Commit 17f06eca authored by mancini's avatar mancini

Merge branch 'LoSoTo.Flag' into 'master'

Add LoSoTo Flag step - Resolves EOSC 25

See merge request lofar-cwl!6
parents 465c7719 7bc9bb09
Pipeline #484 passed with stages
in 3 minutes and 14 seconds
......@@ -86,7 +86,11 @@ losoto_plot:
allow_failure: true
script:
- cwl-runner --no-container steps/LoSoTo.Plot.cwl test_jobs/losoto_plot.json
losoto_flag:
stage: test_steps
allow_failure: true
script:
- cwl-runner --no-container steps/LoSoTo.Flag.cwl test_jobs/losoto_flag.json
losoto_norm:
stage: test_steps
allow_failure: true
......
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.0
id: losoto_flag
$namespaces:
lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
doc: |
This operation for LoSoTo implement a flagging procedure
WEIGHT: compliant
requirements:
InlineJavascriptRequirement:
expressionLib:
- { $include: utils.js}
InitialWorkDirRequirement:
listing:
- entryname: 'parset.config'
entry: $(get_losoto_config('FLAG').join('\n'))
- entryname: $(inputs.input_h5parm.basename)
entry: $(inputs.input_h5parm)
writable: true
baseCommand: "losoto"
arguments:
- $(inputs.input_h5parm.basename)
- parset.config
hints:
DockerRequirement:
dockerPull: lofareosc/lofar-pipeline-ci:latest
inputs:
- id: input_h5parm
type: File
format: lofar:#H5Parm
- id: soltab
type: string
doc: "Solution table"
- id: axesToFlag
type: string[]
doc: Axes along which to smooth+find outlier (e.g. ['time', 'freq']), max 2 values.
- id: order
type: int[]
doc: |
Order of the function fitted during detrending.
Array must have same size of axesToFlag.
If mode=smooth these are the window of the running median (0=all axis).
- id: maxCycles
type: int?
doc: Max number of independent flagging cycles, by default 5.
- id: maxRms
type: float?
doc: Rms to clip outliers, by default 5.
- id: maxRmsNoise
type: float?
doc: |
Do a running rms and then flag those regions that have a rms higher
than MaxRmsNoise*rms_of_rmses, by default 0 (ignored).
- id: fixRms
type: float?
doc: Instead of calculating rms use this value, by default 0 (ignored).
- id: fixRmsNoise
type: float?
doc: |
Instead of calculating rms of the rmses use this value
(it will not be multiplied by the MaxRmsNoise), by default 0 (ignored).
- id: windowNoise
type: int?
doc: Window size for the running rms, by default 11.
- id: replace
type: boolean?
doc: |
Replace bad values with the interpolated ones,
instead of flagging them. By default False.
- id: preflagzeros
type: boolean?
doc:
Flag zeros/ones (bad solutions in BBS/DPPP).
They should be flagged at import time. By default False.
- id: mode
type: string?
doc: |
Detrending/fitting algorithm: smooth / poly / spline.
By default smooth.
- id: refAnt
type: string?
doc: Reference antenna, by default None.
- id: ncpu
type: int?
doc: Number of cpu to use, by default all available.
outputs:
- id: output_h5parm
type: File
format: lofar:#H5Parm
outputBinding:
glob: $(inputs.input_h5parm.basename)
$schema:
- https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
{
"input_h5parm": {"class": "File", "path": "/data/example.h5", "format": "lofar:#H5Parm"},
"soltab": "sol000/phase000",
"axesToFlag": ["time"],
"order": [0]
}
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