def buildTriangulation( self, x, y ):
trig=None
if qgis_qhull_fails:
trig=self._buildtrig_workaround(x,y)
else:
trig=Triangulation(x,y)
analyzer=TriAnalyzer(trig)
mask=analyzer.get_flat_tri_mask()
trig.set_mask(mask)
return trig
def buildTriangulation( self, x, y ):
trig=None
if qgis_qhull_fails:
trig=self._buildtrig_workaround(x,y)
else:
trig=Triangulation(x,y)
analyzer=TriAnalyzer(trig)
mask=analyzer.get_flat_tri_mask()
trig.set_mask(mask)
return trig
def plot_dp(storm, datafile1, datafile2=None):
#Single file netCDF reading
ncf=datafile1
nco=netCDF4.Dataset(ncf)
#Get fields to plot
lon=nco.variables['longitude'][:]
lat=nco.variables['latitude'][:]
timeindays=nco.variables['time'][:]
dp=nco.variables['dp'][:]
triangles=nco.variables['tri'][:,:]
reflon=np.linspace(lon.min(),lon.max(),1000)
reflat=np.linspace(lat.min(),lat.max(),1000)
#reflon=np.linspace(-80.40, -74.75, 1000)
#reflat=np.linspace(32.50, 36.60, 1000)
#reflon=np.linspace(-75.70, -71.05, 1000)
#reflat=np.linspace(38.50, 41.40, 1000)
reflon,reflat=np.meshgrid(reflon,reflat)
plt.figure(figsize = [6.4, 3.8])
flatness=0.10 # flatness is from 0-.5 .5 is equilateral triangle
triangles=triangles-1 # Correct indices for Python's zero-base
tri=Triangulation(lon,lat,triangles=triangles)
mask = TriAnalyzer(tri).get_flat_tri_mask(flatness)
tri.set_mask(mask)
# Loop through each time step and plot results
for ind in range(0, len(timeindays)):
plt.clf()
ax = plt.axes(projection=ccrs.Mercator())
dt = datetime.datetime.combine(datetime.date(1990, 1, 1), datetime.time(0, 0)) + datetime.timedelta(days=timeindays[ind])
dstr = datetime.date.strftime(dt,'%Y%m%d%H:%M:%S')
dstr = dstr[0:8]+' '+dstr[8:17]
print('Plotting '+dstr)
par=np.double(dp[ind,:])
tli=LinearTriInterpolator(tri,par)
par_interp=tli(reflon,reflat)
plt.pcolormesh(reflon,reflat,par_interp,vmin=0.0,vmax=360.0,shading='flat',cmap=plt.cm.jet, transform=ccrs.PlateCarree())
cb = plt.colorbar()
cb.ax.tick_params(labelsize=8)
coast = cfeature.GSHHSFeature(scale='high',edgecolor='black',facecolor='none',linewidth=0.25)
ax.add_feature(coast)
plt.xticks(fontsize=9)
plt.yticks(fontsize=9)
figtitle = storm.capitalize()+': Peak Dir (deg): '+dstr
plt.title(figtitle)
dtlabel = datetime.date.strftime(dt,'%Y%m%d%H%M%S')
dtlabel = dtlabel[0:8]+'_'+dtlabel[8:14]
filenm = 'nsem_'+storm+'_dp_'+dtlabel+'.png'
plt.savefig(filenm,dpi=150,bbox_inches='tight',pad_inches=0.1)
del(par)
del(par_interp)
def plot_magnetic_field_contour(self, ax=None):
if ax is None:
fig, ax = plt.subplots()
else:
fig = plt.gcf()
ax.set_aspect('equal')
from matplotlib.tri import Triangulation, TriAnalyzer, UniformTriRefiner
import matplotlib.cm as cm
element_to_magnetic_field = self.magnetic_field_per_element()
x = []
y = []
Z = []
for group in self.mesh.elements_groups:
for element in group.elements:
x_center, y_center = element.center
x.append(x_center)
y.append(y_center)
Z.append(element_to_magnetic_field[element].Norm())
tri = Triangulation(x, y)
