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CRS handling in xarray provider properties (#1641)

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* update crs handling

* fix epsg code

* config parsing, lean on pyproj

* consolidate code and leverage prior crs work

* update crs handling

* fix epsg code

* config parsing, lean on pyproj

* consolidate code and leverage prior crs work

* fix function call

* bug and flake8 fixes

* documentation updates

* flake8

* Update ogcapi-coverages.rst

* update crs handling

* fix epsg code

* config parsing, lean on pyproj

* consolidate code and leverage prior crs work

* update crs handling

* fix epsg code

* config parsing, lean on pyproj

* consolidate code and leverage prior crs work

* fix function call

* bug and flake8 fixes

* documentation updates

* flake8

* Update ogcapi-coverages.rst

* flake8 fix

* rebase issues

* update import formatting

Co-authored-by: Benjamin Webb <40066515+webb-ben@users.noreply.github.com>

* update conditional logic

Co-authored-by: Benjamin Webb <40066515+webb-ben@users.noreply.github.com>

* update error handling

Co-authored-by: Benjamin Webb <40066515+webb-ben@users.noreply.github.com>

* parse storage crs in init

---------

Co-authored-by: Benjamin Webb <40066515+webb-ben@users.noreply.github.com>
This commit is contained in:
Sarah Jordan
2024-09-12 11:22:25 -05:00
committed by GitHub
parent deb043f928
commit 6682b44928
3 changed files with 104 additions and 10 deletions
Download Patch File Download Diff File Expand all files Collapse all files
docs/source/data-publishing/ogcapi-coverages.rst
+9
View File
@@ -75,6 +75,9 @@ The `Xarray`_ provider plugin reads and extracts `NetCDF`_ and `Zarr`_ data.
x_field: lon
y_field: lat
time_field: time
# optionally specify the coordinate reference system of your dataset
# else pygeoapi assumes it is WGS84 (EPSG:4326).
storage_crs: 4326
format:
name: netcdf
mimetype: application/x-netcdf
@@ -96,6 +99,11 @@ The `Xarray`_ provider plugin reads and extracts `NetCDF`_ and `Zarr`_ data.
be sure to provide the full S3 URL. Any parameters required to open the dataset
using fsspec can be added to the config file under `options` and `s3`.
.. note::
When providing a `storage_crs` value in the xarray configuration, specify the
coordinate reference system using any valid input for
`pyproj.CRS.from_user_input`_.
Data access examples
--------------------
@@ -146,3 +154,4 @@ Data access examples
.. _`NetCDF`: https://en.wikipedia.org/wiki/NetCDF
.. _`Zarr`: https://zarr.readthedocs.io/en/stable
.. _`GDAL raster driver short name`: https://gdal.org/drivers/raster/index.html
.. _`pyproj.CRS.from_user_input`: https://pyproj4.github.io/pyproj/stable/api/crs/coordinate_system.html#pyproj.crs.CoordinateSystem.from_user_input
docs/source/data-publishing/ogcapi-edr.rst
+9
View File
@@ -47,6 +47,9 @@ The `xarray-edr`_ provider plugin reads and extracts `NetCDF`_ and `Zarr`_ data
x_field: lon
y_field: lat
time_field: time
# optionally specify the coordinate reference system of your dataset
# else pygeoapi assumes it is WGS84 (EPSG:4326).
storage_crs: 4326
format:
name: netcdf
mimetype: application/x-netcdf
@@ -81,6 +84,11 @@ The `xarray-edr`_ provider plugin reads and extracts `NetCDF`_ and `Zarr`_ data
S3 URL. Any parameters required to open the dataset using fsspec can be added
to the config file under `options` and `s3`, as shown above.
.. note::
When providing a `storage_crs` value in the EDR configuration, specify the
coordinate reference system using any valid input for
`pyproj.CRS.from_user_input`_.
Data access examples
--------------------
@@ -105,6 +113,7 @@ Data access examples
.. _`xarray`: https://docs.xarray.dev/en/stable/
.. _`NetCDF`: https://en.wikipedia.org/wiki/NetCDF
.. _`Zarr`: https://zarr.readthedocs.io/en/stable
.. _`pyproj.CRS.from_user_input`: https://pyproj4.github.io/pyproj/stable/api/crs/coordinate_system.html#pyproj.crs.CoordinateSystem.from_user_input
