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alihaydaroglu / suite3d

Fast, accurate, volumetric cell detection. Developed for Light Beads Microscopy, usable for other volumetric 2P. In development
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Parameter with number of SVD components seems to be ignored #20

Closed oterocoronel closed 1 year ago

oterocoronel commented 1 year ago

Despite being instructed to do 300 components, it seems like it is using 500

image

It also seems like it was using 500 components when doing the sweep despite instructed to do 200, 300 and 400

image

And when opening the maps with Napari, the 3 maps shown for different SVD components look all the same

alihaydaroglu commented 1 year ago

sorry, the param name should be n_svd_comp. My bad!

From: oterocoronel @.> Sent: Wednesday, July 19, 2023 10:29 PM To: alihaydaroglu/s2p-lbm @.> Cc: Subscribed @.***> Subject: [alihaydaroglu/s2p-lbm] Parameter with number of SVD components seems to be ignored (Issue #20)

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Despite being instructed to do 300 components, it seems like it is using 500

image.png (view on web)https://github.com/alihaydaroglu/s2p-lbm/assets/78885453/b0d5a538-c21a-46d8-afa4-6d9858aac002

It also seems like it was using 500 components when doing the sweep despite instructed to do 200, 300 and 400

image.png (view on web)https://github.com/alihaydaroglu/s2p-lbm/assets/78885453/72fb9df2-d2bf-4174-9cdf-f5735c29de4d

And when opening the maps with Napari, the 3 maps shown for different SVD components look all the same

— Reply to this email directly, view it on GitHubhttps://github.com/alihaydaroglu/s2p-lbm/issues/20, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADSYD3XYNPICFA3CL635S4LXRBGTFANCNFSM6AAAAAA2QQEKDM. You are receiving this because you are subscribed to this thread.Message ID: @.***>

oterocoronel commented 1 year ago

Gotcha. In the first picture, you can see it printed this:

(448, 300, 160000)

Do you know what is that?

alihaydaroglu commented 1 year ago

Yeah it's just a stray print statement I forgot to remove. It's the shape of the spatial components from the SVD. You have 448 blocks, 300 components and 160000 pixels. These are the u.zarr arrays saved in the svd dir. These get loaded to memory and multiplied with the temporal components (448 x 300 x nt) to get 448 reconstructed blocks, which then get patched together to make the movie.

alihaydaroglu commented 1 year ago

reopening so i remember to update the demo notebook

alihaydaroglu commented 1 year ago

fixed in demo notebook https://github.com/alihaydaroglu/s2p-lbm/commit/542c62e86969582d4372a12a7abac09653005bb4