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HiDiHlabs / ovrl.py

A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data.
https://ovrlpy.readthedocs.io
MIT License
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'UMAP' object has no attribute '_knn_search_index'. Did you mean: 'knn_search_index'? #37

Open pakiessling opened 6 days ago

pakiessling commented 6 days ago 
visualizer.save("Xenium-text-visualizer.vis")

/hpcwork/p0020567/enviroments/overlpy2/lib/python3.12/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
Traceback (most recent call last):
  File "/rwthfs/rz/cluster/work/rwth1209/projects/Overlpy_Manuscript/test.py", line 26, in <module>
    visualizer.save("Xenium-text-visualizer.vis")
  File "/hpcwork/p0020567/enviroments/overlpy2/lib/python3.12/site-packages/ovrlpy/_ovrlp.py", line 1206, in save
    pickle.dumps(self.embedder_2d._knn_search_index)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'UMAP' object has no attribute '_knn_search_index'. Did you mean: 'knn_search_index'?

Hi, bekomme den Fehler für umap-learn 0.5.7

Ist das viellecht die falsche Version?

sebastiantiesmeyer commented 6 days ago

Thanks for the report! Our analysis uses umap-learn 0.5.6 I will fix it in the upcoming days, maybe you could try and downgrade for now?

On Tue, 26 Nov 2024 at 15:54, pakiessling @.***> wrote:

visualizer.save("Xenium-text-visualizer.vis")

/hpcwork/p0020567/enviroments/overlpy2/lib/python3.12/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index. warnings.warn("Transforming to str index.", ImplicitModificationWarning) Traceback (most recent call last): File "/rwthfs/rz/cluster/work/rwth1209/projects/Overlpy_Manuscript/test.py", line 26, in visualizer.save("Xenium-text-visualizer.vis") File "/hpcwork/p0020567/enviroments/overlpy2/lib/python3.12/site-packages/ovrlpy/_ovrlp.py", line 1206, in save pickle.dumps(self.embedder_2d._knn_search_index) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'UMAP' object has no attribute '_knn_search_index'. Did you mean: 'knn_search_index'?

Hi, bekomme den Fehler für umap-learn 0.5.7

Ist das viellecht die falsche Version?

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niklasmueboe commented 6 days ago

Maybe it is better to pickle the whole UMAP (and also PCA) object? That way we are not dependent on future API changes in other packages.