def add_times(cube, time): coord_cat.add_month(cube, time, name='month') coord_cat.add_season(cube, time, name='clim_season') coord_cat.add_year(cube, time, name='year') coord_cat.add_day_of_year(cube, time, name='day_number') coord_cat.add_season_year(cube, time, name='season_year') return cube
def add_extra_time_coords(cube):
"""
Adds new coordinate for indexing a given simulation based on model and
ensemble and adds additional time coordinates for unit manipulation
"""
if not cube.coords('year'):
icc.add_year(cube, 'time')
if not cube.coords('month'):
icc.add_month(cube, 'time')
if not cube.coords('month_number'):
icc.add_month_number(cube, 'time')
if not cube.coords('day_of_month'):
icc.add_day_of_month(cube, 'time')
if not cube.coords('hour'):
icc.add_hour(cube, 'time')
return cube
def test_basic(self):
cube = self.cube
time_coord = self.time_coord
ccat.add_year(cube, time_coord, 'my_year')
ccat.add_day_of_month(cube, time_coord, 'my_day_of_month')
ccat.add_day_of_year(cube, time_coord, 'my_day_of_year')
ccat.add_month(cube, time_coord, 'my_month')
with warnings.catch_warnings(record=True):
ccat.add_month_shortname(cube, time_coord, 'my_month_shortname')
ccat.add_month_fullname(cube, time_coord, 'my_month_fullname')
ccat.add_month_number(cube, time_coord, 'my_month_number')
ccat.add_weekday(cube, time_coord, 'my_weekday')
ccat.add_weekday_number(cube, time_coord, 'my_weekday_number')
with warnings.catch_warnings(record=True):
ccat.add_weekday_shortname(cube, time_coord,
'my_weekday_shortname')
ccat.add_weekday_fullname(cube, time_coord, 'my_weekday_fullname')
ccat.add_season(cube, time_coord, 'my_season')
ccat.add_season_number(cube, time_coord, 'my_season_number')
with warnings.catch_warnings(record=True):
ccat.add_season_month_initials(cube, time_coord,
'my_season_month_initials')
ccat.add_season_year(cube, time_coord, 'my_season_year')
# also test 'generic' categorisation interface
def _month_in_quarter(coord, pt_value):
date = coord.units.num2date(pt_value)
return (date.month - 1) % 3
ccat.add_categorised_coord(cube,
'my_month_in_quarter',
time_coord,
_month_in_quarter)
# To ensure consistent results between 32-bit and 64-bit
# platforms, ensure all the numeric categorisation coordinates
# are always stored as int64.
for coord in cube.coords():
if coord.long_name is not None and coord.points.dtype.kind == 'i':
coord.points = coord.points.astype(np.int64)
# check values
self.assertCML(cube, ('categorisation', 'quickcheck.cml'))
def extract_cube_monthmean(infile, stash_codes):
""" Extract specified fields, with multi-annual meaning if req """
import iris.coord_categorisation as ircat
# For easier categorisation of data into months
# Extract fields and check --if less than 12, flag Error
# If more than (and multiple of) 12, derive multi-annual
# monthly means and return
fieldcons = [] # List of stash constraints
for spc in stash_codes:
fieldcons.append(iris.AttributeConstraint(STASH=spc))
incubes = iris.load(infile, constraints=fieldcons, callback=ukca_callback)
#### ---- For now, expect the coordinate to be called 'time' ----
##### %%% Future --use Iris terminology for 'first dimension' -need to find example -- %%%%
tdim = incubes[0].coord('time').shape[0]
log_msg('*** TDIM : {:d} months of data detected. ****'.format(tdim))
if tdim < 12:
raise Evalerror(
'EXTR_CUBE: Atleast 12 (month) records expected. Found {:d}'.
format(tdim))
# If records/ files > 12 and multiple of 12, attempt multi-annual meaning
if tdim > 12:
if tdim % 12 != 0:
raise Evalerror('EXTR_CUBE: Expected multiple of 12 (months).'+\
' Found {:d}'.format(tdim) )
log_msg('EXTR_CUBE: ' + str(tdim / 12) + ' years of data detected.')
log_msg(' Performing multi-annual mean\n')
oucubes = [] # output cube list
for n, cb in enumerate(incubes):
# Add artificial/ auxilliary dim 'month' and average over this.
# First check if this dimension already exists
try:
dumm = cb.coord('month')
except:
# not found --add. %%%% Again assuming coord called 'time' %%%%%%
ircat.add_month(cb, 'time', name='month')
incubes[n] = cb.aggregated_by('month', iris.analysis.MEAN)
return incubes
def climatology(cube, kind='month'):
"""Calculate a climatology for a cube. Can do monthly or yearly.
