Skip to content
Snippets Groups Projects
Commit d88458bf authored by Tammo Jan Dijkema's avatar Tammo Jan Dijkema
Browse files

Revert "restructure workflows" 

This reverts commit 9a827878 [formerly f2405ede].


Former-commit-id: a0ad9a9f
parent e4a2c1a5
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
workflows/HBA_calibrator.cwl
+ 34
− 29
View file @ d88458bf
...@@ -108,123 +108,128 @@ inputs: ...@@ -108,123 +108,128 @@ inputs:
default: 10 default: 10
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 200 'sbg:y': 200
- id: demix - id: raw_data
type: boolean? type: boolean?
default: false default: false
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 300 'sbg:y': 300
- id: ion_3rd - id: demix
type: boolean? type: boolean?
default: false default: false
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 400 'sbg:y': 400
- id: ion_3rd
type: boolean?
default: false
'sbg:x': -1000
'sbg:y': 500
- id: clock_smooth - id: clock_smooth
type: boolean? type: boolean?
default: true default: true
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 500 'sbg:y': 600
- id: tables2export - id: tables2export
type: string? type: string?
default: clock default: clock
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 600 'sbg:y': 700
- id: final_apply - id: final_apply
type: boolean? type: boolean?
default: false default: false
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 700 'sbg:y': 800
- id: memoryperc - id: memoryperc
type: int? type: int?
default: 20 default: 20
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 800 'sbg:y': 900
- id: min_length - id: min_length
type: int? type: int?
default: 50 default: 50
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 900 'sbg:y': 1000
- id: overhead - id: overhead
type: float? type: float?
default: 0.8 default: 0.8
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1000 'sbg:y': 1100
- id: min_separation - id: min_separation
type: int? type: int?
default: 30 default: 30
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1100 'sbg:y': 1200
- id: max_separation_arcmin - id: max_separation_arcmin
type: float? type: float?
default: 1 default: 1
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1200 'sbg:y': 1300
- 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': 1300 'sbg:y': 1400
- 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': 1400 'sbg:y': 1500
- 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': 1500 'sbg:y': 1600
- id: avg_timeresolution - id: avg_timeresolution
type: float? type: float?
default: 4 default: 4
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1600 'sbg:y': 1700
- id: avg_freqresolution - id: avg_freqresolution
type: string? type: string?
default: 48.82kHz default: 48.82kHz
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1700 'sbg:y': 1800
- id: bandpass_freqresolution - id: bandpass_freqresolution
type: string? type: string?
default: 195.3125kHz default: 195.3125kHz
'sbg:x': -1000 'sbg:x': -1000
'sbg:y': 1800 'sbg:y': 1900
outputs: outputs:
- id: msout - id: msout
outputSource: outputSource:
- prefactor/msout - prefactor/msout
type: 'Directory[]' type: 'Directory[]'
'sbg:x': 1000 'sbg:x': 289.5600891113281
'sbg:y': -200 'sbg:y': -144.01869201660156
- 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': 1000 'sbg:x': 317.4496154785156
'sbg:y': -100 'sbg:y': 9.373631477355957
- id: logfile_prep_cal - id: logfile_prep_cal
outputSource: outputSource:
- prefactor/logfile_prep_cal - prefactor/logfile_prep_cal
type: 'File[]?' type: 'File[]?'
'sbg:x': 1000 'sbg:x': 315.0741882324219
'sbg:y': 0 'sbg:y': 180.26284790039062
- 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': 1000 'sbg:x': 287.6455078125
'sbg:y': 100 'sbg:y': 344.1313171386719
- 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': 1000 'sbg:x': 315.5941467285156
'sbg:y': 200 'sbg:y': 494.9656982421875
- id: parset - id: parset
outputSource: outputSource:
- prefactor/parset - prefactor/parset
type: 'File[]' type: 'File[]'
'sbg:x': 1000 'sbg:x': 293.33331298828125
'sbg:y': 300 'sbg:y': -305.4627990722656