#-----------------------------------------------------------------------------
# Improving the triangulation before high-res plots: removing flat triangles
#-----------------------------------------------------------------------------
# masking badly shaped triangles at the border of the triangular mesh.
min_circle_ratio = -1
mask = TriAnalyzer(tri).get_flat_tri_mask(min_circle_ratio)
tri.set_mask(mask)
# refining the data
refiner = UniformTriRefiner(tri)
subdiv = 3
tri_refi, z_test_refi = refiner.refine_field(Z, subdiv=subdiv)
levels = npy.arange(0., 1., 0.05)
cmap = cm.get_cmap(name='Blues', lut=None)
ax.tricontour(tri_refi, z_test_refi, levels=levels, #cmap=cmap,
linewidths=[2.0, 0.5, 1.0, 0.5])
# ax.triplot(tri_refi, color='0.97')
# ax.triplot(tri, color='0.7')
# ax.tricontour(x, y, Z)
return ax
def plot_samples(num):
samples_hundred = BM_sampling_method(num)
tri = Triangulation(samples_hundred[0], samples_hundred[1])
random_gen = np.random.mtrand.RandomState(seed=127260)
init_mask_frac = 0.0
min_circle_ratio = .01
subdiv = 3
ntri = tri.triangles.shape[0]
print 'hi'
mask_init = np.zeros(ntri, dtype=np.bool)
masked_tri = random_gen.randint(0, ntri, int(ntri * init_mask_frac))
mask_init[masked_tri] = True
tri.set_mask(mask_init)
print 'hey'
z_exp = experiment_res(tri.x, tri.y)
print z_exp
mask = TriAnalyzer(tri).get_flat_tri_mask(min_circle_ratio)
tri.set_mask(mask)
# refining the data
refiner = UniformTriRefiner(tri)
tri_refi, z_test_refi = refiner.refine_field(z_exp, subdiv=subdiv)
# analytical 'results' for comparison
z_expected = experiment_res(tri_refi.x, tri_refi.y)
plt.tricontour(tri_refi,
z_expected,
levels=levels,
cmap=cmap,
linestyles='--')
plt.show()
x, y = np.mgrid[-1:1:0.001, -1:1:0.001]
pos = np.empty(x.shape + (2, ))
pos[:, :, 0] = x
pos[:, :, 1] = y
rv = multivariate_normal([0, 0], [[1.0, 0.0], [0.0, 1.0]])
plt.contour(x, y, rv.pdf(pos))
mask = tri_y == 0 # t=0 are not valid datapoints
tri_y = tri_y[~mask]
tri_x = tri_x[~mask]
tri_z = tri_z[~mask]
# }}}
tri = Triangulation(tri_x,
tri_y)
# {{{ refining the data -- see https://matplotlib.org/3.1.0/gallery/images_contours_and_fields/tricontour_smooth_delaunay.html#sphx-glr-gallery-images-contours-and-fields-tricontour-smooth-delaunay-py
# I don't see a difference in the refined (tri_refi) vs. unrefined (tri),
# but I'm quite possibly missing something, or it's more helpful in other cases
refiner = UniformTriRefiner(tri)
subdiv = 3 # Number of recursive subdivisions of the initial mesh for smooth
# plots. Values >3 might result in a very high number of triangles
# for the refine mesh: new triangles numbering = (4**subdiv)*ntri
tri_refi, tri_z_refi = refiner.refine_field(tri_z, subdiv=subdiv)
mask = TriAnalyzer(tri_refi).get_flat_tri_mask(10)
tri_refi = tri_refi.set_mask(~mask)
# }}}
figure(figsize=(5,15),
facecolor=(1,1,1,0))
if not presentation:
plot(tri_x,tri_y,'o',
color='k',alpha=0.3)
triplot(tri,
color='k',alpha=0.3)
tricontourf(tri,tri_z,
levels=linspace(tri_z.min(),tri_z.max(),100),
#cmap=cm,
)
colorbar()
xlabel('frequency\n($\\nu_{\\mu w}-%0.5f$ GHz)/ kHz'%(f_axis.mean()/1e9))
plt.figure(figsize = [6.4, 3.8])
#Loop through each time step and plot results
for ind in range(0, len(timeindays)):
dt = datetime.datetime.combine(datetime.date(1990, 1, 1), datetime.time(0, 0)) + datetime.timedelta(days=timeindays[ind])
dstr = datetime.date.strftime(dt,'%Y%m%d%H:%M:%S')
dstr = dstr[0:8]+' '+dstr[8:17]
print('Plotting '+dstr)
par=np.double(wlv[ind,:])
par2=np.double(ucur[ind,:])
par3=np.double(vcur[ind,:])
flatness=0.10 # flatness is from 0-.5 .5 is equilateral triangle
tri=Triangulation(lon,lat)
mask = TriAnalyzer(tri).get_flat_tri_mask(flatness)
tri.set_mask(mask)
tli=LinearTriInterpolator(tri,par)
par_interp=tli(reflon,reflat)
tli2=LinearTriInterpolator(tri,par2)
par2_interp=tli2(reflon,reflat)
tli3=LinearTriInterpolator(tri,par3)
par3_interp=tli3(reflon,reflat)
#Set up a Mercator projection basemap
plt.clf()
#m=Basemap(projection='merc',llcrnrlon=reflon.min(),urcrnrlon=reflon.max(),\
# llcrnrlat=reflat.min(),urcrnrlat=reflat.max(),resolution='h')
#x,y=m(reflon,reflat)
x = reflon
def __init__(self, **kwargs):
super(ContourMap, self).__init__(**kwargs)
n_test = 200 # Number of test data points, tested from 3 to 5000 for subdiv=3
subdiv = 3 # Number of recursive subdivisions of the initial mesh for smooth
# plots. Values >3 might result in a very high number of triangles
# for the refine mesh: new triangles numbering = (4**subdiv)*ntri
init_mask_frac = 0.0 # Float > 0. adjusting the proportion of
# (invalid) initial triangles which will be masked
# out. Enter 0 for no mask.
min_circle_ratio = .01 # Minimum circle ratio - border triangles with circle
# ratio below this will be masked if they touch a
# border. Suggested value 0.01 ; Use -1 to keep
# all triangles.
# Random points
random_gen = np.random.mtrand.RandomState(seed=127260)
x_test = random_gen.uniform(-1., 1., size=n_test)
y_test = random_gen.uniform(-1., 1., size=n_test)
z_test = experiment_res(x_test, y_test)
# meshing with Delaunay triangulation
tri = Triangulation(x_test, y_test)
ntri = tri.triangles.shape[0]
# Some invalid data are masked out
mask_init = np.zeros(ntri, dtype=np.bool)
masked_tri = random_gen.randint(0, ntri, int(ntri * init_mask_frac))
mask_init[masked_tri] = True
tri.set_mask(mask_init)
