def testSetPlotContourPlain(self):
cube = iris.load_cube(iris.sample_data_path('air_temp.pp'))
plt.subplot(1,2,1)
cc.setPlot(cube, "Contour", "Automatic", 15, False, None, None)
plt.subplot(1,2,2)
qplt.contour(cube, 15)
plt.show()
def test_contour(self):
qplt.contour(self._small())
self.check_graphic()
qplt.contourf(self._small(),
coords=["model_level_number", "grid_longitude"])
self.check_graphic()
def test_map(self):
cube = self._slice(['grid_latitude', 'grid_longitude'])
qplt.contour(cube)
self.check_graphic()
# check that the result of adding 360 to the data is *almost* identically the same result
lon = cube.coord('grid_longitude')
lon.points = lon.points + 360
qplt.contour(cube)
self.check_graphic()
def test_map(self):
cube = self._slice(['grid_latitude', 'grid_longitude'])
qplt.contour(cube)
self.check_graphic()
# check that the result of adding 360 to the data is *almost* identically the same result
lon = cube.coord('grid_longitude')
lon.points = lon.points + 360
qplt.contour(cube)
self.check_graphic()
def simpletest(do_savefig=True, do_showfig=True, savefig_file='./puffer.png'):
figure = make_puffersphere_figure()
axes = make_puffersphere_axes()
axes.stock_img()
data = istk.global_pp()
axes.coastlines()
qplt.contour(data)
draw_gridlines()
#axes.coastlines()
if do_savefig:
save_figure_for_puffersphere(figure=plt.gcf(), filename=savefig_file)
if do_showfig:
plt.show()
def main():
dir='/data/local2/hador/ostia_reanalysis/' # ELD140
filename = dir + '*.nc'
cube = iris.load_cube(filename,'sea_surface_temperature',callback=my_callback)
#reads in data using a special callback, because it is a nasty netcdf file
sst_mean = cube.collapsed('time', iris.analysis.MEAN)
#average all 12 months together
caribbean = iris.Constraint(
longitude=lambda v: 260 <= v <= 320,
latitude=lambda v: 0 <= v <= 40,
name='sea_surface_temperature'
)
caribbean_sst_mean = sst_mean.extract(caribbean)
#extract the Caribbean region
plt.figure()
contour=qplt.contourf(caribbean_sst_mean, 50)
contour=qplt.contour(caribbean_sst_mean, 5,colors='k')
plt.clabel(contour, inline=1, fontsize=10,fmt='%1.1f' )
plt.gca().coastlines()
#plt.gca().set_extent((-100,-60,0,40))
plt.show()
def testSetPlotContourLargeRange(self):
cube = iris.load_cube(iris.sample_data_path('air_temp.pp'))
plt.subplot(1,2,1)
cc.setPlot(cube, "Contour", "brewer_Blues_09", 15, True, 400, 200)
plt.subplot(1,2,2)
contours = qplt.contour(cube, 15, cmap="brewer_Blues_09", vmin=200, vmax=400)
plt.clabel(contours, inline=1, fontsize=8)
plt.show()
def add_sea_floor(cube):
"""
Add a simple sea floor line from the cube mask.
Parameters
----------
cube: iris.cube.Cube
Input cube to use to produce the sea floor.
"""
land_cube = cube.copy()
land_cube.data = np.ma.array(land_cube.data)
mask = 1. * land_cube.data.mask
if mask.shape == ():
mask = np.zeros_like(land_cube.data)
land_cube.data = np.ma.masked_where(mask == 0, mask)
land_cube.data.mask = mask
qplt.contour(land_cube, 2, cmap='Greys_r', rasterized=True)
def set_plot(cube, plot_type, cmap, num_contours, contour_labels,
colorbar_range):
"""
Produces a plot object for the desired cube using quickplot.
Args:
* cube
The cube to be plotted.
* plot_type
String holding the type of plot to be used. Choose from pcolormesh,
Contour and Contourf.
* cmap
String representing the colormap to be used. Can be any of the
Brewer Colormaps supported by Iris, or Automatic.
* num_contour
int holding the number of contours to be plotted.
* contour_labels
Boolean representing whether the contours on a Contour plot
(not contourf) should be labeled.
* colorbar_range
Dictionary containing ints representing the max and min to
which the colorbar will be set.
