Commit 21d1702f authored by mancini's avatar mancini

Merge branch 'LoSoTo-smooth' into 'master'

Add Smooth step

See merge request !11
parents b70fd69f 382cea5b
Pipeline #502 passed with stages
in 5 minutes and 59 seconds
......@@ -109,6 +109,12 @@ losoto_reset:
script:
- cwl-runner --no-container steps/LoSoTo.Reset.cwl test_jobs/losoto_reset.json
losoto_smooth:
stage: test_steps
allow_failure: true
script:
- cwl-runner --no-container steps/LoSoTo.Smooth.cwl test_jobs/losoto_smooth.json
losoto_clip:
stage: test_steps
allow_failure: true
......
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.0
id: losoto_smooth
$namespaces:
lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
doc: |
A smoothing function: running-median on an arbitrary number of axes, running
polyfit and Savitzky-Golay on one axis, or set all solutions to the
mean/median value.
WEIGHT: flag ready.
requirements:
InlineJavascriptRequirement:
expressionLib:
- { $include: utils.js}
InitialWorkDirRequirement:
listing:
- entryname: 'parset.config'
entry: $(get_losoto_config('SMOOTH').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: axesToSmooth
type: string[]
doc: Axes used to compute the smoothing function.
- id: size
type: int[]?
doc: |
Window size for the runningmedian, savitzky-golay, and runningpoly (array
of same size of axesToSmooth), by default [].
- id: mode
default: 'runningmedian'
type:
type: enum
symbols:
- 'runningmedian'
- 'runningpoly'
- 'savitzky-golay'
- 'mean'
- 'median'
doc: Runningmedian or runningpoly or Savitzky-Golay or mean or median (these last two values set all the solutions to the mean/median), by default "runningmedian".
- id: degree
type: int?
doc: Degrees of the polynomia for the runningpoly or savitzky-golay modes, by default 1.
- id: replace
type: boolean?
doc: Flagged data are replaced with smoothed value and unflagged, by default False.
- id: log
type: boolean?
doc: clip is done in log10 space, by default False
- id: refAnt
type: string?
doc: Reference antenna for phases. By default None.
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",
"axesToSmooth": ["time"],
"mode": "median"
}
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