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More lazy fixes (#2450)
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@bouweandela
bouweandela authored Jun 27, 2024
1 parent 5cdc3c2 commit d472381
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Showing 5 changed files with 82 additions and 94 deletions.
73 changes: 15 additions & 58 deletions esmvalcore/cmor/_fixes/cmip5/ec_earth.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,19 +11,18 @@ class Sic(Fix):
"""Fixes for sic."""

def fix_data(self, cube):
"""
Fix data.
"""Fix data.
Fixes discrepancy between declared units and real units
Parameters
----------
cube: iris.cube.Cube
Cube to fix.
Returns
-------
iris.cube.Cube
"""
metadata = cube.metadata
cube *= 100
Expand All @@ -35,19 +34,18 @@ class Sftlf(Fix):
"""Fixes for sftlf."""

def fix_data(self, cube):
"""
Fix data.
"""Fix data.
Fixes discrepancy between declared units and real units
Parameters
----------
cube: iris.cube.Cube
Cube to fix.
Returns
-------
iris.cube.Cube
"""
metadata = cube.metadata
cube *= 100
Expand All @@ -59,19 +57,18 @@ class Tos(Fix):
"""Fixes for tos."""

def fix_data(self, cube):
"""
Fix tos data.
"""Fix tos data.
Fixes mask
Parameters
----------
cube: iris.cube.Cube
Cube to fix.
Returns
-------
iris.cube.Cube
"""
cube.data = da.ma.masked_equal(cube.core_data(), 273.15)
return cube
Expand All @@ -81,8 +78,7 @@ class Tas(Fix):
"""Fixes for tas."""

def fix_metadata(self, cubes):
"""
Fix potentially missing scalar dimension.
"""Fix potentially missing scalar dimension.
Parameters
----------
Expand All @@ -92,9 +88,7 @@ def fix_metadata(self, cubes):
Returns
-------
iris.cube.CubeList
"""

for cube in cubes:
if not cube.coords(var_name='height'):
add_scalar_height_coord(cube)
Expand All @@ -109,8 +103,7 @@ class Areacello(Fix):
"""Fixes for areacello."""

def fix_metadata(self, cubes):
"""
Fix potentially missing scalar dimension.
"""Fix potentially missing scalar dimension.
Parameters
----------
Expand All @@ -120,7 +113,6 @@ def fix_metadata(self, cubes):
Returns
-------
iris.cube.CubeList
"""
areacello = cubes.extract('Areas of grid cell')[0]
lat = cubes.extract('latitude')[0]
Expand All @@ -129,7 +121,9 @@ def fix_metadata(self, cubes):
areacello.add_aux_coord(cube_to_aux_coord(lat), (0, 1))
areacello.add_aux_coord(cube_to_aux_coord(lon), (0, 1))

return iris.cube.CubeList([areacello, ])
return iris.cube.CubeList([
areacello,
])


class Pr(Fix):
Expand All @@ -150,56 +144,19 @@ def fix_metadata(self, cubes):
Returns
-------
iris.cube.CubeList
"""
new_list = iris.cube.CubeList()
for cube in cubes:
try:
old_time = cube.coord('time')
time_coord = cube.coord('time')
except iris.exceptions.CoordinateNotFoundError:
new_list.append(cube)
else:
if old_time.is_monotonic():
if time_coord.is_monotonic():
new_list.append(cube)
else:
time_units = old_time.units
time_data = old_time.points

# erase erroneously copy-pasted points
time_diff = np.diff(time_data)
idx_neg = np.where(time_diff <= 0.)[0]
while len(idx_neg) > 0:
time_data = np.delete(time_data, idx_neg[0] + 1)
time_diff = np.diff(time_data)
idx_neg = np.where(time_diff <= 0.)[0]

# create the new time coord
new_time = iris.coords.DimCoord(time_data,
standard_name='time',
var_name='time',
units=time_units)

# create a new cube with the right shape
dims = (time_data.shape[0],
cube.coord('latitude').shape[0],
cube.coord('longitude').shape[0])
data = cube.data
new_data = np.ma.append(data[:dims[0] - 1, :, :],
data[-1, :, :])
new_data = new_data.reshape(dims)

tmp_cube = iris.cube.Cube(
new_data,
standard_name=cube.standard_name,
long_name=cube.long_name,
var_name=cube.var_name,
units=cube.units,
attributes=cube.attributes,
cell_methods=cube.cell_methods,
dim_coords_and_dims=[(new_time, 0),
(cube.coord('latitude'), 1),
(cube.coord('longitude'), 2)])

new_list.append(tmp_cube)
select = np.unique(time_coord.points, return_index=True)[1]
new_list.append(cube[select])