Args:
cube (iris.cube.Cube)
kind (Optional[str]): 'month' or 'year'
Returns:
iris.cube.Cube
"""
aux_coords = [aux_coord.name() for aux_coord in cube.aux_coords]
if 'year' not in aux_coords:
cat.add_year(cube, 'time')
if 'month' not in aux_coords:
cat.add_month(cube, 'time')
cat.add_month_number(cube, 'time')
out = cube.aggregated_by(kind, iris.analysis.MEAN)
# If the data don't start in January the time coordinate will no longer
# be monotonic. Fix this.
if (kind == 'month') and (not out.coord('time').is_monotonic()):
# Reorder the data so January is first.
jan_index = np.where(out.coord('month').points == 'Jan')[0][0]
ntim = 12
sort_indices = range(jan_index, ntim) + range(0, jan_index)
out = out[sort_indices]
# Create a new time coordinate which is monotonic.
startyear = int(out.coord('time').units.num2date(0).year)
newtime_points = [
netcdftime.datetime(startyear + (m / 12), (m % 12) + 1, 1)
for m in out.coord('month_number').points.astype(int) - 1
]
time_units = out.coord('time').units
newtime_points = time_units.date2num(newtime_points)
newtime = iris.coords.DimCoord(newtime_points,
units=time_units,
standard_name='time')
data_dim = out.coord_dims('time')[0]
out.remove_coord('time')
out.add_dim_coord(newtime, data_dim)
return out
def test_basic(self):
cube = self.cube
time_coord = self.time_coord
ccat.add_year(cube, time_coord, 'my_year')
ccat.add_day_of_month(cube, time_coord, 'my_day_of_month')
ccat.add_day_of_year(cube, time_coord, 'my_day_of_year')
ccat.add_month(cube, time_coord, 'my_month')
with warnings.catch_warnings(record=True):
ccat.add_month_shortname(cube, time_coord, 'my_month_shortname')
ccat.add_month_fullname(cube, time_coord, 'my_month_fullname')
ccat.add_month_number(cube, time_coord, 'my_month_number')
ccat.add_weekday(cube, time_coord, 'my_weekday')
ccat.add_weekday_number(cube, time_coord, 'my_weekday_number')
with warnings.catch_warnings(record=True):
ccat.add_weekday_shortname(cube, time_coord,
'my_weekday_shortname')
ccat.add_weekday_fullname(cube, time_coord, 'my_weekday_fullname')
ccat.add_season(cube, time_coord, 'my_season')
ccat.add_season_number(cube, time_coord, 'my_season_number')
with warnings.catch_warnings(record=True):
ccat.add_season_month_initials(cube, time_coord,
'my_season_month_initials')
ccat.add_season_year(cube, time_coord, 'my_season_year')
# also test 'generic' categorisation interface
def _month_in_quarter(coord, pt_value):
date = coord.units.num2date(pt_value)
return (date.month - 1) % 3
ccat.add_categorised_coord(cube, 'my_month_in_quarter', time_coord,
_month_in_quarter)
# To ensure consistent results between 32-bit and 64-bit
# platforms, ensure all the numeric categorisation coordinates
# are always stored as int64.
for coord in cube.coords():
if coord.long_name is not None and coord.points.dtype.kind == 'i':
coord.points = coord.points.astype(np.int64)
# check values
self.assertCML(cube, ('categorisation', 'quickcheck.cml'))
def test_basic(self):
#make a series of 'day numbers' for the time, that slide across month boundaries
day_numbers = np.arange(0, 600, 27, dtype=np.int32)
cube = iris.cube.Cube(day_numbers, long_name='test cube', units='metres')
#use day numbers as data values also (don't actually use this for anything)
cube.data = day_numbers
time_coord = iris.coords.DimCoord(
day_numbers, standard_name='time', units=iris.unit.Unit('days since epoch', 'gregorian'))
cube.add_dim_coord(time_coord, 0)
#add test coordinates for examples wanted
ccat.add_year(cube, time_coord)
ccat.add_day_of_month(cube, 'time') #NB test passing coord-name instead of coord itself
ccat.add_month(cube, time_coord)
ccat.add_month_shortname(cube, time_coord, name='month_short')
ccat.add_month_fullname(cube, time_coord, name='month_full')
ccat.add_month_number(cube, time_coord, name='month_number')
ccat.add_weekday(cube, time_coord)
ccat.add_weekday_number(cube, time_coord, name='weekday_number')
ccat.add_weekday_shortname(cube, time_coord, name='weekday_short')
ccat.add_weekday_fullname(cube, time_coord, name='weekday_full')
ccat.add_season(cube, time_coord)
ccat.add_season_number(cube, time_coord, name='season_number')
ccat.add_season_month_initials(cube, time_coord, name='season_months')
ccat.add_season_year(cube, time_coord, name='year_ofseason')
#also test 'generic' categorisation interface
def _month_in_quarter(coord, pt_value):
date = coord.units.num2date(pt_value)
return (date.month - 1) % 3
ccat.add_categorised_coord(cube, 'month_in_quarter', time_coord, _month_in_quarter)
for coord_name in ['month_number', 'month_in_quarter', 'weekday_number', 'season_number', 'year_ofseason', 'year', 'day']:
cube.coord(coord_name).points = cube.coord(coord_name).points.astype(np.int64)
#check values
self.assertCML(cube, ('categorisation', 'quickcheck.cml'))
def climatology(cube, kind='month'):
"""Calculate a climatology for a cube. Can do monthly or yearly.
