Commit cfecd9f6 authored by mancini's avatar mancini

Merge branch 'add_losoto_polalign' into 'master'

Add losoto polalign

See merge request !1
parents 968a5ccd 46e4fc97
Pipeline #423 passed with stages
in 3 minutes and 41 seconds
......@@ -105,6 +105,13 @@ losoto_residual:
script:
- cwl-runner --no-container steps/LoSoTo.Residual.cwl test_jobs/losoto_residual.json
losoto_polalign:
stage: test_steps
allow_failure: true
script:
- cwl-runner --no-container steps/LoSoTo.Polalign.cwl test_jobs/losoto_polalign.json
parset_selector:
stage: test_steps
allow_failure: true
......@@ -116,6 +123,7 @@ file_selector:
allow_failure: true
script:
- cwl-runner steps/FileSelector.cwl test_jobs/file_selector.json
NDPPP:
stage: test_steps
......
class: CommandLineTool
cwlVersion: v1.0
id: losoto_polalign
$namespaces:
lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
$schema:
- https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
doc: |
Estimate polarization misalignment as delay
requirements:
InlineJavascriptRequirement:
expressionLib:
- |
function get_config() {
var par = ['soltab = ' + inputs.soltab]
if (inputs.ncpu !== null) par.push('ncpu='+inputs.ncpu);
par.push('[polalign]')
par.push('operation = POLALIGN')
for(var field_name in inputs){
if(field_name === 'input_h5parm' ||
field_name === 'soltab' ||
field_name === 'ncpu') continue;
if(inputs[field_name] === null ||
inputs[field_name] === 'null') continue;
par.push(field_name+'='+inputs[field_name])
}
return par
}
InitialWorkDirRequirement:
listing:
- entryname: 'parset.config'
entry: $(get_config().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: soltabout
default: phasediff
type: string?
doc: output table name (same solset)
- id: maxResidual
type: float?
default: 1
doc: Maximum acceptable rms of the residuals in radians before flagging. Set to zero to avoid the check.
- id: fitOffset
type: boolean?
default: false
doc: Assume that together with a delay each station has also a differential phase offset (important for old LBA observations).
- id: average
type: boolean?
default: false
doc: Mean-average in time the resulting delays/offset.
- id: replace
type: boolean?
default: false
doc: replace using smoothed value instead of flag bad data? Smooth must be active.
- id: refAnt
type: string?
doc: Reference antenna, if not set use the first one.
outputs:
- id: output_h5parm
type: File
format: lofar:#H5Parm
outputBinding:
glob: $(inputs.input_h5parm.basename)
{
"input_h5parm": {
"class": "File",
"path": "/data/example.h5",
"format": "lofar:#H5Parm"
},
"soltab": "sol000/amplitude000",
"average": true
}
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