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Commit 18a1208c authored by Alexander Drabent's avatar Alexander Drabent Committed by Mattia Mancini
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restructure workflows 

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Former-commit-id: e0e46a48
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workflows/HBA_calibrator.cwl
+ 29
− 34
View file @ 18a1208c
...@@ -108,128 +108,123 @@ inputs: ...@@ -108,128 +108,123 @@ inputs:
default: 10 default: 10
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 200 'sbg:y': 200
- id: raw_data
type: boolean?
default: false
'sbg:x': -1000
'sbg:y': 300
- id: demix - id: demix
type: boolean? type: boolean?
default: false default: false
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 400 'sbg:y': 300
- id: ion_3rd - id: ion_3rd
type: boolean? type: boolean?
default: false default: false
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 500 'sbg:y': 400
- id: clock_smooth - id: clock_smooth
type: boolean? type: boolean?
default: true default: true
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 600 'sbg:y': 500
- id: tables2export - id: tables2export
type: string? type: string?
default: clock default: clock
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 700 'sbg:y': 600
- id: final_apply - id: final_apply
type: boolean? type: boolean?
default: false default: false
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 800 'sbg:y': 700
- id: memoryperc - id: memoryperc
type: int? type: int?
default: 20 default: 20
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 900 'sbg:y': 800
- id: min_length - id: min_length
type: int? type: int?
default: 50 default: 50
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1000 'sbg:y': 900
- id: overhead - id: overhead
type: float? type: float?
default: 0.8 default: 0.8
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1100 'sbg:y': 1000
- id: min_separation - id: min_separation
type: int? type: int?
default: 30 default: 30
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1200 'sbg:y': 1100
- id: max_separation_arcmin - id: max_separation_arcmin
type: float? type: float?
default: 1 default: 1
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1300 'sbg:y': 1200
- id: calibrator_path_skymodel - id: calibrator_path_skymodel
type: Directory? type: Directory?
default: /data/skymodels default: /data/skymodels
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1400 'sbg:y': 1300
- id: A-Team_sky_model - id: A-Team_sky_model
type: File? type: File?
default: /data/skymodels/Ateam_LBA_CC.skymodel default: /data/skymodels/Ateam_LBA_CC.skymodel
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1500 'sbg:y': 1400
- id: cal_solutions - id: cal_solutions
type: string? type: string?
default: cal_solutions.h5 default: cal_solutions.h5
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1600 'sbg:y': 1500
- id: avg_timeresolution - id: avg_timeresolution
type: float? type: float?
default: 4 default: 4
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1700 'sbg:y': 1600
- id: avg_freqresolution - id: avg_freqresolution
type: string? type: string?
default: 48.82kHz default: 48.82kHz
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1800 'sbg:y': 1700
- id: bandpass_freqresolution - id: bandpass_freqresolution
type: string? type: string?
default: 195.3125kHz default: 195.3125kHz
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1900 'sbg:y': 1800
outputs: outputs:
- id: msout - id: msout
outputSource: outputSource:
- prefactor/msout - prefactor/msout
type: 'Directory[]' type: 'Directory[]'
'sbg:x': 289.5600891113281 'sbg:x': 1000
'sbg:y': -144.01869201660156 'sbg:y': -200
- id: make_sourcedb_ateam.log - id: make_sourcedb_ateam.log
outputSource: outputSource:
- prefactor/make_sourcedb_ateam.log - prefactor/make_sourcedb_ateam.log
type: File? type: File?
'sbg:x': 317.4496154785156 'sbg:x': 1000
'sbg:y': 9.373631477355957 'sbg:y': -100
- id: logfile_prep_cal - id: logfile_prep_cal
outputSource: outputSource:
- prefactor/logfile_prep_cal - prefactor/logfile_prep_cal
type: 'File[]?' type: 'File[]?'
'sbg:x': 315.0741882324219 'sbg:x': 1000
'sbg:y': 180.26284790039062 'sbg:y': 0
- id: check_Ateam_separation.png - id: check_Ateam_separation.png
outputSource: outputSource:
- prefactor/check_Ateam_separation.png - prefactor/check_Ateam_separation.png
type: 'File[]?' type: 'File[]?'
