def make_scan_plots(self, grid=False, contour=True):
plt.rcParams.update({'font.size': 20})
fig = plt.figure(dpi=600)
if grid:
pts = np.array(list(self.logData.cartesians.keys()))
plt.plot(pts[:, 0], pts[:, 1], 'ok', markersize=1.5)
# plt.close()
if contour:
pts = self.logData.rawenergies
pot = pts[:, 2]
potwv = Constants.convert(pot, "wavenumbers", to_AU=False)
potwv[potwv > 24000] = 24000
plt.tricontourf(pts[:, 0],
pts[:, 1],
potwv,
cmap='viridis',
levels=8)
cb = plt.colorbar()
cb.set_label("Energy ($\mathrm{cm^{-1}}$)")
plt.tricontour(pts[:, 0], pts[:, 1], potwv, colors='k', levels=8)
plt.xlabel("$\mathrm{R_{OO}}$ ($\mathrm{\AA}$)")
plt.ylabel("$\mathrm{r_{XH}}$ ($\mathrm{\AA}$)")
# plt.axis("off")
plt.savefig(
f"{self.fig_dir}/{self.molecule.MoleculeName}_XH_OOpot.png",
dpi=fig.dpi,
bbox_inches="tight")
def my_plot(u,v,t,daystr,levels):
#boston light swim
ax= [-71.10, -70.10, 41.70, 42.70] # region to plot
vel_arrow = 0.2 # velocity arrow scale
subsample = 8 # subsampling of velocity vectors
# find velocity points in bounding box
ind = np.argwhere((lonc >= ax[0]) & (lonc <= ax[1]) & (latc >= ax[2]) & (latc <= ax[3]))
np.random.shuffle(ind)
Nvec = int(len(ind) / subsample)
idv = ind[:Nvec]
# tricontourf plot of water depth with vectors on top
plt.figure(figsize=(20,10))
plt.subplot(111,aspect=(1.0/np.cos(lat[:].mean()*np.pi/180.0)))
#tricontourf(tri, t,levels=levels,shading='faceted',cmap=plt.cm.gist_earth)
plt.tricontourf(tri, t,levels=levels,shading='faceted')
plt.axis(ax)
plt.gca().patch.set_facecolor('0.5')
cbar=plt.colorbar()
cbar.set_label('Forecast Surface Temperature (C)', rotation=-90)
plt.tricontour(tri, t,levels=[0])
Q = plt.quiver(lonc[idv],latc[idv],u[idv],v[idv],scale=10)
maxstr='%3.1f m/s' % vel_arrow
qk = plt.quiverkey(Q,0.92,0.08,vel_arrow,maxstr,labelpos='W')
plt.title('NECOFS Surface Velocity, Layer %d, %s UTC' % (ilayer, daystr))
plt.plot(lon_track,lat_track,'m-o')
plt.plot(lon_buoy,lat_buoy,'y-o')
def plot_surfaces(data, show_samples=False, path=""):
alpha_x = data[:, 0]
alpha_y = data[:, 1]
losses = data[:, 2]
accs = data[:, 3]
fig, ax = plt.subplots(figsize=(12, 9))
if show_samples:
plt.plot(alpha_x, alpha_y, 'ko', color='black', ms=2)
# plt.tricontourf(alpha_x, alpha_y, losses, cmap='viridis', levels=np.arange(0.1, 100, 0.5))
CS = plt.tricontour(alpha_x, alpha_y, losses, cmap='viridis', levels=np.arange(0.1, 10, 0.5))
plt.clabel(CS, inline=1, fontsize=8)
plt.xlim(-1, 1)
plt.ylim(-1, 1)
plt.tick_params(labelsize=12)
plt.tight_layout()
plt.savefig(path + "_loss_landscape.pdf" if path else "loss_landscape.pdf", format='pdf', dpi=1200)
fig, ax = plt.subplots(figsize=(12, 9))
if show_samples:
plt.plot(alpha_x, alpha_y, 'ko', color='black', ms=2)
# plt.tricontourf(alpha_x, alpha_y, accs, cmap='plasma', levels=np.arange(0.01, 1, 0.05))
CS = plt.tricontour(alpha_x, alpha_y, accs, cmap='plasma', levels=np.arange(1, 100, 5))
plt.clabel(CS, inline=1, fontsize=8)
plt.xlim(-1, 1)
plt.ylim(-1, 1)
plt.tick_params(labelsize=12)
plt.tight_layout()
plt.savefig(path + "_accuracy_landscape.pdf" if path else "accuracy_landscape.pdf", format='pdf', dpi=1200)
def plot_frame(df, datforfig, frame):
"""Generates the figure"""
xyzdat, fitraveled, diff = datforfig
extx = (np.min(xyzdat[0]), np.max(xyzdat[0]), np.min(xyzdat[1]), np.max(xyzdat[1]))
fig = plt.figure(figsize=(8,3))
plt.subplot(1, 2, 1)
contour_plot(df)
plt.tricontour(xyzdat[0], xyzdat[1], fitraveled, 5, extent=extx, linewidths=1, colors='k')
plt.title('Fit')
x1d, y1d, z2draw = df_separate(df)
z2d = np.reshape(diff, (len(y1d), len(x1d)))
diffdf = df_join(x1d, y1d, z2d.transpose())
plt.subplot(1, 2, 2)
contour_plot(diffdf)
plt.title('Difference')
plt.subplots_adjust(top=0.8, bottom=0.196, left=0.138, right=0.898, hspace=0.2, wspace=0.55)
fig.patch.set_facecolor('w')
plt.suptitle(str(frame), verticalalignment = 'top')
plt.show()
return fig
def test_tri_smooth_gradient():
