From 6938d209acb1f094eaae45a41fc775fee53905bd Mon Sep 17 00:00:00 2001
From: David Rafferty <drafferty@hs.uni-hamburg.de>
Date: Mon, 23 Oct 2023 13:16:11 +0000
Subject: [PATCH] Adjust merge to exclude duplicate components
---
scripts/merge_skymodels.py | 34 ++++++++++++++++++++++++++++------
steps/merge_skymodels.cwl | 17 +++++++++++++++++
2 files changed, 45 insertions(+), 6 deletions(-)
diff --git a/scripts/merge_skymodels.py b/scripts/merge_skymodels.py
index a7e97f71..2baf2138 100755
--- a/scripts/merge_skymodels.py
+++ b/scripts/merge_skymodels.py
@@ -5,12 +5,28 @@ Append a LOFAR skymodel to an existing one
import os, logging
import lsmtool
-import numpy
########################################################################
-def main(inmodel1, inmodel2, outmodel = 'output.skymodel'):
-
+def main(inmodel1, inmodel2, outmodel = 'output.skymodel', radius=30/3600, keep='from2'):
+ """
+ Merge two LOFAR skymodel text files.
+
+ Parameters
+ ----------
+ inmodel1 : str
+ Name (path) of input model #1
+ inmodel2 : str
+ Name (path) of input model #2
+ outmodel : str, optional
+ Name (path) of output merged model
+ radius : float, optional
+ Matching radius in degrees for determining duplicates
+ keep : str, optional
+ When duplicates are found, keep those from model #1 ('from1') or from
+ model #2 ('from2')
+ """
+
logging.info('Reading ' + inmodel1)
s1 = lsmtool.load(inmodel1)
logging.info('Reading ' + inmodel2)
@@ -22,7 +38,10 @@ def main(inmodel1, inmodel2, outmodel = 'output.skymodel'):
s2.group('single')
logging.info('Adding skymodel ' + inmodel2 + ' to ' + inmodel1)
- s1.concatenate(s2, inheritPatches=True)
+
+ # The following call will merge the two models, identifing (by position) duplicate
+ # sources/components that are present in both
+ s1.concatenate(s2, matchBy='position', radius=radius, keep=keep)
s1.setPatchPositions()
s1.write(outmodel)
@@ -36,11 +55,14 @@ if __name__ == '__main__':
parser.add_argument('--inmodel1', type=str, default=None, help='input/output skymodel.')
parser.add_argument('--inmodel2', type=str, default=None, help='skymodel to append')
parser.add_argument('--outmodel', type=str, default='output.skymodel', help='output skymodel name')
+ parser.add_argument('--radius', type=float, default=30/3600, help='matching radius in degrees')
+ parser.add_argument('--keep', type=str, default='from2', help='keep duplicates from model 1 or 2')
args = parser.parse_args()
format_stream = logging.Formatter("%(asctime)s\033[1m %(levelname)s:\033[0m %(message)s","%Y-%m-%d %H:%M:%S")
format_file = logging.Formatter("%(asctime)s %(levelname)s: %(message)s","%Y-%m-%d %H:%M:%S")
logging.root.setLevel(logging.INFO)
-
- main(inmodel1 = os.path.expandvars(args.inmodel1), inmodel2 = os.path.expandvars(args.inmodel2), outmodel = os.path.expandvars(args.outmodel))
+
+ main(inmodel1 = os.path.expandvars(args.inmodel1), inmodel2 = os.path.expandvars(args.inmodel2),
+ outmodel = os.path.expandvars(args.outmodel), radius=args.radius, keep=args.keep)
diff --git a/steps/merge_skymodels.cwl b/steps/merge_skymodels.cwl
index 45d7b41a..8a99b557 100755
--- a/steps/merge_skymodels.cwl
+++ b/steps/merge_skymodels.cwl
@@ -29,6 +29,23 @@ inputs:
prefix: --outmodel=
separate: false
shellQuote: false
+ - id: radius
+ type: float?
+ default: 0.00833
+ inputBinding:
+ prefix: --radius=
+ separate: false
+ shellQuote: false
+ doc: Matching radius in degrees for identifying duplicate components
+ - id: keep
+ type: string?
+ default: 'from2'
+ inputBinding:
+ prefix: --keep=
+ separate: false
+ shellQuote: false
+ doc: Keep duplicate components from model 1 or model 2
+
outputs:
- id: skymodel_out
type: File
--
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