#-----------------------------------------------------------------------------
# Improving the triangulation before high-res plots: removing flat triangles
#-----------------------------------------------------------------------------
# masking badly shaped triangles at the border of the triangular mesh.
mask = TriAnalyzer(tri).get_flat_tri_mask(min_circle_ratio)
tri.set_mask(mask)
# refining the data
refiner = UniformTriRefiner(tri)
tri_refi, z_test_refi = refiner.refine_field(z_test, subdiv=subdiv)
# analytical 'results' for comparison
z_expected = experiment_res(tri_refi.x, tri_refi.y)
# for the demo: loading the 'flat' triangles for plot
flat_tri = Triangulation(x_test, y_test)
flat_tri.set_mask(~mask)
#-----------------------------------------------------------------------------
# Now the plots
#-----------------------------------------------------------------------------
# User options for plots
plot_tri = True # plot of base triangulation
plot_masked_tri = True # plot of excessively flat excluded triangles
plot_refi_tri = False # plot of refined triangulation
plot_expected = False # plot of analytical function values for comparison
# Graphical options for tricontouring
levels = np.arange(0., 1., 0.025)
cmap = cm.get_cmap(name='Blues', lut=None)
plt.figure()
plt.gca().set_aspect('equal')
plt.title("Filtering a Delaunay mesh\n" +
"(application to high-resolution tricontouring)")
# 1) plot of the refined (computed) data countours:
plt.tricontour(tri_refi,
z_test_refi,
levels=levels,
cmap=cmap,
linewidths=[2.0, 0.5, 1.0, 0.5])
# 2) plot of the expected (analytical) data countours (dashed):
if plot_expected:
plt.tricontour(tri_refi,
z_expected,
levels=levels,
cmap=cmap,
linestyles='--')
# 3) plot of the fine mesh on which interpolation was done:
if plot_refi_tri:
plt.triplot(tri_refi, color='0.97')
# 4) plot of the initial 'coarse' mesh:
if plot_tri:
plt.triplot(tri, color='0.7')
# 4) plot of the unvalidated triangles from naive Delaunay Triangulation:
if plot_masked_tri:
plt.triplot(flat_tri, color='red')
plt.show()
def plot_wnd(storm, datafile1, datafile2=None):
#Single file netCDF reading
ncf = datafile1
nco = netCDF4.Dataset(ncf)
#Get fields to plot
lon = nco.variables['x'][:]
lat = nco.variables['y'][:]
timeinsec = nco.variables['time'][:]
uwnd = nco.variables['windx'][:]
vwnd = nco.variables['windy'][:]
triangles = nco.variables['element'][:, :]
reflon = np.linspace(lon.min(), lon.max(), 1000)
reflat = np.linspace(lat.min(), lat.max(), 1000)
#reflon=np.linspace(-80.40, -74.75, 1000)
#reflat=np.linspace(32.50, 36.60, 1000)
#reflon=np.linspace(-75.70, -71.05, 1000)
#reflat=np.linspace(38.50, 41.40, 1000)
#reflon=np.linspace(-80.40, -73.35, 1000)
#reflat=np.linspace(32.50, 39.50, 1000)
#reflon=np.linspace(-85.30, -78.50, 1000)
#reflat=np.linspace(23.00, 29.70, 1000)
reflon, reflat = np.meshgrid(reflon, reflat)
plt.figure(figsize=[6.4, 3.8])
flatness = 0.10 # flatness is from 0-.5 .5 is equilateral triangle
triangles = triangles - 1 # Correct indices for Python's zero-base
tri = Triangulation(lon, lat, triangles=triangles)
mask = TriAnalyzer(tri).get_flat_tri_mask(flatness)
tri.set_mask(mask)
# Loop through each time step and plot results
for ind in range(0, len(timeinsec)):
besttrack = pd.read_csv(PARMnsem + '/storms/' + STORM +
'/best_track.txt',
header=None,
skiprows=4,
delim_whitespace=True)
plt.clf()
ax = plt.axes(projection=ccrs.Mercator())
ax.set_extent([-100.00, -50.00, 4.00, 48.00], crs=ccrs.PlateCarree())
#ax.set_extent([-80.40, -74.75, 32.50, 36.60], crs=ccrs.PlateCarree())
#ax.set_extent([-80.40, -73.35, 32.50, 39.50], crs=ccrs.PlateCarree())
#ax.set_extent([-85.30, -78.50, 23.00, 29.70], crs=ccrs.PlateCarree())
dt = base_info.tide_spin_start_date + datetime.timedelta(
seconds=timeinsec[ind])
dstr = datetime.date.strftime(dt, '%Y%m%d%H:%M:%S')
dstr = dstr[0:8] + ' ' + dstr[8:17]
print('Plotting ' + dstr)
par = np.sqrt(
np.square(np.double(uwnd[ind, :])) +
np.square(np.double(vwnd[ind, :])))
tli = LinearTriInterpolator(tri, par)
par_interp = tli(reflon, reflat)
plt.pcolormesh(reflon,
reflat,
par_interp,
vmax=60.0,
shading='flat',
cmap=plt.cm.jet,
transform=ccrs.PlateCarree())
cb = plt.colorbar()
cb.ax.tick_params(labelsize=8)
coast = cfeature.GSHHSFeature(scale='high',
edgecolor='black',
facecolor='none',
linewidth=0.25)
ax.add_feature(coast)
plt.plot(besttrack.iloc[:, 3].values,
besttrack.iloc[:, 2].values,
'k--',
linewidth=1.0,
transform=ccrs.PlateCarree())
gl = ax.gridlines(crs=ccrs.PlateCarree(),
draw_labels=True,
linewidth=2,
color='gray',
alpha=0.5,
linestyle='--')
gl.xlabels_top = False
gl.ylabels_right = False
gl.xlines = False
gl.ylines = False
gl.xformatter = LONGITUDE_FORMATTER
gl.yformatter = LATITUDE_FORMATTER
gl.xlabel_style = {'size': 6, 'color': 'black'}
gl.ylabel_style = {'size': 6, 'color': 'black'}
figtitle = storm.capitalize() + ': U10 (m/s): ' + dstr
plt.title(figtitle)
dtlabel = datetime.date.strftime(dt, '%Y%m%d%H%M%S')
dtlabel = dtlabel[0:8] + '_' + dtlabel[8:14]
filenm = 'nsem_' + storm + '_wnd_' + dtlabel + '.png'
plt.savefig(filenm, dpi=150, bbox_inches='tight', pad_inches=0.1)
del (par)
del (par_interp)
def extract_wnd(storm,
datafile1,
stations,
df,
lonmin=None,
lonmax=None,
latmin=None,
latmax=None):
#Single file netCDF reading
