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add kwargs to xarrayReader methods for compatibility (#762)
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* add kwargs to xarrayReader methods for compatibility

* add netcdf backend

* add get_asset_list method

* add STAC+netcdf example
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@vincentsarago
vincentsarago authored Nov 5, 2024
1 parent 9a39c80 commit 9fd7107
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6 changes: 6 additions & 0 deletions CHANGES.md
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# 7.2.0 (2024-11-05)

* Ensure compatibility between XarrayReader and other Readers by adding `**kwargs` on class methods (https://github.com/cogeotiff/rio-tiler/pull/762)

* add `STACReader.get_asset_list()` method to enable easier customization of the asset listing/validation (https://github.com/cogeotiff/rio-tiler/pull/762)

# 7.1.0 (2024-10-29)

* Add `preview()` and `statistics()` methods to XarrayReader (https://github.com/cogeotiff/rio-tiler/pull/755)
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1 change: 1 addition & 0 deletions docs/mkdocs.yml
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Expand Up @@ -44,6 +44,7 @@ nav:
- rio-tiler + STAC: 'examples/Using-rio-tiler-STACReader.ipynb'
- Non-Earth dataset: 'examples/Using-nonEarth-dataset.ipynb'
- Xarray + rio-tiler: 'examples/Using-rio-tiler-XarrayReader.ipynb'
- STAC + Xarray: 'examples/STAC_datacube_support.ipynb'
- Migration Guides:
- v1.0 -> v2.0: 'migrations/v2_migration.md'
- v2.0 -> v3.0: 'migrations/v3_migration.md'
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515 changes: 515 additions & 0 deletions docs/src/examples/STAC_datacube_support.ipynb
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111 changes: 111 additions & 0 deletions docs/src/examples/data/stac_netcdf.json
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{
"type": "Feature",
"stac_version": "1.0.0",
"id": "my_stac",
"properties": {
"proj:epsg": 4326,
"proj:geometry": {
"type": "Polygon",
"coordinates": [
[
[
-170.085,
79.91999999999659
],
[
169.91499999997504,
79.91999999999659
],
[
169.91499999997504,
-80.08
],
[
-170.085,
-80.08
],
[
-170.085,
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]
]
]
},
"proj:bbox": [
-170.085,
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169.91499999997504,
-80.08
],
"proj:shape": [
1000,
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],
"proj:transform": [
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],
"datetime": "2024-11-05T09:03:47.523834Z"
},
"geometry": {
"type": "Polygon",
"coordinates": [
[
[
-170.085,
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],
[
169.91499999997504,
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],
[
169.91499999997504,
-80.08
],
[
-170.085,
-80.08
],
[
-170.085,
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]
]
]
},
"links": [],
"assets": {
"netcdf": {
"href": "dataset_2d.nc",
"type": "application/x-netcdf",
"roles": ["data"],
"cube:variables": {
"dataset": {
"dimensions": [
"y",
"x"
],
"type": "data"
}
}
}
},
"bbox": [
-170.085,
-80.08,
169.91499999997504,
79.91999999999659
],
"stac_extensions": [
"https://stac-extensions.github.io/projection/v1.1.0/schema.json",
"https://stac-extensions.github.io/datacube/v2.2.0/schema.json"
]
}
1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up @@ -43,6 +43,7 @@ test = [
# XarrayReader
"xarray",
"rioxarray",
"h5netcdf",
# S3
"boto3",
# Some tests will fail with 5.0
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23 changes: 19 additions & 4 deletions rio_tiler/io/stac.py
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Expand Up @@ -3,7 +3,18 @@
import json
import os
import warnings
from typing import Any, Dict, Iterator, Optional, Sequence, Set, Tuple, Type, Union
from typing import (
Any,
Dict,
Iterator,
List,
Optional,
Sequence,
Set,
Tuple,
Type,
Union,
)
from urllib.parse import urlparse

import attr
Expand Down Expand Up @@ -273,7 +284,13 @@ def __attrs_post_init__(self):
self.minzoom = self.minzoom if self.minzoom is not None else self._minzoom
self.maxzoom = self.maxzoom if self.maxzoom is not None else self._maxzoom