"""
# We unpack the colorbar_range dictionary
colorbar_max = colorbar_range['max']
colorbar_min = colorbar_range['min']
# We obtain the levels used to define the contours.
levels = get_levels(cube, colorbar_max, colorbar_min, num_contours)
if plot_type == "Filled Contour":
qplt.contourf(cube,
num_contours,
cmap=get_colormap(cmap),
levels=levels,
vmax=colorbar_max,
vmin=colorbar_min)
elif plot_type == "Contour":
contours = qplt.contour(cube,
num_contours,
cmap=get_colormap(cmap),
levels=levels,
vmax=colorbar_max,
vmin=colorbar_min)
if contour_labels:
plt.clabel(contours, inline=1, fontsize=8)
else:
qplt.pcolormesh(cube,
cmap=get_colormap(cmap),
vmax=colorbar_max,
vmin=colorbar_min)
def plot_band_list(List, fname, lev, O3_bands, rates_in_bands):
fig = plt.figure(figsize=(13, 18), dpi=100)
index_grid = np.arange(9).reshape([3, 3])
gs = gridspec.GridSpec(4, 3)
for i in range(3):
for j in range(3):
plt1 = plt.subplot(gs[i, j])
divs = List[index_grid[i, j]]
qplt.contourf(divs, lev, cmap='bwr')
qplt.contour(divs, levels=[0], colors='black')
plt.title(
str(rates_in_bands[index_grid[i, j]]) +
' events/year, O$_3$ Percentile ' +
str(10 * index_grid[i, j]) + '-' +
str(10 + 10 * index_grid[i, j]))
plt1.set_yscale('log', basey=10, subsy=None)
plt.ylim(5, 10000)
plt1.invert_yaxis()
plt.ylabel('Pressure (Pa)')
plt.xlabel('Latitude')
plt1 = plt.subplot(gs[3, 0])
divs = List[9]
qplt.contourf(divs, lev, cmap='bwr')
qplt.contour(divs, levels=[0], colors='black')
plt.title(
str(rates_in_bands[index_grid[i, j]]) +
' events/year, O$_3$ Percentile 90-100')
plt1.set_yscale('log', basey=10, subsy=None)
plt.ylim(5, 10000)
plt1.invert_yaxis()
plt.ylabel('Pressure (Pa)')
plt.xlabel('Latitude')
plt.tight_layout()
plt.show()
fig.savefig('./figures/' + fname, dpi=200)
return
def plot_data(ax, z, t=360):
ax = plt.subplot(111)
assert z in zc.points
assert t in time.points
alt = iris.Constraint(**{zc.name(): z})
ts = iris.Constraint(time=t)
w = data['W'].extract(alt & ts)
v = data['V'].extract(alt & ts)
u = data['U'].extract(alt & ts)
qc = data['QC'].extract(alt & ts)
c = qplt.contour(qc,
coords=[xc.name(), yc.name()],
colors='grey',
levels=[
1e-3,
],
alpha=0.8,
linewidths=2.5,
title="")
ax.set_title("")
levels = np.linspace(-20, 20, 201)
#cw = qplt.contourf(w, coords=[xc.name(), yc.name()],
# cmap=plt.cm.RdBu, vmin=-20., vmax=20.)
cw = ax.contourf(xc.points,
yc.points,
w.data,
cmap=plt.cm.RdBu_r,
levels=levels,
extend="both")
cb = plt.colorbar(cw, cax=cax, orientation='vertical')
ax.set_title("")
sl = 10
ax.quiver(xc.points[::sl],
yc.points[::sl],
u.data[::sl, ::sl],
v.data[::sl, ::sl],
units='inches',
scale=75,
headwidth=2)
hour = t // 3600
minute = (t % 3600) / 60
ax.set_title("Time = %02d:%02d | Alt = %5d m" % (hour, minute, z),
loc='left',
fontsize=11)
def main():
"""
"""
cs = iris.Constraint(pressure=900)
for i in xrange(1, 37):
# Load the front variables
cubes = files.load(datadir + '/xjjhq/xjjhq_fronts' + str(i).zfill(3) +
'.pp')
loc = convert.calc('front_locator_parameter_thw', cubes)
m1 = convert.calc('thermal_front_parameter_thw', cubes)
m2 = convert.calc('local_frontal_gradient_thw', cubes)
# Apply the masking criteria
mask = np.logical_or(m1.data < 4 * 0.3e-10, m2.data < 4 * 1.35e-5)
loc.data = np.ma.masked_where(mask, loc.data)
loc = cs.extract(loc)
# Plot the locating variable
qplt.contour(loc, [0], colors='k')
plt.gca().coastlines()
plt.gca().gridlines()
plt.title('Fronts at 900 hPa, T+' + str(i) + ' hours')
plt.savefig(plotdir + 'fronts' + str(i).zfill(3) + '.png')
def set_plot(cube, plot_type, cmap, num_contours, contour_labels, colorbar_range):
"""
Produces a plot object for the desired cube using quickplot.
Args:
* cube
The cube to be plotted.
* plot_type
String holding the type of plot to be used. Choose from pcolormesh,
Contour and Contourf.
* cmap
String representing the colormap to be used. Can be any of the
Brewer Colormaps supported by Iris, or Automatic.
* num_contour
int holding the number of contours to be plotted.
* contour_labels
Boolean representing whether the contours on a Contour plot
(not contourf) should be labeled.
* colorbar_range
Dictionary containing ints representing the max and min to
which the colorbar will be set.
