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Workaround for some cases that end up in #347 #419

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Mar 17, 2021
Merged

Workaround for some cases that end up in #347 #419

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bccd5f2
workaround for some cases that end up in #347
forman Mar 9, 2021
ef54d24
Merge branch 'master' into forman-347-dont_reorder_lat
forman Mar 10, 2021
df83144
Preparing 0.7.1 release
forman Mar 16, 2021
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12 changes: 8 additions & 4 deletions CHANGES.md
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Original file line number Diff line number Diff line change
@@ -1,7 +1,11 @@
## Changes in 0.7.1.dev1 (in development)

* Added `s3fs` requirement that has been removed by accident.
* Added missing requirements `requests` and `urllib3`.
## Changes in 0.7.1

* Dataset normalisation no longer includes reordering increasing
latitude coordinates, as this creates datasets that are no longer writable
to Zarr. (#347)
* Updated package requirements
- Added `s3fs` requirement that has been removed by accident.
- Added missing requirements `requests` and `urllib3`.

## Changes in 0.7.0

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32 changes: 10 additions & 22 deletions test/core/test_normalize.py
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Expand Up @@ -12,11 +12,11 @@
from jdcal import gcal2jd
from numpy.testing import assert_array_almost_equal

from xcube.core.normalize import adjust_spatial_attrs
from xcube.core.normalize import adjust_temporal_attrs
from xcube.core.normalize import normalize_coord_vars
from xcube.core.normalize import normalize_dataset
from xcube.core.normalize import normalize_missing_time
from xcube.core.normalize import adjust_spatial_attrs
from xcube.core.normalize import adjust_temporal_attrs


# noinspection PyPep8Naming
Expand Down Expand Up @@ -85,25 +85,23 @@ def test_normalize_lon_lat(self):
dataset = xr.Dataset({'first': (['latitude',
'longitude'], [[1, 2, 3],
[2, 3, 4]])})
# Since normalization puts latitudes into descending order, we
# expect the rows to be swapped.
expected = xr.Dataset({'first': (['lat', 'lon'], [[2, 3, 4],
[1, 2, 3]])})
expected = xr.Dataset({'first': (['lat', 'lon'], [[1, 2, 3],
[2, 3, 4]])})
actual = normalize_dataset(dataset)
assertDatasetEqual(actual, expected)

dataset = xr.Dataset({'first': (['lat', 'long'], [[1, 2, 3],
[2, 3, 4]])})
expected = xr.Dataset({'first': (['lat', 'lon'], [[2, 3, 4],
[1, 2, 3]])})
expected = xr.Dataset({'first': (['lat', 'lon'], [[1, 2, 3],
[2, 3, 4]])})
actual = normalize_dataset(dataset)
assertDatasetEqual(actual, expected)

dataset = xr.Dataset({'first': (['latitude',
'spacetime'], [[1, 2, 3],
[2, 3, 4]])})
expected = xr.Dataset({'first': (['lat', 'spacetime'], [[2, 3, 4],
[1, 2, 3]])})
expected = xr.Dataset({'first': (['lat', 'spacetime'], [[1, 2, 3],
[2, 3, 4]])})
actual = normalize_dataset(dataset)
assertDatasetEqual(actual, expected)

Expand All @@ -114,7 +112,7 @@ def test_normalize_lon_lat(self):
actual = normalize_dataset(dataset)
assertDatasetEqual(actual, expected)

def test_normalize_inverted_lat(self):
def test_normalize_does_not_reorder_increasing_lat(self):
first = np.zeros([3, 45, 90])
first[0, :, :] = np.eye(45, 90)
ds = xr.Dataset({
Expand All @@ -125,18 +123,8 @@ def test_normalize_inverted_lat(self):
'time': [datetime(2000, x, 1) for x in range(1, 4)]}).chunk(
chunks={'time': 1})

first = np.zeros([3, 45, 90])
first[0, :, :] = np.flip(np.eye(45, 90), axis=0)
expected = xr.Dataset({
'first': (['time', 'lat', 'lon'], first),
'second': (['time', 'lat', 'lon'], np.zeros([3, 45, 90])),
'lat': np.linspace(88, -88, 45),
'lon': np.linspace(-178, 178, 90),
'time': [datetime(2000, x, 1) for x in range(1, 4)]}).chunk(
chunks={'time': 1})

actual = normalize_dataset(ds)
xr.testing.assert_equal(actual, expected)
xr.testing.assert_equal(actual, ds)
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The check of this test is now that latitude is not inverted anymore. One might argue that we don't need it anymore at all. At least, remove the lines were the 'expected' dataset is built and rename the test to 'test_lat_not_inverted'.

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I agree that the variable expected (lines 128-134) can be removed entirely, but I think it's still useful to keep the test itself as a definition of current behaviour, even if it's trivial. For the name I'd prefer test_normalize_on_increasing_latitudes, which just refers the input format rather than the expected behaviour, and means that there's one less place to update if/when we change it again. (I try to avoid/remove "inverted" where possible, because I find it ambiguous -- to me it just implies "the opposite of whatever we currently want in this context". "increasing" / "decreasing" are far clearer.)


def test_normalize_with_missing_time_dim(self):
ds = xr.Dataset({'first': (['lat', 'lon'], np.zeros([90, 180])),
Expand Down
26 changes: 1 addition & 25 deletions xcube/core/normalize.py
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Expand Up @@ -56,34 +56,11 @@ def normalize_dataset(ds: xr.Dataset) -> xr.Dataset:
ds = _normalize_lat_lon_2d(ds)
ds = _normalize_dim_order(ds)
ds = _normalize_lon_360(ds)

# xcube viewer currently requires decreasing latitude co-ordinates, so
# we invert them here if necessary.
ds = _ensure_lat_decreasing(ds)

ds = normalize_missing_time(ds)
ds = _normalize_jd2datetime(ds)
return ds


def _ensure_lat_decreasing(ds: xr.Dataset) -> xr.Dataset:
"""
If the latitude is increasing, invert it to make it decreasing.
:param ds: some xarray dataset
:return: a normalized xarray dataset
"""
try:
if not _is_lat_decreasing(ds.lat):
ds = ds.sel(lat=slice(None, None, -1))
except AttributeError:
# The dataset doesn't have 'lat', probably not geospatial
pass
except ValueError:
# The dataset still has an ND 'lat' array
pass
return ds


def _normalize_lat_lon(ds: xr.Dataset) -> xr.Dataset:
"""
Rename variables named 'longitude' or 'long' to 'lon', and 'latitude' to 'lon'.
Expand Down Expand Up @@ -366,7 +343,7 @@ def normalize_missing_time(ds: xr.Dataset) -> xr.Dataset:
return ds


def adjust_spatial_attrs(ds: xr.Dataset, allow_point: bool=False) -> xr.Dataset:
def adjust_spatial_attrs(ds: xr.Dataset, allow_point: bool = False) -> xr.Dataset:
"""
Adjust the global spatial attributes of the dataset by doing some
introspection of the dataset and adjusting the appropriate attributes
Expand Down Expand Up @@ -692,7 +669,6 @@ def _is_lat_decreasing(lat: xr.DataArray) -> bool:


def _normalize_dim_order(ds: xr.Dataset) -> xr.Dataset:

copy_created = False

for var_name in ds.data_vars:
Expand Down
2 changes: 1 addition & 1 deletion xcube/version.py
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Expand Up @@ -19,4 +19,4 @@
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.

version = '0.7.1.dev1'
version = '0.7.1'