tomnicholas1

Joined 2 years ago

Karma
160
Submissions
47
Member since
Aug 19
OSS python software for science, currently employed at earthmover.io. I help maintain Xarray, Zarr, Icechunk, VirtualiZarr, and other pangeo.io projects.

https://github.com/TomNicholas

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Recent submissions

Comment · 2 months ago
> The problem in climatology is that when the models don't fit the data they just change the data and claim victory

That is... not remotely true, nor supported by either of the links you shared. (Nor by any cursory look at the state of the world today, with well-anticipated Himalayan glacial floods as front-page news.) You therefore appear to be leaping over the line from healthy skepticism to irrational conspiratorial thinking, so I'm going to stop engaging, sorry.

Comment · 2 months ago
Comment · 2 months ago
Comment · 3 months ago
Yes! But if you want to share it with anyone else that would be great, since we're advocating for fairly radical changes within a big bureaucracy here, as I'm sure you will appreciate :)
Comment · 3 months ago
Comment · 5 months ago
The last 2 years of my professional life have in some sense all been working towards this blog post.

It shows how you can make an enormous archive of public scientific data[1] much easier to use for everyone, without having to copy all the data, which would be prohibitively expensive at this scale.

I also made some sweet gifs and images of the Earth from space from the raw data so check those out!

[1] In this case satellite data, but this could work for data from many other fields - my background is original nuclear fusion plasma physics then oceanography.

Comment · 7 months ago
Comment · 8 months ago
Comment · 9 months ago
Comment · 9 months ago
IMO Zarr is that newer format. It abstracts over the features of all these other formats so neatly that it can literally subsume them.

I feel that we no longer really need TIFF etc. - for scientific use cases in the cloud Zarr is all that's needed going forwards. The other file formats become just archival blobs that either are converted to Zarr or pointed at by virtual Zarr stores.

Comment · 9 months ago
The generalized form of this range-request-based streaming approach looks something like my project VirtualiZarr [0].

Many of these scientific file formats (HDF5, netCDF, TIFF/COG, FITS, GRIB, JPEG and more) are essentially just contiguous multidimensional array(/"tensor") chunks embedded alongside metadata about what's in the chunks. Efficiently fetching these from object storage is just about efficiently fetching the metadata up front so you know where the chunks you want are [1].

The data model of Zarr [2] generalizes this pattern pretty well, so that when backed by Icechunk [3], you can store a "datacube" of "virtual chunk references" that point at chunks anywhere inside the original files on S3.

This allows you to stream data out as fast as the S3 network connection allows [4], and then you're free to pull that directly, or build tile servers on top of it [5].

In the Pangeo project and at Earthmover we do all this for Weather and Climate science data. But the underlying OSS stack is domain-agnostic, so works for all sorts of multidimensional array data, and VirtualiZarr has a plugin system for parsing different scientific file formats.

I would love to see if someone could create a virtual Zarr store pointing at this WSI data!

[0]: https://virtualizarr.readthedocs.io/en/stable/

[1]: https://earthmover.io/blog/fundamentals-what-is-cloud-optimi...

[2]: https://earthmover.io/blog/what-is-zarr

[3]: https://earthmover.io/blog/icechunk-1-0-production-grade-clo...

[4]: https://earthmover.io/blog/i-o-maxing-tensors-in-the-cloud

[5]: https://earthmover.io/blog/announcing-flux

Comment · 10 months ago
God this article is 10000% better than the posted one. This is great:

> Names should not describe what you currently think the thing you’re naming is for. Imagine naming your newborn child "Doctor", or "SupportsMeInMyOldAge". Poor kid.

Comment · 1 year ago
Thank you for the explanation! But what a mess.

I would love to bring these benefits to the multidimensional array world, via integration with the Zarr/Icechunk formats somehow (which I work on). But this fragmentation of formats makes it very hard to know where to start.

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