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NASA-IMPACT / veda-docs

Documentation for the VEDA Project
https://nasa-impact.github.io/veda-docs
Apache License 2.0
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Add notebook for reading zarr from veda stac catalog and visualizing it #19

Closed slesaad closed 1 year ago

slesaad commented 1 year ago

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review-notebook-app[bot] commented 1 year ago

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slesaad commented 1 year ago

I noticed in the ReviewNB preview that the map visualization wasn't rendered, does it have to do something with the warning I received about "GH001: Large files detected" ?

Also, the notebook reads data from the dev veda stac catalog, should we wait till the data is published to staging (might take a while) or is it okay to publish this right now and once it's published to staging, update this notebook?

cc @jsignell @ranchodeluxe @abarciauskas-bgse

jsignell commented 1 year ago

Yeah I think for now don't worry about the viz not showing up on github. It shows up fine when using nbviewer: https://nbviewer.org/github/NASA-IMPACT/veda-docs/blob/994b71a8e390ecc96aa93e77da65b2ba3b5a92f2/example-notebooks/veda-stac-zarr-viz.ipynb

Just as a quick question, do you think that this should replace the current visualizing-zarr notebook or I guess more generally how does it relate to that notebook?

abarciauskas-bgse commented 1 year ago

I ran the notebook in SMCE and it LGTM!

I defer to you all on if we should remove the existing visualizing-zarr.ipynb notebook - I do think it's helpful to identify some ways to downsample large zarr datasets for visualization but I'm not married to keeping it (especially if it causes confusion to users)

slesaad commented 1 year ago

@jsignell @abarciauskas-bgse I did think about updating the existing notebook that aimee created to read from the stac catalog instead of directly from the s3 bucket, but i also think that's it's worth having examples for two different datasets so we can link those from two dataset pages especially since the two zarr datasets are in different projection systems.

jsignell commented 1 year ago

Ok! It's really helpful to hear that as a vision. So the current notebooks are kind of more instructional and are intended to demonstrate how to use tools. With that lens on I think this notebook is a clearer example of "how to open and visualize zarr". We can create a new section for more dataset-centric analyses. That is where the old notebook that Aimee wrote can go and that's where the new notebooks that @kathrynberger is writing can go. I can set up that structure and move Aimee's notebook in a separate PR.

review-notebook-app[bot] commented 1 year ago

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jsignell commented on 2023-03-03T16:42:09Z ----------------------------------------------------------------

I've bee trying to follow a pre-defined pattern for these notebooks. You did a lot of it which I appreciate! But I'd love to see an "Approach" section that outlines the steps that this notebook will go through.


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jsignell commented on 2023-03-03T16:42:11Z ----------------------------------------------------------------

In the other notebooks I've been including a matching block that explains what the stac catalog is and how to pick a collection. It would be great to include that here.


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jsignell commented on 2023-03-03T16:42:11Z ----------------------------------------------------------------

I'm an intake fan, but I'm not really sure it is giving us much in this example. I would prefer to see this use pystac_client like the other examples. See https://github.com/NASA-IMPACT/veda-docs/blob/main/example-notebooks/open-and-plot.ipynb for instance.


review-notebook-app[bot] commented 1 year ago

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jsignell commented on 2023-03-03T16:42:13Z ----------------------------------------------------------------

In general this notebook could use a bit more text. If there is nothing interesting to say then consider if it really deserves to be its own section.


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jsignell commented on 2023-03-03T16:42:14Z ----------------------------------------------------------------

nice plot!!


jsignell commented 1 year ago

@slesaad just let me know if you want to talk my comment over or if you would like me to just push changes to your branch.

slesaad commented 1 year ago

@jsignell should i merge this?

jsignell commented 1 year ago

@jsignell should i merge this?

Do you see my review comments?

slesaad commented 1 year ago

@jsignell oof sorry, my mind somehow skipped all those comments from review-notebook-app 😅 ; i'll make those changes you mentioned!

jsignell commented 1 year ago

No worries at all! And if it's easier I am also happy to take it from here :)

slesaad commented 1 year ago

No worries at all! And if it's easier I am also happy to take it from here :)

you would do that? 🥺 that'd be great! thank you so much ❤️

jsignell commented 1 year ago

No problem! I am taking a look now.

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