Args:
cube (iris.cube.Cube)
kind (Optional[str]): 'month' or 'year'
Returns:
iris.cube.Cube
"""
aux_coords = [aux_coord.name() for aux_coord in cube.aux_coords]
if 'year' not in aux_coords:
cat.add_year(cube, 'time')
if 'month' not in aux_coords:
cat.add_month(cube, 'time')
cat.add_month_number(cube, 'time')
out = cube.aggregated_by(kind, iris.analysis.MEAN)
# If the data don't start in January the time coordinate will no longer
# be monotonic. Fix this.
if (kind == 'month') and (not out.coord('time').is_monotonic()):
# Reorder the data so January is first.
jan_index = np.where(out.coord('month').points == 'Jan')[0][0]
ntim = 12
sort_indices = range(jan_index, ntim) + range(0, jan_index)
out = out[sort_indices]
# Create a new time coordinate which is monotonic.
startyear = int(out.coord('time').units.num2date(0).year)
newtime_points = [netcdftime.datetime(startyear + (m / 12), (m % 12) + 1, 1)
for m in out.coord('month_number').points.astype(int)-1]
time_units = out.coord('time').units
newtime_points = time_units.date2num(newtime_points)
newtime = iris.coords.DimCoord(newtime_points, units=time_units,
standard_name='time')
data_dim = out.coord_dims('time')[0]
out.remove_coord('time')
out.add_dim_coord(newtime, data_dim)
return out
def test_basic(self):
cube = self.cube
time_coord = self.time_coord
ccat.add_year(cube, time_coord, "my_year")
ccat.add_day_of_month(cube, time_coord, "my_day_of_month")
ccat.add_day_of_year(cube, time_coord, "my_day_of_year")
ccat.add_month(cube, time_coord, "my_month")
ccat.add_month_fullname(cube, time_coord, "my_month_fullname")
ccat.add_month_number(cube, time_coord, "my_month_number")
ccat.add_weekday(cube, time_coord, "my_weekday")
ccat.add_weekday_number(cube, time_coord, "my_weekday_number")
ccat.add_weekday_fullname(cube, time_coord, "my_weekday_fullname")
ccat.add_season(cube, time_coord, "my_season")
ccat.add_season_number(cube, time_coord, "my_season_number")
ccat.add_season_year(cube, time_coord, "my_season_year")
# also test 'generic' categorisation interface
def _month_in_quarter(coord, pt_value):
date = coord.units.num2date(pt_value)
return (date.month - 1) % 3
ccat.add_categorised_coord(
cube, "my_month_in_quarter", time_coord, _month_in_quarter
)
# To ensure consistent results between 32-bit and 64-bit
# platforms, ensure all the numeric categorisation coordinates
# are always stored as int64.
for coord in cube.coords():
if coord.long_name is not None and coord.points.dtype.kind == "i":
coord.points = coord.points.astype(np.int64)
# check values
self.assertCML(cube, ("categorisation", "quickcheck.cml"))
def get_niwa_obs(o3_file, conv_fact=1.0e6, monthly_mean=True):
""" Reads NIWA data and returns as monthly means, if requested """
# o3_file - expects NetCDF data
niwao3, = iris.load(o3_file)
# Apply any conversion requested - default :mole/mole volume to ppmv
niwao3.data = niwao3.data * conv_fact
if monthly_mean:
# Collapse data to multi-annual monthly mean
# Add 'month' aux coord and tag records by months
# for easier meaning over the years.
# --verified with explicit meaning at sample pts
import iris.coord_categorisation as ircat
ircat.add_month(niwao3, 'time', name='month')
niwao3m = niwao3.aggregated_by('month', iris.analysis.MEAN)
niwao3m.rename(niwao3.name())
return niwao3m
else:
return niwao3
# Create a VectorWind instance to handle the computations.
w = VectorWind(uwnd, vwnd)
# Compute components of rossby wave source: absolute vorticity, divergence,
# irrotational (divergent) wind components, gradients of absolute vorticity.
eta = w.absolutevorticity()
div = w.divergence()
uchi, vchi = w.irrotationalcomponent()
etax, etay = w.gradient(eta)
etax.units = 'm**-1 s**-1'
etay.units = 'm**-1 s**-1'
# Combine the components to form the Rossby wave source term.
S = eta * -1. * div - (uchi * etax + vchi * etay)
S.coord('longitude').attributes['circular'] = True
# Pick out the field for December at 200 hPa.
time_constraint = iris.Constraint(month='Dec')
add_month(S, 'time')
S_dec = S.extract(time_constraint)
# Plot Rossby wave source.
clevs = [-30, -25, -20, -15, -10, -5, 0, 5, 10, 15, 20, 25, 30]
ax = plt.subplot(111, projection=ccrs.PlateCarree(central_longitude=180))
fill = iplt.contourf(S_dec * 1e11, clevs, cmap=plt.cm.RdBu_r, extend='both')
ax.coastlines()
ax.gridlines()
plt.colorbar(fill, orientation='horizontal')
plt.title('Rossby Wave Source ($10^{-11}$s$^{-1}$)', fontsize=16)
plt.show()
def add_time_coord_cats(cube):
"""
This function takes in an iris cube, and adds a range of
numeric co-ordinate categorisations to it. Depending
on the data, not all of the coords added will be relevant.
args
----
cube: iris cube that has a coordinate called 'time'
Returns
-------
Cube: cube that has new time categorisation coords added
Notes
-----
test
A simple example:
>>> file = os.path.join(conf.DATA_DIR, 'mslp.daily.rcm.viet.nc')
>>> cube = iris.load_cube(file)
>>> coord_names = [coord.name() for coord in cube.coords()]
>>> print((', '.join(coord_names)))
time, grid_latitude, grid_longitude
>>> ccube = add_time_coord_cats(cube)
>>> coord_names = [coord.name() for coord in ccube.coords()]
>>> print((', '.join(coord_names)))
time, grid_latitude, grid_longitude, day_of_month, day_of_year, month, \
month_number, season, season_number, year
>>> # print every 50th value of the added time cat coords
... for c in coord_names[3:]:
... print(ccube.coord(c).long_name)
... print(ccube.coord(c).points[::50])
...
