/subtract_with_wsclean.py' )" "--applybeam" "--applycal" "--forwidefield" "--inverse" "--speedup_facet_subtract" "--cleanup_input_ms" ) ;
cwl:baseCommand ( "python3" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "vlbi-cwl"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(inputs.ncpu)"
] ;
cwl:inputs , , , , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "${\n // Set 'writable' on the \"subtracted_ms\" entry only if copy_to_local_scratch is true.\n let stagedListing = [\n { entry: inputs.subtracted_ms },\n { entry: inputs.model_image_folder },\n { entry: inputs.polygon_region },\n { entry: inputs.h5parm },\n { entry: inputs.polygon_info }\n ];\n if (!inputs.copy_to_local_scratch) {\n stagedListing[0].writable = true;\n }\n return stagedListing;\n}\n"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stderr "predict_facet_err.log" ;
cwl:stdout "predict_facet.log" .
rdfs:comment "Merged h5parms" ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:comment "Run DP3 with a parset" ;
rdfs:label "DP3 with parset" ;
ns1:original_cwlVersion "v1.2" ;
cwl:baseCommand ( "DP3" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "vlbi-cwl"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 6
] ;
cwl:inputs , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "$(inputs.msin)" ]
] ;
cwl:stderr "dp3_parset_err.log" ;
cwl:stdout "dp3_parset.log" .
cwl:source .
cwl:source ;
cwl:valueFrom "$(self[0])" .
rdfs:comment "The facet regions." ;
cwl:outputBinding [ CommandOutputBinding:glob
"poly*.reg" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "Number of cores to use during predict and subtract." ;
sld:default 16 ;
sld:type xsd:int , sld:null .
cwl:source .
rdfs:comment "The HDF5 solution file containing the solutions for prediction." ;
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "--h5parm_predict"
] ;
sld:type cwl:File .
rdfs:comment "Multi-directional HDF5 file." ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--h5"
] ;
sld:type cwl:File .
rdfs:comment "Number of bits per float used for columns containing visibilities." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--bitrate" ;
CommandLineBinding:separate true
] ;
sld:default 8 ;
sld:type xsd:int , sld:null .
cwl:source .
cwl:source .
cwl:source .
rdfs:comment "The lofar_helpers directory." ;
sld:type cwl:Directory .
rdfs:comment "MeasurementSet after predicting back facet model visibilities" ;
cwl:outputBinding [ CommandOutputBinding:glob
"facet*.ms" ] ;
sld:type cwl:Directory .
rdfs:label "Get DS9 facet layout" ;
cwl:in , , ;
cwl:out ;
cwl:run .
rdfs:comment "The output DS9 region file." ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.regionfile)" ] ;
sld:type cwl:File .
rdfs:comment "Specific option for using --bypass-file-store on the Spider cluster to run predict and subtract on local scratch." ;
sld:default false ;
sld:type xsd:boolean , sld:null .
rdfs:comment "DS9 region file with facets for prediction." ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--region"
] ;
sld:type cwl:File .
rdfs:comment "Name of the output DS9 region file." ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--DS9regionout"
] ;
sld:default "facets.reg" ;
sld:type xsd:string .
rdfs:comment "Input data in MeasurementSet format." ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--mslist"
] ;
sld:type cwl:Directory .
cwl:source .
cwl:outputSource , ;
cwl:pickValue "first_non_null" ;
sld:type [ sld:items cwl:Directory ;
sld:type sld:array
] .
cwl:source .
rdfs:comment "MeasurementSet for source subtraction." ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--mslist"
] ;
sld:type cwl:Directory .
cwl:source .
rdfs:comment "Multi-directional HDF5 file." ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--h5"
] ;
sld:type cwl:File .
cwl:source .
rdfs:comment "MS subtracted data" ;
cwl:outputBinding [ CommandOutputBinding:glob
"subfov_*.ms" ] ;
sld:type cwl:Directory .
rdfs:comment "The DS9 region file that defines the facets." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--reg"
] ;
sld:type cwl:File .
rdfs:comment "The files containing the stdout\nand stderr from the step.\n" ;
cwl:outputBinding [ CommandOutputBinding:glob
"dp3_parset*.log" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "Output measurement set" ;
cwl:outputBinding [ CommandOutputBinding:glob
"*.concat.ms" ] ;
sld:type cwl:Directory .
