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+10,14 @@ name = "cog3pio" crate-type = ["cdylib"] [dependencies] +bytes = "1.5.0" ndarray = "0.15.6" 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 = { version = "1.36.0", features = ["rt-multi-thread"] } +url = "2.5.0" [dev-dependencies] tempfile = "3.10.1" diff --git a/README.md b/README.md index aea4da9..da307af 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,80 @@ Cloud-optimized GeoTIFF ... Parallel I/O Yet another attempt at creating a GeoTIFF reader, in Rust, with Python bindings. + +## Installation + +### Rust + + cargo add --git https://github.com/weiji14/cog3pio.git + +### Python + + pip install git+https://github.com/weiji14/cog3pio.git + +> [!TIP] +> The API for this crate/library is still unstable and subject to change, so you may +> want to pin to a specific git commit using either: +> - `cargo add --git https://github.com/weiji14/cog3pio.git --rev ` +> - `pip install git+https://github.com/weiji14/cog3pio.git@` +> +> where `` is a commit hashsum obtained from +> https://github.com/weiji14/cog3pio/commits/main + + +## Usage + +### Rust + +```rust +use std::io::Cursor; + +use bytes::Bytes; +use cog3pio::io::geotiff::read_geotiff; +use ndarray::Array2; +use object_store::path::Path; +use object_store::{parse_url, GetResult, ObjectStore}; +use tokio; +use url::Url; + +#[tokio::main] +async fn main() { + let cog_url: &str = + "https://github.com/cogeotiff/rio-tiler/raw/6.4.0/tests/fixtures/cog_nodata_nan.tif"; + let tif_url: Url = Url::parse(cog_url).unwrap(); + let (store, location): (Box, Path) = parse_url(&tif_url).unwrap(); + + let stream: Cursor = { + let result: GetResult = store.get(&location).await.unwrap(); + let bytes: Bytes = result.bytes().await.unwrap(); + Cursor::new(bytes) + }; + + let arr: Array2 = read_geotiff(stream).unwrap(); + assert_eq!(arr.dim(), (549, 549)); + assert_eq!(arr[[500, 500]], 0.13482364); +} +``` + +### Python + +```python +import numpy as np +from cog3pio import read_geotiff + +array: np.ndarray = read_geotiff( + path="https://github.com/cogeotiff/rio-tiler/raw/6.4.0/tests/fixtures/cog_nodata_nan.tif" +) +assert array.shape == (549, 549) +assert array.dtype == "float32" +``` + +> [!NOTE] +> Currently, this crate/library only supports reading single-band float32 GeoTIFF files, +> i.e. multi-band and other dtypes (e.g. uint16) don't work yet. See roadmap below on +> future plans. + + ## Roadmap Short term (Q1 2024): @@ -11,7 +85,7 @@ Short term (Q1 2024): [`ndarray`](https://github.com/rust-ndarray/ndarray) - [ ] Multi-band reader (relying on [`image-tiff`](https://github.com/image-rs/image-tiff)) -- [ ] Read from remote storage (using +- [x] Read from remote storage (using [`object-store`](https://github.com/apache/arrow-rs/tree/object_store_0.9.0/object_store)) Medium term (Q2 2024): @@ -20,6 +94,7 @@ Medium term (Q2 2024): - [ ] Parallel reader (TBD on multi-threaded or asynchronous) - [ ] Direct-to-GPU loading + ## Related crates - https://github.com/georust/geotiff diff --git a/python/tests/test_io_geotiff.py b/python/tests/test_io_geotiff.py index 3b48a40..0a461b7 100644 --- a/python/tests/test_io_geotiff.py +++ b/python/tests/test_io_geotiff.py @@ -8,7 +8,7 @@ from cog3pio import read_geotiff - +# %% @pytest.fixture(scope="module", name="geotiff_path") def fixture_geotiff_path(): """ @@ -31,3 +31,57 @@ def test_read_geotiff_local(geotiff_path): array = read_geotiff(path=geotiff_path) assert array.shape == (20, 20) assert array.dtype == "float32" + + +@pytest.mark.benchmark +def test_read_geotiff_remote(): + """ + Read a GeoTIFF file from a remote URL. + """ + array = 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" + + +def test_read_geotiff_invalid_filepath(): + """ + Check that a ValueError is raised when an invalid filepath is passed to read_geotiff. + """ + with pytest.raises(ValueError, match=r"Cannot parse path: \\invalid\\path"): + read_geotiff(path=r"\invalid\path") + + +def test_read_geotiff_invalid_remote_url(): + """ + Check that a ValueError is raised when an invalid remote url is passed to read_geotiff. + """ + with pytest.raises(ValueError, match="Cannot parse url: protocol://file.ext"): + read_geotiff(path="protocol://file.ext") + + +def test_read_geotiff_missing_url(): + """ + Check that a FileNotFoundError is raised when a url pointing to a non-existent file + is passed to read_geotiff. + """ + with pytest.raises( + FileNotFoundError, match="Cannot find file: https://example.com/geo.tif" + ): + read_geotiff(path="https://example.com/geo.tif") + + +def test_read_geotiff_unsupported_dtype(): + """ + Check that a ValueError is raised when an unsupported GeoTIFF (of ComplexInt16 type) + is passed to read_geotiff. + """ + with pytest.raises( + ValueError, + match="Cannot read GeoTIFF because: " + "The Decoder does not support the image format ", + ): + read_geotiff( + path="https://github.com/corteva/rioxarray/raw/0.15.1/test/test_data/input/cint16.tif" + ) diff --git a/src/io/geotiff.rs