day_of_month
[ 1 21 11 1 21 11 1 21]
day_of_year
[ 1 51 101 151 201 251 301 351]
month
['Jan' 'Feb' 'Apr' 'Jun' 'Jul' 'Sep' 'Nov' 'Dec']
month_number
[ 1 2 4 6 7 9 11 12]
season
['djf' 'djf' 'mam' 'jja' 'jja' 'son' 'son' 'djf']
season_number
[0 0 1 2 2 3 3 0]
year
[2000 2000 2000 2000 2000 2000 2000 2000]
"""
# most errors pop up when you try to add a coord that has
# previously been added, or the cube doesn't contain the
# necessary attribute.
ccube = cube.copy()
# numeric
try:
iccat.add_day_of_year(ccube, "time")
except AttributeError as err:
print(("add_time_coord_cats: {}, skipping . . . ".format(err)))
except ValueError as err:
print(("add_time_coord_cats: {}, skipping . . . ".format(err)))
try:
iccat.add_day_of_month(ccube, "time")
except AttributeError as err:
print(("add_time_coord_cats: {}, skipping . . . ".format(err)))
except ValueError as err:
print(("add_time_coord_cats: {}, skipping . . . ".format(err)))
try:
iccat.add_month_number(ccube, "time")
except AttributeError as err:
print(("add_time_coord_cats: {}, skipping . . . ".format(err)))
except ValueError as err:
print(("add_time_coord_cats: {}, skipping . . . ".format(err)))
try:
iccat.add_season_number(ccube, "time")
except AttributeError as err:
print(("add_time_coord_cats: {}, skipping . . . ".format(err)))
except ValueError as err:
print(("add_time_coord_cats: {}, skipping . . . ".format(err)))
try:
iccat.add_year(ccube, "time")
except AttributeError as err:
print(("add_time_coord_cats: {}, skipping . . . ".format(err)))
except ValueError as err:
print(("add_time_coord_cats: {}, skipping . . . ".format(err)))
# strings
try:
iccat.add_month(ccube, "time")
except AttributeError as err:
print(("add_time_coord_cats: {}, skipping . . . ".format(err)))
except ValueError as err:
print(("add_time_coord_cats: {}, skipping . . . ".format(err)))
try:
iccat.add_season(ccube, "time")
except AttributeError as err:
print(("add_time_coord_cats: {}, skipping . . . ".format(err)))
except ValueError as err:
print(("add_time_coord_cats: {}, skipping . . . ".format(err)))
return ccube
warnings.simplefilter('ignore', UserWarning)
uwnd = iris.load_cube(example_data_path('uwnd_mean.nc'))
vwnd = iris.load_cube(example_data_path('vwnd_mean.nc'))
uwnd.coord('longitude').circular = True
vwnd.coord('longitude').circular = True
# Create a VectorWind instance to handle the computation of streamfunction and
# velocity potential.
w = VectorWind(uwnd, vwnd)
# Compute the streamfunction and velocity potential.
sf, vp = w.sfvp()
# Pick out the field for December.
time_constraint = iris.Constraint(month='Dec')
add_month(sf, 'time', name='month')
add_month(vp, 'time', name='month')
sf_dec = sf.extract(time_constraint)
vp_dec = vp.extract(time_constraint)
# Plot streamfunction.
clevs = [-120, -100, -80, -60, -40, -20, 0, 20, 40, 60, 80, 100, 120]
ax = plt.subplot(111, projection=ccrs.PlateCarree(central_longitude=180))
fill_sf = iplt.contourf(sf_dec * 1e-06, clevs, cmap=plt.cm.RdBu_r,
extend='both')
ax.coastlines()
ax.gridlines()
plt.colorbar(fill_sf, orientation='horizontal')
plt.title('Streamfunction ($10^6$m$^2$s$^{-1}$)', fontsize=16)
# Plot velocity potential.
def main():
cube = myload()
icat.add_month(cube, 'time')
months = cube.coord('month')
# Set the limits for the loop over years.
minTime = 0
maxTime = 90
for time in range(minTime, maxTime):
# Set up for larger image.
figSize = [12, 6]
fig = plt.figure(figsize=figSize, dpi=200)
rect = 0, 0, 200 * figSize[0], 200 * figSize[1]
fig.add_axes(rect)
geo_axes = plt.axes(projection=ccrs.PlateCarree())
# We need to fix the boundary of the figure (otherwise we get a black border at left & top).
# Cartopy removes matplotlib's axes.patch (which normally defines the boundary) and
# replaces it with outline_patch and background_patch. It's the former which is causing
# the black border. Get the axis object and make its outline patch invisible.
geo_axes.outline_patch.set_visible(False)
plt.margins(0, 0)
fig.subplots_adjust(left=0, right=1, bottom=0, top=1)
# Contour plot the temperatures and add the coastline.
iplt.contourf(cube[time],
levels=(0.000008, 0.00002, 0.00007, 0.0002, 0.001, 0.05),
colors=('cyan', 'blue', 'yellow', 'orange', 'red'))
#-6.4358826, 27.94899
plt.gca().coastlines()
#plt.colorbar(boundaries = (-6, -3, 0, 4, 8, 12, 16, 20, 25), values = (-6, -3, 0, 4, 8, 12, 16, 20))
# Extract the year value and display it (coordinates used in locating the text are
# those of the data).
month = months[time].points[0]
# Display year on both sides of the display.
plt.text(-110,
0,
month,
horizontalalignment='center',
verticalalignment='top',
size='large',
fontdict={'family': 'monospace'})
plt.text(70,
0,
month,
horizontalalignment='center',
verticalalignment='top',
size='large',
fontdict={'family': 'monospace'})
# Now save the plot in an image file. The files are numbered sequentially, starting
# from 000.png; this is so that the ffmpeg command can grok them.
filename = "rainfall/image-%04d.png" % time
# plt.savefig(filename, bbox_inches='tight', pad_inches=0)
plt.savefig(filename, dpi=200)
# Discard the figure (otherwise the text will be overwritten
# by the next iteration).
plt.close()
print("images made! Now converting to .mp4...")
create_video()
print("Opening video...")
def mainfunc(run):
"""Main function in stratospheric assessment code."""
metrics = dict()
# Set up to only run for 10 year period (eventually)
year_cons = dict(from_dt=run['from_monthly'], to_dt=run['to_monthly'])
# Read zonal mean U (lbproc=192) and add month number to metadata
ucube = load_run_ss(
run, 'monthly', 'eastward_wind', lbproc=192, **year_cons)
# Although input data is a zonal mean, iris does not recognise it as such
# and just reads it as having a single longitudinal coordinate. This
# removes longitude as a dimension coordinate and makes it a scalar
# coordinate in line with how a zonal mean would be described.
# Is there a better way of doing this?
ucube_cds = [cdt.standard_name for cdt in ucube.coords()]
if 'longitude' in ucube_cds:
ucube = ucube.collapsed('longitude', iris.analysis.MEAN)
if not ucube.coord('latitude').has_bounds():
ucube.coord('latitude').guess_bounds()
# check for month_number
aux_coord_names = [aux_coord.var_name for aux_coord in ucube.aux_coords]
if 'month_number' not in aux_coord_names:
icc.add_month_number(ucube, 'time', name='month_number')
# Read zonal mean T (lbproc=192) and add clim month and season to metadata
tcube = load_run_ss(
run, 'monthly', 'air_temperature', lbproc=192,
**year_cons) # m01s30i204
# Although input data is a zonal mean, iris does not recognise it as such
# and just reads it as having a single longitudinal coordinate. This
# removes longitude as a dimension coordinate and makes it a scalar
# coordinate in line with how a zonal mean would be described.
# Is there a better way of doing this?
tcube_cds = [cdt.standard_name for cdt in tcube.coords()]
if 'longitude' in tcube_cds:
tcube = tcube.collapsed('longitude', iris.analysis.MEAN)
if not tcube.coord('latitude').has_bounds():
tcube.coord('latitude').guess_bounds()
aux_coord_names = [aux_coord.var_name for aux_coord in tcube.aux_coords]
if 'month' not in aux_coord_names:
icc.add_month(tcube, 'time', name='month')
if 'clim_season' not in aux_coord_names:
icc.add_season(tcube, 'time', name='clim_season')
# Read zonal mean q (lbproc=192) and add clim month and season to metadata
qcube = load_run_ss(
run, 'monthly', 'specific_humidity', lbproc=192,
**year_cons) # m01s30i205
# Although input data is a zonal mean, iris does not recognise it as such
# and just reads it as having a single longitudinal coordinate. This
# removes longitude as a dimension coordinate and makes it a scalar
# coordinate in line with how a zonal mean would be described.
# Is there a better way of doing this?
qcube_cds = [cdt.standard_name for cdt in qcube.coords()]
if 'longitude' in qcube_cds:
qcube = qcube.collapsed('longitude', iris.analysis.MEAN)
if not qcube.coord('latitude').has_bounds():
qcube.coord('latitude').guess_bounds()
aux_coord_names = [aux_coord.var_name for aux_coord in qcube.aux_coords]
if 'month' not in aux_coord_names:
icc.add_month(qcube, 'time', name='month')
if 'clim_season' not in aux_coord_names:
icc.add_season(qcube, 'time', name='clim_season')
# Calculate PNJ metrics
pnj_metrics(run, ucube, metrics)
# Calculate QBO metrics
qbo_metrics(run, ucube, metrics)
# Calculate polar temperature metrics
tpole_metrics(run, tcube, metrics)
# Calculate equatorial temperature metrics
teq_metrics(run, tcube, metrics)
# Calculate tropical temperature metrics
t_metrics(run, tcube, metrics)
# Calculate tropical water vapour metric
q_metrics(run, qcube, metrics)
# Summary metric
summary_metric(metrics)
# Make sure all metrics are of type float
# Need at the moment to populate metrics files
for key, value in metrics.items():
metrics[key] = float(value)
return metrics
def main():
gppcube = myload('gpp')
chlrphylcube = myload('chlrphyl')
#data = np.add(gppcube.data, chlrphylcube.data)
gppLbound = np.amin(gppcube.data)
gppUbound = np.amax(gppcube.data)
chlrphylLbound = np.amin(chlrphylcube.data)
chlrphylUbound = np.amax(chlrphylcube.data)
print(gppLbound, gppUbound)
print(chlrphylLbound, chlrphylUbound)
icat.add_month(gppcube, 'time')
months = gppcube.coord('month')
# Set the limits for the loop over years.
minTime = 0
maxTime = 360
fileIndex = 0
for time in range(minTime, maxTime):
# Avoid timesteps that are broken - ie, cause a stop with this error:
# ValueError: A LinearRing must have at least 3 coordinate tuple
if time in [12, 310, 320, 347, 351, 354]:
continue
# Set up for larger image.
figSize = [12, 6]
fig = plt.figure(figsize=figSize, dpi=200)
rect = 0,0,200*figSize[0],200*figSize[1]
fig.add_axes(rect)
geo_axes = plt.axes(projection=ccrs.PlateCarree())
