From fd89c06fd51aa5086180628e62e926295372b67b Mon Sep 17 00:00:00 2001
From: Alexander Drabent <alex@tls-tautenburg.de>
Date: Thu, 15 Jul 2021 10:39:38 +0200
Subject: [PATCH] bugfixes + only apply element beam for target
Former-commit-id: d85209357c1f06e1e73a89253446a1ef1b629360
---
lofar-cwl/steps/makesourcedb.cwl | 9 +++++++--
steps/find_skymodel_cal.cwl | 2 +-
steps/transfer_solutions.cwl | 2 +-
subworkflow/prep_target_applycal.cwl | 2 +-
subworkflow/smooth_calibrate.cwl | 2 +-
workflows/prefactor_target/finalize.cwl | 4 +++-
6 files changed, 14 insertions(+), 7 deletions(-)
diff --git a/lofar-cwl/steps/makesourcedb.cwl b/lofar-cwl/steps/makesourcedb.cwl
index 97b23e5f..521981fa 100755
--- a/lofar-cwl/steps/makesourcedb.cwl
+++ b/lofar-cwl/steps/makesourcedb.cwl
@@ -10,11 +10,12 @@ inputs:
type:
- File
- string
- default: '/data/skymodels/Ateam_LBA_CC.skymodel'
+ default: '$PREFACTOR_DATA_ROOT/skymodels/Ateam_LBA_CC.skymodel'
inputBinding:
position: 0
prefix: in=
separate: false
+ shellQuote: false
- default: Ateam.sourcedb
id: output_file_name
type: string?
@@ -23,6 +24,7 @@ inputs:
prefix: out=
separate: false
valueFrom: $(inputs.output_file_name)
+ shellQuote: false
- default: blob
id: outtype
type: string?
@@ -30,13 +32,15 @@ inputs:
position: 2
prefix: outtype=
separate: false
- - default: <
+ shellQuote: false
+ - default: '"<"'
id: format
type: string?
inputBinding:
position: 3
prefix: format=
separate: false
+ shellQuote: false
- default: make_sourcedb.log
id: logname
type: string?
@@ -58,3 +62,4 @@ hints:
stdout: $(inputs.logname)
requirements:
- class: InlineJavascriptRequirement
+ - class: ShellCommandRequirement
\ No newline at end of file
diff --git a/steps/find_skymodel_cal.cwl b/steps/find_skymodel_cal.cwl
index 98c665d5..e5ad659a 100644
--- a/steps/find_skymodel_cal.cwl
+++ b/steps/find_skymodel_cal.cwl
@@ -71,7 +71,7 @@ requirements:
max_separation_arcmin = 1.0 if max_separation_arcmin is None else max_separation_arcmin
extension = "$(inputs.skymodels_extension)"
if skymodels is None:
- skymodels = "/data/skymodels"
+ skymodels = os.path.expandvars("$PREFACTOR_DATA_ROOT/skymodels")
else:
skymodels = skymodels["path"]
output = {}
diff --git a/steps/transfer_solutions.cwl b/steps/transfer_solutions.cwl
index e92ba2e4..65c53c38 100644
--- a/steps/transfer_solutions.cwl
+++ b/steps/transfer_solutions.cwl
@@ -17,7 +17,7 @@ inputs:
type:
- File?
- string?
- default: '/data/solutions/3C48.h5'
+ default: '$PREFACTOR_DATA_ROOT/solutions/3C48.h5'
inputBinding:
position: 0
prefix: '--refh5parm'
diff --git a/subworkflow/prep_target_applycal.cwl b/subworkflow/prep_target_applycal.cwl
index e3968609..04036992 100644
--- a/subworkflow/prep_target_applycal.cwl
+++ b/subworkflow/prep_target_applycal.cwl
@@ -131,7 +131,7 @@ steps:
- id: invert
default: true
- id: beammode
- default: default
+ default: element
out:
- id: augmented_steps
run: ../lofar-cwl/steps/DP3.ApplyBeamStepGenerator.cwl
diff --git a/subworkflow/smooth_calibrate.cwl b/subworkflow/smooth_calibrate.cwl
index 29fb52a9..8995c3b0 100644
--- a/subworkflow/smooth_calibrate.cwl
+++ b/subworkflow/smooth_calibrate.cwl
@@ -65,7 +65,7 @@ steps:
label: smooth_corrected
scatter:
- msin
- scatterMethod: flat_crossproduct
+# scatterMethod: flat_crossproduct
'sbg:x': -394
'sbg:y': -29
- id: calib_cal
diff --git a/workflows/prefactor_target/finalize.cwl b/workflows/prefactor_target/finalize.cwl
index 8543d90c..fb5429cb 100644
--- a/workflows/prefactor_target/finalize.cwl
+++ b/workflows/prefactor_target/finalize.cwl
@@ -140,7 +140,7 @@ steps:
scatter:
- msin
- msout_name
- scatterMethod: flat_crossproduct
+ scatterMethod: dotproduct
'sbg:x': 400
'sbg:y': 0
- id: average
@@ -171,6 +171,8 @@ steps:
label: average
scatter:
- msin
+ - msout_name
+ scatterMethod: dotproduct
'sbg:x': 600
'sbg:y': -200
- id: wsclean
--
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