Rasterio error: Input shapes do not overlap raster but reprojection not working

Question

I'm trying to use rasterio (v1.0.13) and fiona to perform a raster clip on a geotiff using a geojson polygon. For reference, the clip works perfectly from the command line using GDAL:

gdalwarp -cutline tmp_yard.geojson -crop_to_cutline -of GTiff -r cubic leaf_index.tif tmp.tif

enter image description here

enter image description here

But the following does not (as per rasterio docs: https://rasterio.readthedocs.io/en/latest/topics/masking-by-shapefile.html#)

with fiona.open("tmp_yard.geojson", "r") as geojson:
 features = [feature["geometry"] for feature in geojson]
 pprint.pprint(features)
 with rasterio.open("leaf_index.tif") as src:
 out_image, out_transform = rasterio.mask.mask(src, features,
 crop=True)
 out_meta = src.meta.copy()

Produces error:

[{'coordinates': [[(-11680153.379982425, 4825380.211452511), (-11680101.881582342, 4825359.649286965), (-11680099.47141429, 4825337.825410188), (-11680153.677325355, 4825348.074481825), (-11680153.379982425, 4825380.211452511)]], 'type': 'Polygon'}]

ValueError: Input shapes do not overlap raster.

I tried to apply the solution here: Masking GeoTIFF file after GeoJSON through rasterio - "Input shapes do not overlap raster" to reproject my geoson, using:

import shapely
import pyproj
def project_wsg_shape_to_csr(shape, csr):
 project = lambda x, y: pyproj.transform(
 pyproj.Proj(init='epsg:4326'),
 pyproj.Proj(init=csr),
 x,
 y
 )
 return shapely.ops.transform(project, shape)
yard=project_wsg_shape_to_csr(features, 'epsg:4326')

However, this produces the error:

AttributeError: 'list' object has no attribute 'is_empty'

Anyone got any ideas?

• James: Without the full traceback for your error, it's tough to say for sure where the error is happening, BUT, it sounds like your shape might be a list instead of a Shapely geometry. Could you check that your geometry is correct?
• metalaureate: Yes, I had that wrong but I couldn't figure out how to fix it. I solved the problem by giving up on reprojecting on the geoJSON side and instead reprojecting the geoTIFF to WSG84 instead before applying the clip.

Answer 1

Your code tries to convert from EPSG:4326 to EPSG:4326. But your data is actually in EPSG:3857 (wild guess on my end). You need to use EPSG:3857 as "source" CRS.

Try this (untested):

project = lambda x, y: pyproj.transform(
 pyproj.Proj(init='epsg:3857'),
 pyproj.Proj(init='epsg:4326'),
 x,
 y
)
yard = shapely.ops.transform(project, features)

GeoJSON had no specification until https://www.rfc-editor.org/rfc/rfc7946 so older GeoJSON might not be in WGS84 which rasterio might assume to be the case.

Answer 2

In the end, reprojecting the geoTIFF using QGIS (instead of trying to unsuccessfully reproject geoJSON) to WSG84 did the trick and made the rasterio example work.