From 274162b064bc70364d29bec54df953a970f6aedf Mon Sep 17 00:00:00 2001
From: Alexander Drabent <alex@tls-tautenburg.de>
Date: Wed, 28 Oct 2020 13:57:40 +0100
Subject: [PATCH] add structure function
Former-commit-id: 635f6d0a11c4f6e7a11e14df0a9b3a200d7b310d
---
steps/structure_function.cwl | 62 +++++++++++++++++++++++++
workflows/prefactor_target.cwl | 2 +
workflows/prefactor_target/finalize.cwl | 51 ++++++++++++++++++--
3 files changed, 112 insertions(+), 3 deletions(-)
create mode 100644 steps/structure_function.cwl
diff --git a/steps/structure_function.cwl b/steps/structure_function.cwl
new file mode 100644
index 00000000..434d75f0
--- /dev/null
+++ b/steps/structure_function.cwl
@@ -0,0 +1,62 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
+ sbg: 'https://www.sevenbridges.com/'
+id: structure_function
+baseCommand:
+ - python3
+ - /usr/local/bin/getStructure_from_phases.py
+inputs:
+ - format: 'lofar:#H5Parm'
+ id: h5parmFile
+ type: File
+ inputBinding:
+ position: 0
+ doc: List of h5parm files
+ - default: 'target'
+ id: solset
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--solset'
+ doc: Input solset name
+ - default: 'phase000'
+ id: soltab
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--soltab'
+ doc: Name of the soltab
+ - default: 'POINTING'
+ id: outbasename
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: '--outbasename'
+ doc: Namebase of the output files
+outputs:
+ - id: structure_plot
+ doc: Output plot
+ type: File
+ outputBinding:
+ glob: $(inputs.outbasename+'_structure.png')
+ - id: structure_txt
+ doc: Output text
+ type: File
+ outputBinding:
+ glob: $(inputs.outbasename+'_structure.txt')
+ - id: log
+ type: File[]
+ outputBinding:
+ glob: 'structure_function*.log'
+label: structure_function
+requirements:
+ - class: InlineJavascriptRequirement
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor:HBAcalibrator
+stdout: structure_function.log
+stderr: structure_function_err.log
+$schema:
+ - 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
diff --git a/workflows/prefactor_target.cwl b/workflows/prefactor_target.cwl
index b1ab4477..f2082880 100644
--- a/workflows/prefactor_target.cwl
+++ b/workflows/prefactor_target.cwl
@@ -242,6 +242,7 @@ outputs:
- id: inspection
outputSource:
- prep/inspection
+ - finalize/inspection
type: 'File[]'
linkMerge: merge_flattened
'sbg:x': 2000
@@ -404,6 +405,7 @@ steps:
out:
- id: msout
- id: solutions
+ - id: inspection
- id: logfiles
run: ./prefactor_target/finalize.cwl
label: finalize
diff --git a/workflows/prefactor_target/finalize.cwl b/workflows/prefactor_target/finalize.cwl
index f4949a37..1b3ab905 100644
--- a/workflows/prefactor_target/finalize.cwl
+++ b/workflows/prefactor_target/finalize.cwl
@@ -46,22 +46,30 @@ outputs:
outputSource:
- apply_gsmcal/msout
type: 'Directory[]'
- 'sbg:x': 1000
+ 'sbg:x': 1300
'sbg:y': 0
- id: solutions
outputSource:
- h5parm_pointingname/outh5parm
type: File
- 'sbg:x': 1000
+ 'sbg:x': 1300
'sbg:y': 200
- id: logfiles
outputSource:
- concat_logfiles_applygsm/output
- concat_logfiles_solutions/output
+ - concat_logfiles_structure/output
type: 'File[]'
linkMerge: merge_flattened
- 'sbg:x': 1000
+ 'sbg:x': 1300
'sbg:y': 800
+ - id: inspection
+ outputSource:
+ - structure_function/structure_plot
+ type: 'File[]?'
+ linkMerge: merge_flattened
+ 'sbg:x': 1300
+ 'sbg:y': 500
steps:
- id: add_missing_stations
in:
@@ -169,6 +177,27 @@ steps:
label: h5parm_pointingname
'sbg:x': 400
'sbg:y': 200
+ - id: structure_function
+ in:
+ - id: h5parmFile
+ source: write_solutions/outh5parm
+ - id: solset
+ default: 'target'
+ - id: soltab
+ source:
+ - skymodel_source
+ - gsmcal_step
+ valueFrom: $(self.join(''))
+ - id: outbasename
+ source: get_targetname/targetname
+ out:
+ - id: structure_plot
+ - id: structure_txt
+ - id: log
+ run: ../../steps/structure_function.cwl
+ label: structure_function
+ 'sbg:x': 500
+ 'sbg:y': 300
- id: concat_logfiles_applygsm
in:
- id: file_list
@@ -200,6 +229,22 @@ steps:
label: concat_logfiles_solutions
'sbg:x': 500
'sbg:y': 500
+ - id: concat_logfiles_structure
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - structure_function/log
+ - structure_function/structure_txt
+ - id: file_prefix
+ source: get_targetname/targetname
+ valueFrom: $(self+'_structure')
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_structure
+ 'sbg:x': 950
+ 'sbg:y': 500
- id: get_targetname
in:
- id: msin
--
GitLab