'sbg:x': 287.6455078125 'sbg:x': 1000
'sbg:y': 344.1313171386719 'sbg:y': 100
- id: check_Ateam_separation.log - id: check_Ateam_separation.log
outputSource: outputSource:
- prefactor/check_Ateam_separation.log - prefactor/check_Ateam_separation.log
type: 'File[]?' type: 'File[]?'
'sbg:x': 315.5941467285156 'sbg:x': 1000
'sbg:y': 494.9656982421875 'sbg:y': 200
- id: parset - id: parset
outputSource: outputSource:
- prefactor/parset - prefactor/parset
type: 'File[]' type: 'File[]'
'sbg:x': 293.33331298828125 'sbg:x': 1000
'sbg:y': -305.4627990722656 'sbg:y': 300
steps: steps:
- id: prefactor - id: prefactor
in: in:
...@@ -312,7 +307,7 @@ steps: ...@@ -312,7 +307,7 @@ steps:
- id: msout - id: msout
- id: logfile_prep_cal - id: logfile_prep_cal
- id: parset - id: parset
run: ./prefactor_calibrator_test.cwl run: ./prefactor_calibrator.cwl
label: prefactor_calibrator label: prefactor_calibrator
'sbg:x': 0 'sbg:x': 0
'sbg:y': 0 'sbg:y': 0
......
workflows/prefactor_calibrator.cwl
+ 220
− 153
View file @ 18a1208c
...@@ -5,64 +5,189 @@ label: prefactor_calibrator ...@@ -5,64 +5,189 @@ label: prefactor_calibrator
$namespaces: $namespaces:
sbg: 'https://www.sevenbridges.com/' sbg: 'https://www.sevenbridges.com/'
inputs: inputs:
- id: raw_data
type: boolean
'sbg:x': -634
'sbg:y': -688
- id: demix
type: boolean
'sbg:x': -639.3313598632812
'sbg:y': -271
- id: msin - id: msin
type: 'Directory[]' type: 'Directory[]'
'sbg:x': -635 'sbg:x': -1000
'sbg:y': -543 'sbg:y': -1700
- id: skymodels - id: refant
type: Directory type: string?
'sbg:x': -123 default: CS001HBA0
'sbg:y': -850 'sbg:x': -1000
- id: memoryperc 'sbg:y': -1600
type: int - id: flag_baselines
default: 20 type: 'string[]?'
'sbg:x': -634
'sbg:y': -411
- id: baselines_to_flag
type: 'string[]'
default: [] default: []
'sbg:x': -635.8651123046875 'sbg:x': -1000
'sbg:y': -148 'sbg:y': -1500
- id: uvw - id: process_baselines_cal
type: File? type: string?
'sbg:x': -356.9723205566406 default: '*&'
'sbg:y': -804.0709838867188 'sbg:x': -1000
- id: strategy 'sbg:y': -1400
type: File? - id: filter_baselines
'sbg:x': -352 type: string?
'sbg:y': -713 default: '*&'
- id: propagate_solutions 'sbg:x': -1000
type: boolean 'sbg:y': -1300
- id: do_smooth
type: boolean?
default: false
'sbg:x': -1000
'sbg:y': -1200
- id: rfistrategy
type: string?
default: HBAdefault.rfis
'sbg:x': -1000
'sbg:y': -1100
- id: max2interpolate
type: int?
default: 30
'sbg:x': -1000
'sbg:y': -1000
- id: ampRange
type: 'int[]?'
default:
- 0
- 0
'sbg:x': -1000
'sbg:y': -900
- id: skip_international
type: boolean?
default: true default: true
'sbg:x': -112 'sbg:x': -1000
'sbg:y': -737 'sbg:y': -800
- id: flagunconverged - id: raw_data
type: boolean type: boolean?
default: false
'sbg:x': -1000
'sbg:y': -700
- id: propagatesolutions
type: boolean?
default: true default: true
'sbg:x': -92 'sbg:x': -1000
'sbg:y': -600
- id: flagunconverged
type: boolean?
default: false
'sbg:x': -1000
'sbg:y': -500
- id: maxStddev
type: float?
default: -1.0
'sbg:x': -1000
'sbg:y': -400 'sbg:y': -400
- id: do_smooth - id: solutions2transfer
type: boolean type: File?
