From 7365542dd1cfbd645796c1a5cd573ac8740f51ba Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Tue, 14 Jan 2020 10:11:46 +0100
Subject: [PATCH] Add Smooth step
Former-commit-id: 382cea5b2a969c4c6e530a32cf2dc0b1de5a79da
---
.gitlab-ci.yml | 6 +++
steps/LoSoTo.Smooth.cwl | 86 ++++++++++++++++++++++++++++++++++++
test_jobs/losoto_smooth.json | 6 +++
3 files changed, 98 insertions(+)
create mode 100644 steps/LoSoTo.Smooth.cwl
create mode 100644 test_jobs/losoto_smooth.json
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d31f3ae7..ba19298f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -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
diff --git a/steps/LoSoTo.Smooth.cwl b/steps/LoSoTo.Smooth.cwl
new file mode 100644
index 00000000..cdf67851
--- /dev/null
+++ b/steps/LoSoTo.Smooth.cwl
@@ -0,0 +1,86 @@
+#!/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
diff --git a/test_jobs/losoto_smooth.json b/test_jobs/losoto_smooth.json
new file mode 100644
index 00000000..00672d3c
--- /dev/null
+++ b/test_jobs/losoto_smooth.json
@@ -0,0 +1,6 @@
+{
+ "input_h5parm": {"class": "File", "path": "/data/example.h5", "format": "lofar:#H5Parm"},
+ "soltab": "sol000/phase000",
+ "axesToSmooth": ["time"],
+ "mode": "median"
+}
--
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