#ncf='ww3.field.2018_wnd.nc'
ncf = datafile1
nco = netCDF4.Dataset(ncf)
#ncf2='ww3.field.2018_dp.nc'
#ncf2=datafile2
#nco2=netCDF4.Dataset(ncf2)
#Get fields to plot
lon = nco.variables['longitude'][:]
lat = nco.variables['latitude'][:]
pnt_lon = stations.iloc[0, :].values
pnt_lat = stations.iloc[1, :].values
timeindays = nco.variables['time'][:]
uwnd = nco.variables['uwnd'][:]
vwnd = nco.variables['vwnd'][:]
#timeindays2=nco2.variables['time'][:]
#dir=nco2.variables['dp'][:]
if lonmin != None:
reflon = np.linspace(lonmin, lonmax, 1000)
reflat = np.linspace(latmin, latmax, 1000)
else:
reflon = np.linspace(lon.min(), lon.max(), 1000)
reflat = np.linspace(lat.min(), lat.max(), 1000)
reflon, reflat = np.meshgrid(reflon, reflat)
flatness = 0.10 # flatness is from 0-.5 .5 is equilateral triangle
tri = Triangulation(lon, lat)
mask = TriAnalyzer(tri).get_flat_tri_mask(flatness)
tri.set_mask(mask)
#Read obs point locations
#data=np.loadtxt('erie_ndbc.loc', comments = '$')
#buoylon=data[:,0]
#buoylat=data[:,1]
plt.figure(figsize=[6.4, 3.8])
df_dates = pd.DataFrame(columns=['Date'])
# Loop through each time step and plot results
for ind in range(0, len(timeindays)):
plt.clf()
ax = plt.axes(projection=ccrs.Mercator())
dt = datetime.datetime.combine(datetime.date(
1990, 1, 1), datetime.time(
0, 0)) + datetime.timedelta(days=timeindays[ind])
dstr = datetime.date.strftime(dt, '%Y%m%d%H:%M:%S')
dstr = dstr[0:8] + ' ' + dstr[8:17]
print('Extracting ' + dstr)
par = np.sqrt(
np.square(np.double(uwnd[ind, :])) +
np.square(np.double(vwnd[ind, :])))
#par2=np.double(dir[ind,:])
tli = LinearTriInterpolator(tri, par)
par_interp = tli(pnt_lon, pnt_lat)
#print(par_interp)
df.loc[len(df)] = par_interp
df_dates.loc[len(df_dates)] = pd.to_datetime(
dt, format="%Y-%m-%d %H:%M:%S")
#line = pd.to_datetime(dt, format="%Y-%m-%d %H:%M:%S")
#new_row = pd.DataFrame(par_interp, columns=stations.columns, index=line)
#df = pd.concat([df, pd.DataFrame(new_row)], ignore_index=False)
del (par)
del (par_interp)
df['Date'] = df_dates
df.set_index('Date', inplace=True)
return df
def density(model, refinement=0):
"""
Create a Voronoi mesh and calculate the local particle density on its vertices.
The local density is calculated as follows:
for each vertex, compute the density of each neighbour region as
one over the area and assign the average of
the neighbouring density to the vertex.
Parameters
----------
model : simulation.builder.Model
the Model object containing
refinement : int (defaults : 0)
number of subdivision for refining the mesh (0 == None)
Returns
-------
tri : matplotlib.tri.Triangulation
the triangulation mesh (refined if set as)
vert_density : numpy.array
the array containing the local denstity associated with the tri mesh
Example
-------
To plot the result using matplotlib use :
.. code-block:: python
import matplotlib.pyplot as plt
tri, density = data_proc.density(model)
plt.tricontour(tri, density) # to draw contours
plt.tricontourf(tri, density) # ot draw filled contours
plt.show()
Note
----
As of now, the numerical results may not be quantitatively accurate
but should qualitatively represent the density.
"""
vor = Voronoi(model.pos)
vert_density = np.zeros(max(vor.vertices.shape)) # density vector
reg_num = np.zeros(max(
vor.vertices.shape)) # nbr of regions per vertex --> averaging
for point_index, reg in enumerate(vor.point_region):
vertices = vor.regions[reg]
if vertices:
if -1 not in vertices:
area = ConvexHull(vor.vertices[vertices]).area # gets the area
vert_density[
vertices] += 1 / area # makes it a density (sort-of)
reg_num[vertices] += 1
vert_density /= reg_num # averaging
# getting rid of really ugly border points
new_vert, vert_density = (
vor.vertices[vor.vertices[:, 0] >= np.min(model.pos[:, 0])],
vert_density[vor.vertices[:, 0] >= np.min(model.pos[:, 0])])
new_vert, vert_density = (
new_vert[new_vert[:, 0] <= np.max(model.pos[:, 0])],
vert_density[new_vert[:, 0] <= np.max(model.pos[:, 0])])
new_vert, vert_density = (
new_vert[new_vert[:, 1] >= np.min(model.pos[:, 1])],
vert_density[new_vert[:, 1] >= np.min(model.pos[:, 1])])
new_vert, vert_density = (
new_vert[new_vert[:, 1] <= np.max(model.pos[:, 1])],
vert_density[new_vert[:, 1] <= np.max(model.pos[:, 1])])
# for triangulation refinement
tri2 = Triangulation(*new_vert.T)
if refinement:
tri2.set_mask(TriAnalyzer(tri2).get_flat_tri_mask(0.1))
refiner = UniformTriRefiner(tri2)
print(len(tri2.neighbors), vert_density.shape)
tri, vert_density = refiner.refine_field(vert_density,
subdiv=refinement)
else:
tri, vert_density = tri2, vert_density
return tri, vert_density
def mesh_2D(fname,
var=None,
flabels=None,
fformat='csv',
xlabel='X axis',
ylabel='Y axis',
vmins=None,
output_path=None):
"""Visualization of specific variable on a user provided 2D mesh.
The provided mesh should contain two columns (x,y coordinates for each
mesh point) and be one of :func:`batman.input_output.available_formats`.
(x, y) must be respectively the first and second column. Any other column
is treated as an extra variable and will be used to plot a figure.
If :attr:`var` is not `None`, its content will be used as plotting
variables.
:param str fname: name of mesh file.
:param array_like var: data to be plotted shape (n_coords, n_vars).
:param list(str) flabels: names of the variables.