self.assets = list(
self.assets = self.get_asset_list()
if not self.assets:
raise MissingAssets("No valid asset found. Asset's media types not supported")

def get_asset_list(self) -> List[str]:
"""Get valid asset list"""
return list(
_get_assets(
self.item,
include=self.include_assets,
Expand All @@ -282,8 +299,6 @@ def __attrs_post_init__(self):
exclude_asset_types=self.exclude_asset_types,
)
)
if not self.assets:
raise MissingAssets("No valid asset found. Asset's media types not supported")

def _get_reader(self, asset_info: AssetInfo) -> Tuple[Type[BaseReader], Dict]:
"""Get Asset Reader."""
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8 changes: 7 additions & 1 deletion rio_tiler/io/xarray.py
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Expand Up @@ -3,7 +3,7 @@
from __future__ import annotations

import warnings
from typing import Dict, List, Optional
from typing import Any, Dict, List, Optional

import attr
import numpy
Expand Down Expand Up @@ -156,6 +156,7 @@ def statistics(
percentiles: Optional[List[int]] = None,
hist_options: Optional[Dict] = None,
nodata: Optional[NoData] = None,
**kwargs: Any,
) -> Dict[str, BandStatistics]:
"""Return statistics from a dataset."""
hist_options = hist_options or {}
Expand Down Expand Up @@ -188,6 +189,7 @@ def tile(
reproject_method: WarpResampling = "nearest",
auto_expand: bool = True,
nodata: Optional[NoData] = None,
**kwargs: Any,
) -> ImageData:
"""Read a Web Map tile from a dataset.
Expand Down Expand Up @@ -264,6 +266,7 @@ def part(
height: Optional[int] = None,
width: Optional[int] = None,
resampling_method: RIOResampling = "nearest",
**kwargs: Any,
) -> ImageData:
"""Read part of a dataset.
Expand Down Expand Up @@ -362,6 +365,7 @@ def preview(
dst_crs: Optional[CRS] = None,
reproject_method: WarpResampling = "nearest",
resampling_method: RIOResampling = "nearest",
**kwargs: Any,
) -> ImageData:
"""Return a preview of a dataset.
Expand Down Expand Up @@ -446,6 +450,7 @@ def point(
lat: float,
coord_crs: CRS = WGS84_CRS,
nodata: Optional[NoData] = None,
**kwargs: Any,
) -> PointData:
"""Read a pixel value from a dataset.
Expand Down Expand Up @@ -499,6 +504,7 @@ def feature(
height: Optional[int] = None,
width: Optional[int] = None,
resampling_method: RIOResampling = "nearest",
**kwargs: Any,
) -> ImageData:
"""Read part of a dataset defined by a geojson feature.
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106 changes: 106 additions & 0 deletions tests/fixtures/stac_netcdf.json
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{
"type": "Feature",
"stac_version": "1.0.0",
"id": "my_stac",
"properties": {
"proj:epsg": 4326,
"proj:geometry": {
"type": "Polygon",
"coordinates": [
[
[
-170.085,
79.91999999999659
],
[
169.91499999997504,
79.91999999999659
],
[
169.91499999997504,
-80.08
],
[
-170.085,
-80.08
],
[
-170.085,
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]
]
]
},
"proj:bbox": [
-170.085,
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169.91499999997504,
-80.08
],
"proj:shape": [
1000,
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],
"proj:transform": [
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0,
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0,
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],
"datetime": "2024-11-05T09:03:47.523834Z"
},
"geometry": {
"type": "Polygon",
"coordinates": [
[
[
-170.085,
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[
169.91499999997504,
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[
169.91499999997504,
-80.08
],
[
-170.085,
-80.08
],
[
-170.085,
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]
]
]
},
"links": [],
"assets": {
"geotiff": {
"href": "dataset_2d.tif",
"type": "image/tiff; application=geotiff",
"roles": ["data"]
},
"netcdf": {
"href": "dataset_2d.nc",
"type": "application/x-netcdf",
"roles": ["data"]
}
},
"bbox": [
-170.085,
-80.08,
169.91499999997504,
79.91999999999659
],
"stac_extensions": [
"https://stac-extensions.github.io/projection/v1.1.0/schema.json"
]
}
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