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Fix bug that arose when users would supply --fixed-posns in the cli #181

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Merged
HannoSpreeuw merged 4 commits into from
Dec 2, 2025
Merged

Fix bug that arose when users would supply --fixed-posns in the cli #181

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1c255da
Fix bug that arose when users would supply --fixed-posns in the cli
tmillenaar Nov 28, 2025
c4ca71c
Add test for fixed-posns arg in pyse and check the number of csv rows…
tmillenaar Dec 1, 2025
2384641
Raise appropriate error if fixed-posns is used in conjunction with ei…
tmillenaar Dec 2, 2025
2ef2caf
Fix silly formulation of error
tmillenaar Dec 2, 2025
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8 changes: 4 additions & 4 deletions sourcefinder/utility/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -160,10 +160,10 @@ def construct_argument_parser():
"--structuring-element",
type=ast.literal_eval,
help="""
Structuring element for morphological operations, provided as a
Python-style nested list, e.g. '[[1,1,1], [1,1,1], [1,1,1]]' for
Structuring element for morphological operations, provided as a
Python-style nested list, e.g. '[[1,1,1], [1,1,1], [1,1,1]]' for
8-connectivity and '[[0,1,0], [1,1,1], [0,1,0]]' for 4-connectivity.
This is used for defining the connectivity in connected-component
This is used for defining the connectivity in connected-component
labelling.
""",
)
Expand Down Expand Up @@ -577,7 +577,7 @@ def run_sourcefinder(files, conf, mode):
if mode == "fixed":
# FIXME: conf.image.fixed_coords does not exist
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sr = imagedata.fit_fixed_positions(
conf.image.fixed_coords,
eval(conf.image.fixed_posns), # fixed_posns is a string, use eval to obtain it's contents
conf.image.ffbox * max(imagedata.beam[0:2]),
)

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2 changes: 1 addition & 1 deletion test/test_scripts/test_pyse.py
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Expand Up @@ -36,7 +36,7 @@ def test_pyse_export(tmpdir):
"--residuals",
"--islands",
]
extra_args = ["--detection-thr", "6", "--analysis-thr", "5", *export_args]
extra_args = ["--detection-thr", "6", "--analysis-thr", "5", "--fixed-posns", "[[136.896, 14.0222]]", *export_args]
nr_sources_per_image = run_pyse(files, extra_args, tmpdir)

for n in nr_sources_per_image:
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