:param str fformat: format of the mesh file.
:param str xlabel: name of the x-axis.
:param str ylabel: name of the y-axis.
:param lst(double) vmins: value of the minimal output for data filtering.
:param str output_path: name of the output path.
:returns: figure.
:rtype: Matplotlib figure instances.
"""
# Read the mesh file
io = formater(fformat)
mesh = io.read(fname)
if var is not None:
var = np.asarray(var)
else:
var = mesh[:, 2:]
if flabels is None:
flabels = ['y' + str(i) for i in range(var.shape[1])]
# Input variables
var_len = var.shape[0]
if var_len != len(mesh):
raise ValueError(
'Variable size not equal: Variable {} - Mesh {}'.format(
var_len, len(mesh)))
if vmins is None:
vmins = [None] * var_len
# Meshing with Delaunay triangulation
tri = Triangulation(mesh[:, 0], mesh[:, 1])
# Masking badly shaped triangles at the border of the triangular mesh
mask = TriAnalyzer(tri).get_flat_tri_mask(0.01)
tri.set_mask(mask)
# Loop over input parameters
figs, axs = [], []
for i, _ in enumerate(var[0]):
fig, ax = plt.subplots()
figs.append(fig)
axs.append(ax)
cmap = cm.viridis
cmap.set_bad(alpha=0.0)
cmap.set_under('w', alpha=0.0)
plt.tricontourf(tri,
var[:, i],
antialiased=True,
cmap=cmap,
vmin=vmins[i])
plt.xlabel(xlabel)
plt.ylabel(ylabel)
plt.tick_params(axis='x')
plt.tick_params(axis='y')
cbar = plt.colorbar()
cbar.set_label(flabels[i])
cbar.ax.tick_params()
bat.visualization.save_show(output_path, figs, extend='neither')
return figs, axs
def extract_wlv(storm,
datafile1,
stations,
df,
lonmin=None,
lonmax=None,
latmin=None,
latmax=None):
print('Reading', datafile1)
#Single file netCDF reading
#ncf='ww3.field.2018_wnd.nc'
ncf = datafile1
nco = netCDF4.Dataset(ncf)
#ncf2='ww3.field.2018_dp.nc'
#ncf2=datafile2
#nco2=netCDF4.Dataset(ncf2)
#Get fields to plot
lon = nco.variables['x'][:]
lat = nco.variables['y'][:]
pnt_lon = stations.iloc[0, :].values
pnt_lat = stations.iloc[1, :].values
timeinsec = nco.variables['time'][:]
#base_date=nco.variables['time:base_date']
#print(base_date)
wlv = nco.variables['zeta'][:]
triangles = nco.variables['element'][:, :]
#timeindays2=nco2.variables['time'][:]
#dir=nco2.variables['dp'][:]
if lonmin != None:
reflon = np.linspace(lonmin, lonmax, 1000)
reflat = np.linspace(latmin, latmax, 1000)
else:
reflon = np.linspace(lon.min(), lon.max(), 1000)
reflat = np.linspace(lat.min(), lat.max(), 1000)
reflon, reflat = np.meshgrid(reflon, reflat)
flatness = 0.10 # flatness is from 0-.5 .5 is equilateral triangle
triangles = triangles - 1 # Correct indices for Python's zero-base
tri = Triangulation(lon, lat, triangles=triangles)
mask = TriAnalyzer(tri).get_flat_tri_mask(flatness)
tri.set_mask(mask)
#Read obs point locations
#data=np.loadtxt('erie_ndbc.loc', comments = '$')
#buoylon=data[:,0]
#buoylat=data[:,1]
df_dates = pd.DataFrame(columns=['Date'])
# Loop through each time step and plot results
for ind in range(0, len(timeinsec)):
#plt.clf()
#ax = plt.axes(projection=ccrs.Mercator())
dt = base_info.tide_spin_start_date + datetime.timedelta(
seconds=timeinsec[ind])
dstr = datetime.date.strftime(dt, '%Y%m%d%H:%M:%S')
dstr = dstr[0:8] + ' ' + dstr[8:17]
print('Plotting ' + dstr)
par = np.double(wlv[ind, :])
tli = LinearTriInterpolator(tri, par)
par_interp = tli(pnt_lon, pnt_lat)
#print(par_interp)
df.loc[len(df)] = par_interp
df_dates.loc[len(df_dates)] = pd.to_datetime(
dt, format="%Y-%m-%d %H:%M:%S")
#line = pd.to_datetime(dt, format="%Y-%m-%d %H:%M:%S")
#new_row = pd.DataFrame(par_interp, columns=stations.columns, index=line)
#df = pd.concat([df, pd.DataFrame(new_row)], ignore_index=False)
del (par)
del (par_interp)
df['Date'] = df_dates
df.set_index('Date', inplace=True)
return df
def spatial_autocorr_fft(tri,
U,
V,
N_grid=512,
auto=False,
transform=False,
tree=None,
interp='Lanczos'):
"""
Function to estimate autocorrelation from a single increment in cartesian
coordinates(tau, eta)
Input:
-----
tri - Delaunay triangulation object of unstructured grid.
N_grid - Squared, structured grid resolution to apply FFT.
U, V - Arrays with cartesian components of wind speed.
Output:
------
r_u,r_v - 2D arrays with autocorrelation function rho(tau,eta)
for U and V, respectively.
