Commit 1bafabfa authored by mancini's avatar mancini

Merge branch 'HBA_calibrator' of git.astron.nl:eosc/prefactor3-cwl into HBA_calibrator

parents b9599951 6a7f9527
Pipeline #3439 failed with stages
in 9 minutes and 55 seconds
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: check_ateam_separation
baseCommand:
- python3
- /usr/local/bin/Ateamclipper.py
inputs:
- id: msin
type:
- Directory
- type: array
items: Directory
inputBinding:
position: 0
doc: Input measurement set
outputs:
- id: msout
doc: Output MS
type: File?
outputBinding:
glob: $(inputs.msin)
- id: logfile
type: 'File[]?'
outputBinding:
glob: Ateamclipper.log
label: Ateamclipper
hints:
- class: DockerRequirement
dockerPull: lofareosc/prefactor:HBAcalibrator
- class: InlineJavascriptRequirement
stdout: Ateamclipper.log
......@@ -38,6 +38,8 @@ inputs:
- fulljones
- polalign
- bandpass
- RMextract
- phaseOrig
doc: |
Type of correction to perform, can be one of 'gain', 'tec', 'clock',
'(common)rotationangle' / 'rotation', '(common)scalarphase',
......
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: predict
baseCommand:
- DPPP
inputs:
- id: msin
type: Directory
inputBinding:
position: 0
prefix: msin=
separate: false
doc: Input Measurement Set
- default: DATA
id: msin_datacolumn
type: string
inputBinding:
position: 0
prefix: msin.datacolumn=
separate: false
doc: Input data Column
- default: MODEL_DATA
id: msout_datacolumn
type: string
inputBinding:
position: 0
prefix: msout.datacolumn=
separate: false
- id: sources_db
type: File
inputBinding:
position: 0
prefix: predict.sourcedb=
separate: false
- default: null
id: sources
type: 'string[]'
inputBinding:
position: 0
prefix: predict.sources=
separate: false
itemSeparator: ','
valueFrom: '[$(self)]'
- default: false
id: usebeammodel
type: boolean
inputBinding:
position: 0
prefix: predict.usebeammodel=True
- default: false
id: onebeamperpatch
type: boolean
inputBinding:
position: 0
prefix: predict.onebeamperpatch=True
- default: null
id: filter_baselines
type: string
inputBinding:
position: 0
prefix: filter.baseline=
separate: false
valueFrom: '$(self)'
- default: false
id: filter_remove
type: boolean
inputBinding:
position: 0
prefix: filter.remove=True
- id: writefullresflag
type: boolean
default: false
inputBinding:
prefix: msout.writefullresflag=True
- id: overwrite
type: boolean
default: false
inputBinding:
prefix: msout.overwrite=True
- id: storagemanager
type: string
default: ""
inputBinding:
prefix: msout.storagemanager=
separate: false
- id: databitrate
type: int?
inputBinding:
prefix: msout.storagemanager.databitrate=
separate: false
outputs:
- id: msout
doc: Output Measurement Set
type: Directory
outputBinding:
glob: $(inputs.msin.basename)
- id: logfile
type: File[]
outputBinding:
glob: 'predict_cal*.log'
arguments:
- 'steps=[filter,predict]'
- predict.beammode=array_factor
- predict.usechannelfreq=False
- msout=.
requirements:
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.msin)
writable: true
- class: InlineJavascriptRequirement
hints:
- class: DockerRequirement
dockerPull: lofareosc/prefactor:HBAcalibrator
stdout: filter_predict.log
stderr: filter_predict_err.log
\ No newline at end of file
function get_losoto_config(step_name) {
var par = ['soltab = ' + inputs.soltab]
if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);
console.log(inputs, par)
par.push("[" + step_name + "]")
par.push('operation=' + step_name)
for(var field_name in inputs){
......
......@@ -32,6 +32,6 @@ requirements:
FILE_LIST=("\${@}")
FILE_PREFIX=$(inputs.file_prefix)
FILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)
cat "\${FILE_LIST[@]}" > "\$FILE_PREFIX.\$FILE_SUFFIX"
cat "\${FILE_LIST[@]}" > $FILE_PREFIX.$FILE_SUFFIX
writable: false
- class: InlineJavascriptRequirement
......@@ -53,7 +53,7 @@ inputs:
type: int
'sbg:x': 1465.0855712890625
'sbg:y': 450.8930358886719
- id: demix_baseline
- id: process_baselines_target
type: string
'sbg:x': 1585.496826171875
'sbg:y': 588.0062866210938
......@@ -97,25 +97,41 @@ inputs:
type: string
'sbg:x': 1880
'sbg:y': -380
- id: updateweights
type: boolean
'sbg:x': 2234.90185546875
'sbg:y': -393.8929748535156
outputs:
- id: logfile
- id: prep_logfile
outputSource:
- concat_logfiles_dppp/output
type: File
'sbg:x': 4982.51416015625
'sbg:y': 121.597900390625
type: File?