"""
# We unpack the colorbar_range dictionary
colorbar_max = colorbar_range["max"]
colorbar_min = colorbar_range["min"]
# We obtain the levels used to define the contours.
levels = get_levels(cube, colorbar_max, colorbar_min, num_contours)
if plot_type == "Filled Contour":
qplt.contourf(cube, num_contours, cmap=get_colormap(cmap), levels=levels, vmax=colorbar_max, vmin=colorbar_min)
elif plot_type == "Contour":
contours = qplt.contour(
cube, num_contours, cmap=get_colormap(cmap), levels=levels, vmax=colorbar_max, vmin=colorbar_min
)
if contour_labels:
plt.clabel(contours, inline=1, fontsize=8)
else:
qplt.pcolormesh(cube, cmap=get_colormap(cmap), vmax=colorbar_max, vmin=colorbar_min)
def plot_data(ax, z, t=360):
ax = plt.subplot(111)
assert z in zc.points
assert t in time.points
alt = iris.Constraint(**{zc.name(): z})
ts = iris.Constraint(time=t)
w = data['W'].extract(alt & ts)
v = data['V'].extract(alt & ts)
u = data['U'].extract(alt & ts)
qc = data['QC'].extract(alt & ts)
c = qplt.contour(qc, coords=[xc.name(), yc.name()],
colors='grey', levels=[1e-3, ],
alpha=0.8, linewidths=2.5,
title="")
ax.set_title("")
levels = np.linspace(-20, 20, 201)
#cw = qplt.contourf(w, coords=[xc.name(), yc.name()],
# cmap=plt.cm.RdBu, vmin=-20., vmax=20.)
cw = ax.contourf(xc.points, yc.points, w.data,
cmap=plt.cm.RdBu_r, levels=levels, extend="both")
cb = plt.colorbar(cw, cax=cax, orientation='vertical')
ax.set_title("")
sl = 10
ax.quiver(xc.points[::sl], yc.points[::sl],
u.data[::sl, ::sl], v.data[::sl, ::sl],
units='inches', scale=75, headwidth=2)
hour = t // 3600
minute = (t % 3600) / 60
ax.set_title("Time = %02d:%02d | Alt = %5d m" % (hour, minute, z),
loc='left', fontsize=11)
def test_xaxis_labels(self):
qplt.contour(self.cube, coords=("str_coord", "bar"))
self.assertPointsTickLabels("xaxis")
def test_contour(self):
qplt.contour(self._small())
self.check_graphic()
qplt.contourf(self._small(), coords=['model_level_number', 'grid_longitude'])
self.check_graphic()
from __future__ import (absolute_import, division, print_function)
from six.moves import (filter, input, map, range, zip) # noqa
import matplotlib.pyplot as plt
import iris
import iris.quickplot as qplt
fname = iris.sample_data_path('air_temp.pp')
temperature_cube = iris.load_cube(fname)
# Add a contour, and put the result in a variable called contour.
contour = qplt.contour(temperature_cube)
# Add coastlines to the map created by contour.
plt.gca().coastlines()
# Add contour labels based on the contour we have just created.
plt.clabel(contour, inline=False)
plt.show()
def test_xaxis_labels(self):
qplt.contour(self.cube, coords=("str_coord", "bar"))
self.assertPointsTickLabels("xaxis")
def PV_along_trajectories(folder='IOP3/T42',
time_string='20160922_12',
name='',
theta_min=24,
no_of_trajs=10,
plotnotmean=True):
TrEn = load('/storage/silver/scenario/bn826011/WCB_outflow/Final/' +
folder + '/inflow/' + time_string +
'_3DTrajectoryEnsemble_new' + name)
# load arbitrary set of 3D trajectories
times = TrEn.times
# get array containing pertinent times
clpv = iris.load(
'/storage/silver/NCAS-Weather/ben/nawdex/mi-ar482/' + time_string +
'/prodm_op_gl-mn_' + time_string + '_c*_thsfcs.nc',
'ertel_potential_vorticity')
clpv[-1] = iris.util.new_axis(clpv[-1], 'time')
pvcube = clpv.concatenate_cube()
# load full 3D PV fields for corresponding case
# could restrict this to pertinent times to save processing time
cldt = iris.load('/storage/silver/NCAS-Weather/ben/nawdex/mi-ar482/' +
time_string + '/prodm_op_gl-mn_' + time_string +
'_b*_thsfcs.nc', 'total_minus_adv_only_theta'
) # '_c*_thsfcs_5K.nc', 'ertel_potential_vorticity')
cldt[-1] = iris.util.new_axis(cldt[-1], 'time')
dtcube = cldt.concatenate_cube()
# same for diabatic heating proxy
delta_lat = np.mean(np.diff(pvcube.coord('latitude').points[:10])) / 2
# spacing of latitude grid
delta_lon = np.mean(np.diff(pvcube.coord('longitude').points[:10])) / 2
# spacing of longitude grid
trajectory_bin = []