"""
if transform:
U_mean = avetriangles(np.c_[tri.x, tri.y], U, tri)
V_mean = avetriangles(np.c_[tri.x, tri.y], V, tri)
# Wind direction
gamma = np.arctan2(V_mean, U_mean)
# Components in matrix of coefficients
S11 = np.cos(gamma)
S12 = np.sin(gamma)
T = np.array([[S11, S12], [-S12, S11]])
vel = np.array(np.c_[U, V]).T
vel = np.dot(T, vel)
X = np.array(np.c_[tri.x, tri.y]).T
X = np.dot(T, X)
U = vel[0, :]
V = vel[1, :]
tri = Triangulation(X[0, :], X[1, :])
mask = TriAnalyzer(tri).get_flat_tri_mask(.05)
tri = Triangulation(tri.x, tri.y, triangles=tri.triangles[~mask])
U_mean = avetriangles(np.c_[tri.x, tri.y], U, tri)
V_mean = avetriangles(np.c_[tri.x, tri.y], V, tri)
else:
# Demeaning
U_mean = avetriangles(np.c_[tri.x, tri.y], U, tri)
V_mean = avetriangles(np.c_[tri.x, tri.y], V, tri)
grid = np.meshgrid(np.linspace(np.min(tri.x), np.max(tri.x), N_grid),
np.linspace(np.min(tri.y), np.max(tri.y), N_grid))
U = U - U_mean
V = V - V_mean
# Interpolated values of wind field to a squared structured grid
if interp == 'cubic':
U_int = CubicTriInterpolator(tri, U)(grid[0].flatten(),
grid[1].flatten()).data
V_int = CubicTriInterpolator(tri, V)(grid[0].flatten(),
grid[1].flatten()).data
U_int = np.reshape(U_int, grid[0].shape)
V_int = np.reshape(V_int, grid[0].shape)
else:
# U_int= lanczos_int_sq(grid,tree,U)
# V_int= lanczos_int_sq(grid,tree,V)
U_int = LinearTriInterpolator(tri, U)(grid[0].flatten(),
grid[1].flatten()).data
V_int = LinearTriInterpolator(tri, V)(grid[0].flatten(),
grid[1].flatten()).data
U_int = np.reshape(U_int, grid[0].shape)
V_int = np.reshape(V_int, grid[0].shape)
#zero padding
U_int[np.isnan(U_int)] = 0.0
V_int[np.isnan(V_int)] = 0.0
fftU = np.fft.fft2(U_int)
fftV = np.fft.fft2(V_int)
if auto:
# Autocorrelation
r_u = np.real(np.fft.fftshift(np.fft.ifft2(np.absolute(fftU)**
2))) / len(U_int.flatten())
r_v = np.real(np.fft.fftshift(np.fft.ifft2(np.absolute(fftV)**
2))) / len(U_int.flatten())
r_uv = np.real(
np.fft.fftshift(np.fft.ifft2(np.real(
fftU * np.conj(fftV))))) / len(U_int.flatten())
dx = np.max(np.diff(grid[0].flatten()))
dy = np.max(np.diff(grid[1].flatten()))
n = grid[0].shape[0]
m = grid[1].shape[0]
# Spectra
fftU = np.fft.fftshift(fftU)
fftV = np.fft.fftshift(fftV)
fftUV = fftU * np.conj(fftV)
Suu = 2 * (np.abs(fftU)**2) * (dx * dy) / (n * m)
Svv = 2 * (np.abs(fftV)**2) * (dx * dy) / (n * m)
Suv = 2 * np.real(fftUV) * (dx * dy) / (n * m)
k1 = np.fft.fftshift((np.fft.fftfreq(n, d=dx)))
k2 = np.fft.fftshift((np.fft.fftfreq(m, d=dy)))
if auto:
return (r_u, r_v, r_uv, Suu, Svv, Suv, k1, k2)
else:
return (Suu, Svv, Suv, k1, k2)
def plot_wlv(storm, datafile1, datafile2=None, lonmin=None, lonmax=None, latmin=None, latmax=None, domain=None):
#Single file netCDF reading
ncf=datafile1
nco=netCDF4.Dataset(ncf)
ncf2=datafile2
nco2=netCDF4.Dataset(ncf2)
#Get fields to plot
lon=nco.variables['longitude'][:]
lat=nco.variables['latitude'][:]
timeindays=nco.variables['time'][:]
wlv=nco.variables['wlv'][:]
triangles=nco.variables['tri'][:,:]
dpt=nco2.variables['dpt'][:]
if lonmin != None:
reflon=np.linspace(lonmin, lonmax, 1000)
reflat=np.linspace(latmin, latmax, 1000)
else:
reflon=np.linspace(lon.min(),lon.max(),1000)
reflat=np.linspace(lat.min(),lat.max(),1000)
reflon,reflat=np.meshgrid(reflon,reflat)
plt.figure(figsize = [6.4, 3.8])
flatness=0.10 # flatness is from 0-.5 .5 is equilateral triangle
triangles=triangles-1 # Correct indices for Python's zero-base
tri=Triangulation(lon,lat,triangles=triangles)
mask = TriAnalyzer(tri).get_flat_tri_mask(flatness)
tri.set_mask(mask)
# Loop through each time step and plot results
for ind in range(0, len(timeindays)):
besttrack = pd.read_csv(PARMnsem+'/storms/'+STORM+'/best_track.txt', header=None, skiprows=4, delim_whitespace=True)
plt.clf()
ax = plt.axes(projection=ccrs.Mercator())
if lonmin != None:
ax.set_extent([lonmin, lonmax, latmin, latmax], crs=ccrs.PlateCarree())
dt = datetime.datetime.combine(datetime.date(1990, 1, 1), datetime.time(0, 0)) + datetime.timedelta(days=timeindays[ind])
dstr = datetime.date.strftime(dt,'%Y%m%d%H:%M:%S')
dstr = dstr[0:8]+' '+dstr[8:17]
print('Plotting '+dstr)
par=np.double(wlv[ind,:])
tli=LinearTriInterpolator(tri,par)
par_interp=tli(reflon,reflat)
plt.pcolormesh(reflon,reflat,par_interp,vmin=-2.0,vmax=2.0, shading='flat',cmap=plt.cm.bwr, transform=ccrs.PlateCarree())
cb = plt.colorbar()
cb.ax.tick_params(labelsize=8)
coast = cfeature.GSHHSFeature(scale='high',edgecolor='black',facecolor='none',linewidth=0.25)
