✨ Read GeoTIFF files from remote urls via object_store #5

weiji14 · 2024-03-01T18:51:16Z

Enable GeoTIFFs stored on remote urls (e.g. http, s3, azure, gcp, etc) to be read into numpy arrays.

Uses the object_store crate, which pulls data via an async API. Note that only the network read is async, the TIFF decoding (using the tiff crate) is still synchronous.

Usage (in Python):

import numpy as np
from cog3pio import read_geotiff

array: np.ndarray = read_geotiff(
    path="https://github.com/pka/georaster/raw/v0.1.0/data/tiff/float32.tif"
)
assert array.shape == (20, 20)
assert array.dtype == "float32"

TODO:

Add failing unit test reading a GeoTIFF via HTTP
Use object_store's parse_url function to handle remote URL reads
Ensure that local relative filepaths (e.g. data/float32.tif) work alongside remote URLs (e.g. https://somewhere.com/float32.tif)
Refactor to remove .unwrap() statements
Document in main README.md on new usage

Other things done in this PR out of necessity:

Move to compiling on manylinux_2_28, therefore dropping compilation on i686 (x86) targets on Linux

References:

Similar PR to read FlatGeobuf via object_store at Async flatgeobuf reading via object-store geoarrow/geoarrow-rs#494

A generic object store interface for uniformly interacting with AWS S3, Google Cloud Storage, Azure Blob Storage and local files! Also added the url crate.

An event-driven, non-blocking I/O platform for writing asynchronous I/O backed applications!

Doing test driven development by trying to load a remote GeoTIFF file via http into a numpy array.

Allow passing remote URLs to the read_geotiff_py function. URLs are handled via object_store's parse_url function. Data is read asynchronously into an in-memory buffer (within a tokio runtime), and passed into the synchronous io::geotiff::read_geotiff function. Also added a short example in the Python docstring on how this can be used.

weiji14 · 2024-03-01T19:10:47Z

src/lib.rs

+        // Parse URL
+        let url = Url::parse(path).expect(&format!("Cannot parse path: {path}"));
+        let (store, location) = parse_url(&url).expect(&format!("Cannot parse url: {url}"));
+
+        // Return cursor to in-memory buffer
+        let result = store.get(&location).await.unwrap();


Need to find a way here to let object_store read from local filepaths like /tmp/float32.tif or data/float32.tif. Currently at commit 33faafb, one would need to prepend the filepath with file:// for the read to work, otherwise there will be an error like pyo3_runtime.PanicException: Cannot parse path: /tmp/tmp6ip79h4_/float32.tif: RelativeUrlWithoutBase (see https://github.com/weiji14/cog3pio/actions/runs/8115987634/job/22185036928?pr=5#step:6:89).

Maybe add some logic to determine the URL scheme, and if it is local, prepend the url with file://?

Oh wait, RelativeUrlWithoutBase is raised on Url::parse, not ObjectStore 😅 Edit: Should be handled in f9607f3

Great, need to figure out how to handle Windows paths - https://github.com/weiji14/cog3pio/actions/runs/8118215740/job/22192052940?pr=5#step:6:95:

E pyo3_runtime.PanicException: Cannot parse url: c:\Users\RUNNER~1\AppData\Local\Temp\tmpv5aci1cm\float32.tif: Generic { store: "URL", source: Unrecognised { url: Url { scheme: "c", cannot_be_a_base: true, username: "", password: None, host: None, port: None, path: "\\Users\\RUNNER~1\\AppData\\Local\\Temp\\tmpv5aci1cm\\float32.tif", query: None, fragment: None } } }

Ok, figured out that there's a Url::from_file_path function that handles Windows paths (and also prepends file:// to local filepaths). Implemented in commit 3c8a604

weiji14 · 2024-03-01T19:12:19Z

Cargo.toml

 numpy = "0.20.0"
+object_store = { version = "0.9.0", features = ["http"] }
 pyo3 = { version = "0.20.3", features = ["abi3-py310", "extension-module"] }
 tiff = "0.9.1"
+tokio = "1.36.0"
+url = "2.5.0"


Probably need to hide some of the Python-specific crates behind a feature flag (if the pure Rust parts will be published as a crate). Hoping that most of the Rust code can be upstreamed though. See PyO3/pyo3#2271 for reference.

Handle the RelativeUrlWithoutBase parsing error raised when local filepaths are given without `file://` in front. Also moved the parse url logic out of the async block.

codspeed-hq · 2024-03-01T23:05:33Z

CodSpeed Performance Report

Merging #5 will degrade performances by 33.24%

_{Comparing object_store (5c412da) with main (0c37e32)}

Summary

❌ 1 (👁 1) regressions

🆕 1 new benchmarks

Benchmarks breakdown

	Benchmark	`main`	`object_store`	Change
👁	`test_read_geotiff_local`	423 µs	633.6 µs	-33.24%
🆕	`test_read_geotiff_remote`	N/A	48.9 ms	N/A

Resolve `warning: ring@0.17.8: #error "ARM assembler must define __ARM_ARCH"` on aarch64. Xref PyO3/maturin-action#222

Getting an error like `/usr/bin/python3: No module named pip` when using the quay.io/pypa/manylinux_2_28_x86_64:latest docker image, so trying with ghcr.io/rust-cross/manylinux_2_28-cross instead. Note that the aarch64/armv7/s390x/ppc64le targets use this rust-cross image by default.

Don't compile on i686 since manylinux_2_28 doesn't support it according to https://github.com/rust-cross/manylinux-cross/blob/1c46d3b27a55eff53d675bf515d6361d7cc1abde/README.md?plain=1#L25-L35 and https://github.com/pypa/manylinux/blob/dbe0aa5c374c5b69769253d2a77820b08fe80a7d/README.rst?plain=1#L46. Note that x86 is an alias of i686 (see https://github.com/PyO3/maturin-action/blob/60d11847b29f81ca5375519a8eb33cc336ba4bfa/src/index.ts#L119).

