Biomass reproject + update links

[HarshiniGirish]

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[wildintellect]

I'm redirecting review to @hrodmn and @smk0033 who are working the OGC App Pack example.

[HarshiniGirish]

@smk0033 @hrodmn need a review on this notebook please!

[hrodmn]

@HarshiniGirish I'm sorry this PR slipped past me a few months ago!

The STAC item bbox approach is clever but we don't need to do that! I am not sure why these files have a null crs but they are georeferenced. Instead of a crs they have gcps defined (gcps = Ground Control Points).

Here is how you can use it to do the reprojection without guessing using the STAC metadata:

rio_env = rasterio.Env(GDAL_HTTP_HEADERS=f"Authorization: Bearer {token}")
with rio_env:
    with rasterio.open(asset_href) as ds:
        arr = ds.read(1)
        gcps_list, gcp_crs = ds.gcps
        valid = arr[np.isfinite(arr)]
        print("Shape:", arr.shape)
        print("CRS:", ds.crs)
        print("GCPS list:", gcps_list)
        print("GCP CRS:", gcp_crs)
        print("Transform:", ds.transform)
        print("Min/Max:", float(valid.min()), float(valid.max()))

src_arr = arr.copy()
src_height, src_width = src_arr.shape

# Reproject to EPSG:4326 on a clean output grid
dst_crs = "EPSG:4326"  # don't use EPSG:4326 for raster data if possible!

dst_transform, dst_width, dst_height = calculate_default_transform(
    src_crs=gcp_crs,
    dst_crs=dst_crs,
    width=src_width,
    height=src_height,
    gcps=gcps_list
)

reprojected = np.empty((dst_height, dst_width), dtype=src_arr.dtype)

reproject(
    source=src_arr,
    destination=reprojected,
    gcps=gcps_list,
    src_crs=gcp_crs,
    dst_transform=dst_transform,
    dst_crs=dst_crs,
    resampling=Resampling.nearest
)

print("Destination CRS:", dst_crs)
print("Reprojected shape:", reprojected.shape)
print("Destination transform:", dst_transform)

I think we should encourage users to use a different CRS than epsg:4326 for array data like this, so you could figure out roughly where the sample file is then pick a projected CRS that fits the area.

[HarshiniGirish]

thanks for the feedback @hrodmn. It's up for review again!

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hrodmn commented on 2026-06-04T14:03:26Z
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I would just drop the "Because the file already contains ..." sentence because we don't need to reference the STAC item for anything.

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hrodmn commented on 2026-06-04T14:03:27Z
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Line #4.    

we can drop references to STAC item bbox everywhere!

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hrodmn commented on 2026-06-04T14:03:28Z
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Here's another STAC item bbox reference to remove.

[hrodmn]

Thanks @HarshiniGirish! I left a few more suggestions - let's remove all references to the STAC item bbox approach since we don't need to plant that seed in any reader's mind 😆

The plot at the end suggests that nodata values are not getting masked out so you should take another look at your approach.