Fill missing data_vars during concat by reindexing (#7400)

* Fill missing data variables during concat by reindexing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * FIX: use `Any` for type of `fill_value` as this seems consistent with other places * ENH: add tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * typing Co-authored-by: Illviljan <[email protected]> * typing Co-authored-by: Illviljan <[email protected]> * typing Co-authored-by: Illviljan <[email protected]> * use None instead of False Co-authored-by: Illviljan <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * concatenate variable in any case if variable has concat_dim * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add tests from @scottcha #3545 * typing * fix typing * fix tests with, finalize typing * add whats-new.rst entry * Update xarray/tests/test_concat.py Co-authored-by: Illviljan <[email protected]> * Update xarray/tests/test_concat.py Co-authored-by: Illviljan <[email protected]> * add TODO, fix numpy.random.default_rng * change np.random to use Generator * move code for variable order into dedicated function, merge with _parse_datasets, provide fast lane for variable order estimation * fix comment * Use order from first dataset, append missing variables to the end * ensure fill_value is dict * ensure fill_value in align * simplify combined_var, fix test * revert fill_value for alignment.py * derive variable order in order of appearance as suggested per review * remove unneeded enumerate * Use alignment.reindex_variables instead. This also removes the need to handle fill_value * small cleanup * Update doc/whats-new.rst Co-authored-by: Deepak Cherian <[email protected]> * adapt tests as per review request, fix ensure_common_dims * adapt tests as per review request * fix whats-new.rst * add whats-new.rst entry * Add additional test with scalar data_var * remove erroneous content from whats-new.rst Co-authored-by: Scott Chamberlin <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Illviljan <[email protected]> Co-authored-by: Deepak Cherian <[email protected]>
pydata · Jan 20, 2023 · b4e3cbc · b4e3cbc
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diff --git a/doc/whats-new.rst b/doc/whats-new.rst
@@ -35,6 +35,9 @@ Deprecations
 Bug fixes
 ~~~~~~~~~
 
+- :py:func:`xarray.concat` can now concatenate variables present in some datasets but
+  not others (:issue:`508`, :pull:`7400`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_ and `Scott Chamberlin <https://github.com/scottcha>`_.
 
 Documentation
 ~~~~~~~~~~~~~

diff --git a/xarray/core/concat.py b/xarray/core/concat.py
@@ -5,7 +5,7 @@
 import pandas as pd
 
 from xarray.core import dtypes, utils
-from xarray.core.alignment import align
+from xarray.core.alignment import align, reindex_variables
 from xarray.core.duck_array_ops import lazy_array_equiv
 from xarray.core.indexes import Index, PandasIndex
 from xarray.core.merge import (
@@ -378,7 +378,9 @@ def process_subset_opt(opt, subset):
 
             elif opt == "all":
                 concat_over.update(
-                    set(getattr(datasets[0], subset)) - set(datasets[0].dims)
+                    set().union(
+                        *list(set(getattr(d, subset)) - set(d.dims) for d in datasets)
+                    )
                 )
             elif opt == "minimal":
                 pass
@@ -406,19 +408,26 @@ def process_subset_opt(opt, subset):
 
 # determine dimensional coordinate names and a dict mapping name to DataArray
 def _parse_datasets(
-    datasets: Iterable[T_Dataset],
-) -> tuple[dict[Hashable, Variable], dict[Hashable, int], set[Hashable], set[Hashable]]:
-
+    datasets: list[T_Dataset],
+) -> tuple[
+    dict[Hashable, Variable],
+    dict[Hashable, int],
+    set[Hashable],
+    set[Hashable],
+    list[Hashable],
+]:
     dims: set[Hashable] = set()
     all_coord_names: set[Hashable] = set()
     data_vars: set[Hashable] = set()  # list of data_vars
     dim_coords: dict[Hashable, Variable] = {}  # maps dim name to variable
     dims_sizes: dict[Hashable, int] = {}  # shared dimension sizes to expand variables
+    variables_order: dict[Hashable, Variable] = {}  # variables in order of appearance
 
     for ds in datasets:
         dims_sizes.update(ds.dims)
         all_coord_names.update(ds.coords)
         data_vars.update(ds.data_vars)
+        variables_order.update(ds.variables)
 
