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Commit 86c94e94 authored by alex's avatar alex
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finish bandpass step

parent 148cb0a6
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2 merge requests!69Change the name of the pre-calibrated output MS,!20Merge request HBA_calibrator to master
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......@@ -45,29 +45,30 @@ inputs:
inputBinding:
prefix: msout.storagemanager=
- id: updateweights
type: boolean?
type: string?
inputBinding:
position: 0
prefix: -applybeam.updateweights=
prefix: applybeam.updateweights=
separate: false
- id: beammode
- id: usechannelfreq
type: string?
inputBinding:
position: 0
prefix: -applybeam.beammode=
prefix: applybeam.usechannelfreq=
separate: false
- id: usechannelfreq
type: boolean?
- id: invert
type: string?
inputBinding:
position: 0
prefix: -applybeam.usechannelfreq=
prefix: applybeam.invert=
separate: false
- id: invert
type: boolean?
- id: beammode
type: string?
inputBinding:
position: 0
prefix: -applybeam.invert=
prefix: applybeam.beammode=
separate: false
outputs:
- id: msout
doc: Output Measurement Set
......
......@@ -54,10 +54,10 @@ inputs:
inputBinding:
prefix: msout.storagemanager=
- id: updateweights
type: boolean?
type: string?
inputBinding:
position: 0
prefix: -applycal.updateweights=
prefix: applycal.updateweights=
separate: false
outputs:
- id: msout
......
File mode changed from 100755 to 100644
......@@ -2,7 +2,7 @@ class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: bulk_rename
id: concatfiles
baseCommand:
- bash
- bulk_rename.sh
......@@ -21,7 +21,7 @@ outputs:
type: File
outputBinding:
glob: "$(inputs.file_prefix).$(inputs.file_suffix)"
label: bulk_rename
label: concatfiles
requirements:
- class: InitialWorkDirRequirement
listing:
......
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: h5parm_pointingname
baseCommand:
- python3
- /usr/local/bin/h5parm_pointingname.py
inputs:
- id: h5parm
type: File
inputBinding:
position: 1
doc: H5parm whose pointing direction should be corrected the solutions should be transferred.
- id: solsetName
type: string?
inputBinding:
position: 0
prefix: '--solsetName'
doc: Name of the input h5parm solution set
- id: pointing
type: string?
inputBinding:
position: 0
prefix: '--pointing'
doc: Name of the output h5parm solution set
outputs:
- id: outh5parm
type: File
outputBinding:
glob: $(inputs.h5parm.basename)
- id: log
type: File[]
outputBinding:
glob: 'h5parm_name*.log'
stdout: h5parm_name.log
stderr: h5parm_name_err.log
label: h5parm_pointingname
hints:
- class: DockerRequirement
dockerPull: 'lofareosc/prefactor:HBAcalibrator'
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.h5parm)
writable: true
\ No newline at end of file
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: transfer_solutions
baseCommand:
- python3
- /usr/local/bin/transfer_solutions.py
inputs:
- default: output.h5
id: h5parm
type: File
inputBinding:
position: 1
doc: H5parm to which the solutions should be transferred.
- id: refh5parm
type:
- File?
- string?
default: '/data/solutions/3C48.h5'
inputBinding:
position: 0
prefix: '--refh5parm'
doc: Name of the h5parm from which the solutions should be transferred.
- id: insolset
type: string?
inputBinding:
position: 0
prefix: '--insolset'
doc: Name of the input h5parm solution set
- id: outsolset
type: string?
inputBinding:
position: 0
prefix: '--outsolset'
doc: Name of the output h5parm solution set
- id: insoltab
type: string?
inputBinding:
position: 0
prefix: '--insoltab'
doc: Name of the input h5parm solution set
- id: outsoltab
type: string?
inputBinding:
position: 0
prefix: '--outsoltab'
doc: Name of the output h5parm solution set
- id: antenna
type: string?
inputBinding:
position: 0
prefix: '--antenna'
doc: Regular expression of antenna solutions to be transferred
- id: parset
type: File?
inputBinding:
position: 0
prefix: '--parset'
doc: Parset for plotting diagnostic plots after transfer with LoSoTo
outputs:
- id: outh5parm
type: File
outputBinding:
glob: $(inputs.h5parm.basename)
- id: log
type: File[]
outputBinding:
glob: 'transfer_solutions*.log'
- id: plots
type: File[]
outputBinding:
glob: "*.png"
stdout: transfer_solutions.log
stderr: transfer_solutions_err.log
label: transfer_solutions
hints:
- class: DockerRequirement
dockerPull: 'lofareosc/prefactor:HBAcalibrator'
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.h5parm)
writable: true
......@@ -95,7 +95,7 @@ steps:
- id: msin_datacolumn
default: CORRECTED_DATA
- id: updateweights
default: true
default: 'True'
- id: parmdb
source: input_h5parm
- id: msout_datacolumn
......@@ -116,13 +116,13 @@ steps:
- id: msout_datacolumn
default: CORRECTED_DATA
- id: updateweights
default: true
default: 'true'
- id: invert
default: true
default: 'true'
- id: beammode
default: element
- id: usechannelfreq
default: false
default: 'false'
- id: msin
source: applyBP/msout
- id: type
......