ax.add_feature(coast)
plt.plot(besttrack.iloc[:,3].values, besttrack.iloc[:,2].values, 'k--', linewidth=1.0, transform=ccrs.PlateCarree())
gl = ax.gridlines(crs=ccrs.PlateCarree(), draw_labels=True,
linewidth=2, color='gray', alpha=0.5, linestyle='--')
gl.xlabels_top = False
gl.ylabels_right = False
gl.xlines = False
gl.ylines = False
gl.xformatter = LONGITUDE_FORMATTER
gl.yformatter = LATITUDE_FORMATTER
gl.xlabel_style = {'size': 6, 'color': 'black'}
gl.ylabel_style = {'size': 6, 'color': 'black'}
figtitle = storm.capitalize()+': WL (m MSL): '+dstr
plt.title(figtitle)
dtlabel = datetime.date.strftime(dt,'%Y%m%d%H%M%S')
dtlabel = dtlabel[0:8]+'_'+dtlabel[8:14]
filenm = 'nsem_'+storm+'_wlv_'+dtlabel+'_'+domain+'.png'
plt.savefig(filenm,dpi=150,bbox_inches='tight',pad_inches=0.1)
del(par)
del(par_interp)
CS = ax.tricontour(tri,
z,
breaks,
linewidths=[0.5, 0.25],
colors='saddlebrown')
plt.clabel(CS, inline=5, fontsize=8)
ax.set_ylabel('X[m]')
ax.set_xlabel('Y[m]')
plt.grid()
plt.savefig('plot.png', dpi=300)
plt.show()
# Tworzenie mapy hipsometrycznej
matplotlib.rcParams['contour.negative_linestyle'] = 'solid'
tri = Triangulation(y, x)
mask = TriAnalyzer(tri).get_flat_tri_mask(0.02)
tri.set_mask(mask)
fig, ax = plt.subplots()
fig.set_size_inches(10, 15)
ax.tick_params(labelsize=15)
ax.yaxis.set_major_formatter(FormatStrFormatter('%d'))
ax.xaxis.set_major_formatter(FormatStrFormatter('%d'))
ax.set_aspect('equal')
ax.set_title("Mapa warstwicowa")
CS = ax.tricontourf(tri, z, cmap='RdBu')
ax.tricontour(tri, z, breaks, linewidths=[0.5, 0.25], colors='saddlebrown')
plt.clabel(CS, inline=1, fontsize=10)
ax.set_ylabel('X[m]')
ax.set_xlabel('Y[m]')
plt.grid()
plt.savefig('plotHipso.png', dpi=300)
def plot_cur(storm, datafile1, datafile2=None):
#Single file netCDF reading
ncf=datafile1
nco=netCDF4.Dataset(ncf)
#ncf2=datafile2
#nco2=netCDF4.Dataset(ncf2)
#Get fields to plot
lon=nco.variables['longitude'][:]
lat=nco.variables['latitude'][:]
timeindays=nco.variables['time'][:]
ucur=nco.variables['ucur'][:]
vcur=nco.variables['vcur'][:]
triangles=nco.variables['tri'][:,:]
#timeindays2=nco2.variables['time'][:]
#dir=nco2.variables['dp'][:]
reflon=np.linspace(lon.min(),lon.max(),1000)
reflat=np.linspace(lat.min(),lat.max(),1000)
#reflon=np.linspace(-80.40, -74.75, 1000)
#reflat=np.linspace(32.50, 36.60, 1000)
#reflon=np.linspace(-75.70, -71.05, 1000)
#reflat=np.linspace(38.50, 41.40, 1000)
reflon,reflat=np.meshgrid(reflon,reflat)
plt.figure(figsize = [6.4, 3.8])
flatness=0.10 # flatness is from 0-.5 .5 is equilateral triangle
triangles=triangles-1 # Correct indices for Python's zero-base
tri=Triangulation(lon,lat,triangles=triangles)
mask = TriAnalyzer(tri).get_flat_tri_mask(flatness)
tri.set_mask(mask)
# Loop through each time step and plot results
for ind in range(0, len(timeindays)):
plt.clf()
ax = plt.axes(projection=ccrs.Mercator())
dt = datetime.datetime.combine(datetime.date(1990, 1, 1), datetime.time(0, 0)) + datetime.timedelta(days=timeindays[ind])
dstr = datetime.date.strftime(dt,'%Y%m%d%H:%M:%S')
dstr = dstr[0:8]+' '+dstr[8:17]
print('Plotting '+dstr)
par=np.sqrt( np.square(np.double(ucur[ind,:])) + np.square(np.double(vcur[ind,:])) )
#par2=np.double(dir[ind,:])
tli=LinearTriInterpolator(tri,par)
par_interp=tli(reflon,reflat)
#u=np.cos(np.pi/180*(270-par_interp))
#v=np.sin(np.pi/180*(270-par_interp))
plt.pcolormesh(reflon,reflat,par_interp,vmin=0.0,vmax=2.0,shading='flat',cmap=plt.cm.jet, transform=ccrs.PlateCarree())
#plt.contourf(reflon, reflat, par_interp, vmax=60.0, cmap=plt.cm.jet, transform=ccrs.PlateCarree())
cb = plt.colorbar()
cb.ax.tick_params(labelsize=8)
#rowskip=np.floor(par_interp.shape[0]/25)
#colskip=np.floor(par_interp.shape[1]/25)
rowskip = 50
colskip = 50
#plt.quiver(reflon[0::rowskip,0::colskip],reflat[0::rowskip,0::colskip],\
# u[0::rowskip,0::colskip],v[0::rowskip,0::colskip], \
# scale = 50, color='black',pivot='middle',units='xy',alpha=0.7)
coast = cfeature.GSHHSFeature(scale='high',edgecolor='black',facecolor='none',linewidth=0.25)
ax.add_feature(coast)
plt.xticks(fontsize=9)
plt.yticks(fontsize=9)
figtitle = storm.capitalize()+': Cur (m/s): '+dstr
plt.title(figtitle)
dtlabel = datetime.date.strftime(dt,'%Y%m%d%H%M%S')
dtlabel = dtlabel[0:8]+'_'+dtlabel[8:14]
filenm = 'nsem_'+storm+'_cur_'+dtlabel+'.png'
plt.savefig(filenm,dpi=150,bbox_inches='tight',pad_inches=0.1)
del(par)
del(par_interp)