default: /data/solutions/3C48.h5
'sbg:x': -1000
'sbg:y': -300
- id: antennas2transfer
type: File?
default: '[FUSPID].*'
'sbg:x': -1000
'sbg:y': -200
- id: demix_sources
type: 'string[]?'
default:
- CasA
- CygA
'sbg:x': -1000
'sbg:y': -100
- id: demix_target
type: string?
default: ''
'sbg:x': -1000
'sbg:y': 0
- id: demix_freqstep
type: int?
default: 16
'sbg:x': -1000
'sbg:y': 100
- id: demix_timestep
type: int?
default: 10
'sbg:x': -1000
'sbg:y': 200
- id: demix
type: boolean?
default: false
'sbg:x': -1000
'sbg:y': 300
- id: ion_3rd
type: boolean?
default: false
'sbg:x': -1000
'sbg:y': 400
- id: clock_smooth
type: boolean?
default: true default: true
'sbg:x': -89 'sbg:x': -1000
'sbg:y': -276 'sbg:y': 500
- id: min_separation - id: tables2export
type: int type: string?
default: clock
'sbg:x': -1000
'sbg:y': 600
- id: final_apply
type: boolean?
default: false
'sbg:x': -1000
'sbg:y': 700
- id: memoryperc
type: int?
default: 20 default: 20
'sbg:x': -638.4987182617188 'sbg:x': -1000
'sbg:y': 31.238996505737305 'sbg:y': 800
- id: min_length
type: int?
default: 50
'sbg:x': -1000
'sbg:y': 900
- id: overhead
type: float?
default: 0.8
'sbg:x': -1000
'sbg:y': 1000
- id: min_separation
type: int?
default: 30
'sbg:x': -1000
'sbg:y': 1100
- id: max_separation_arcmin
type: float?
default: 1
'sbg:x': -1000
'sbg:y': 1200
- id: calibrator_path_skymodel
type: Directory?
default: /data/skymodels
'sbg:x': -1000
'sbg:y': 1300
- id: A-Team_sky_model - id: A-Team_sky_model
type: string type: File?
'sbg:x': -889.9927978515625 default: /data/skymodels/Ateam_LBA_CC.skymodel
'sbg:y': -845.9927978515625 'sbg:x': -1000
'sbg:y': 1400
- id: cal_solutions
type: string?
default: cal_solutions.h5
'sbg:x': -1000
'sbg:y': 1500
- id: avg_timeresolution
type: float?
default: 4
'sbg:x': -1000
'sbg:y': 1600
- id: avg_freqresolution
type: string?
default: 48.82kHz
'sbg:x': -1000
'sbg:y': 1700
- id: bandpass_freqresolution
type: string?
default: 195.3125kHz
'sbg:x': -1000
'sbg:y': 1800
outputs: outputs:
- id: outh5parm - id: outh5parm
outputSource: outputSource:
...@@ -95,121 +220,63 @@ outputs: ...@@ -95,121 +220,63 @@ outputs:
'sbg:x': 495.6245422363281 'sbg:x': 495.6245422363281
'sbg:y': -1257.4857177734375 'sbg:y': -1257.4857177734375
steps: steps:
- id: ndppp_prep_cal - id: prep
in: in:
- id: baselines_to_flag - id: msin
default: [] source: msin
source: - id: flag_baselines
- baselines_to_flag source: flag_baselines
- id: elevation_to_flag - id: process_baselines_cal
default: 0deg..20deg source: process_baselines_cal
- id: min_amplitude_to_flag - id: filter_baselines
default: 1.e-30 source: filter_baselines
- id: memoryperc - id: do_smooth
default: 20 source: do_smooth
source: memoryperc - id: rfistrategy
source: rfistrategy
- id: raw_data - id: raw_data
source: raw_data source: raw_data
- id: demix_sources
source: demix_sources
- id: demix_target
source: demix_target
- id: demix_freqstep
source: demix_freqstep
- id: demix_timestep
source: demix_timestep
- id: demix_target
source: demix_target
- id: demix_target
source: demix_target
- id: demix - id: demix
source: demix source: demix
- id: msin - id: memoryperc
linkMerge: merge_flattened source: memoryperc
source: - id: min_length
- msin source: min_length
- id: skymodel - id: overhead
source: make_sourcedb/sourcedb source: overhead