......@@ -89,13 +89,13 @@ steps:
- id: msout_datacolumn
default: CORRECTED_DATA
- id: updateweights
default: true
default: 'true'
- id: invert
default: true
default: 'true'
- id: beammode
default: element
- id: usechannelfreq
default: false
default: 'false'
- id: msin
source: applyPA/msout
- id: type
......
......@@ -45,7 +45,7 @@ inputs:
'sbg:x': -1000
'sbg:y': -1000
- id: ampRange
type: 'int[]?'
type: 'float[]?'
default:
- 0
- 0
......@@ -77,8 +77,7 @@ inputs:
'sbg:x': -1000
'sbg:y': -400
- id: solutions2transfer
type: string?
default: /data/solutions/3C48.h5
type: File?
'sbg:x': -1000
'sbg:y': -300
- id: antennas2transfer
......
......@@ -45,7 +45,7 @@ inputs:
'sbg:x': -1000
'sbg:y': -1000
- id: ampRange
type: 'int[]?'
type: 'float[]?'
default:
- 0
- 0
......@@ -77,8 +77,7 @@ inputs:
'sbg:x': -1000
'sbg:y': -400
- id: solutions2transfer
type: string?
default: /data/solutions/3C48.h5
type: File?
'sbg:x': -1000
'sbg:y': -300
- id: antennas2transfer
......@@ -289,6 +288,7 @@ steps:
- id: check_Ateam_separation.png
- id: msout
- id: parset
- id: calibrator_name
run: ./prefactor_calibrator/prep.cwl
label: prep
'sbg:x': 0
......@@ -386,6 +386,12 @@ steps:
source: do_smooth
- id: insolutions
source: fr/outsolutions
- id: solutions2transfer
source: solutions2transfer
- id: antennas2transfer
source: antennas2transfer
- id: calibrator_name
source: prep/calibrator_name
out:
- id: msout
- id: outsolutions
......
......@@ -5,6 +5,10 @@ label: BP
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: calibrator_name
type: string
'sbg:x': -1000
'sbg:y': -700
- id: ampRange
type: 'float[]?'
'sbg:x': -1000
......@@ -43,8 +47,12 @@ inputs:
type: File
'sbg:x': -1000
'sbg:y': 200
- id: solutions2transfer
type: File?
'sbg:x': -1000
'sbg:y': 300
- id: inh5parm_logfile
type: File
type: File[]
'sbg:x': -1000
'sbg:y': 400
- id: do_smooth
......@@ -56,6 +64,10 @@ inputs:
type: File
'sbg:x': -1000
'sbg:y': 600
- id: antennas2transfer
type: string?
'sbg:x': -1000
'sbg:y': 700
outputs:
- id: outh5parm
outputSource:
......@@ -76,13 +88,14 @@ outputs:
- losoto_plot_B1/output_plots
- losoto_plot_B2/output_plots
- losoto_plot_B3/output_plots
type: 'File[]'
- transfer_solutions/plots
type: 'File[]?'
linkMerge: merge_flattened
'sbg:x': 1000
'sbg:y': 0
- id: outsolutions
outputSource:
- write_solutions/outh5parm
- transfer_solutions/outh5parm
type: File
'sbg:x': 1000
'sbg:y': 100
......@@ -101,7 +114,7 @@ outputs:
- id: outh5parm_logfile
outputSource:
- h5parm_collector/log
type: File
type: File[]
'sbg:x': 1000
'sbg:y': 300
steps:
......@@ -147,7 +160,7 @@ steps:
- id: logfile
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_A1
'sbg:x': 0
'sbg:x': -200
'sbg:y': -200
- id: losoto_plot_A2
in:
......@@ -170,7 +183,7 @@ steps:
- id: logfile
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_A2
'sbg:x': 0
'sbg:x': -200
'sbg:y': -100
- id: losoto_plot_B1
in:
......@@ -193,7 +206,7 @@ steps:
- id: logfile
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_B1
'sbg:x': 0
'sbg:x': -200
'sbg:y': 0
- id: losoto_plot_B2
in:
......@@ -222,7 +235,7 @@ steps:
- id: logfile
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_B2
'sbg:x': 0
'sbg:x': -200
'sbg:y': 100
- id: losoto_plot_B3
in:
......@@ -249,8 +262,84 @@ steps:
- id: logfile
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_B3
'sbg:x': 0
'sbg:x': -200
'sbg:y': 200
- id: losoto_plot_B1_trans
in:
- id: input_h5parm
source: bandpass/output_h5parm
- id: soltab
default: sol000/bandpass
- id: axesInPlot
default:
- time
- freq
- id: axisInTable
default: ant
- id: plotFlag
default: true
- id: prefix
default: bandpass_transfer_
out:
- id: parset
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_B1_trans
'sbg:x': -200
'sbg:y': 300