# Image comparison based on example trigradient_demo.
def dipole_potential(x, y):
""" An electric dipole potential V """
r_sq = x**2 + y**2
theta = np.arctan2(y, x)
z = np.cos(theta) / r_sq
return (np.max(z) - z) / (np.max(z) - np.min(z))
# Creating a Triangulation
n_angles = 30
n_radii = 10
min_radius = 0.2
radii = np.linspace(min_radius, 0.95, n_radii)
angles = np.linspace(0, 2 * np.pi, n_angles, endpoint=False)
angles = np.repeat(angles[..., np.newaxis], n_radii, axis=1)
angles[:, 1::2] += np.pi / n_angles
x = (radii * np.cos(angles)).flatten()
y = (radii * np.sin(angles)).flatten()
V = dipole_potential(x, y)
triang = mtri.Triangulation(x, y)
xmid = x[triang.triangles].mean(axis=1)
ymid = y[triang.triangles].mean(axis=1)
mask = np.where(xmid * xmid + ymid * ymid < min_radius * min_radius, 1, 0)
triang.set_mask(mask)
# Refine data - interpolates the electrical potential V
refiner = mtri.UniformTriRefiner(triang)
tri_refi, z_test_refi = refiner.refine_field(V, subdiv=3)
# Computes the electrical field (Ex, Ey) as gradient of -V
tci = mtri.CubicTriInterpolator(triang, -V)
(Ex, Ey) = tci.gradient(triang.x, triang.y)
E_norm = np.sqrt(Ex**2 + Ey**2)
# Plot the triangulation, the potential iso-contours and the vector field
plt.figure()
plt.gca().set_aspect('equal')
plt.triplot(triang, color='0.8')
levels = np.arange(0., 1., 0.01)
cmap = cm.get_cmap(name='hot', lut=None)
plt.tricontour(tri_refi,
z_test_refi,
levels=levels,
cmap=cmap,
linewidths=[2.0, 1.0, 1.0, 1.0])
# Plots direction of the electrical vector field
plt.quiver(triang.x,
triang.y,
Ex / E_norm,
Ey / E_norm,
units='xy',
scale=10.,
zorder=3,
color='blue',
width=0.007,
headwidth=3.,
headlength=4.)
def draw_nodal_values_contour(values,
coords,
edof,
levels=12,
title=None,
dofs_per_node=None,
el_type=None,
draw_elements=False):
"""Draws element nodal values as filled contours. Element topologies
supported are triangles, 4-node quads and 8-node quads."""
edof_tri = topo_to_tri(edof)
ax = plt.gca()
ax.set_aspect('equal')
x, y = coords.T
v = np.asarray(values)
plt.tricontour(x, y, edof_tri - 1, v.ravel(), levels)
if draw_elements:
if dofs_per_node != None and el_type != None:
draw_mesh(coords,
edof,
dofs_per_node,
el_type,
color=(0.2, 0.2, 0.2))
else:
info(
"dofs_per_node and el_type must be specified to draw the mesh."
