ENH: Read from http sources
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dzenanz
reviewed
Aug 1, 2023
dzenanz
reviewed
Aug 1, 2023
Add support for reading from Zarr stores available remotely via `http` or `https`, such as those served over a local network or hosted on the cloud with AWS S3. Includes automated tests referencing OME-Zarr data detailed in the Open Microscopy Environment (OME) GitHub organization: https://github.com/ome/ome-ngff-prototypes Also includes non-automated Python tests for reading from local disk over HTTP and C++ utility for generic OME-Zarr reading.
dzenanz
approved these changes
Aug 2, 2023
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Overview
Adds support for reading from remote OME-Zarr stores compatible with the tensorstore
httpkey-value store driver.Notes
The Tensorstore
httpkey-value store driver provides an interface to access remote OME-Zarr data viahttporhttpsconnection. Remote OME-Zarr file resources must be available as a URL, i.e.https://1.2.3.4:8080/path/to/image.zarr/.zgroup,https://1.2.3.4:8080/path/to/image.zarr/0/..., etc.Compatible with reading from Amazon AWS S3 buckets, formed as
https://<bucket-name>.s3.amazonaws.com/path/to/image.zarr.Automatedtest coverage is provided in Python by spawning a background Python web server to serve files from the local test directory overhttp. A C++ test is included as a utility for manual testing, but is not automated.EDIT: I now recall that Python tests are not included in ITK test automation.
httpsupport may be tested manually with the following command:Output
Relevant output from Python HTTP test run on my local machine shows that local zarr store is successfully queried via the Python HTTP web server:
References
https://google.github.io/tensorstore/kvstore/http/index.html