Update _dataset_from_files to allow merging conflicting null and non-…

…null values. Raise a warning if conflicting non-null values are merged, but supress the MergeError. Move null-masking into dataset creation util functions to ensure that nulls are set BEFORE merging to allow the above to work as designed. (#29)

test/test_utils.py

@@ -150,14 +150,14 @@ def test_parse_invalid_time_warns():
 def test_dataarray_from_file():
     """Test that an xarray.DataArray can be created from a valid GeoTIFF."""
     file_path = TEST_IMAGE_PATHS[0]
-    da = wxee.utils._dataarray_from_file(file_path)
+    da = wxee.utils._dataarray_from_file(file_path, masked=True, nodata=0)
 
     assert da.name == "pr"
 
 
 def test_dataset_from_files():
     """Test than an xarray.Dataset can be created from a list of valid GeoTIFFs."""
-    ds = wxee.utils._dataset_from_files(TEST_IMAGE_PATHS)
+    ds = wxee.utils._dataset_from_files(TEST_IMAGE_PATHS, masked=True, nodata=0)
 
     assert ds.time.size == 3
     assert all([var in ds.variables for var in ["pr", "rmax"]])

wxee/collection.py

@@ -131,11 +131,7 @@ def to_xarray(
                 max_attempts=max_attempts,
             )
 
-            ds = _dataset_from_files(files)
-
-        # Mask the nodata values. This will convert int datasets to float.
-        if masked:
-            ds = ds.where(ds != nodata)
+            ds = _dataset_from_files(files, masked, nodata)
 
         if path:
             ds.to_netcdf(path, mode="w")

wxee/image.py

@@ -91,11 +91,7 @@ def to_xarray(
                 progress=progress,
             )
 
-            ds = _dataset_from_files(files)
-
-        # Mask the nodata values. This will convert int datasets to float.
-        if masked:
-            ds = ds.where(ds != nodata)
+            ds = _dataset_from_files(files, masked, nodata)
 
         if path:
             ds.to_netcdf(path, mode="w")

wxee/utils.py

@@ -124,14 +124,24 @@ def _create_retry_session(max_attempts: int) -> requests.Session:
     return session
 
 
-def _dataset_from_files(files: List[str]) -> xr.Dataset:
+def _dataset_from_files(files: List[str], masked: bool, nodata: int) -> xr.Dataset:
     """Create an xarray.Dataset from a list of raster files."""
-    das = [_dataarray_from_file(file) for file in files]
+    das = [_dataarray_from_file(file, masked, nodata) for file in files]
 
-    return xr.merge(das)
+    try:
+        # Allow conflicting values if one is null, take the non-null value
+        merged = xr.merge(das, compat="no_conflicts")
+    except xr.core.merge.MergeError:
+        # If non-null conflicting values occur, take the first value and warn the user
+        merged = xr.merge(das, compat="override")
+        warnings.warn(
+            "Different non-null values were encountered for the same variable at the same time coordinate. The first value was taken."
+        )
 
+    return merged
 
-def _dataarray_from_file(file: str) -> xr.DataArray:
+
+def _dataarray_from_file(file: str, masked: bool, nodata: int) -> xr.DataArray:
     """Create an xarray.DataArray from a single file by parsing datetimes and variables from the file name.
 
     The file name must follow the format "{dimension}.{coordinate}.{variable}.{extension}".
@@ -141,6 +151,10 @@ def _dataarray_from_file(file: str) -> xr.DataArray:
 
     da = da.expand_dims({dim: [coord]}).rename(var).squeeze("band").drop_vars("band")
 
+    # Mask the nodata values. This will convert int datasets to float.
+    if masked:
+        da = da.where(da != nodata)
+
     return da