- id: timeresolution - id: min_separation
default: 1 source: min_separation
- id: freqresolution - id: max_separation_arcmin
default: 1 source: max_separation_arcmin
- id: calibrator_path_skymodel
source: calibrator_path_skymodel
- id: A-Team_skymodel
source: A-Team_skymodel
- id: avg_timeresolution
source: avg_timeresolution
- id: avg_freqresolution
source: avg_freqresolution
out: out:
- id: msout - id: msout
run: ../subworkflow/ndppp_prep_cal.cwl run: prefactor_calibrator/prep.cwl
label: ndppp_prep_cal label: prep
scatter: scatter:
- msin - msin
'sbg:x': -359 'sbg:x': -359
'sbg:y': -519 'sbg:y': -519
- id: aoflagger
in:
- id: msin
source:
- ndppp_prep_cal/msout
- id: strategy
source: strategy
- id: uvw
source: uvw
out:
- id: output_ms
run: ../lofar-cwl/steps/AOFlagger.cwl
label: AOFlagger
scatterMethod: flat_crossproduct
'sbg:x': -164
'sbg:y': -565
- id: calib_cal
in:
- id: msin
source: aoflagger/output_ms
- id: skymodels
source: skymodels
- id: flagunconverged
source: flagunconverged
- id: propagate_solutions
source: propagate_solutions
- id: do_smooth
source: do_smooth
out:
- id: h5parm
- id: msout
run: ../subworkflow/calib_cal.cwl
label: calib_cal
scatter:
- msin
'sbg:x': 47
'sbg:y': -583
- id: h5parm_collector
in:
- id: h5parmFiles
source:
- calib_cal/h5parm
- 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': 292.1979675292969
'sbg:y': -543.7208251953125
- id: check_ateam_separation
in:
- id: ms
source:
- msin
- id: min_separation
source: min_separation
out:
- id: output_imag
- id: logfile
run: ../lofar-cwl/steps/check_ateam_separation.cwl
label: check_Ateam_separation
'sbg:x': -331.452392578125
'sbg:y': 23.596216201782227
- id: make_sourcedb
in:
- id: sky_model
source: A-Team_sky_model
out:
- id: sourcedb
- id: log
run: ../lofar-cwl/steps/makesourcedb.cwl
label: make_sourcedb_ateam
'sbg:x': -628.7400512695312
'sbg:y': -847.117919921875
requirements: requirements:
- class: SubworkflowFeatureRequirement - class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement - class: ScatterFeatureRequirement
workflows/prefactor_calibrator_test.cwl → workflows/prefactor_calibrator/prep.cwl
+ 3
− 3
View file @ 18a1208c
...@@ -113,7 +113,7 @@ steps: ...@@ -113,7 +113,7 @@ steps:
- id: msout - id: msout
- id: logfile - id: logfile
- id: parset - id: parset
run: ../subworkflow/ndppp_prep_cal.cwl run: ../../subworkflow/ndppp_prep_cal.cwl
label: ndppp_prep_cal label: ndppp_prep_cal
scatter: scatter:
- msin - msin
...@@ -129,7 +129,7 @@ steps: ...@@ -129,7 +129,7 @@ steps:
out: out:
- id: output_imag - id: output_imag
- id: logfile - id: logfile
run: ../lofar-cwl/steps/check_ateam_separation.cwl run: ../../lofar-cwl/steps/check_ateam_separation.cwl
label: check_Ateam_separation label: check_Ateam_separation
'sbg:x': -331.452392578125 'sbg:x': -331.452392578125
'sbg:y': 23.596216201782227 'sbg:y': 23.596216201782227
...@@ -140,7 +140,7 @@ steps: ...@@ -140,7 +140,7 @@ steps:
out: out:
- id: sourcedb - id: sourcedb
- id: log - id: log
run: ../lofar-cwl/steps/makesourcedb.cwl run: ../../lofar-cwl/steps/makesourcedb.cwl
label: make_sourcedb_ateam label: make_sourcedb_ateam
'sbg:x': -647.0108642578125 'sbg:x': -647.0108642578125
'sbg:y': -981.3153076171875 'sbg:y': -981.3153076171875
......
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