Merge branch 'LoSoTo-Reweight' into 'master'

Add LoSoTo reweight

See merge request eosc/lofar-cwl!10

Former-commit-id: e2e6fb51 [formerly b70fd69f]
Former-commit-id: 4cd6a884
Former-commit-id: 3aa5cbc0

.gitlab-ci.yml

@@ -135,6 +135,14 @@ losoto_interpolate:
   allow_failure: true
   script:
     - cwl-runner --no-container steps/LoSoTo.Interpolate.cwl test_jobs/losoto_interpolate.json
+
+losoto_reweight:
+  stage: test_steps
+  allow_failure: true
+  script:
+   - cwl-runner --no-container steps/LoSoTo.Reweight.cwl test_jobs/losoto_reweight.json
+
+
 losoto_residual:
   stage: test_steps
   allow_failure: true

steps/LoSoTo.Reweight.cwl

+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+id: losoto_reweight
+
+$namespaces:
+  lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+doc: |
+  Change the the weight values.
+  Parameters
+
+
+requirements:
+  InlineJavascriptRequirement:
+    expressionLib:
+      - { $include: utils.js}
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: 'parset.config'
+        entry: $(get_losoto_config('REWEIGHT').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: mode
+    default: 'uniform'
+    type:
+      - type: enum
+        symbols:
+          - uniform
+          - window
+          - copy
+    doc: One of 'uniform' (single value), 'window' (sliding window in time), or 'copy' (copy from another table), by default 'uniform'.
+  - id: weightVal
+    type: float?
+    doc: Set weights to this values (0=flagged), by default 1.
+  - id: nmedian
+    type: int?
+    doc: |
+      Median window size in number of timeslots for 'window' mode.
+      If nonzero, a median-smoothed version of the input values is
+      subtracted to detrend them. If 0, no smoothing or subtraction is
+      done, by default 3.
+  - id: nstddev
+    type: int?
+    doc: Standard deviation window size in number of timeslots for 'window' mode, by default 251.
+  - id: soltabImport
+    type: string?
+    doc: Name of a soltab. Copy weights from this soltab (must have same axes shape), by default none.
+  - id: flagBad
+    type: boolean?
+    doc: Re-apply flags to bad values (1 for amp, 0 for other tables), 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

steps/utils.js

 function get_losoto_config(step_name) {
     var par = ['soltab = ' + inputs.soltab]
-    if (inputs.ncpu !== null) par.push('ncpu='+inputs.ncpu);
+    if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);
+    console.log(inputs, par)
     par.push("[" + step_name + "]")
     par.push('operation=' + step_name)
     for(var field_name in inputs){

test_jobs/losoto_reweight.json

+{
+  "input_h5parm": {"class": "File", "path": "/data/example.h5", "format": "lofar:#H5Parm"},
+  "soltab":  "sol000/phase000"
+}