From 1d7b892ef4457c23b03e878490781714615981b9 Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Fri, 10 Jan 2020 14:27:50 +0100
Subject: [PATCH] Add LoSoTo Flag step
Former-commit-id: 7bc9bb09a5cfab206a38ce6b38d8e12910467b9f
---
.gitlab-ci.yml | 6 ++-
steps/LoSoTo.Flag.cwl | 105 +++++++++++++++++++++++++++++++++++++
test_jobs/losoto_flag.json | 6 +++
3 files changed, 116 insertions(+), 1 deletion(-)
create mode 100644 steps/LoSoTo.Flag.cwl
create mode 100644 test_jobs/losoto_flag.json
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 78e53fe0..e82264fd 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -86,7 +86,11 @@ losoto_plot:
allow_failure: true
script:
- cwl-runner --no-container steps/LoSoTo.Plot.cwl test_jobs/losoto_plot.json
-
+losoto_flag:
+ stage: test_steps
+ allow_failure: true
+ script:
+ - cwl-runner --no-container steps/LoSoTo.Flag.cwl test_jobs/losoto_flag.json
losoto_norm:
stage: test_steps
allow_failure: true
diff --git a/steps/LoSoTo.Flag.cwl b/steps/LoSoTo.Flag.cwl
new file mode 100644
index 00000000..30dbd164
--- /dev/null
+++ b/steps/LoSoTo.Flag.cwl
@@ -0,0 +1,105 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+id: losoto_flag
+
+$namespaces:
+ lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+doc: |
+ This operation for LoSoTo implement a flagging procedure
+ WEIGHT: compliant
+
+
+requirements:
+ InlineJavascriptRequirement:
+ expressionLib:
+ - { $include: utils.js}
+ InitialWorkDirRequirement:
+ listing:
+ - entryname: 'parset.config'
+ entry: $(get_losoto_config('FLAG').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: axesToFlag
+ type: string[]
+ doc: Axes along which to smooth+find outlier (e.g. ['time', 'freq']), max 2 values.
+ - id: order
+ type: int[]
+ doc: |
+ Order of the function fitted during detrending.
+ Array must have same size of axesToFlag.
+ If mode=smooth these are the window of the running median (0=all axis).
+ - id: maxCycles
+ type: int?
+ doc: Max number of independent flagging cycles, by default 5.
+ - id: maxRms
+ type: float?
+ doc: Rms to clip outliers, by default 5.
+ - id: maxRmsNoise
+ type: float?
+ doc: |
+ Do a running rms and then flag those regions that have a rms higher
+ than MaxRmsNoise*rms_of_rmses, by default 0 (ignored).
+ - id: fixRms
+ type: float?
+ doc: Instead of calculating rms use this value, by default 0 (ignored).
+ - id: fixRmsNoise
+ type: float?
+ doc: |
+ Instead of calculating rms of the rmses use this value
+ (it will not be multiplied by the MaxRmsNoise), by default 0 (ignored).
+ - id: windowNoise
+ type: int?
+ doc: Window size for the running rms, by default 11.
+
+ - id: replace
+ type: boolean?
+ doc: |
+ Replace bad values with the interpolated ones,
+ instead of flagging them. By default False.
+ - id: preflagzeros
+ type: boolean?
+ doc:
+ Flag zeros/ones (bad solutions in BBS/DPPP).
+ They should be flagged at import time. By default False.
+ - id: mode
+ type: string?
+ doc: |
+ Detrending/fitting algorithm: smooth / poly / spline.
+ By default smooth.
+ - id: refAnt
+ type: string?
+ doc: Reference antenna, by default None.
+ - id: ncpu
+ type: int?
+ doc: Number of cpu to use, 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
diff --git a/test_jobs/losoto_flag.json b/test_jobs/losoto_flag.json
new file mode 100644
index 00000000..f1ce6b2f
--- /dev/null
+++ b/test_jobs/losoto_flag.json
@@ -0,0 +1,6 @@
+{
+ "input_h5parm": {"class": "File", "path": "/data/example.h5", "format": "lofar:#H5Parm"},
+ "soltab": "sol000/phase000",
+ "axesToFlag": ["time"],
+ "order": [0]
+}
--
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