From 526658462120c63e2daf38a138ba07ce19362ecc Mon Sep 17 00:00:00 2001
From: Alexander Drabent <alex@tls-tautenburg.de>
Date: Mon, 4 Dec 2023 09:56:08 +0100
Subject: [PATCH] fix predict step in LBA_target
---
steps/wsclean.cwl | 9 ++++++-
workflows/linc_target/imaging_subtract.cwl | 28 +++++++++++++++++++---
2 files changed, 33 insertions(+), 4 deletions(-)
diff --git a/steps/wsclean.cwl b/steps/wsclean.cwl
index e435d8bb..42c08c02 100644
--- a/steps/wsclean.cwl
+++ b/steps/wsclean.cwl
@@ -265,7 +265,9 @@ inputs:
shellQuote: false
- id: image_name
default: 'pointing'
- type: string?
+ type:
+ - string?
+ - File?
inputBinding:
position: 1
prefix: '-name'
@@ -284,6 +286,11 @@ inputs:
position: 1
prefix: '-predict'
shellQuote: false
+ - id: padding
+ type: float?
+ inputBinding:
+ position: 1
+ prefix: -padding
- id: baseline_averaging
default: false
type: float?
diff --git a/workflows/linc_target/imaging_subtract.cwl b/workflows/linc_target/imaging_subtract.cwl
index 8f4e6264..74e3b942 100644
--- a/workflows/linc_target/imaging_subtract.cwl
+++ b/workflows/linc_target/imaging_subtract.cwl
@@ -233,7 +233,7 @@ steps:
- id: tempdir
source: wsclean_tmpdir
- id: do_predict
- default: true
+ default: false
- id: reuse_dirty
source: make_mask_image/dirty_image
- id: reuse_psf
@@ -245,10 +245,30 @@ steps:
- id: logfile
run: ../../steps/wsclean.cwl
label: image_predict
+ - id: predict_wsclean
+ in:
+ - id: msin
+ source: make_mask_image/msout # workaround for CWL bug (https://github.com/common-workflow-language/cwltool/issues/1785)
+ - id: image_name
+ source: image_predict/image
+ - id: padding
+ default: 1.8
+ - id: channels-out
+ source: total_bandwidth
+ valueFrom: '$(Math.round(self/4.e6) > 0 ? Math.round(self/4.e6) : 1)'
+ - id: tempdir
+ source: wsclean_tmpdir
+ - id: do_predict
+ default: true
+ out:
+ - id: msout
+ - id: logfile
+ run: ../../steps/wsclean.cwl
+ label: predict_wsclean
- id: subtract_model
in:
- id: msin
- source: image_predict/msout
+ source: predict_wsclean/msout
- id: command
default: "set CORRECTED_DATA = CORRECTED_DATA - MODEL_DATA"
out:
@@ -559,7 +579,6 @@ steps:
- make_mask_image/logfile
- make_mask/logfile
- blank_image_reg/logfile
- - image_predict/logfile
linkMerge: merge_flattened
pickValue: all_non_null
- id: file_prefix
@@ -588,6 +607,8 @@ steps:
in:
- id: file_list
source:
+ - image_predict/logfile
+ - predict_wsclean/logfile
- merge_array_files/output
linkMerge: merge_flattened
- id: file_prefix
@@ -600,6 +621,7 @@ steps:
in:
- id: file_list
source:
+ - image_tmp/logfile
- make_beam_reg/logfile
- blank_image_reg_1/logfile
- blank_image_reg_2/logfile
--
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