'sbg:x': 5500
'sbg:y': 100
- id: predict_logfile
outputSource:
- concat_logfiles_predict/output
type: File?
'sbg:x': 5500
'sbg:y': 0
- id: clipper_logfile
outputSource:
- concat_logfiles_clipper/output
type: File?
'sbg:x': 5500
'sbg:y': -100
- id: msout
outputSource:
- dp3_execute/msout
- predict/msout
type: Directory
'sbg:x': 4884.83251953125
'sbg:y': -232.5366973876953
'sbg:x': 5502.318359375
'sbg:y': -279.49835205078125
- id: parset
outputSource:
- dp3_execute/parset
type: File
'sbg:x': 4862.033203125
'sbg:y': -541.10693359375
'sbg:x': 5427.662109375
'sbg:y': -765.5377197265625
steps:
- id: flagbaseline
in:
......@@ -228,7 +244,7 @@ steps:
- id: step_name
default: demixer
- id: baseline
source: demix_baseline
source: process_baselines_target
- id: demixtimestep
source: demix_timestep
- id: demixfreqstep
......@@ -278,6 +294,32 @@ steps:
label: concat_logfiles_dppp
'sbg:x': 4543.36376953125
'sbg:y': -6.564670085906982
- id: concat_logfiles_predict
in:
- id: file_list
source:
- predict/logfile
- id: file_prefix
default: predict_targ
out:
- id: output
run: ../steps/concatenate_files.cwl
label: concat_logfiles_predict
'sbg:x': 4700
'sbg:y': -6.564670085906982
- id: concat_logfiles_clipper
in:
- id: file_list
source:
- Ateamclipper/logfile
- id: file_prefix
default: Ateamclipper
out:
- id: output
run: ../steps/concatenate_files.cwl
label: concat_logfiles_clipper
'sbg:x': 4900
'sbg:y': -6.564670085906982
- id: dp3_execute
in:
- id: msout_name
......@@ -323,6 +365,8 @@ steps:
default: apply_pa_1
- id: parmdb
source: parmdb
- id: solset
default: calibrator
- id: correction
default: polalign
out:
......@@ -339,6 +383,8 @@ steps:
default: apply_bandpass_1
- id: parmdb
source: parmdb
- id: solset
default: calibrator
- id: correction
default: bandpass
out:
......@@ -363,11 +409,57 @@ steps:
source: apply_phase_correction
- id: parmdb
source: parmdb
- id: updateweights
source: updateweights
out:
- id: selected_steps
run: ./prep_target_applycal.cwl
label: prep_target_applycal
'sbg:x': 2728.697998046875
'sbg:y': -18.151018142700195
- id: predict
in:
- id: msin
source: dp3_execute/msout
- id: msin_datacolumn
default: DATA
- id: msout_datacolumn
default: MODEL_DATA
- id: sources_db
source: skymodel
- id: storagemanager
default: Dysco
- id: databitrate
default: 0
- id: filter_baselines
source: process_baselines_target
- id: sources
default:
- 'VirA_4_patch'
- 'CygAGG'
- 'CasA_4_patch'
- 'TauAGG'
- id: usebeammodel
default: true
- id: onebeamperpatch
default: true
out:
- id: msout
- id: logfile
run: ../lofar-cwl/steps/filter_predict.cwl
'sbg:x': 4500
'sbg:y': -344.5472106933594
- id: Ateamclipper
in:
- id: msin
source: predict/msout
out:
- id: msout
- id: logfile
run: ../lofar-cwl/steps/Ateamclipper.cwl
'sbg:x': 4700
'sbg:y': -344.5472106933594
requirements:
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
......@@ -18,13 +18,13 @@ inputs:
'sbg:x': 1990.8035888671875
'sbg:y': -230.75811767578125
- id: apply_rm_correction
type: boolean
'sbg:x': 2273.170166015625
'sbg:y': -251.86672973632812
- id: apply_beam_correction
type: boolean
'sbg:x': 2502.2421875
'sbg:y': -225.68701171875
- id: apply_beam_correction
type: boolean
'sbg:x': 2273.170166015625
'sbg:y': -251.86672973632812
- id: apply_phase_correction
type: boolean
'sbg:x': 2750.948974609375
......@@ -33,6 +33,10 @@ inputs:
type: File
'sbg:x': 2007.115234375
'sbg:y': 685.0719604492188
- id: updateweights
type: boolean
'sbg:x': 2167.219970703125
'sbg:y': 422.6792297363281
outputs:
- id: selected_steps
outputSource:
......@@ -50,6 +54,8 @@ steps:
default: apply_clock
- id: parmdb
source: parmdb
- id: solset
default: calibrator
- id: correction
default: clock
out:
......@@ -66,6 +72,8 @@ steps:
default: apply_tec
- id: parmdb
source: parmdb
- id: solset
default: calibrator
- id: correction
default: tec