         # preserves ordering of dimensions
         for dim in ds.dims:
@@ -429,7 +438,7 @@ def _parse_datasets(
                 dim_coords[dim] = ds.coords[dim].variable
         dims = dims | set(ds.dims)
 
-    return dim_coords, dims_sizes, all_coord_names, data_vars
+    return dim_coords, dims_sizes, all_coord_names, data_vars, list(variables_order)
 
 
 def _dataset_concat(
@@ -439,7 +448,7 @@ def _dataset_concat(
     coords: str | list[str],
     compat: CompatOptions,
     positions: Iterable[Iterable[int]] | None,
-    fill_value: object = dtypes.NA,
+    fill_value: Any = dtypes.NA,
     join: JoinOptions = "outer",
     combine_attrs: CombineAttrsOptions = "override",
 ) -> T_Dataset:
@@ -471,7 +480,9 @@ def _dataset_concat(
         align(*datasets, join=join, copy=False, exclude=[dim], fill_value=fill_value)
     )
 
-    dim_coords, dims_sizes, coord_names, data_names = _parse_datasets(datasets)
+    dim_coords, dims_sizes, coord_names, data_names, vars_order = _parse_datasets(
+        datasets
+    )
     dim_names = set(dim_coords)
     unlabeled_dims = dim_names - coord_names
 
@@ -525,7 +536,7 @@ def _dataset_concat(
 
     # we've already verified everything is consistent; now, calculate
     # shared dimension sizes so we can expand the necessary variables
-    def ensure_common_dims(vars):
+    def ensure_common_dims(vars, concat_dim_lengths):
         # ensure each variable with the given name shares the same
         # dimensions and the same shape for all of them except along the
         # concat dimension
@@ -553,16 +564,35 @@ def get_indexes(name):
                     data = var.set_dims(dim).values
                     yield PandasIndex(data, dim, coord_dtype=var.dtype)
 
+    # create concatenation index, needed for later reindexing
+    concat_index = list(range(sum(concat_dim_lengths)))
+
     # stack up each variable and/or index to fill-out the dataset (in order)
     # n.b. this loop preserves variable order, needed for groupby.
-    for name in datasets[0].variables:
+    for name in vars_order:
         if name in concat_over and name not in result_indexes:
-            try:
-                vars = ensure_common_dims([ds[name].variable for ds in datasets])
-            except KeyError:
-                raise ValueError(f"{name!r} is not present in all datasets.")
-
-            # Try concatenate the indexes, concatenate the variables when no index
+            variables = []
+            variable_index = []
+            var_concat_dim_length = []
+            for i, ds in enumerate(datasets):
+                if name in ds.variables:
+                    variables.append(ds[name].variable)
+                    # add to variable index, needed for reindexing
+                    var_idx = [
+                        sum(concat_dim_lengths[:i]) + k
+                        for k in range(concat_dim_lengths[i])
+                    ]
+                    variable_index.extend(var_idx)
+                    var_concat_dim_length.append(len(var_idx))
+                else:
+                    # raise if coordinate not in all datasets
+                    if name in coord_names:
+                        raise ValueError(
+                            f"coordinate {name!r} not present in all datasets."
+                        )
+            vars = ensure_common_dims(variables, var_concat_dim_length)
+
+            # Try to concatenate the indexes, concatenate the variables when no index
             # is found on all datasets.
             indexes: list[Index] = list(get_indexes(name))
             if indexes:
@@ -589,6 +619,15 @@ def get_indexes(name):
                 combined_var = concat_vars(
                     vars, dim, positions, combine_attrs=combine_attrs
                 )
+                # reindex if variable is not present in all datasets
+                if len(variable_index) < len(concat_index):
+                    combined_var = reindex_variables(
+                        variables={name: combined_var},
+                        dim_pos_indexers={
+                            dim: pd.Index(variable_index).get_indexer(concat_index)
+                        },
+                        fill_value=fill_value,
+                    )[name]
                 result_vars[name] = combined_var
 
         elif name in result_vars: