Fix path_length silently ignored in CalculateImageStats - #393
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animmosmith wants to merge 3 commits into
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Fix path_length silently ignored in CalculateImageStats#393animmosmith wants to merge 3 commits into
animmosmith wants to merge 3 commits into
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data['settings']['general'] is a plain dict, so
getattr(general, 'path_length', 40) always returned the default,
silently ignoring any path_length configured in config.toml when
calculating volume concentration (vc) and sample_volume. Every
existing test happened to use path_length=40, masking the bug.
Use general.get('path_length', 40) instead, and add a regression
test with a non-default path_length to catch this in future.
Fixes #363
animmosmith
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animmosmith
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* add 'pyopia --version' command * bump version (merge PR #393 first) * adjust version --------- Co-authored-by: Alex Nimmo Smith <animmosmith@users.noreply.github.com>
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Summary
CalculateImageStats.__call__read the configuredpath_lengthviagetattr(data['settings']['general'], 'path_length', 40). Sincedata['settings']['general']is a plaindict,getattrnever finds the key (dicts don't expose their contents as attributes), so this always silently returned the default40regardless of what was configured inconfig.toml. This affects the volume concentration (vc) andsample_volumeoutputs.path_length=40.0, so the bug produced no test failures.general.get('path_length', 40)), consistent with howPerClassConcentrationalready reads it.path_length(123.0) that fails against the old code and passes against the fix.This closes out #363, which asked for
imx/imy(CCD pixel dimensions) to be propagated intonc_vc_from_stats— that part was already fixed by #369 for the related/duplicate issue #366, which derivesimx/imyfrom the actual raw image shape rather than threading them through config. This PR fixes thepath_lengthregression that #369 introduced along the way.Test plan
pytest pyopia/tests/test_pipeline.pypasses (4 passed)flake8shows no new issues