steps: steps:
- id: prefactor - id: prefactor
in: in:
...@@ -307,7 +312,7 @@ steps: ...@@ -307,7 +312,7 @@ steps:
- id: msout - id: msout
- id: logfile_prep_cal - id: logfile_prep_cal
- id: parset - id: parset
run: ./prefactor_calibrator.cwl run: ./prefactor_calibrator_test.cwl
label: prefactor_calibrator label: prefactor_calibrator
'sbg:x': 0 'sbg:x': 0
'sbg:y': 0 'sbg:y': 0
......
workflows/prefactor_calibrator.cwl
+ 153
− 220
View file @ d88458bf
...@@ -5,189 +5,64 @@ label: prefactor_calibrator ...@@ -5,189 +5,64 @@ 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': -1000 'sbg:x': -635
'sbg:y': -1700 'sbg:y': -543
- id: refant - id: skymodels
type: string? type: Directory
default: CS001HBA0 'sbg:x': -123
'sbg:x': -1000 'sbg:y': -850
'sbg:y': -1600 - id: memoryperc
- id: flag_baselines type: int
type: 'string[]?' default: 20
'sbg:x': -634
'sbg:y': -411
- id: baselines_to_flag
type: 'string[]'
default: [] default: []
'sbg:x': -1000 'sbg:x': -635.8651123046875
'sbg:y': -1500 'sbg:y': -148
- id: process_baselines_cal - id: uvw
type: string? type: File?
default: '*&' 'sbg:x': -356.9723205566406
'sbg:x': -1000 'sbg:y': -804.0709838867188
'sbg:y': -1400 - id: strategy
- id: filter_baselines type: File?
type: string? 'sbg:x': -352
default: '*&' 'sbg:y': -713
'sbg:x': -1000 - id: propagate_solutions
'sbg:y': -1300 type: boolean
- 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
'sbg:x': -1000
'sbg:y': -800
- id: raw_data
type: boolean?
default: false
'sbg:x': -1000
'sbg:y': -700
- id: propagatesolutions
type: boolean?
default: true default: true
'sbg:x': -1000 'sbg:x': -112
'sbg:y': -600 'sbg:y': -737
- id: flagunconverged - id: flagunconverged
type: boolean? type: boolean
default: false default: true
'sbg:x': -1000 'sbg:x': -92
'sbg:y': -500
- id: maxStddev
type: float?
default: -1.0
'sbg:x': -1000
'sbg:y': -400 'sbg:y': -400
- id: solutions2transfer - id: do_smooth
type: File? type: boolean
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': -1000 'sbg:x': -89
'sbg:y': 500 'sbg:y': -276
- id: tables2export
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
'sbg:x': -1000
'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 - id: min_separation
type: int? type: int
default: 30 default: 20
'sbg:x': -1000 'sbg:x': -638.4987182617188
'sbg:y': 1100 'sbg:y': 31.238996505737305
- 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: File? type: string
default: /data/skymodels/Ateam_LBA_CC.skymodel 'sbg:x': -889.9927978515625
'sbg:x': -1000 'sbg:y': -845.9927978515625
'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:
...@@ -220,63 +95,121 @@ outputs: ...@@ -220,63 +95,121 @@ outputs:
'sbg:x': 495.6245422363281 'sbg:x': 495.6245422363281
'sbg:y': -1257.4857177734375 'sbg:y': -1257.4857177734375
steps: steps:
- id: prep - id: ndppp_prep_cal
in: in:
- id: msin - id: baselines_to_flag
source: msin default: []
- id: flag_baselines source:
source: flag_baselines - baselines_to_flag
- id: process_baselines_cal - id: elevation_to_flag
source: process_baselines_cal default: 0deg..20deg
- id: filter_baselines - id: min_amplitude_to_flag
source: filter_baselines default: 1.e-30
- id: do_smooth - id: memoryperc
source: do_smooth default: 20
- id: rfistrategy source: memoryperc
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: memoryperc - id: msin
source: memoryperc linkMerge: merge_flattened
- id: min_length source:
source: min_length - msin
- id: overhead - id: skymodel
source: overhead source: make_sourcedb/sourcedb
- id: min_separation - id: timeresolution
source: min_separation default: 1
- id: max_separation_arcmin - id: freqresolution
source: max_separation_arcmin default: 1
- 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: prefactor_calibrator/prep.cwl run: ../subworkflow/ndppp_prep_cal.cwl
label: prep label: ndppp_prep_cal
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/prep.cwl → workflows/prefactor_calibrator_test.cwl
+ 3
− 3
View file @ d88458bf
...@@ -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
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment