CSV download

[ehoops-cz]

Resolves #78

• Modifies zarr generation script to include parentTrackId in the data field
• Reads in the data field and stores it on the track object on the canvas
• Reads out the data when the user clicks on "Export Cell Tracks" button

TODO:

• verify that the correct values are in there
• write some tests I ended up testing manually - should these be automated?
• get this data in the webapp and add it to the csv download

To test:
run the script to generate a new zarr bundle and serve it locally

NOTE: We will need to update the data on S3 to include the data field. There will be downtime if this is not done first.

[vercel]

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Name	Status	Preview	Comments	Updated (UTC)
points-web-viewer	✅ Ready (Inspect)	Visit Preview	💬 Add feedback	Jun 20, 2024 7:38pm

[aganders3]

Note: there's some bug. When the points load, they are clearly not in the same place on the canvas, but I'm not sure why.

I saw this too - it's likely a bug on main as well. I will make a new issue.

[ehoops-cz]

an example csv is on sheet 2 here: https://docs.google.com/spreadsheets/d/1akqPHvt_Yu7lZ7L6E_2bxM7D0u6lYDpiLheouJ_l3Kk/edit?gid=1909503628#gid=1909503628

I think there's something wrong with the data, but still looking into it

[aganders3]

Can you grant access to that sheet?

[ehoops-cz]

Can you grant access to that sheet?

done! sorry!

I think the input CSV is in t, z, y, x order. Is it possible that is the problem here?

I don't think so. The values seem to be trackIds, just not the right ones. Maybe I'm putting them in the data rows instead of columns?

[ehoops-cz]

update: I tried switching the rows/columns and that was very obviously wrong. All of the tracks were listed as having no parentTrackId.

[aganders3]

I'm going to try to look at this more closely today.

[andy-sweet]

Still need to finish looking at everything, but generally looks good. There's seems one bug maybe related to the track geometry changes that needs to be addressed before this can be merged though.

[aganders3]

Generally looks good and I was able to export some tracks and read them in napari, where all looked okay to me.

I have a couple questions and nitpicks, and also interested about some of @andy-sweet's comments.

[andy-sweet]

Looks good to me and the feature is a great to tie this back to the napari plugin. Some nice improvements in the CSV to Zarr converter too! I have one optional suggestion/simplification, but it's non-blocking.

Given that Ashley has more experience with the three.js data structures here, you should wait for approval from him before merging!

[aganders3]

LGTM! Thanks for taking this one on.