for traj in TrEn:
if abs(traj.data[0, 3] - traj.data[-1, 3]) > theta_min and min(
traj.data[:, 3]) > 300:
trajectory_bin.append(traj)
# make a list of trajectories which ascend the most
# NOTE: the data I have for some reason only goes down to 300K - possible drawback
n = int(max(np.floor(len(trajectory_bin) / no_of_trajs), 1))
# interval of selection based on desired number of trajectories
for figno, trajex in enumerate(trajectory_bin[::n]):
lat = trajex.data[:, 1]
lon = trajex.data[:, 0]
theta = trajex.data[:, 3]
pvs = []
dts = []
for i in range(len(times)):
lat_constraint = iris.Constraint(latitude=lambda cell: lat[
i] - delta_lat < cell < lat[i] + delta_lat)
lon_constraint = iris.Constraint(longitude=lambda cell: lon[
i] - delta_lon < cell < lon[i] + delta_lon)
time_constraint = iris.Constraint(time=times[i])
pvs.append(
pvcube.extract(lat_constraint & lon_constraint
& time_constraint))
dts.append(
dtcube.extract(lat_constraint & lon_constraint
& time_constraint))
### hack fix for points not being found
ncl = []
tcl = []
try:
for cube in pvs:
if cube.ndim == 1:
ncl.append(cube)
elif cube.ndim == 2:
ncl.append(cube[:, 0])
else:
ncl.append(cube[:, 0, 0])
### hack fix for points not being found
for cube in dts:
if cube.ndim == 1:
tcl.append(cube)
elif cube.ndim == 2:
tcl.append(cube[:, 0])
else:
tcl.append(cube[:, 0, 0])
### hack fix for points not being found
pvtrajcubes = iris.cube.CubeList(ncl)
dttrajcubes = iris.cube.CubeList(tcl)
pvmerge = pvtrajcubes.merge_cube()
dtmerge = dttrajcubes.merge_cube()
if plotnotmean:
plt.figure(figsize=(12, 12))
plt.subplot(2, 2, 1)
qplt.contourf(pvmerge, np.linspace(-3, 3, 25), cmap='RdBu_r')
plt.plot(times, theta)
plt.subplot(2, 2, 2)
qplt.contourf(dtmerge, np.linspace(-25, 25, 26), cmap='RdBu_r')
plt.plot(times, theta)
plt.subplot(2, 1, 2)
qplt.contour(pvcube[14, 10], [2])
plt.gca().coastlines()
plt.plot(lon - 360, lat, linewidth=3)
plt.savefig('PV_dtheta_trajectory_crosssection_' + str(figno) +
'_' + time_string + '.png')
plt.show()
except AttributeError as e:
print e
else:
if figno == 0:
pvarray = np.array([pvmerge.data])
dtarray = np.array([dtmerge.data])
thetarray = np.array([theta])
# for the first profile, initialise a numpy array
else:
pvarray = np.append(pvarray, [pvmerge.data], axis=0)
dtarray = np.append(dtarray, [dtmerge.data], axis=0)
thetarray = np.append(thetarray, [theta], axis=0)
if not plotnotmean:
lts = len(times)
pvmean = np.mean(pvarray, axis=0)
dtmean = np.mean(dtarray, axis=0)
thetamean = np.mean(thetarray, axis=0)
# create mean fields along trajectories
ytheta = np.repeat([np.linspace(300, 340, 17)], lts, axis=0)
xtime = np.repeat([np.linspace(0, (lts - 1) * 6, lts)], 17, axis=0).T
# create arrays for axes
plt.figure(figsize=(12, 8))
plt.subplot(1, 2, 1)
plt.contourf(xtime,
ytheta,
pvmean,
np.linspace(-3, 3, 25),
cmap='RdBu_r')
plt.plot(np.linspace((lts - 1) * 6, 0, lts), thetamean)
plt.title('Average PV along trajectory for > 20K ascent')
plt.xlabel('time from start, hours')
plt.ylabel('theta, kelvin')
plt.subplot(1, 2, 2)
plt.contourf(xtime,
ytheta,
dtmean,
np.linspace(-25, 25, 26),
cmap='RdBu_r')
plt.plot(np.linspace((lts - 1) * 6, 0, lts), thetamean)
plt.title('Average diabatic heating')
plt.xlabel('time, hours')
plt.savefig('PV_dtheta_trajectory_crosssection_mean_' + time_string +
'.png')
plt.show()
def test_xaxis_labels(self):
qplt.contour(self.cube, coords=('str_coord', 'bar'))
self.assertPointsTickLabels('xaxis')
def make_transect_contours(
cfg,
metadata,
filename,
):
"""
Make a contour plot of the transect for an indivudual model.
This tool loads the cube from the file, checks that the units are
sensible BGC units, checks for layers, adjusts the titles accordingly,
determines the ultimate file name and format, then saves the image.
Parameters
----------
cfg: dict
the opened global config dictionairy, passed by ESMValTool.
metadata: dict
The metadata dictionairy for a specific model.
filename: str
The preprocessed model file.
"""
# Load cube and set up units
cube = iris.load_cube(filename)
cube = diagtools.bgc_units(cube, metadata['short_name'])
cube = make_depth_safe(cube)
# Load threshold/thresholds.
plot_details = {}
colours = []
thresholds = diagtools.load_thresholds(cfg, metadata)
linewidths = [1 for thres in thresholds]
linestyles = ['-' for thres in thresholds]
cubes = make_cube_region_dict(cube)
for region, cube in cubes.items():
for itr, thres in enumerate(thresholds):
colour = diagtools.get_colour_from_cmap(itr, len(thresholds))
label = str(thres) + ' ' + str(cube.units)
colours.append(colour)
plot_details[thres] = {
'c': colour,
'lw': 1,
'ls': '-',
'label': label
}
qplt.contour(cube,
thresholds,
colors=colours,
linewidths=linewidths,
linestyles=linestyles,
rasterized=True)
# Determine y log scale.
if determine_set_y_logscale(cfg, metadata):
plt.axes().set_yscale('log')
add_sea_floor(cube)
# Add legend
diagtools.add_legend_outside_right(plot_details,
plt.gca(),
column_width=0.08,
loc='below')
# Add title to plot
title = ' '.join([
metadata['dataset'], metadata['long_name'],
determine_transect_str(cube, region)
])
titlify(title)
# Load image format extention
image_extention = diagtools.get_image_format(cfg)
# Determine image filename:
if metadata['dataset'].find('MultiModel') > -1:
path = diagtools.folder(
cfg['plot_dir']) + os.path.basename(filename)
path.replace('.nc', region + '_transect_contour' + image_extention)
else:
path = diagtools.get_image_path(
cfg,
metadata,
suffix=region + 'transect_contour' + image_extention,
)
# Saving files:
if cfg['write_plots']:
logger.info('Saving plots to %s', path)
plt.savefig(path)
plt.close()
def multi_model_contours(
cfg,
metadatas,
):
"""
Make a multi model comparison plot showing several transect contour plots.
This tool loads several cubes from the files, checks that the units are
sensible BGC units, checks for layers, adjusts the titles accordingly,
determines the ultimate file name and format, then saves the image.
Parameters
----------
cfg: dict
the opened global config dictionairy, passed by ESMValTool.
metadatas: dict
The metadatas dictionairy for a specific model.
"""
####
# Load the data for each layer as a separate cube
model_cubes = {}
regions = {}
thresholds = {}
set_y_logscale = True
for filename in sorted(metadatas):
cube = iris.load_cube(filename)
cube = diagtools.bgc_units(cube, metadatas[filename]['short_name'])
cube = make_depth_safe(cube)
cubes = make_cube_region_dict(cube)
model_cubes[filename] = cubes
for region in model_cubes[filename]:
regions[region] = True
# Determine y log scale.
set_y_logscale = determine_set_y_logscale(cfg, metadatas[filename])
# Load threshold/thresholds.
tmp_thresholds = diagtools.load_thresholds(cfg, metadatas[filename])
for threshold in tmp_thresholds:
thresholds[threshold] = True
# Load image format extention
image_extention = diagtools.get_image_format(cfg)
# Make a plot for each layer and each threshold
for region, threshold in itertools.product(regions, thresholds):
logger.info('plotting threshold: \t%s', threshold)
title = ''
plot_details = {}
# Plot each file in the group
for index, filename in enumerate(sorted(metadatas)):
color = diagtools.get_colour_from_cmap(index, len(metadatas))
linewidth = 1.
linestyle = '-'
# Determine line style for MultiModel statistics:
if 'MultiModel' in metadatas[filename]['dataset']:
linewidth = 2.
linestyle = ':'
# Determine line style for Observations
if metadatas[filename]['project'] in diagtools.get_obs_projects():
color = 'black'
linewidth = 1.7
linestyle = '-'
qplt.contour(model_cubes[filename][region], [
threshold,
],
colors=[
color,
],
linewidths=linewidth,
linestyles=linestyle,
rasterized=True)
plot_details[filename] = {
'c': color,
'ls': linestyle,
'lw': linewidth,
'label': metadatas[filename]['dataset']
}
if set_y_logscale:
plt.axes().set_yscale('log')
title = metadatas[filename]['long_name']
units = str(model_cubes[filename][region].units)
add_sea_floor(model_cubes[filename][region])
# Add title, threshold, legend to plots
title = ' '.join([
title,
str(threshold), units,
determine_transect_str(model_cubes[filename][region], region)
])
titlify(title)
plt.legend(loc='best')
# Saving files:
if cfg['write_plots']:
path = diagtools.get_image_path(
cfg,
metadatas[filename],
prefix='MultipleModels',
suffix='_'.join([
'contour_tramsect', region,
str(threshold) + image_extention
]),
metadata_id_list=[
'field', 'short_name', 'preprocessor', 'diagnostic',
'start_year', 'end_year'
],
)
# Resize and add legend outside thew axes.
plt.gcf().set_size_inches(9., 6.)
diagtools.add_legend_outside_right(plot_details,
plt.gca(),
column_width=0.15)
logger.info('Saving plots to %s', path)
plt.savefig(path)
plt.close()
def make_map_contour(
cfg,
metadata,
filename,
):
"""
Make a simple contour map plot for an individual model.
Parameters
----------
cfg: dict
the opened global config dictionary, passed by ESMValTool.
metadata: dict
the metadata dictionary
filename: str
the preprocessed model file.
"""
# Load cube and set up units
cube = iris.load_cube(filename)
cube = diagtools.bgc_units(cube, metadata['short_name'])
# Is this data is a multi-model dataset?
multi_model = metadata['dataset'].find('MultiModel') > -1
# Make a dict of cubes for each layer.
cubes = diagtools.make_cube_layer_dict(cube)
# Load image format extention and threshold.thresholds.
image_extention = diagtools.get_image_format(cfg)
# Load threshold/thresholds.
plot_details = {}
colours = []
thresholds = diagtools.load_thresholds(cfg, metadata)
for itr, thres in enumerate(thresholds):
if len(thresholds) > 1:
colour = plt.cm.jet(float(itr) / float(len(thresholds) - 1.))
else:
colour = plt.cm.jet(0)
label = str(thres) + ' ' + str(cube.units)
colours.append(colour)
plot_details[thres] = {'c': colour, 'lw': 1, 'ls': '-', 'label': label}
linewidths = [1 for thres in thresholds]
linestyles = ['-' for thres in thresholds]
# Making plots for each layer
for layer_index, (layer, cube_layer) in enumerate(cubes.items()):
layer = str(layer)
qplt.contour(cube_layer,
thresholds,
colors=colours,
linewidths=linewidths,
linestyles=linestyles,
rasterized=True)
try:
plt.gca().coastlines()
except AttributeError:
logger.warning('Not able to add coastlines')
try:
plt.gca().add_feature(cartopy.feature.LAND,
zorder=10,
facecolor=[0.8, 0.8, 0.8])
except AttributeError:
logger.warning('Not able to add coastlines')
# Add legend
diagtools.add_legend_outside_right(plot_details,
plt.gca(),
column_width=0.02,
loc='below')
# Add title to plot
title = ' '.join([metadata['dataset'], metadata['long_name']])
depth_units = str(cube_layer.coords('depth')[0].units)
if layer:
title = '{} ({} {})'.format(title, layer, depth_units)
plt.title(title)
# Determine image filename:
if multi_model:
path = os.path.join(diagtools.folder(cfg['plot_dir']),
os.path.basename(filename))
path = path.replace('.nc', '_contour_map_' + str(layer_index))
path = path + image_extention
else:
path = diagtools.get_image_path(
cfg,
metadata,
suffix='_contour_map_' + str(layer_index) + image_extention,
)
# Saving files:
if cfg['write_plots']:
logger.info('Saving plots to %s', path)
plt.savefig(path)
plt.close()
def multi_model_contours(
cfg,
metadata,
):
"""
Make a contour map showing several models.
Parameters
----------
cfg: dict
the opened global config dictionary, passed by ESMValTool.
metadata: dict
the metadata dictionary.
"""
####
# Load the data for each layer as a separate cube
model_cubes = {}
layers = {}
for filename in sorted(metadata):
cube = iris.load_cube(filename)
cube = diagtools.bgc_units(cube, metadata[filename]['short_name'])
cubes = diagtools.make_cube_layer_dict(cube)
model_cubes[filename] = cubes
for layer in cubes:
layers[layer] = True
# Load image format extention
image_extention = diagtools.get_image_format(cfg)
# Load threshold/thresholds.
thresholds = diagtools.load_thresholds(cfg, metadata)
# Make a plot for each layer and each threshold
for layer, threshold in itertools.product(layers, thresholds):
title = ''
z_units = ''
plot_details = {}
cmap = plt.cm.get_cmap('jet')
land_drawn = False
# Plot each file in the group
for index, filename in enumerate(sorted(metadata)):
if len(metadata) > 1:
color = cmap(index / (len(metadata) - 1.))
else:
color = 'blue'
linewidth = 1.