out:
......@@ -77,11 +85,13 @@ steps:
in:
- id: steps
source:
- apply_beam/selected_steps
- apply_rm/selected_steps
- id: step_name
default: apply_phase
- id: parmdb
source: parmdb
- id: solset
default: calibrator
- id: correction
default: phaseOrig
out:
......@@ -93,32 +103,40 @@ steps:
in:
- id: steps
source:
- apply_tec/selected_steps
- apply_beam/selected_steps
- id: step_name
default: apply_rm
- id: parmdb
source: parmdb
- id: solset
default: target
- id: correction
default: RMextract
out:
- id: augmented_steps
run: ../lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
'sbg:x': 2321
'sbg:y': 285.3694763183594
'sbg:x': 2545.4775390625
'sbg:y': 291.2240295410156
- id: applybeam
in:
- id: steps
source:
- apply_rm/selected_steps
- apply_tec/selected_steps
- id: step_name
default: apply_beam
- id: usechannelfreq
default: true
- id: updateweights
source: updateweights
- id: invert
default: true
- id: beammode
default: default
out:
- id: augmented_steps
run: ../lofar-cwl/steps/DP3.ApplyBeamStepGenerator.cwl
'sbg:x': 2545.4775390625
'sbg:y': 291.2240295410156
'sbg:x': 2321
'sbg:y': 285.3694763183594
- id: apply_beam
in:
- id: select_a
......@@ -129,13 +147,13 @@ steps:
- id: b_steps
default: []
source:
- apply_rm/selected_steps
- apply_tec/selected_steps
out:
- id: selected_steps
run: ../lofar-cwl/steps/DP3.Selector.cwl
label: apply_beam
'sbg:x': 2648.432373046875
'sbg:y': 167.062255859375
'sbg:x': 2441.14599609375
'sbg:y': 167.0730438232422
- id: apply_rm
in:
- id: select_a
......@@ -146,13 +164,13 @@ steps:
- id: b_steps
default: []
source:
- apply_tec/selected_steps
- apply_beam/selected_steps
out:
- id: selected_steps
run: ../lofar-cwl/steps/DP3.Selector.cwl
label: apply_rm?
'sbg:x': 2441.14599609375
'sbg:y': 167.0730438232422
'sbg:x': 2648.432373046875
'sbg:y': 167.062255859375
- id: apply_clock
in:
- id: select_a
......@@ -197,7 +215,7 @@ steps:
- id: b_steps
default: []
source:
- apply_beam/selected_steps
- apply_rm/selected_steps
out:
- id: selected_steps
run: ../lofar-cwl/steps/DP3.Selector.cwl
......
......@@ -208,6 +208,8 @@ outputs:
- losoto_plot_RM/logfile
- compare_station_list/logfile
- concat_logfiles_prep_targ/output
- concat_logfiles_predict_targ/output
- concat_logfiles_clipper_targ/output
type: 'File[]'
linkMerge: merge_flattened
'sbg:x': 1000
......@@ -347,7 +349,7 @@ steps:
- id: demix_freqstep
default: 1
source: demix_freqstep
- id: demix_baseline
- id: process_baselines_target
default: '*'
source: process_baselines_target
- id: target_source
......@@ -377,9 +379,13 @@ steps:
default: true
- id: filter_baselines
source: compare_station_list/filter_out
- id: updateweights
source: updateweights
out:
- id: msout
- id: logfile
- id: prep_logfile
- id: predict_logfile
- id: clipper_logfile
- id: parset
run: ../../subworkflow/ndppp_prep_targ.cwl
label: ndppp_prep_target
......@@ -391,14 +397,40 @@ steps:
in:
- id: file_list
linkMerge: merge_flattened
source: dppp_prep_target/logfile
source: dppp_prep_target/prep_logfile
- id: file_prefix
default: ndppp_prep_targ
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_prep_targ
label: concat_logfiles_prep_target
'sbg:x': 250
'sbg:y': 300
- id: concat_logfiles_predict_targ
in:
- id: file_list
linkMerge: merge_flattened
source: dppp_prep_target/predict_logfile
- id: file_prefix
default: predict_targ
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_predict_targ
'sbg:x': 250
'sbg:y': 400
- id: concat_logfiles_clipper_targ
in:
- id: file_list
linkMerge: merge_flattened
source: dppp_prep_target/clipper_logfile
- id: file_prefix
default: Ateamclipper
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_clipper_targ
'sbg:x': 250
'sbg:y': 500
requirements:
- class: ScatterFeatureRequirement
\ No newline at end of file
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