Skip to content

Preserve metadata during anomalies computation when using iris cubes difference #652

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
mattiarighi merged 8 commits into from
Jun 5, 2020
Merged

Preserve metadata during anomalies computation when using iris cubes difference #652

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
062ffdd
fix to preserve orig cube metadata
valeriupredoi May 26, 2020
b2047ee
test to check for metadata preservation
valeriupredoi May 26, 2020
de9b03e
codacy faff
valeriupredoi May 26, 2020
2285fd7
more in depth check on cube metadata
valeriupredoi May 27, 2020
9c46e6c
Bouwe suggestion
valeriupredoi May 27, 2020
3510565
import missing
valeriupredoi May 27, 2020
80a371f
Bouwe suggestion
valeriupredoi May 28, 2020
15ff704
fixed imports
valeriupredoi May 28, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 5 additions & 2 deletions esmvalcore/preprocessor/_time.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,18 +3,19 @@
Allows for selecting data subsets using certain time bounds;
constructing seasonal and area averages.
"""
import copy
import datetime
import logging
from warnings import filterwarnings

import dask.array as da
import iris
import iris.cube
import iris.coord_categorisation
import iris.cube
import iris.exceptions
import iris.util
from iris.time import PartialDateTime
import numpy as np
from iris.time import PartialDateTime

from ._shared import get_iris_analysis_operation, operator_accept_weights

Expand Down Expand Up @@ -460,7 +461,9 @@ def anomalies(cube, period, reference=None, standardize=False):
reference_cube = extract_time(cube, **reference)
reference = climate_statistics(reference_cube, period=period)
if period in ['full']:
metadata = copy.deepcopy(cube.metadata)
cube = cube - reference
cube.metadata = metadata
if standardize:
cube_stddev = climate_statistics(
cube, operator='std_dev', period=period)
Expand Down
41 changes: 28 additions & 13 deletions tests/unit/preprocessor/_time/test_time.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,25 +1,26 @@
"""Unit tests for the :func:`esmvalcore.preprocessor._time` module."""

import copy
import unittest
import pytest
import tests

import numpy as np
from numpy.testing import assert_array_equal, assert_array_almost_equal

from cf_units import Unit
import iris
import iris.coord_categorisation
import iris.coords
import numpy as np
import pytest
from cf_units import Unit
from iris.cube import Cube
from numpy.testing import assert_array_almost_equal, assert_array_equal

from esmvalcore.preprocessor._time import (
extract_month, extract_season, extract_time,
regrid_time,
decadal_statistics, annual_statistics, seasonal_statistics,
monthly_statistics, daily_statistics, timeseries_filter,
climate_statistics, anomalies
)
import tests
from esmvalcore.preprocessor._time import (annual_statistics, anomalies,
climate_statistics,
daily_statistics,
decadal_statistics, extract_month,
extract_season, extract_time,
monthly_statistics, regrid_time,
seasonal_statistics,
timeseries_filter)


def _create_sample_cube():
Expand Down Expand Up @@ -1022,6 +1023,20 @@ def test_standardized_anomalies(period, standardize=True):
)


@pytest.mark.parametrize('period, reference', PARAMETERS)
def test_anomalies_preserve_metadata(period, reference, standardize=False):
cube = make_map_data(number_years=2)
cube.var_name = "si"
cube.units = "m"
metadata = copy.deepcopy(cube.metadata)
result = anomalies(cube, period, reference, standardize=standardize)
assert result.metadata == metadata
for coord_cube, coord_res in zip(cube.coords(), result.coords()):
Copy link
Member

@bouweandela bouweandela May 28, 2020 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Note that if one array is longer than the other, zip will only iterate over the number of elements in the shortest iterable, so this does not test that the cubes have the same coordinates

Copy link
Contributor Author

@valeriupredoi valeriupredoi May 28, 2020

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

good point actually! but the cubes should have the same number of coords otherwise the iris cube difference would fail beforehand

if coord_cube.has_bounds() and coord_res.has_bounds():
assert_array_equal(coord_cube.bounds, coord_res.bounds)
assert coord_cube == coord_res
Comment on lines +1034 to +1037
Copy link
Member

@bouweandela bouweandela May 28, 2020

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I'm not sure if this is needed, because you're testing that the metadata was preserved, right?

Copy link
Contributor Author

@valeriupredoi valeriupredoi May 28, 2020

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

the metadata object does not contain information on the coords, I was quite surprised by that too



@pytest.mark.parametrize('period, reference', PARAMETERS)
def test_anomalies(period, reference, standardize=False):
cube = make_map_data(number_years=2)
Expand Down