)
if title != None:
ax.set(title=title)
def plot_patch(mesh_container, x, d, vmin=0, vmax=1, contours=True):
px = zkronv(tt.xfun(2, d), tt.ones(2, d))
py = zkronv(tt.ones(2, d), tt.xfun(2, d))
px = px.full().flatten('F').astype(np.int)
py = py.full().flatten('F').astype(np.int)
pts = np.array([mesh_container._pts(ex, ey) for ex, ey in zip(px, py)])
tri = Delaunay(pts)
plt.tripcolor(pts[:, 0],
pts[:, 1],
tri.simplices.copy(),
x,
shading='gouraud',
vmin=vmin,
vmax=vmax)
if contours:
plt.tricontour(pts[:, 0],
pts[:, 1],
tri.simplices.copy(),
x,
np.linspace(vmin, vmax, 11),
colors='k')
d = mesh_container.d
p1 = mesh_container._pts(0, 0)
p2 = mesh_container._pts(2**d - 1, 0)
p3 = mesh_container._pts(2**d - 1, 2**d - 1)
p4 = mesh_container._pts(0, 2**d - 1)
plt.plot([p1[0], p2[0], p3[0], p4[0]], [p1[1], p2[1], p3[1], p4[1]], 'm')
def plot(filename):
import os
from matplotlib.pyplot import clf, tricontour, tricontourf, \
gca, savefig, rc, minorticks_on
if not os.path.exists(filename):
return -1
rc('text', usetex=True)
clf()
x, y, tri, ux, uy = load_velocity(filename)
tricontourf(x, y, tri, ux, 16)
tricontour(x, y, tri, ux, 16, linestyles='-',
colors='black', linewidths=0.5)
minorticks_on()
gca().set_aspect('equal')
gca().tick_params(direction='out', which='both')
gca().set_xticklabels([])
gca().set_yticklabels([])
name, _ = os.path.splitext(filename)
name = os.path.basename(name)
savefig('{0}.png'.format(name), dpi=300, bbox_inches='tight')
savefig('{0}.pdf'.format(name), bbox_inches='tight')
def plot2():
with open("data_plate_thing.txt", 'r') as f:
s = f.read().splitlines()
non_zero_data = np.array(
[split_line(line) for line in s[1:] if split_line(line)[8] != 0])
min_char_interval = non_zero_data[:, 0]
max_char_interval = non_zero_data[:, 1]
min_plate_interval = non_zero_data[:, 2]
max_plate_interval = non_zero_data[:, 3]
tempo = non_zero_data[:, 4]
acertos = non_zero_data[:, 8]
# Definição dos objetos de triangulação para plotagem
triang = tri.Triangulation(min_plate_interval, max_plate_interval)
# Plot 1 - Curvas de nível
plt.subplot(1, 2, 2)
# plt.gca().set_aspect('equal')
plt.tricontourf(triang,
acertos,
levels=np.linspace(np.min(acertos), np.max(acertos), 30))
plt.colorbar()
plt.tricontour(triang, acertos, colors='k')
def drawplot(filein, fileout, model, offtot=0, offBs=0, offRK=0):
'''
Draw the plot using shaded areas for the global fit and contour lines for Bs-only and RK-only fits
'''
fig = texfig.figure()
trgtot, ztot = triang(readfile(filein, -1, 9, offtot))
plt.tricontourf(trgtot,
ztot,
levels=[0.0, 1.0, 4.0, 9.0],
colors=('#00B400', '#00FF00', '#BFFF80'))
trgBs, zBs = triang(readfile(filein, -2, 6, offBs))
plt.tricontour(trgBs,
zBs,
levels=[1.0, 4.0],
colors='b',
linestyles=('-', '--'))
trgRK, zRK = triang(readfile(filein, -3, 6, offRK))
plt.tricontour(trgRK,
zRK,
levels=[1.0, 4.0],
colors='#800000',
linestyles=('-.', ':'))
if model == 'LQ':
plt.xlabel(r"$M_{S_3} [\mathrm{TeV}]$")
plt.ylabel(r'$\mathrm{Im}\ y^{QL}_{32}y^{QL*}_{32}$')
if model == 'Z':
plt.xlabel(r"$M_{Z'} [\mathrm{TeV}]$")
plt.ylabel(r'$\mathrm{Im}\ \lambda^Q_{23}$')
texfig.savefig(fileout)
def plot(self, N=6, cm=plt.cm.jet):
plt.figure()
plt.gca().set_aspect('equal')
plt.tricontourf(self.triang, self.density, N, cm=cm)
plt.colorbar()
plt.tricontour(self.triang, self.density, N, colors='k')
plt.show()
def plot_tricontour(self):