return new_list
68 changes: 49 additions & 19 deletions esmvalcore/cmor/_fixes/cmip6/access_esm1_5.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,25 +20,51 @@ def fix_metadata(self, cubes):
Returns
-------
iris.cube.CubeList
"""
for cube in cubes:
try:
bcoeff = cube.coord(var_name='b')
# values taken from HadGEM2-ES model (CMIP5), which uses the
# same atmospheric component as ACCESS-ESM1-5 (HadGAM2, N96L38)
bcoeff.points = [
0.99771648645401, 0.990881502628326, 0.979542553424835,
0.9637770652771, 0.943695485591888, 0.919438362121582,
0.891178011894226, 0.859118342399597, 0.823493480682373,
0.784570515155792, 0.742646217346191, 0.698050200939178,
0.651142716407776, 0.602314412593842, 0.55198872089386,
0.500619947910309, 0.44869339466095, 0.39672577381134,
0.34526526927948, 0.294891387224197, 0.24621507525444,
0.199878215789795, 0.156554222106934, 0.116947874426842,
0.0817952379584312, 0.0518637150526047, 0.0279368180781603,
0.0107164792716503, 0.00130179093685001,
0, 0, 0, 0, 0, 0, 0, 0, 0,
0.99771648645401,
0.990881502628326,
0.979542553424835,
0.9637770652771,
0.943695485591888,
0.919438362121582,
0.891178011894226,
0.859118342399597,
0.823493480682373,
0.784570515155792,
0.742646217346191,
0.698050200939178,
0.651142716407776,
0.602314412593842,
0.55198872089386,
0.500619947910309,
0.44869339466095,
0.39672577381134,
0.34526526927948,
0.294891387224197,
0.24621507525444,
0.199878215789795,
0.156554222106934,
0.116947874426842,
0.0817952379584312,
0.0518637150526047,
0.0279368180781603,
0.0107164792716503,
0.00130179093685001,
0,
0,
0,
0,
0,
0,
0,
0,
0,
]
bcoeff.bounds = [
[1, 0.994296252727509],
Expand Down Expand Up @@ -70,8 +96,15 @@ def fix_metadata(self, cubes):
[0.0389823913574219, 0.0183146875351667],
[0.0183146875351667, 0.00487210927531123],
[0.00487210927531123, 0],
[0, 0], [0, 0], [0, 0], [0, 0], [0, 0], [0, 0], [0, 0],
[0, 0], [0, 0],
[0, 0],
[0, 0],
[0, 0],
[0, 0],
[0, 0],
[0, 0],
[0, 0],
[0, 0],
[0, 0],
]
except iris.exceptions.CoordinateNotFoundError:
pass
Expand All @@ -80,7 +113,6 @@ def fix_metadata(self, cubes):

Cli = Cl


Clw = Cl


Expand All @@ -98,7 +130,6 @@ def fix_metadata(self, cubes):
Returns
-------
iris.cube.Cube
"""
cube = self.get_cube_from_list(cubes)
cube.coord('air_pressure').points = \
Expand All @@ -122,11 +153,10 @@ def fix_metadata(self, cubes):
Returns
-------
iris.cube.Cube
"""
cube = self.get_cube_from_list(cubes)
cube.coord('air_pressure').points = \
np.round(cube.coord('air_pressure').points, 0)
np.round(cube.coord('air_pressure').core_points(), 0)
cube.coord('air_pressure').bounds = \
np.round(cube.coord('air_pressure').bounds, 0)
np.round(cube.coord('air_pressure').core_bounds(), 0)
return cubes
6 changes: 2 additions & 4 deletions esmvalcore/cmor/_fixes/cmip6/cnrm_cm6_1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@
from ..fix import Fix
from ..shared import (
add_aux_coords_from_cubes,
fix_ocean_depth_coord,
get_bounds_cube,
fix_ocean_depth_coord
)


Expand All @@ -24,7 +24,6 @@ def fix_metadata(self, cubes):
Returns
-------
iris.cube.Cube
"""
cube = self.get_cube_from_list(cubes)

Expand All @@ -40,7 +39,7 @@ def fix_metadata(self, cubes):
# Fix vertical coordinate bounds
for coord_name in ('ap', 'b'):
bounds_cube = get_bounds_cube(cubes, coord_name)
bounds = bounds_cube.data.reshape(-1, 2)
bounds = bounds_cube.core_data().reshape(-1, 2)
new_bounds_cube = iris.cube.Cube(bounds,
**bounds_cube.metadata._asdict())
cubes.remove(bounds_cube)
Expand Down Expand Up @@ -91,7 +90,6 @@ def fix_metadata(self, cubes):
Returns
-------
iris.cube.CubeList
"""
for cube in cubes:
if cube.coords(axis='Z'):
Expand Down
21 changes: 14 additions & 7 deletions esmvalcore/cmor/_fixes/cmip6/fgoals_g3.py
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
"""Fixes for FGOALS-g3 model."""
import dask.array as da
import iris

from ..common import OceanFixGrid
Expand All @@ -22,7 +23,13 @@ def fix_metadata(self, cubes):
"""Fix metadata.
FGOALS-g3 data contain latitude and longitude data set to >1e30 in some
places.
places. Note that the corresponding data is all masked.
Example files:
v20191030/siconc_SImon_FGOALS-g3_piControl_r1i1p1f1_gn_070001-079912.nc
v20191030/siconc_SImon_FGOALS-g3_piControl_r1i1p1f1_gn_080001-089912.nc
v20200706/siconc_SImon_FGOALS-g3_ssp534-over_r1i1p1f1_gn_201501-210012
.nc
Parameters
----------
Expand All @@ -32,13 +39,13 @@ def fix_metadata(self, cubes):
Returns
-------
iris.cube.CubeList
"""
cube = self.get_cube_from_list(cubes)
cube.coord('latitude').points[
cube.coord('latitude').points > 1000.0] = 0.0
cube.coord('longitude').points[
cube.coord('longitude').points > 1000.0] = 0.0
for coord_name in ['latitude', 'longitude']:
coord = cube.coord(coord_name)
bad_indices = coord.core_points() > 1000.0
coord.points = da.ma.where(bad_indices, 0.0, coord.core_points())

return super().fix_metadata(cubes)


Expand All @@ -51,7 +58,7 @@ class Mrsos(Fix):
def fix_metadata(self, cubes):
"""Fix metadata.
FGOALS-g3 mrsos data contains error in co-ordinate bounds.
FGOALS-g3 mrsos data contains error in coordinate bounds.
Parameters
----------
Expand Down
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