✨ A read_geotiff function for reading GeoTIFF into ndarray

[weiji14]

Rust-based function for reading GeoTIFF files!

Uses the tiff crate for the I/O, ndarray crate to store the 2D array in Rust, and numpy crate to convert to numpy.ndarray in Python.

Note: This only works on single-band GeoTIFF files with float32 dtype for now

Usage:

In Rust:

use ndarray::Array2;
use std::fs::File;
use cog3pio::io::geotiff::read_geotiff;

let path: &str = "path/to/file.tif";
let file: File = File::open(path).expect("Cannot find GeoTIFF file");
let arr: Array2<f32> = read_geotiff(file).unwrap();
assert_eq!(arr.dim(), (20, 20));
assert_eq!(arr.mean(), Some(19.0));

In Python:

import numpy as np
from cog3pio import read_geotiff

array: np.ndarray = read_geotiff(path="georaster/data/tiff/float32.tif")
assert array.shape == (20, 20)
assert array.dtype == "float32"

TODO:

• Initial implementation to allow reading single-band Float32 dtype GeoTIFF files
• Improve documentation
• Add unit tests in Python and Rust

TODO in future:

• Refactor to handle other dtypes
• Reconsider project layout? Done at 🚚 Move pyo3 functions to src/python/adapters.rs #9

References:

• https://stackoverflow.com/questions/76145217/how-to-transform-a-tiff-file-to-ndarray-in-rust
• https://en.anyquestion.info/q/how-to-transform-a-tiff-file-to-ndarray-in-rust
• https://github.com/image-rs/image-tiff/pull/216/files

[weiji14]

Original error on s390x build at https://github.com/weiji14/cog3pio/actions/runs/8071580043/job/22051501437#step:7:410 before this line was added:

    error: subprocess-exited-with-error
    
    × Preparing metadata (pyproject.toml) did not run successfully.
    │ exit code: 1
    ╰─> [20 lines of output]
        + /usr/bin/python3 /tmp/pip-install-6l_88pqi/numpy_281cd73ebd0a445c8bd7bbbb7479992b/vendored-meson/meson/meson.py setup /tmp/pip-install-6l_88pqi/numpy_281cd73ebd0a445c8bd7bbbb7479992b /tmp/pip-install-6l_88pqi/numpy_281cd73ebd0a445c8bd7bbbb7479992b/.mesonpy-q6jzljl7 -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/tmp/pip-install-6l_88pqi/numpy_281cd73ebd0a445c8bd7bbbb7479992b/.mesonpy-q6jzljl7/meson-python-native-file.ini
        The Meson build system
        Version: 1.2.99
        Source dir: /tmp/pip-install-6l_88pqi/numpy_281cd73ebd0a445c8bd7bbbb7479992b
        Build dir: /tmp/pip-install-6l_88pqi/numpy_281cd73ebd0a445c8bd7bbbb7479992b/.mesonpy-q6jzljl7
        Build type: native build
        Project name: NumPy
        Project version: 1.26.4
        
        ../meson.build:1:0: ERROR: Unknown compiler(s): [['cc'], ['gcc'], ['clang'], ['nvc'], ['pgcc'], ['icc'], ['icx']]
        The following exception(s) were encountered:
        Running `cc --version` gave "[Errno 2] No such file or directory: 'cc'"
        Running `gcc --version` gave "[Errno 2] No such file or directory: 'gcc'"
        Running `clang --version` gave "[Errno 2] No such file or directory: 'clang'"
        Running `nvc --version` gave "[Errno 2] No such file or directory: 'nvc'"
        Running `pgcc --version` gave "[Errno 2] No such file or directory: 'pgcc'"
        Running `icc --version` gave "[Errno 2] No such file or directory: 'icc'"
        Running `icx --version` gave "[Errno 2] No such file or directory: 'icx'"
        
        A full log can be found at /tmp/pip-install-6l_88pqi/numpy_281cd73ebd0a445c8bd7bbbb7479992b/.mesonpy-q6jzljl7/meson-logs/meson-log.txt
        [end of output]
    
    note: This error originates from a subprocess, and is likely not a problem with pip.
  error: metadata-generation-failed
  
  × Encountered error while generating package metadata.
  ╰─> See above for output.
  
  note: This is an issue with the package mentioned above, not pip.
  hint: See above for details.
  25h::error::The process '/home/runner/work/_actions/uraimo/run-on-arch-action/517085f0367c8256bcfa753e3e13e1550af09954/src/run-on-arch.sh' failed with exit code 1

So at b54ab26, I added this apt build-dep numpy line following https://numpy.org/devdocs/building/#system-level-dependencies, but got E: You must put some 'deb-src' URIs in your sources.list at https://github.com/weiji14/cog3pio/actions/runs/8071955898/job/22052723659?pr=3#step:7:330.

Maybe best to just install the compilers individually instead of messing with /etc/apt/sources.list

[weiji14]

Ok, added the NumPy build deps manually at 41259a1, and also needed to apt install ninja-build to get NumPy to compile on armv7/s390x/ppc64le (9dfa03a). The CI on those three platforms take ~24min to run though, compared to <5min for linux/aarch64 🙃