# We need to fix the boundary of the figure (otherwise we get a black border at left & top).
# Cartopy removes matplotlib's axes.patch (which normally defines the boundary) and
# replaces it with outline_patch and background_patch. It's the former which is causing
# the black border. Get the axis object and make its outline patch invisible.
geo_axes.outline_patch.set_visible(False)
plt.margins(0,0)
fig.subplots_adjust(left=0, right=1, bottom=0, top=1)
# Contour plot the temperatures and add the coastline.
iplt.contourf(chlrphylcube[time], vmin = chlrphylLbound, vmax = chlrphylUbound, cmap = 'BuGn')
iplt.contourf(gppcube[time], vmin = gppLbound, vmax = gppUbound, cmap = 'YlGn')
#-6.4358826, 27.94899
plt.gca().coastlines()
#plt.colorbar(boundaries = (-6, -3, 0, 4, 8, 12, 16, 20, 25), values = (-6, -3, 0, 4, 8, 12, 16, 20))
# We need to fix the boundary of the figure (otherwise we get a black border at left & top).
# Cartopy removes matplotlib's axes.patch (which normally defines the boundary) and
# replaces it with outline_patch and background_patch. It's the former which is causing
# the black border. Get the axis object and make its outline patch invisible.
ax = plt.gca()
ax.outline_patch.set_visible(False)
# Extract the year value and display it (coordinates used in locating the text are
# those of the data).
month = months[time].points[0]
# Display year on both sides of the display.
plt.text(-110, 0, month, horizontalalignment='center',
verticalalignment='top', size='large',
fontdict={'family' : 'monospace'})
plt.text( 70, 0, month, horizontalalignment='center',
verticalalignment='top', size='large',
fontdict={'family' : 'monospace'})
# Now save the plot in an image file. The files are numbered sequentially, starting
# from 000.png; this is so that the ffmpeg command can grok them.
filename = "gpp_chlrphyl_movie/image-%04d.png" % fileIndex
fileIndex += 1
# plt.savefig(filename, bbox_inches='tight', pad_inches=0)
plt.savefig(filename, dpi=200)
# Discard the figure (otherwise the text will be overwritten
# by the next iteration).
plt.close()
print("images made! Now converting to .mp4...")
create_video()
print("Opening video...")
def read_pr_sm_topo(project_info, model):
"""
;; Arguments
;; project_info: dictionary
;; all info from namelist
;;
;; Return
;; pr: iris cube [time, lat, lon]
;; precipitation time series
;; sm: iris cube [time, lat, lon]
;; soil moisture time series
;; topo: array [lat, lon]
;; topography
;; lon: array [lon]
;; longitude
;; lat: array [lat]
;; latitude
;; time: iris cube coords
;; time info of cube
;; time_bnds_1: float
;; first time_bnd of time series
;;
;;
;; Description
;; Read cmip5 input data for computing the diagnostic
;;
"""
import projects
E = ESMValProject(project_info)
verbosity = E.get_verbosity()
#-------------------------
# Read model info
#-------------------------
currProject = getattr(vars()['projects'], model.split_entries()[0])()
model_info = model.split_entries()
mip = currProject.get_model_mip(model)
exp = currProject.get_model_exp(model)
start_year = currProject.get_model_start_year(model)
end_year = currProject.get_model_end_year(model)
years = range(int(start_year), int(end_year) + 1)
'''
#-------------------------
# Read model info
#-------------------------
model_name = model_info[1]
time_step = model_info[2]
exp_fam = model_info[3]
model_run = model_info[4]
year_start = model_info[5]
year_end = model_info[6]
filedir = model_info[7]
years = range(int(year_start), int(year_end)+1)
'''
#-------------------------
# Input data directories
#-------------------------
currDiag = project_info['RUNTIME']['currDiag']
pr_index = currDiag.get_variables().index('pr')
pr_field = currDiag.get_field_types()[pr_index]
sm_index = currDiag.get_variables().index('mrsos')
sm_field = currDiag.get_field_types()[sm_index]
indir = currProject.get_cf_outpath(project_info, model)
in_file = currProject.get_cf_outfile(project_info, model, pr_field, 'pr', mip, exp)
pr_files = [os.path.join(indir, in_file)]
in_file = currProject.get_cf_outfile(project_info, model, sm_field, 'mrsos', mip, exp)
sm_files = [os.path.join(indir, in_file)]
'''
#-------------------------
# Input data directories
#-------------------------
pr_files = []
sm_files = []
for yy in years:
Patt = filedir+'pr_'+time_step+'_'+model_name+'_'+exp_fam+'_'+\
model_run+'_'+str(yy)+'*.nc'
pr_files.append(glob.glob(Patt))
Patt = filedir+'mrsos_'+time_step+'_'+model_name+'_'+exp_fam+'_'+\
model_run+'_'+str(yy)+'*.nc'
sm_files.append(glob.glob(Patt))