rdfs:comment "The output data with corrected\ndata in MeasurementSet format.\n" ;
cwl:outputBinding [ CommandOutputBinding:glob
"*.parset" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
a cwl:CommandLineTool ;
rdfs:comment "Gather the correct WSClean model images from model_image_folder" ;
ns1:original_cwlVersion "v1.2" ;
cwl:baseCommand ( "gather_model_images.sh" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "vlbi-cwl"
] ;
cwl:inputs ;
cwl:outputs .
cwl:source .
cwl:source .
rdfs:comment "Unaveraged MeasurementSets with coverage of the target directions." ;
sld:type [ sld:items cwl:Directory ;
sld:type sld:array
] .
rdfs:comment "Parset for DP3" ;
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:type cwl:File .
rdfs:comment "LOFAR helpers directory." ;
sld:type cwl:Directory .
rdfs:comment "The files containing the stdout\nand stderr from the step.\n" ;
cwl:outputBinding [ CommandOutputBinding:glob
"python_concat*.log" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "CSV file with polygon information (RA/DEC of calibrator and facet centers and averaging factor)" ;
sld:type cwl:File .
rdfs:comment "input MS" ;
sld:type [ sld:items cwl:Directory ;
sld:type sld:array
] .
cwl:source .
rdfs:comment "log files from get_facet_layout" ;
cwl:outputBinding [ CommandOutputBinding:glob
"get_facet_layout*.log" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
rdfs:comment "LOFAR helpers directory." ;
sld:type cwl:Directory .
cwl:source .
rdfs:comment "Polygon CSV file." ;
cwl:outputBinding [ CommandOutputBinding:glob
"*.csv" ] ;
sld:type cwl:File .
rdfs:comment "Pixel scale in arcseconds per pixel." ;
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "--pixelscale"
] ;
sld:default 4e-01 ;
sld:type xsd:float .
rdfs:comment "Specific option for using --bypass-file-store on the Spider cluster to run predict and subtract on local scratch." ;
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "--copy_to_local_scratch" ;
CommandLineBinding:separate false
] ;
sld:default false ;
sld:type xsd:boolean , sld:null .
rdfs:label "Get WSClean model images" ;
cwl:in ;
cwl:out ;
cwl:run .
rdfs:comment "Input data in MeasurementSet format." ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--msin" ;
CommandLineBinding:separate true
] ;
sld:type [ sld:items cwl:Directory ;
sld:type sld:array
] .
rdfs:comment "Log files from current step." ;
cwl:outputBinding [ CommandOutputBinding:glob
"subtract_fov*.log" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
rdfs:comment "Directory with model images" ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:Directory .
rdfs:comment "Number of bits per float used for columns containing visibilities." ;
sld:default 8 ;
sld:type xsd:int , sld:null .
rdfs:label "Split polygon file" ;
cwl:in , , ;
cwl:out , ;
cwl:run .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
rdfs:comment "Folder containing 1.2\" model images." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--model_image_folder"
] ;
sld:type cwl:Directory .
cwl:source .
cwl:source .
rdfs:comment "The DS9 region file that defines the facets for prediction." ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--facets_predict"
] ;
sld:type cwl:File .
rdfs:comment "HDF5 file containing the solutions for prediction." ;
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "--h5parm_predict"
] ;
sld:type cwl:File .
rdfs:comment "Path to lofar_helpers directory." ;
sld:type cwl:Directory .
rdfs:comment "Specific option for using --bypass-file-store on the Spider cluster to run predict and subtract on local scratch." ;
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "--copy_to_local_scratch" ;
CommandLineBinding:separate false
] ;
sld:default false ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Number of cores to use during the subtract." ;
sld:default 16 ;
sld:type xsd:int , sld:null .
cwl:source .
rdfs:comment "Image size in pixels (larger than image fov to help wsclean 1.2\" imaging at boundaries)." ;
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "--imsize"
] ;
sld:default 25000 ;
sld:type xsd:int .
rdfs:comment "Directory with filtered WSClean model images" ;
cwl:outputBinding [ CommandOutputBinding:glob
"output_images" ] ;
sld:type cwl:Directory .
rdfs:comment "LOFAR helpers directory." ;
sld:type cwl:Directory .
rdfs:comment "facetselfcal directory." ;
sld:type cwl:Directory .