Commit c5d6ae5c authored by mancini's avatar mancini

Add Interpolate step

parent 2e6c1f1d
......@@ -130,6 +130,11 @@ losoto_faraday:
script:
- cwl-runner --no-container steps/LoSoTo.Faraday.cwl test_jobs/losoto_faraday.json
losoto_interpolate:
stage: test_steps
allow_failure: true
script:
- cwl-runner --no-container steps/LoSoTo.Interpolate.cwl test_jobs/losoto_interpolate.json
losoto_residual:
stage: test_steps
allow_failure: true
......
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.0
id: losoto_interpolate
$namespaces:
lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
doc: |
This operation for LoSoTo implements regridding and linear interpolation of data for an axis.
WEIGHT: compliant
requirements:
InlineJavascriptRequirement:
expressionLib:
- { $include: utils.js}
InitialWorkDirRequirement:
listing:
- entryname: 'parset.config'
entry: $(get_losoto_config('INTERPOLATE').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: axisToRegrid
type: string
doc: Name of the axis for which regridding/interpolation will be done
- id: outSoltab
type: string
doc: Output sol tab name
- id: newdelta
type: string
doc: Fundamental width between samples after regridding. E.g., "100kHz" or "10s"
- id: delta
type: string?
doc: |
Fundamental width between samples in axisToRegrid. E.g., "100kHz" or "10s". If "",
it is calculated from the axisToRegrid values
- id: maxFlaggedWidth
type: int?
doc: |
Maximum allowable width in number of samples (after regridding) above which
interpolated values are flagged (e.g., maxFlaggedWidth = 5 would allow gaps of
5 samples or less to be interpolated across but gaps of 6 or more would be
flagged)
- id: log
type: boolean?
doc: Interpolation is done in log10 space, by default False
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",
"axisToRegrid": "time",
"newdelta": "1s",
"outSoltab": "timeout"
}
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