[ENH] MDS: Show Kruskal stress#6309
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lanzagar merged 1 commit intobiolab:masterfrom Feb 17, 2023
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Additional details and impacted files@@ Coverage Diff @@
## master #6309 +/- ##
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Coverage 87.47% 87.48%
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Files 316 316
Lines 68085 68115 +30
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+ Hits 59556 59589 +33
+ Misses 8529 8526 -3 |
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lanzagar
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Feb 2, 2023
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| self.embedding = None # type: Optional[np.ndarray] | ||
| self.effective_matrix = None # type: Optional[DistMatrix] | ||
| self.stress = None |
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As shown by failing tests, this conflicts with the static method with the same name.
This results in a crash when setting the size of points to "Stress".
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It's not that I don't warn students about this exact mistake.
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lanzagar
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| def _compute_stress(self): | ||
| if self.embedding is None or self.effective_matrix is None: | ||
| return None | ||
| actual = scipy.spatial.distance.pdist(self.embedding) | ||
| actual = scipy.spatial.distance.squareform(actual) | ||
| return np.sqrt(np.sum((actual - self.effective_matrix) ** 2) | ||
| / (np.sum(self.effective_matrix ** 2) or 1)) |
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It would probably be better to call get_stress and normalize the returned result.
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Issue
Fixes #6070.
Description of changes
To reviewer: please check that I indeed called
update_stressfrom all places where it's needed -- and that it's not called multiple times.I don't know where to show the stress. Optimization box was about the best place. I don't want to put it on the graph, because then we'd need to at least allow the user to move it and ... no.
Includes