b/src/io/geotiff.rs index b7ddd95..37760bf 100644 --- a/src/io/geotiff.rs +++ b/src/io/geotiff.rs @@ -1,27 +1,26 @@ use std::io::{Read, Seek}; -use ndarray::{Array2, ShapeError}; +use ndarray::Array2; use tiff::decoder::{DecodingResult, Limits}; +use tiff::{TiffError, TiffFormatError}; /// Synchronously read a GeoTIFF file into an [`ndarray::Array`] -pub fn read_geotiff(stream: R) -> Result, ShapeError> { +pub fn read_geotiff(stream: R) -> Result, TiffError> { // Open TIFF stream with decoder - let mut decoder = tiff::decoder::Decoder::new(stream).expect("Cannot create tiff decoder"); + let mut decoder = tiff::decoder::Decoder::new(stream)?; decoder = decoder.with_limits(Limits::unlimited()); // Get image dimensions - let dimensions: (u32, u32) = decoder.dimensions().expect("Cannot parse image dimensions"); - let width = dimensions.0 as usize; - let height = dimensions.1 as usize; + let (width, height): (u32, u32) = decoder.dimensions()?; // Get image pixel data - let DecodingResult::F32(img_data) = decoder.read_image().expect("Cannot decode tiff image") - else { + let DecodingResult::F32(img_data) = decoder.read_image()? else { panic!("Cannot read band data") }; // Put image pixel data into an ndarray - let vec_data = Array2::from_shape_vec((height, width), img_data)?; + let vec_data = Array2::from_shape_vec((height as usize, width as usize), img_data) + .map_err(|_| TiffFormatError::InvalidDimensions(height, width))?; Ok(vec_data) } diff --git a/src/lib.rs b/src/lib.rs index 7530a31..2f066f2 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -8,38 +8,113 @@ //! **Note**: For Python users, there are also bindings (via [`pyo3`]) to read GeoTIFF files into //! `numpy.ndarray` objects (i.e. similar to [`rasterio`](https://github.com/rasterio/rasterio)). //! This is done via the [`numpy`] crate which enables passing data from Rust to Python. +//! +//! # Examples +//! +//! Read a GeoTIFF file retrieved via the [`object_store`] crate, and pass it into the +//! [`read_geotiff`](./io/geotiff/fn.read_geotiff.html) function. +//! +//! ```rust +//! use std::io::Cursor; +//! +//! use bytes::Bytes; +//! use cog3pio::io::geotiff::read_geotiff; +//! use ndarray::Array2; +//! use object_store::path::Path; +//! use object_store::{parse_url, GetResult, ObjectStore}; +//! use tokio; +//! use url::Url; +//! +//! #[tokio::main] +//! async fn main() { +//! let cog_url: &str = +//! "https://github.com/cogeotiff/rio-tiler/raw/6.4.0/tests/fixtures/cog_nodata_nan.tif"; +//! let tif_url: Url = Url::parse(cog_url).unwrap(); +//! let (store, location): (Box, Path) = parse_url(&tif_url).unwrap(); +//! +//! let stream: Cursor = { +//! let result: GetResult = store.get(&location).await.unwrap(); +//! let bytes: Bytes = result.bytes().await.unwrap(); +//! Cursor::new(bytes) +//! }; +//! +//! let arr: Array2 = read_geotiff(stream).unwrap(); +//! assert_eq!(arr.dim(), (549, 549)); +//! assert_eq!(arr[[500, 500]], 0.13482364); +//! } +//! ``` /// Modules for handling Input/Output of GeoTIFF data pub mod io; -use std::fs::File; +use std::io::Cursor; +use bytes::Bytes; use ndarray::Dim; use numpy::{PyArray, ToPyArray}; +use object_store::{parse_url, ObjectStore}; +use pyo3::exceptions::{PyBufferError, PyFileNotFoundError, PyValueError}; use pyo3::prelude::{pyfunction, pymodule, PyModule, PyResult, Python}; -use pyo3::wrap_pyfunction; +use pyo3::{wrap_pyfunction, PyErr}; +use url::Url; /// Read a GeoTIFF file from a path on disk into an ndarray /// /// Parameters /// ---------- /// path : str -/// The path to the file. +/// The path to the file, or a url to a remote file. /// /// Returns /// ------- /// array : np.ndarray /// 2D array containing the GeoTIFF pixel data. +/// +/// Examples +/// -------- +/// from cog3pio import read_geotiff +/// +/// array = read_geotiff("https://github.com/pka/georaster/raw/v0.1.0/data/tiff/float32.tif") +/// assert array.shape == (20, 20) #[pyfunction] #[pyo3(name = "read_geotiff")] fn read_geotiff_py<'py>( path: &str, py: Python<'py>, ) -> PyResult<&'py PyArray>> { - // 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}")))?; + + // Initialize async runtime + let runtime = tokio::runtime::Builder::new_current_thread() + .enable_all() + .build()?; + + // Get TIFF file stream asynchronously + let stream = runtime.block_on(async { + let result = store + .get(&location) + .await + .map_err(|_| PyFileNotFoundError::new_err(format!("Cannot find file: {path}")))?; + let bytes = result.bytes().await.map_err(|_| { + PyBufferError::new_err(format!("Failed to stream data from {path} into bytes.")) + })?; + // Return cursor to in-memory buffer + Ok::, PyErr>(Cursor::new(bytes)) + })?; + // Get image pixel data as an ndarray - let vec_data = io::geotiff::read_geotiff(file).expect("Cannot read GeoTIFF"); + let vec_data = io::geotiff::read_geotiff(stream) + .map_err(|err| PyValueError::new_err(format!("Cannot read GeoTIFF because: {err}")))?; + // Convert from ndarray (Rust) to numpy ndarray (Python) Ok(vec_data.to_pyarray(py)) }