Add compositing #331
Add compositing #331
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Read position metadata of tiles from nd2 file Closes #244
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I think it would be better to put the compositing checkbox just to the right of the Positions (XY) UI as indicated below.
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I have noticed an issue with the file "normmedia_8well_col2_livecellgfp.nd2". If I upload it, it gets stuck on the "Variables" and "Assignments" screen and clicking "Submit" doesn't work. This problem appears to arise both when "Enable compositing" is checked or unchecked. |
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Can confirm this is also a problem for the OASL_SOX10_VGF.nd2 dataset. |
I noticed that the submit button was slow, but it works for me, I have to wait 7/8 seconds after clicking I found where the problem is |
bruyeret
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Yes, I did notice that the interface did eventually go through. But when it did, it still seemed to have an error on the next page. Also, this slowdown was not there before, so it must have been something introduced with this new code. |
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What is the error you get on the next page? I don't get any error |
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Also, in general, navigation is very slow through the file once uploaded now. It is qualitatively worse than before. I think something is wrong now with how things are specified. |
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Yes I agree, I had a quick talk with David about that and he told me that
I don't know how we could make things faster, I'll discuss that with David |
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Speed on composited images (and only composited image) will be slower on first load. They should eventually be cached and just as snappy as other files. To get, for instance, a thumbnail, we can't just read one section of a file, we have to read a bunch of sections to composite it. |
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@manthey It's actually slow even WITHOUT compositing, though, which is puzzling. |
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I think it would be fine if it is slower for composited files, but I think it should be the same for non-composited files, right? |
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David will try to fix the problem on girder's side (it is something with file caching) |
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Sounds good, thanks! |
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Tried the file normmedia_8well_col2_livecellgfp.nd2 and still had problems. It was faster to process, but still quite slow to upload even if you do not check "composite". Once loaded, navigating the file (e.g. moving the XY slider) was much less responsive than before. |
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On the same file, composite doesn't seem to work… |
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Like, it doesn't show any image. |
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I haven't bump David's changes into this branch yet, did you do it? |
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I didn't bump them in… |
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I'll do it tomorrow, sorry for that! |
Add comments, typescript, verbose variables Tweak some logic When generating the JSON, create a source object for each frame Modify the UI Add a checkbox and logic for compositing Fix an error in getDataset when there is no image
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@bruyeret can you add / update tests ? |
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Also, the updates from @manthey did lead to some speed up, but didn't solve the underlying problem of the order(s) of magnitude slowdown. |
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@manthey OK, I updated large_image to the latest version (19.*). I am still getting an issue with this file:
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I tested it and I think it is good! |
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Does this completely get rid of the JSON parsing if there is no compositing? |
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I tried checking "composite positions" for PMAIP1_NGFR_WNT5A.nd2" and no image showed up. But without checking that box, it was fine. |
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I added PMAIP1_NGFR_WNT5A.nd2 to the Dropbox: https://www.dropbox.com/sh/89axp9vwtt81o4v/AADHKe4Hon64InYWtnY9hRjFa?dl=0 |
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OK, I think we can merge now! |
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LGTM |
Add compositing option when importing compatible a single nd2 file.
Change the UI.
Closes #244