.. _`OGC Environmental Data Retrieval (EDR) (API)`: https://github.com/opengeospatial/ogcapi-coverages
pygeoapi/provider/xarray_.py
+86 -10
View File
@@ -37,12 +37,16 @@ import zipfile
import xarray
import fsspec
import numpy as np
import pyproj
from pyproj.exceptions import CRSError
from pygeoapi.api import DEFAULT_STORAGE_CRS
from pygeoapi.provider.base import (BaseProvider,
ProviderConnectionError,
ProviderNoDataError,
ProviderQueryError)
from pygeoapi.util import read_data
from pygeoapi.util import get_crs_from_uri, read_data
LOGGER = logging.getLogger(__name__)
@@ -82,6 +86,7 @@ class XarrayProvider(BaseProvider):
data_to_open = self.data
self._data = open_func(data_to_open)
self.storage_crs = self._parse_storage_crs(provider_def)
self._coverage_properties = self._get_coverage_properties()
self.axes = [self._coverage_properties['x_axis_label'],
@@ -341,6 +346,7 @@ class XarrayProvider(BaseProvider):
def _get_coverage_properties(self):
"""
Helper function to normalize coverage properties
:param provider_def: provider definition
:returns: `dict` of coverage properties
"""
@@ -401,16 +407,21 @@ class XarrayProvider(BaseProvider):
'restime': self.get_time_resolution()
}
if 'crs' in self._data.variables.keys():
try:
properties['bbox_crs'] = f'http://www.opengis.net/def/crs/OGC/1.3/{self._data.crs.epsg_code}' # noqa
properties['inverse_flattening'] = self._data.crs.\
inverse_flattening
# Update properties based on the xarray's CRS
epsg_code = self.storage_crs.to_epsg()
LOGGER.debug(f'{epsg_code}')
if epsg_code == 4326 or self.storage_crs == 'OGC:CRS84':
pass
LOGGER.debug('Confirmed default of WGS 84')
else:
properties['bbox_crs'] = \
f'https://www.opengis.net/def/crs/EPSG/0/{epsg_code}'
properties['inverse_flattening'] = \
self.storage_crs.ellipsoid.inverse_flattening
if self.storage_crs.is_projected:
properties['crs_type'] = 'ProjectedCRS'
except AttributeError:
pass
LOGGER.debug(f'properties: {properties}')
properties['axes'] = [
properties['x_axis_label'],
@@ -476,6 +487,71 @@ class XarrayProvider(BaseProvider):
return ', '.join(times)
def _parse_grid_mapping(self):
"""
Identifies grid_mapping.
:returns: name of xarray data variable that contains CRS information.
"""
LOGGER.debug('Parsing grid mapping...')
spatiotemporal_dims = (self.time_field, self.y_field, self.x_field)
LOGGER.debug(spatiotemporal_dims)
grid_mapping_name = None
for var_name, var in self._data.variables.items():
if all(dim in var.dims for dim in spatiotemporal_dims):
try:
grid_mapping_name = self._data[var_name].attrs['grid_mapping'] # noqa
LOGGER.debug(f'Grid mapping: {grid_mapping_name}')
except KeyError as err:
LOGGER.debug(err)
LOGGER.debug('No grid mapping information found.')
return grid_mapping_name
def _parse_storage_crs(
self,
provider_def: dict
) -> pyproj.CRS:
"""
Parse the storage CRS from an xarray dataset.
:param provider_def: provider definition
:returns: `pyproj.CRS` instance parsed from dataset
"""
storage_crs = None
try:
storage_crs = provider_def['storage_crs']
crs_function = pyproj.CRS.from_user_input
except KeyError as err:
LOGGER.debug(err)
LOGGER.debug('No storage_crs found. Attempting to parse the CRS.')
if storage_crs is None:
grid_mapping = self._parse_grid_mapping()
if grid_mapping is not None:
storage_crs = self._data[grid_mapping].attrs
crs_function = pyproj.CRS.from_cf
elif 'crs' in self._data.variables.keys():
storage_crs = self._data['crs'].attrs
crs_function = pyproj.CRS.from_dict
else:
storage_crs = DEFAULT_STORAGE_CRS
crs_function = get_crs_from_uri
LOGGER.debug('Failed to parse dataset CRS. Assuming WGS84.')
LOGGER.debug(f'Parsing CRS {storage_crs} with {crs_function}')
try:
crs = crs_function(storage_crs)
except CRSError as err:
LOGGER.debug(f'Unable to parse projection with pyproj: {err}')
LOGGER.debug('Assuming default WGS84.')
crs = get_crs_from_uri(DEFAULT_STORAGE_CRS)
LOGGER.debug(crs)
return crs
def _to_datetime_string(datetime_obj):
"""