pr_files = [l[0] for l in pr_files if len(l)>0]
pr_files = sorted(pr_files)
sm_files = [l[0] for l in sm_files if len(l)>0]
sm_files = sorted(sm_files)
'''
#----------------------
# Read in precipitation
#----------------------
pr_list = []
for pr_file in pr_files:
info('Reading precipitation from ' + pr_file, verbosity, required_verbosity=1)
pr = iris.load(pr_file)[0]
for at_k in pr.attributes.keys():
pr.attributes.pop(at_k)
pr_list.append(pr)
pr = iris.cube.CubeList(pr_list)
pr = pr.concatenate()[0]
# Convert longitude from 0_360 to -180_180
pr = coord_change([pr])[0]
# Add metadata: day, month, year
add_month(pr, 'time')
add_day_of_month(pr, 'time', name='dom')
add_year(pr, 'time')
# Convert units to kg m-2 hr-1
pr.convert_units('kg m-2 hr-1')
#-----------------------
# Read in soil moisture
#-----------------------
sm_list = []
for sm_file in sm_files:
info('Reading soil moisture from ' + sm_file, verbosity, required_verbosity=1)
sm = iris.load(sm_file)[0]
for at_k in sm.attributes.keys():
sm.attributes.pop(at_k)
sm_list.append(sm)
sm = iris.cube.CubeList(sm_list)
sm = sm.concatenate()[0]
# Convert longitude from 0_360 to -180_180
sm = coord_change([sm])[0]
# Add metadata: day, month, year
add_month(sm, 'time')
add_day_of_month(sm, 'time', name='dom')
add_year(sm, 'time')
#----------------------------------------------
# Constrain pr and sm data to latitude 60S_60N
#----------------------------------------------
latconstraint = iris.Constraint(latitude=lambda cell: -59.0 <= cell <= 59.0)
pr = pr.extract(latconstraint)
sm = sm.extract(latconstraint)
#---------------------------------------------------
# Read in grid info: latitude, longitude, timestamp
#---------------------------------------------------
lon = sm.coords('longitude')[0].points
lat = sm.coords('latitude')[0].points
time = sm.coords('time')
# --------------------------------------
# Convert missing data (if any) to -999.
# --------------------------------------
try:
sm.data.set_fill_value(-999)
sm.data.data[sm.data.mask] = -999.
except:
info('no missing data conversion', verbosity, required_verbosity=1)
#----------------------
# Read in topography
#----------------------
# Topography map specs:
# latitude 60S_60N
# longitude 180W_180E
# model resolution
#ftopo = currProject.get_cf_fx_file(project_info, model)
#dt = '>f4'
#topo = (np.fromfile(ftopo, dtype=dt)).reshape(len(lat), len(lon))
topo = get_topo(project_info, lon, lat, model)
#----------------------
# Read in time bounds
#----------------------
indir, infiles = currProject.get_cf_infile(project_info, model, pr_field, 'pr', mip, exp)
Patt = os.path.join(indir, infiles)
pr_files = sorted(glob.glob(Patt))
ncf = nc4.Dataset(pr_files[0])
time_bnds_1 = ncf.variables['time_bnds'][0][0]
time_bnds_1 = time_bnds_1 - int(time_bnds_1)
ncf.close()
#-----------------------------------------------
# Return input data to compute sm_pr diagnostic
#-----------------------------------------------
return pr, sm, topo, lon, lat, time, time_bnds_1
# Create a VectorWind instance to handle the computations.
w = VectorWind(uwnd, vwnd)
# Compute components of rossby wave source: absolute vorticity, divergence,
# irrotational (divergent) wind components, gradients of absolute vorticity.
eta = w.absolutevorticity()
div = w.divergence()
uchi, vchi = w.irrotationalcomponent()
etax, etay = w.gradient(eta)
etax.units = 'm**-1 s**-1'
etay.units = 'm**-1 s**-1'
# Combine the components to form the Rossby wave source term.
S = eta * -1. * div - (uchi * etax + vchi * etay)
S.coord('longitude').attributes['circular'] = True
# Pick out the field for December at 200 hPa.
time_constraint = iris.Constraint(month='Dec')
add_month(S, 'time')
S_dec = S.extract(time_constraint)
# Plot Rossby wave source.
clevs = [-30, -25, -20, -15, -10, -5, 0, 5, 10, 15, 20, 25, 30]
ax = plt.subplot(111, projection=ccrs.PlateCarree(central_longitude=180))
fill = iplt.contourf(S_dec * 1e11, clevs, cmap=plt.cm.RdBu_r, extend='both')
ax.coastlines()
ax.gridlines()
plt.colorbar(fill, orientation='horizontal')
plt.title('Rossby Wave Source ($10^{-11}$s$^{-1}$)', fontsize=16)
plt.show()
# Create a VectorWind instance to handle the computations.
w = VectorWind(uwnd, vwnd)
# Compute components of rossby wave source: absolute vorticity, divergence,
# irrotational (divergent) wind components, gradients of absolute vorticity.
eta = w.absolutevorticity()
div = w.divergence()
uchi, vchi = w.irrotationalcomponent()
etax, etay = w.gradient(eta)
etax.units = "m**-1 s**-1"
etay.units = "m**-1 s**-1"