- id: losoto_plot_B2_trans
in:
- id: input_h5parm
source: bandpass/output_h5parm
- id: soltab
default: sol000/bandpass
- id: axesInPlot
default:
- freq
- id: axisInTable
default: ant
- id: axisInCol
default: pol
- id: plotFlag
default: true
- id: time.minmaxstep
default:
- 0
- 1e20
- 500000
- id: prefix
default: bandpass_transfer_
out:
- id: parset
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_B2_trans
'sbg:x': -200
'sbg:y': 400
- id: losoto_plot_B3_trans
in:
- id: input_h5parm
source: bandpass/output_h5parm
- id: soltab
default: sol000/bandpass
- id: axesInPlot
default:
- freq
- id: axisInCol
default: ant
- id: plotFlag
default: true
- id: time.minmaxstep
default:
- 0
- 1e20
- 500000
- id: prefix
default: bbandpass_transfer_
out:
- id: parset
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_B3_trans
'sbg:x': -200
'sbg:y': 500
- id: concat_logfiles_bp
in:
- id: file_list
......@@ -264,6 +353,8 @@ steps:
- losoto_plot_B2/logfile
- losoto_plot_B3/logfile
- write_solutions/log
- h5parm_pointingname/log
- transfer_solutions/log
- id: file_prefix
default: losoto_bandpass
out:
......@@ -293,8 +384,8 @@ steps:
- id: log
run: ../../steps/h5parmcat.cwl
label: write_solutions
'sbg:x': 0
'sbg:y': 500
'sbg:x': -200
'sbg:y': 700
- id: apply_calibrate_bp
in:
- id: msin
......@@ -306,7 +397,7 @@ steps:
- id: propagatesolutions
source: propagatesolutions
- id: input_h5parm
source: write_solutions/outh5parm
source: transfer_solutions/outh5parm
out:
- id: msout
- id: BLsmooth.log
......@@ -404,6 +495,65 @@ steps:
label: H5parm_collector
'sbg:x': 750
'sbg:y': -300
- id: h5parm_pointingname
in:
- id: h5parm
source: write_solutions/outh5parm
- id: solsetName
default: calibrator
- id: pointing
source: calibrator_name
out:
- id: outh5parm
- id: log
run: ../../steps/h5parm_pointingname.cwl
label: h5parm_pointingname
'sbg:x': 0
'sbg:y': 300
- id: transfer_solutions
in:
- id: h5parm
source: h5parm_pointingname/outh5parm
- id: refh5parm
source: solutions2transfer
- id: insolset
default: calibrator
- id: outsolset
default: calibrator
- id: insoltab
default: bandpass
- id: outsoltab
default: bandpass
- id: antenna
source: antennas2transfer
- id: parset
source: concat_parset/output
out:
- id: outh5parm
- id: log
- id: plots
run: ../../steps/transfer_solutions.cwl
label: transfer_solutions
'sbg:x': 200
'sbg:y': 300
- id: concat_parset
in:
- id: file_list
linkMerge: merge_flattened
source:
- losoto_plot_B1_trans/parset
- losoto_plot_B2_trans/parset
- losoto_plot_B3_trans/parset
- id: file_prefix
default: losoto
- id: file_suffix
default: parset
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_parset
'sbg:x': 0
'sbg:y': 500
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
......
......@@ -28,7 +28,7 @@ inputs:
'sbg:x': -1000
'sbg:y': 100
- id: inh5parm_logfile
type: File
type: File[]
'sbg:x': -1000
'sbg:y': 200
- id: do_smooth
......@@ -85,7 +85,7 @@ outputs:
- id: outh5parm_logfile
outputSource:
- h5parm_collector/log
type: File
type: File[]
'sbg:x': 1000
'sbg:y': 300
steps:
......
......@@ -28,7 +28,7 @@ inputs:
'sbg:x': -1000
'sbg:y': 100
- id: inh5parm_logfile
type: File
type: File[]
'sbg:x': -1000
'sbg:y': 200
- id: do_smooth
......@@ -82,7 +82,7 @@ outputs:
- id: outh5parm_logfile
outputSource:
- h5parm_collector/log
type: File
type: File[]
'sbg:x': 1000
'sbg:y': 300
steps:
......
......@@ -134,10 +134,16 @@ outputs:
type: 'File[]'
'sbg:x': 1000
'sbg:y': 200
- id: calibrator_name
outputSource:
- find_skymodel_cal/model_name
type: string
'sbg:x': 1000
'sbg:y': 400
- id: outh5parm_logfile
outputSource:
- h5parm_collector/log
type: File
type: File[]
'sbg:x': 1000
'sbg:y': 650
- id: logfiles
......
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