# meshing with Delaunay triangulation tri = Triangulation(x_test, y_test) ntri = tri.triangles.shape[0] # Some invalid data are masked out mask_init = np.zeros(ntri, dtype=bool) masked_tri = random_gen.randint(0, ntri, int(ntri * init_mask_frac)) mask_init[masked_tri] = True tri.set_mask(mask_init) #----------------------------------------------------------------------------- # Improving the triangulation before high-res plots: removing flat triangles #----------------------------------------------------------------------------- # masking badly shaped triangles at the border of the triangular mesh. mask = TriAnalyzer(tri).get_flat_tri_mask(min_circle_ratio) tri.set_mask(mask) # refining the data refiner = UniformTriRefiner(tri) tri_refi, z_test_refi = refiner.refine_field(z_test, subdiv=subdiv) # analytical 'results' for comparison z_expected = experiment_res(tri_refi.x, tri_refi.y) # for the demo: loading the 'flat' triangles for plot flat_tri = Triangulation(x_test, y_test) flat_tri.set_mask(~mask) #-----------------------------------------------------------------------------
def plot_cur(storm, datafile1, datafile2=None):
#Single file netCDF reading
ncf = datafile1
nco = netCDF4.Dataset(ncf)
#ncf2=datafile2
#nco2=netCDF4.Dataset(ncf2)
#Get fields to plot
lon = nco.variables['longitude'][:]
lat = nco.variables['latitude'][:]
timeindays = nco.variables['time'][:]
ucur = nco.variables['ucur'][:]
vcur = nco.variables['vcur'][:]
triangles = nco.variables['tri'][:, :]
#timeindays2=nco2.variables['time'][:]
#dir=nco2.variables['dp'][:]
reflon = np.linspace(lon.min(), lon.max(), 1000)
reflat = np.linspace(lat.min(), lat.max(), 1000)
#reflon=np.linspace(-80.40, -73.35, 1000)
#reflat=np.linspace(32.50, 39.50, 1000)
reflon, reflat = np.meshgrid(reflon, reflat)
plt.figure(figsize=[6.4, 3.8])
flatness = 0.10 # flatness is from 0-.5 .5 is equilateral triangle
triangles = triangles - 1 # Correct indices for Python's zero-base
tri = Triangulation(lon, lat, triangles=triangles)
mask = TriAnalyzer(tri).get_flat_tri_mask(flatness)
tri.set_mask(mask)
# Loop through each time step and plot results
for ind in range(0, len(timeindays)):
besttrack = pd.read_csv(PARMnsem + '/storms/' + STORM +
'/best_track.txt',
header=None,
skiprows=4,
delim_whitespace=True)
plt.clf()
ax = plt.axes(projection=ccrs.Mercator())
ax.set_extent([-100.00, -50.00, 4.00, 48.00], crs=ccrs.PlateCarree())
#ax.set_extent([-80.40, -73.35, 32.50, 39.50], crs=ccrs.PlateCarree())
dt = base_info.tide_spin_start_date + datetime.timedelta(
days=timeindays[ind])
dstr = datetime.date.strftime(dt, '%Y%m%d%H:%M:%S')
dstr = dstr[0:8] + ' ' + dstr[8:17]
print('Plotting ' + dstr)
par = np.sqrt(
np.square(np.double(ucur[ind, :])) +
np.square(np.double(vcur[ind, :])))
#par2=np.double(dir[ind,:])
tli = LinearTriInterpolator(tri, par)
par_interp = tli(reflon, reflat)
#u=np.cos(np.pi/180*(270-par_interp))
#v=np.sin(np.pi/180*(270-par_interp))
plt.pcolormesh(reflon,
reflat,
par_interp,
vmin=0.0,
vmax=2.0,
shading='flat',
cmap=plt.cm.jet,
transform=ccrs.PlateCarree())
#plt.contourf(reflon, reflat, par_interp, vmax=60.0, cmap=plt.cm.jet, transform=ccrs.PlateCarree())
cb = plt.colorbar()
cb.ax.tick_params(labelsize=8)
#rowskip=np.floor(par_interp.shape[0]/25)
#colskip=np.floor(par_interp.shape[1]/25)
rowskip = 50
colskip = 50
#plt.quiver(reflon[0::rowskip,0::colskip],reflat[0::rowskip,0::colskip],\
# u[0::rowskip,0::colskip],v[0::rowskip,0::colskip], \
# scale = 50, color='black',pivot='middle',units='xy',alpha=0.7)
coast = cfeature.GSHHSFeature(scale='high',
edgecolor='black',
facecolor='none',
linewidth=0.25)
ax.add_feature(coast)
plt.plot(besttrack.iloc[:, 3].values,
besttrack.iloc[:, 2].values,
'k--',
linewidth=1.0,
transform=ccrs.PlateCarree())
gl = ax.gridlines(crs=ccrs.PlateCarree(),
draw_labels=True,
linewidth=2,
color='gray',
alpha=0.5,
linestyle='--')
gl.xlabels_top = False
gl.ylabels_right = False
gl.xlines = False
gl.ylines = False
gl.xformatter = LONGITUDE_FORMATTER
gl.yformatter = LATITUDE_FORMATTER
gl.xlabel_style = {'size': 6, 'color': 'black'}
gl.ylabel_style = {'size': 6, 'color': 'black'}
figtitle = storm.capitalize() + ': Cur (m/s): ' + dstr
plt.title(figtitle)
dtlabel = datetime.date.strftime(dt, '%Y%m%d%H%M%S')
dtlabel = dtlabel[0:8] + '_' + dtlabel[8:14]
filenm = 'nsem_' + storm + '_cur_' + dtlabel + '.png'
plt.savefig(filenm, dpi=150, bbox_inches='tight', pad_inches=0.1)
del (par)
del (par_interp)