# Combine the components to form the Rossby wave source term.
S = eta * -1.0 * div - (uchi * etax + vchi * etay)
S.coord("longitude").attributes["circular"] = True
# Pick out the field for December at 200 hPa.
time_constraint = iris.Constraint(month="Dec")
add_month(S, "time")
S_dec = S.extract(time_constraint)
# Plot Rossby wave source.
clevs = [-30, -25, -20, -15, -10, -5, 0, 5, 10, 15, 20, 25, 30]
ax = plt.subplot(111, projection=ccrs.PlateCarree(central_longitude=180))
fill = iplt.contourf(S_dec * 1e11, clevs, cmap=plt.cm.RdBu_r, extend="both")
ax.coastlines()
ax.gridlines()
plt.colorbar(fill, orientation="horizontal")
plt.title("Rossby Wave Source ($10^{-11}$s$^{-1}$)", fontsize=16)
plt.show()
def read_pr_sm_topo(filedir, years):
"""
;; Arguments
;; filedir: dir
;; directory with input data
;; years: list of int
;; list of years for the analysis
;;
;; Return
;; pr: iris cube [time, lat, lon]
;; precipitation time series
;; sm: iris cube [time, lat, lon]
;; soil moisture time series
;; topo: array [lat, lon]
;; topography
;; lon: array [lon]
;; longitude
;; lat: array [lat]
;; latitude
;; time: iris cube coords
;; time info of cube
;;
;;
;; Description
;; Read cmip5 input data for computing the diagnostic
;;
"""
#-------------------------
# Input data directories
#-------------------------
Patt = filedir + 'pr_3hr_inmcm4_amip_r1i1p1_{}010101-{}123122.nc'
pr_files = [Patt.format(y, y) for y in years]
Patt = filedir + 'mrsos_3hr_inmcm4_amip_r1i1p1_{}010100-{}123121.nc'
sm_files = [Patt.format(y, y) for y in years]
#----------------------
# Read in precipitation
#----------------------
pr_list = []
for pr_file in pr_files:
print 'Reading precipitation from ' + pr_file
pr = iris.load(pr_file)[0]
for at_k in pr.attributes.keys():
pr.attributes.pop(at_k)
pr_list.append(pr)
pr = iris.cube.CubeList(pr_list)
pr = pr.concatenate()[0]
# Convert longitude from 0_360 to -180_180
pr = coord_change([pr])[0]
# Add metadata: day, month, year
add_month(pr, 'time')
add_day_of_month(pr, 'time', name='dom')
add_year(pr, 'time')
# Convert units to kg m-2 hr-1
pr.convert_units('kg m-2 hr-1')
#-----------------------
# Read in soil moisture
#-----------------------
sm_list = []
for sm_file in sm_files:
print 'Reading soil moisture from ' + sm_file
sm = iris.load(sm_file)[0]
for at_k in sm.attributes.keys():
sm.attributes.pop(at_k)
sm_list.append(sm)
sm = iris.cube.CubeList(sm_list)
sm = sm.concatenate()[0]
# Convert longitude from 0_360 to -180_180
sm = coord_change([sm])[0]
# Add metadata: day, month, year
add_month(sm, 'time')
add_day_of_month(sm, 'time', name='dom')
add_year(sm, 'time')
#----------------------------------------------
# Constrain pr and sm data to latitude 60S_60N
#----------------------------------------------
latconstraint = iris.Constraint(
latitude=lambda cell: -59.0 <= cell <= 59.0)
pr = pr.extract(latconstraint)
sm = sm.extract(latconstraint)
#---------------------------------------------------
# Read in grid info: latitude, longitude, timestamp
#---------------------------------------------------
lon = sm.coords('longitude')[0].points
lat = sm.coords('latitude')[0].points
time = sm.coords('time')
# --------------------------------------
# Convert missing data (if any) to -999.
# --------------------------------------
try:
sm.data.set_fill_value(-999)
sm.data.data[sm.data.mask] = -999.
except:
print 'no missing data conversion'
#----------------------
# Read in topography
#----------------------
# Topography map specs:
# latitude 60S_60N
# longitude 180W_180E
# model resolution
ftopo = filedir + 'topo_var_5x5_inmcm4.gra'
dt = '>f4'
topo = (np.fromfile(ftopo, dtype=dt)).reshape(len(lat), len(lon))
#-----------------------------------------------
# Return input data to compute sm_pr diagnostic
#-----------------------------------------------
return pr, sm, topo, lon, lat, time
warnings.simplefilter('ignore', UserWarning)
uwnd = iris.load_cube(example_data_path('uwnd_mean.nc'))
vwnd = iris.load_cube(example_data_path('vwnd_mean.nc'))
uwnd.coord('longitude').circular = True
vwnd.coord('longitude').circular = True
# Create a VectorWind instance to handle the computation of streamfunction and
# velocity potential.
w = VectorWind(uwnd, vwnd)
# Compute the streamfunction and velocity potential.
sf, vp = w.sfvp()
# Pick out the field for December.
time_constraint = iris.Constraint(month='Dec')
add_month(sf, 'time', name='month')
add_month(vp, 'time', name='month')
sf_dec = sf.extract(time_constraint)
vp_dec = vp.extract(time_constraint)
# Plot streamfunction.
clevs = [-120, -100, -80, -60, -40, -20, 0, 20, 40, 60, 80, 100, 120]
ax = plt.subplot(111, projection=ccrs.PlateCarree(central_longitude=180))
fill_sf = iplt.contourf(sf_dec * 1e-06,
clevs,
cmap=plt.cm.RdBu_r,
extend='both')
ax.coastlines()
ax.gridlines()
plt.colorbar(fill_sf, orientation='horizontal')
plt.title('Streamfunction ($10^6$m$^2$s$^{-1}$)', fontsize=16)