linestyle = '-'
# Determine line style for Observations
if metadata[filename]['project'] in diagtools.get_obs_projects():
color = 'black'
linewidth = 1.7
linestyle = '-'
# Determine line style for MultiModel statistics:
if 'MultiModel' in metadata[filename]['dataset']:
color = 'black'
linestyle = ':'
linewidth = 1.4
cube = model_cubes[filename][layer]
qplt.contour(cube, [
threshold,
],
colors=[
color,
],
linewidths=linewidth,
linestyles=linestyle,
rasterized=True)
plot_details[filename] = {
'c': color,
'ls': linestyle,
'lw': linewidth,
'label': metadata[filename]['dataset']
}
if not land_drawn:
try:
plt.gca().coastlines()
except AttributeError:
logger.warning('Not able to add coastlines')
plt.gca().add_feature(cartopy.feature.LAND,
zorder=10,
facecolor=[0.8, 0.8, 0.8])
land_drawn = True
title = metadata[filename]['long_name']
if layer != '':
z_units = model_cubes[filename][layer].coords('depth')[0].units
units = str(model_cubes[filename][layer].units)
# Add title, threshold, legend to plots
title = ' '.join([title, str(threshold), units])
if layer:
title = ' '.join([title, '(', str(layer), str(z_units), ')'])
plt.title(title)
plt.legend(loc='best')
# Saving files:
if cfg['write_plots']:
path = diagtools.get_image_path(
cfg,
metadata[filename],
prefix='MultipleModels_',
suffix='_'.join([
'_contour_map_',
str(threshold),
str(layer) + image_extention
]),
metadata_id_list=[
'field', 'short_name', 'preprocessor', 'diagnostic',
'start_year', 'end_year'
],
)
# Resize and add legend outside thew axes.
plt.gcf().set_size_inches(9., 6.)
diagtools.add_legend_outside_right(plot_details,
plt.gca(),
column_width=0.15)
logger.info('Saving plots to %s', path)
plt.savefig(path)
plt.close()
def make_map_extent_plots(
cfg,
metadata,
filename,
):
"""
Make an extent map plot showing several times for an individual model.
Parameters
----------
cfg: dict
the opened global config dictionairy, passed by ESMValTool.
metadata: dict
The metadata dictionairy for a specific model.
filename: str
The preprocessed model file.
"""
# Load cube and set up units
cube = iris.load_cube(filename)
iris.coord_categorisation.add_year(cube, 'time')
cube = diagtools.bgc_units(cube, metadata['short_name'])
cube = agregate_by_season(cube)
# Is this data is a multi-model dataset?
multi_model = metadata['dataset'].find('MultiModel') > -1
# Make a dict of cubes for each layer.
cubes = diagtools.make_cube_layer_dict(cube)
# Load image format extention
image_extention = diagtools.get_image_format(cfg)
# Load threshold, pole and season
threshold = float(cfg['threshold'])
pole = get_pole(cube)
season = get_season(cube)
# Start making figure
for layer_index, (layer, cube_layer) in enumerate(cubes.items()):
fig = plt.figure()
fig.set_size_inches(7, 7)
if pole == 'North': # North Hemisphere
projection = cartopy.crs.NorthPolarStereo()
ax1 = plt.subplot(111, projection=projection)
ax1.set_extent([-180, 180, 50, 90], cartopy.crs.PlateCarree())
if pole == 'South': # South Hemisphere
projection = cartopy.crs.SouthPolarStereo()
ax1 = plt.subplot(111, projection=projection)
ax1.set_extent([-180, 180, -90, -50], cartopy.crs.PlateCarree())
try:
ax1.add_feature(cartopy.feature.LAND,
zorder=10,
facecolor=[0.8, 0.8, 0.8])
except ConnectionRefusedError:
logger.error('Cartopy was unable add coastlines due to a '
'connection error.')
ax1.gridlines(linewidth=0.5,
color='black',
zorder=20,
alpha=0.5,
linestyle='--')
try:
plt.gca().coastlines()
except AttributeError:
logger.warning('make_polar_map: Not able to add coastlines')
times = np.array(cube.coord('time').points.astype(float))
plot_desc = {}
for time_itr, time in enumerate(times):
cube = cube_layer[time_itr]
line_width = 1
color = plt.cm.jet(float(time_itr) / float(len(times)))
label = get_year(cube)
plot_desc[time] = {
'label': label,
'c': [
color,
],
'lw': [
line_width,
],
'ls': [
'-',
]
}
layer = str(layer)
qplt.contour(cube, [
threshold,
],
colors=plot_desc[time]['c'],
linewidths=plot_desc[time]['lw'],
linestyles=plot_desc[time]['ls'],
rasterized=True)
# Add legend
legend_size = len(plot_desc) + 1
ncols = int(legend_size / 25) + 1
ax1.set_position([
ax1.get_position().x0,
ax1.get_position().y0,
ax1.get_position().width * (1. - 0.1 * ncols),
ax1.get_position().height
])
fig.set_size_inches(7 + ncols * 1.2, 7)
# Construct dummy plots.
for i in sorted(plot_desc):
plt.plot(
[],
[],
c=plot_desc[i]['c'][0],
lw=plot_desc[i]['lw'][0],
ls=plot_desc[i]['ls'][0],
label=plot_desc[i]['label'],
)
legd = ax1.legend(loc='center left',
ncol=ncols,
prop={'size': 10},
bbox_to_anchor=(1., 0.5))
legd.draw_frame(False)
legd.get_frame().set_alpha(0.)
