Error with rio.pad_box() When Padding Multiple GeoTIFFs with Consistent Geometry

[dimplejaiin]

I am working on aligning multiple GeoTIFF datasets to ensure they have consistent dimensions based on a predefined bounding box. Initially, I attempted to use the padding option available in xarray, but due to limitations/requirements specific to my use case, I transitioned to using rioxarray's pad_box() method. Unfortunately, I've encountered an issue where the dataset dimensions seem to conflict when updating a Zarr store, despite the expectation that padding should result in consistent dimensions across datasets.

Error Message

raise ValueError(ValueError: variable 'x' already exists with different dimension sizes: {'x': 4900} != {'x': 4899}. to_zarr() only supports changing dimension sizes when explicitly appending, but append_dim='time'.

Expected Behavior

The expectation is for the rio.pad_box() method to successfully pad the datasets, maintaining consistent x, y dimensions for both images when the bounding box is the same, and subsequently allowing updates to the Zarr store without encountering dimension size mismatch errors.

Steps to Reproduce

• Obtain two tiles of Sentinel2 from this link.
• Use the bounding box from a given geometry to attempt dataset padding.
• Try to update a Zarr store with the padded data.

Code to Reproduce

import os
import xarray
from fsspec.mapping import FSMap
import rioxarray
from fsspec.implementations.local import LocalFileSystem
from typing import Dict
import numpy as np

def get_bounding_box(aoi_geometry: dict):
    polygon = Polygon(aoi_geometry["coordinates"][0])
    min_x, min_y, max_x, max_y = polygon.bounds
    return min_x, min_y, max_x, max_y

def _update_zarr_store_with_mosaic(
    path_to_mosaic_file: str,
    date: str,
    index: int,
    min_x: float,
     min_y: float,
     max_x: float,
     max_y: float,
) -> bool:
    local_fs: LocalFileSystem = LocalFileSystem()
    parent_path = "/Users/work/test/"
    zarr_store_path = os.path.join(parent_path, "datacube")
    zarr_store: FSMap = local_fs.get_mapper(root=zarr_store_path)
    data = rioxarray.open_rasterio(path_to_mosaic_file, chunks=True)

    data = data.rio.pad_box(minx=min_x, miny=min_y, maxx=max_x, maxy=max_y)
    
    data = data.expand_dims({"time": 1})
    data = data.assign_coords(time=[date])
    data.attrs = {}
    dataset = data.to_dataset(name="data")
    try:
        if index == 0:
            # during first push, we need to create time dimension hence we don't call append dim
            zarr_out = dataset.to_zarr(store=zarr_store)
        else:
            # during consequent pushes to zarr store, we want new data along the time dimension
            zarr_out = dataset.to_zarr(store=zarr_store, append_dim="time")
    except Exception:
        return False
    return True

if __name__ == "__main__":
    date_to_mosaic_file_path_dict = {
        "2024-03-19": "2024_03_19_mosaic.tif",
        "2024-03-09": "2024_03_09_mosaic.tif"
    }

    aoi_geometry = {
        "type": "Polygon",
        "coordinates": [
            [
                [-109.02659262228212, 39.011530803336974], [-109.02348912568533, 38.593684208582765],
                [-108.52488383982984, 38.593684208582765], [-108.52798733642663, 39.011530803336974],
                [-109.02659262228212, 39.011530803336974]
            ]
        ],
    }
    min_x, min_y, max_x, max_y = get_bounding_box(aoi_geometry)
    for idx, date in enumerate(sorted(date_to_mosaic_file_path_dict.keys())):
        _update_zarr_store_with_mosaic(date_to_mosaic_file_path_dict[date], date, idx, min_x, min_y, max_x, max_y)

Environment

Python version: 3.9
rioxarray: 0.13.3
rasterio: 1.3.8
xarray: 2022.12.0
GDAL: 3.6.4

Seeking Suggestions

Is there a recommended method for achieving this padding without encountering dimension size conflicts, especially in scenarios requiring updates to Zarr stores? Any insights or alternative approaches would be greatly appreciated.

[RichardScottOZ]

Can a reproject match template based on your zarr store help?

[snowman2]

Related #155