Gather coords with zarr
MODIFY
pangeo_forge_recipes/recipes/xarray_zarr.py
pangeo_forge_recipes/recipes/xarray_zarr.py
@@ -3,6 +3,7 @@ A Pangeo Forge Recipe
"""
import functools
+import itertools
import logging
import os
import warnings
@@ -26,6 +27,7 @@ from .base import BaseRecipe, FilePatternRecipeMixin
# use this filename to store global recipe metadata in the metadata_cache
# it will be written once (by prepare_target) and read many times (by store_chunk)
_GLOBAL_METADATA_KEY = "pangeo-forge-recipe-metadata.json"
+_ARRAY_DIMENSIONS = "_ARRAY_DIMENSIONS"
MAX_MEMORY = (
int(os.getenv("PANGEO_FORGE_MAX_MEMORY")) # type: ignore
if os.getenv("PANGEO_FORGE_MAX_MEMORY")
@@ -621,6 +623,12 @@ def store_chunk(
zarr_array[zarr_region] = data
+def _gather_coordinate_dimensions(group: zarr.Group) -> List[str]:
+ return list(
+ set(itertools.chain(*(group[var].attrs.get(_ARRAY_DIMENSIONS, []) for var in group)))
+ )
+
+
def finalize_target(
target: CacheFSSpecTarget,
consolidate_zarr: bool,
@@ -632,9 +640,9 @@ def finalize_target(
if consolidate_dimension_coordinates:
logger.info("Consolidating dimension coordinate arrays")
target_mapper = target.get_mapper()
- ds = xr.open_zarr(target_mapper) # Probably a better way to get the dimension coords?
group = zarr.open(target_mapper, mode="a")
- for dim in ds.dims:
+ dims = _gather_coordinate_dimensions(group)
+ for dim in dims:
arr = group[dim]
attrs = dict(arr.attrs)
new = group.array(

Gather coords with zarr