# tricontour.
x = self._x
y = self._y
z = self._z
n_labels = self._n_labels
zi = self._zi
x_min = self._x_min
y_min = self._y_min
x_max = self._x_max
y_max = self._y_max
title = self._title
x_label = self._x_label
y_label = self._y_label
plt.subplot(111) # change this if you want to plot both
triang = tri.Triangulation(x, y)
plt.tricontour(x, y, z, n_labels, linewidths=0.5, colors='k')
plt.tricontourf(x,
y,
z,
n_labels,
cmap=plt.cm.rainbow,
norm=plt.normalize(vmax=abs(zi).max(),
vmin=-abs(zi).max()))
plt.colorbar()
plt.plot(x, y, 'ko', ms=3)
plt.xlim(x_min, x_max)
plt.ylim(y_min, y_max)
plt.xlabel(x_label)
plt.ylabel(y_label)
plt.title(title)
print('tricontour plotted')
def plot(self, N=6, cm=plt.cm.jet):
plt.figure()
plt.gca().set_aspect('equal')
plt.tricontourf(self.triang, self.density, N, cm=cm)
plt.colorbar()
plt.tricontour(self.triang, self.density, N, colors='k')
plt.show()
def test_tri_smooth_gradient():
# Image comparison based on example trigradient_demo.
def dipole_potential(x, y):
""" An electric dipole potential V """
r_sq = x ** 2 + y ** 2
theta = np.arctan2(y, x)
z = np.cos(theta) / r_sq
return (np.max(z) - z) / (np.max(z) - np.min(z))
# Creating a Triangulation
n_angles = 30
n_radii = 10
min_radius = 0.2
radii = np.linspace(min_radius, 0.95, n_radii)
angles = np.linspace(0, 2 * np.pi, n_angles, endpoint=False)
angles = np.repeat(angles[..., np.newaxis], n_radii, axis=1)
angles[:, 1::2] += np.pi / n_angles
x = (radii * np.cos(angles)).flatten()
y = (radii * np.sin(angles)).flatten()
V = dipole_potential(x, y)
triang = mtri.Triangulation(x, y)
xmid = x[triang.triangles].mean(axis=1)
ymid = y[triang.triangles].mean(axis=1)
mask = np.where(xmid * xmid + ymid * ymid < min_radius * min_radius, 1, 0)
triang.set_mask(mask)
# Refine data - interpolates the electrical potential V
refiner = mtri.UniformTriRefiner(triang)
tri_refi, z_test_refi = refiner.refine_field(V, subdiv=3)
# Computes the electrical field (Ex, Ey) as gradient of -V
tci = mtri.CubicTriInterpolator(triang, -V)
(Ex, Ey) = tci.gradient(triang.x, triang.y)
E_norm = np.sqrt(Ex ** 2 + Ey ** 2)
# Plot the triangulation, the potential iso-contours and the vector field
plt.figure()
plt.gca().set_aspect("equal")
plt.triplot(triang, color="0.8")
levels = np.arange(0.0, 1.0, 0.01)
cmap = cm.get_cmap(name="hot", lut=None)
plt.tricontour(tri_refi, z_test_refi, levels=levels, cmap=cmap, linewidths=[2.0, 1.0, 1.0, 1.0])
# Plots direction of the electrical vector field
plt.quiver(
triang.x,
triang.y,
Ex / E_norm,
Ey / E_norm,
units="xy",
scale=10.0,
zorder=3,
color="blue",
width=0.007,
headwidth=3.0,
headlength=4.0,
)
def genPredPlot(X, Y):
plt.style.use('bmh')
feature1, feature2 = X[:, 1], X[:, 2]
feature1Neg = [
feature1.item(i) for i in range(Y.shape[1]) if Y.item(i) == 0
]
feature1Pos = [
feature1.item(i) for i in range(Y.shape[1]) if Y.item(i) == 1
]
feature2Neg = [
feature2.item(i) for i in range(Y.shape[1]) if Y.item(i) == 0
]
feature2Pos = [
feature2.item(i) for i in range(Y.shape[1]) if Y.item(i) == 1
]
# plot scatters of original data
plt.subplot(2, 1, 1)
negPlot, = plt.plot(feature1Neg, feature2Neg, 'bo')
posPlot, = plt.plot(feature1Pos, feature2Pos, 'ro')
xAxis = np.linspace(np.min(feature1) - 1, np.max(feature1) + 1, num=11)
# generate samples of theta
sampleSize = 8000
thetas = generateSamplesMat(