# Add title to plot
title = ' '.join([
metadata['dataset'],
])
if layer:
title = ' '.join([
title, '(', layer,
str(cube_layer.coords('depth')[0].units), ')'
])
plt.title(title)
# Determine image filename:
suffix = '_'.join(['ortho_map', pole, season, str(layer_index)])
suffix = suffix.replace(' ', '') + image_extention
if multi_model:
path = diagtools.folder(cfg['plot_dir'])
path = path + os.path.basename(filename)
path = path.replace('.nc', suffix)
else:
path = diagtools.get_image_path(
cfg,
metadata,
suffix=suffix,
)
# Saving files:
if cfg['write_plots']:
logger.info('Saving plots to %s', path)
plt.savefig(path)
plt.close()
def permafrost_area(soiltemp, airtemp, landfrac, run):
"""Calculate the permafrost area and make a plot."""
# Define parameters of the test to calculate the existence of permafrost
thresh_temperature = 273.2
frozen_months = 24
prop_months_frozen = 0.5 # frozen for at least half of the simulation
# make a mask of land fraction over non iced areas and extract northern
# latitudes
nonice = get_nonice_mask(run)
mask = iris.analysis.maths.multiply(nonice, landfrac)
mask = mask.extract(iris.Constraint(latitude=lambda cell: cell > 0))
# extract northern high latitudes [and deeepst soil level]
soiltemp = soiltemp.extract(iris.Constraint(depth=2.0)) # from 1m to 3m
# Make an aggregator to define the permafrost extent
# I dont really understand this but it works
frozen_count = iris.analysis.Aggregator('frozen_count',
num_frozen,
units_func=lambda units: 1)
# Calculate the permafrost locations
pf_periods = soiltemp.collapsed('time',
frozen_count,
threshold=thresh_temperature,
frozen_length=frozen_months)
tot_time = len(soiltemp.coord('time').points)
pf_periods = pf_periods / float(tot_time)
pf_periods.rename('Fraction of months layer 4 (-1m to -3m) soil is frozen')
# mask out non permafrost points, sea points and ice points
pf_periods.data = np.ma.masked_less(pf_periods.data, prop_months_frozen)
# set all non-masked values to 1 for area calculation
# (may be a better way of doing this but I'm not sure what it is)
pf_periods = pf_periods / pf_periods
# mask for land area also
pf_periods = pf_periods * mask
# calculate the area of permafrost
# Generate area-weights array. This method requires bounds on lat/lon
# coords, add some in sensible locations using the "guess_bounds"
# method.
for coord in ['latitude', 'longitude']:
if not pf_periods.coord(coord).has_bounds():
pf_periods.coord(coord).guess_bounds()
grid_areas = iris.analysis.cartography.area_weights(pf_periods)
# calculate the areas not masked in pf_periods
pf_area = pf_periods.collapsed(['longitude', 'latitude'],
iris.analysis.SUM,
weights=grid_areas).data
# what is the area where the temperature is less than 0 degrees C?
airtemp = airtemp.collapsed('time', iris.analysis.MEAN)
# if more than 2 dims, select the ground level
if airtemp.ndim > 2:
airtemp = airtemp[0]
airtemp_below_zero = np.where(airtemp.data < 273.2, 1, 0)
airtemp_area = np.sum(airtemp_below_zero * grid_areas)
pf_prop = pf_area / airtemp_area
pf_area = pf_area / 1e12
# Figure Permafrost extent north america
plt.figure(figsize=(8, 8))
ax = plt.axes(projection=ccrs.Orthographic(central_longitude=-80.0,
central_latitude=60.0))
qplt.pcolormesh(pf_periods)
ax.gridlines()
ax.coastlines()
levels = [thresh_temperature]
qplt.contour(airtemp, levels, colors='k', linewidths=3)
plt.title('Permafrost extent & zero degree isotherm ({})'.format(
run['runid']))
plt.savefig('pf_extent_north_america_' + run['runid'] + '.png')
# Figure Permafrost extent asia
plt.figure(figsize=(8, 8))
ax = plt.axes(projection=ccrs.Orthographic(central_longitude=100.0,
central_latitude=50.0))
qplt.pcolormesh(pf_periods)
ax.gridlines()
ax.coastlines()
levels = [thresh_temperature]
qplt.contour(airtemp, levels, colors='k', linewidths=3)
plt.title('Permafrost extent & zero degree isotherm ({})'.format(
run['runid']))
plt.savefig('pf_extent_asia_' + run['runid'] + '.png')
# defining metrics for return up to top level
metrics = {
'permafrost area': pf_area,
'fraction area permafrost over zerodeg': pf_prop,
}
return metrics
from __future__ import (absolute_import, division, print_function)
from six.moves import (filter, input, map, range, zip) # noqa
import matplotlib.pyplot as plt
import iris
import iris.quickplot as qplt
fname = iris.sample_data_path('air_temp.pp')
temperature_cube = iris.load_cube(fname)
# Add a contour, and put the result in a variable called contour.
contour = qplt.contour(temperature_cube)
# Add coastlines to the map created by contour.
plt.gca().coastlines()
# Add contour labels based on the contour we have just created.
plt.clabel(contour, inline=False)
plt.show()