Commit 3514a5b4 authored by mancini's avatar mancini

Merge branch 'LoSoTo-Flagextend' into 'master'

Add Flagextend - Resolves EOSC-26

See merge request !7
parents 17f06eca ed15f74f
Pipeline #486 passed with stages
in 3 minutes and 31 seconds
......@@ -114,6 +114,11 @@ losoto_clip:
allow_failure: true
script:
- cwl-runner --no-container steps/LoSoTo.Clip.cwl test_jobs/losoto_clip.json
losoto_flagextend:
stage: test_steps
allow_failure: true
script:
- cwl-runner --no-container steps/LoSoTo.Flagextend.cwl test_jobs/losoto_flagextend.json
losoto_faraday:
stage: test_steps
......
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.0
id: losoto_flagextend
$namespaces:
lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
doc: |
This operation for LoSoTo implement a extend flag procedure.
It can work in multi dimensional space and for each datum check if the
surrounding data are flagged to a certain %, then flag also that datum.
The size of the surrounding footprint can be tuned
requirements:
InlineJavascriptRequirement:
expressionLib:
- { $include: utils.js}
InitialWorkDirRequirement:
listing:
- entryname: 'parset.config'
entry: $(get_losoto_config('FLAGEXTEND').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: axesToExt
type: string[]
doc: Axes used to find close flags.
- id: size
type: int[]
doc: |
Size of the window (diameter), per axis. If 0 is given then the entire
length of the axis is assumed.
Must be a vector of same length of Axes.
- id: percent
type: float?
doc: Percent of flagged data around the point to flag it, by default 50.
- id: maxCycles
type: int?
doc: Number of independent cycles of flag expansion, by default 3.
- id: ncpu
type: int?
doc: Number of CPU used, 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",
"axesToExt": ["time"],
"size": [0]
}
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