segmentation_shape consistency - #463
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TeunHuijben
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #463 +/- ##
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- Coverage 88.87% 88.86% -0.02%
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Files 59 59
Lines 5844 5845 +1
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Hits 5194 5194
- Misses 650 651 +1 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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🔴 Blocked by Funtracks PR: funkelab/funtracks#260 (which is merged, but not yet released) |
…two places in the zattrs (within geff, and in top level)
cmalinmayor
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Aug 20, 2026
| df = pd.DataFrame( | ||
| { | ||
| "Benchmark": new_df["Benchmark"], | ||
| f"Median (s) HEAD {new_commit}": new_df["median"].map("{:.5f}".format), |
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Are the benchmarking diffs still needed? Or covered by main by now?
cmalinmayor
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Aug 20, 2026
cmalinmayor
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Claude assures me the benchmark changes are nice improvements 🙃 You might want to look at my changes before you merge, so I'll leave clicking the button to you @TeunHuijben
🍅 👍 🎉 🌮
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Problem:
Solution:
This PR removes the segmentation_shape logic, and fully uses the existing tracksdata format of saving the shape in metadata.extra.tracksdata.shape. When reading the shape from the metadata we do a double check for backwards compatibility.
For geffs that are exported from motile_tracker and then imported, it doesn't matter where we save the shape, because that is an internal discussion. But for geffs exported by other tracksdata-based tracking tools (ultrack, hoct, etc.), we are now natively compatible.