Use built-in function at https://docs.rs/url/2.5.0/url/struct.Url.html#method.from_file_path to add the file:// prefix instead of the DIY method at f9607f3. Hoping that this would handle Windows paths too. Also changed .expect to .map_err to raise PyValueError instead of panicking.

Add instructions on how to install cog3pio in Rust or Python (need to pull development version from git for now), and sample code to read a GeoTIFF file from a http url. Included some tips on pinning the specific commit hash, and mentioned that the current crate/library only supports reading single-band float32 GeoTIFF files. Also checked the box that reading from remote storage is implemented.

Gracefully handle errors when retrieving the GeoTIFF data in the async block, using turbofish operator as suggested by https://rust-lang.github.io/async-book/07_workarounds/02_err_in_async_blocks.html. Fixed some errors missing the format! macro, and added unit tests to catch parsing and decoding errors. In the read_geotiff function, changed the function to return a TiffError instead of ShapeError, so that ? can be used in the decoding portions.

Copy the Rust code from 15b0dbc to src/lib.rs as a doctest. Need to change `crate-type = ["rlib"]` in Cargo.toml so that `cargo test --doc` works, but will configure that in CI later.

weiji14 · 2024-03-04T03:31:48Z

src/lib.rs

-    // Open TIFF file from path
-    let file = File::open(path).expect("Cannot find GeoTIFF file");
+    // Parse URL into ObjectStore and path
+    let file_or_url = match Url::from_file_path(path) {
+        // Parse local filepath
+        Ok(filepath) => filepath,
+        // Parse remote URL
+        Err(_) => Url::parse(path)
+            .map_err(|_| PyValueError::new_err(format!("Cannot parse path: {path}")))?,
+    };
+    let (store, location) = parse_url(&file_or_url)
+        .map_err(|_| PyValueError::new_err(format!("Cannot parse url: {file_or_url}")))?;


CodSpeed Performance Report

Merging #5 will degrade performances by 32.21%

Comparing object_store (33f4a73) with main (0c37e32)

Summary

❌ 1 (👁 1) regressions

🆕 1 new benchmarks

Benchmarks breakdown

Benchmark main object_store Change
👁 test_read_geotiff_local 423 µs 624 µs -32.21%
🆕 test_read_geotiff_remote N/A 49 ms N/A

Acknowledging the slowdown in reading local GeoTIFF files as acceptable for now since it is only ~200µs slower, but could revisit this next time if we should have separate branches for remote files (read using object_store) and local files (read using std::fs::File).

weiji14 added 3 commits March 2, 2024 07:36

➕ Add object_store

dad4d15

A generic object store interface for uniformly interacting with AWS S3, Google Cloud Storage, Azure Blob Storage and local files! Also added the url crate.

➕ Add tokio

98a75fc

An event-driven, non-blocking I/O platform for writing asynchronous I/O backed applications!

🧪 Add unit test to read GeoTIFF from remote http url

6cc8f4b

Doing test driven development by trying to load a remote GeoTIFF file via http into a numpy array.

weiji14 added the feature New feature or request label Mar 1, 2024

weiji14 added this to the 0.1.0 milestone Mar 1, 2024

weiji14 self-assigned this Mar 1, 2024

weiji14 commented Mar 1, 2024

View reviewed changes

👔 Handle local filepaths by prepending with file://

f9607f3

Handle the RelativeUrlWithoutBase parsing error raised when local filepaths are given without `file://` in front. Also moved the parse url logic out of the async block.

weiji14 added 2 commits March 3, 2024 15:35

💚 Build wheels on manylinux_2_28

315282f

Resolve `warning: ring@0.17.8: #error "ARM assembler must define __ARM_ARCH"` on aarch64. Xref PyO3/maturin-action#222

weiji14 force-pushed the object_store branch from a5e2ee7 to c477eba Compare March 3, 2024 03:34

weiji14 added 5 commits March 3, 2024 16:49

📝 Copy example usage to crate-level docs as doctest

5c412da

Copy the Rust code from 15b0dbc to src/lib.rs as a doctest. Need to change `crate-type = ["rlib"]` in Cargo.toml so that `cargo test --doc` works, but will configure that in CI later.

weiji14 commented Mar 4, 2024

View reviewed changes

weiji14 marked this pull request as ready for review March 4, 2024 03:32

weiji14 enabled auto-merge (squash) March 4, 2024 03:33

weiji14 merged commit fefa543 into main Mar 4, 2024
13 checks passed

weiji14 deleted the object_store branch March 4, 2024 03:54

weiji14 mentioned this pull request Apr 10, 2024

Using cog3pio to determine byte ranges in COG files? #16

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✨ Read GeoTIFF files from remote urls via object_store #5

✨ Read GeoTIFF files from remote urls via object_store #5

weiji14 commented Mar 1, 2024 •

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weiji14 Mar 1, 2024 •

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codspeed-hq bot commented Mar 1, 2024 •

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✨ Read GeoTIFF files from remote urls via object_store #5

✨ Read GeoTIFF files from remote urls via object_store #5

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CodSpeed Performance Report

Merging #5 will degrade performances by 33.24%

Summary

Benchmarks breakdown

weiji14 Mar 4, 2024

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CodSpeed Performance Report

Merging #5 will degrade performances by 32.21%

Summary

Benchmarks breakdown

weiji14 commented Mar 1, 2024 •

edited

weiji14 Mar 1, 2024 •

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weiji14 Mar 1, 2024 •

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codspeed-hq bot commented Mar 1, 2024 •

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