Commit fef5c9f0 authored by mancini's avatar mancini

Merge branch 'LoSoTo-prefactor-bandpass' into 'master'

Add bandpass step

See merge request lofar-cwl!15
parents 21d1702f 586fa97b
Pipeline #508 passed with stages
in 3 minutes and 50 seconds
......@@ -115,6 +115,12 @@ losoto_smooth:
- cwl-runner --no-container steps/LoSoTo.Smooth.cwl test_jobs/losoto_smooth.json
stage: test_steps
allow_failure: true
- cwl-runner --no-container steps/LoSoTo.PrefactorBandpass.cwl test_jobs/losoto_prefactorbandpass.json
stage: test_steps
allow_failure: true
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.0
id: losoto_prefactor_bandpass
doc: |
This operation for LoSoTo implements the Prefactor bandpass operation
WEIGHT: flag-only compliant, no need for weight
- { $include: utils.js}
- entryname: 'parset.config'
entry: $(get_losoto_config('PREFACTOR_BANDPASS').join('\n'))
- entryname: $(inputs.input_h5parm.basename)
entry: $(inputs.input_h5parm)
writable: true
baseCommand: "losoto"
- $(inputs.input_h5parm.basename)
- parset.config
dockerPull: lofareosc/lofar-pipeline-ci:latest
- id: input_h5parm
type: File
format: lofar:#H5Parm
- id: soltab
type: string
doc: "Solution table"
- id: chanWidth
type: string?
doc: |
the width of each channel in the data from which solutions were obtained. Can be
either a string like "48kHz" or a float in Hz. If interpolate = True, chanWidth
must be specified
- id: BadSBList
type: string?
doc: a list of bad subbands that will be flagged
- id: outSoltabName
type: string?
doc: |
Name of the output bandpass soltab. An existing soltab with this name will be
- id: interpolate
type: boolean?
default: false
doc: |
If True, interpolate to a regular frequency grid and then smooth, ignoring bad
subbands. If False, neither interpolation nor smoothing is done and the output
frequency grid is the same as the input one. If interpolate = True, chanWidth
must be specified
- id: removeTimeAxis
type: boolean?
doc: |
If True, the time axis of the output bandpass soltab is removed by doing a median
over time. If False, the output time grid is the same as the input one
- id: autoFlag
type: boolean?
doc: If True, automatically flag bad frequencies and stations
- id: nSigma
type: float?
doc: Number of sigma for autoFlagging. Amplitudes outside of nSigma*stddev are flagged
- id: maxFlaggedFraction
type: float?
doc: |
Maximum allowable fraction of flagged frequencies for autoFlagging. Stations with
higher fractions will be completely flagged
- id: maxStddev
type: float?
doc: Maximum allowable standard deviation for autoFlagging
- id: ncpu
type: int?
doc: Number of CPUs to use during autoFlagging (0 = all)
- id: output_h5parm
type: File
format: lofar:#H5Parm
glob: $(inputs.input_h5parm.basename)
"input_h5parm": {"class": "File", "path": "/data/example.h5", "format": "lofar:#H5Parm"},
"soltab": "sol000/amplitude000"
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