[theta_opt.item(i) for i in range(theta_opt.shape[0])],
np.linalg.inv(hessian_opt), sampleSize)
# plot predicted boundary
XPredMat = 7 * np.random.rand(10000, 2) - 3
X_bias = np.hstack((np.ones((XPredMat.shape[0], 1)), XPredMat)).transpose()
yPred = predict(X_bias, np.matrix(thetas))
n_levels = 20
levels = np.linspace(1.1 * np.min(yPred), 1.1 * np.max(yPred), n_levels)
plt.tricontour(X_bias[1, :],
X_bias[2, :],
[yPred.item(i) for i in range(yPred.shape[1])],
levels=levels)
plt.axis([
1.1 * np.min(feature1), 1.1 * np.max(feature1), 1.1 * np.min(feature2),
1.1 * np.max(feature2)
])
plt.xlabel('hours studied')
plt.ylabel('grade in class')
plt.legend((negPlot, posPlot), ('failed', 'passed'), loc=3)
plt.title('Posterior Predictive Distribution')
plt.subplot(2, 1, 2)
value = sigmoid(theta_opt.transpose() * X_bias) - yPred
plt.hist([value.item(i) for i in range(value.shape[1])], bins=100)
plt.title('Histogram of Prediction Difference in MCMC and MAP')
plt.savefig('p3.pdf', format='pdf')
plt.tight_layout()
plt.show()
def _add_SSE_contour(x, y, color, label, columns, SSE, compare):
ax = plt.gca()
xvar, yvar, loc = _get_variables(ax, columns)
x = SSE[xvar]
y = SSE[yvar]
z = SSE['SSE']
triang = tri.Triangulation(x, y)
plt.tricontour(triang, z, [compare], colors='r')
def _add_LR_contour(x,y,color,label,columns,data,theta_star,threshold):
ax = plt.gca()
xvar, yvar, loc = _get_variables(ax,columns)
X, Y, Z = _get_data_slice(xvar,yvar,columns,data,theta_star)
triang = tri.Triangulation(X, Y)
plt.tricontour(triang,Z,[threshold], colors='r')
def main():
loaded_matrix = unpickle_elevation_matrix("matrix_pickle_k2.bin")
x, y, z = convert_matrix(loaded_matrix, 300)
plot_mlab(x, y, z)
plt.tricontour(x.ravel(), y.ravel(), z.ravel(), 100)
plt.show()
print("stop")
def _add_LR_contour(x, y, color, label, columns, data, theta_star, threshold):
ax = plt.gca()
xvar, yvar, loc = _get_variables(ax, columns)
X, Y, Z = _get_data_slice(xvar, yvar, columns, data, theta_star)
triang = tri.Triangulation(X, Y)
plt.tricontour(triang, Z, [threshold], colors='r')
def plot_surf_disp(m,
side,
field,
name,
vmin=None,
vmax=None,
filename=None,
view_R=1.0,
proj=None,
latlon_step=0.5):
fC, R = get_fault_centered_view(m)
if vmin is None:
vmin = np.min(field)
if vmax is None:
vmax = np.max(field)
cmap = 'PuOr_r'
levels = np.linspace(vmin, vmax, 17)
plt.figure(figsize=(10, 10))
fault_start_idx = m.get_start('fault')
for i in range(2):
which_tris = np.where(
np.logical_or(side[:fault_start_idx] == 0,
side[:fault_start_idx] == i + 1))[0]
reduced_m = mesh_fncs.remove_unused_pts((m.pts, m.tris[which_tris]))
soln_vals = np.empty(reduced_m[0].shape[0])
soln_vals[reduced_m[1]] = field[which_tris]
triang = tri.Triangulation(reduced_m[0][:, 0],
reduced_m[0][:, 1],
triangles=reduced_m[1])
tri_refi, interp_vals = triang, soln_vals
cntf = plt.tricontourf(tri_refi,
interp_vals,
cmap=cmap,
levels=levels,
extend='both')
plt.tricontour(tri_refi,
interp_vals,
levels=levels,
colors='#333333',
linestyles='solid',
linewidths=0.75)
plot_fault_trace(m)
cbar = plt.colorbar(cntf)
cbar.set_label('$\\text{displacement (m)}$')
map_axis(fC, R, view_R, proj, latlon_step)
plt.title(name)
if filename is not None:
plt.savefig(filename)
plt.show()
def plot_fnc(triang, f):
levels = np.linspace(np.min(f) - 1e-12, np.max(f) + 1e-12, 21)
cntf = plt.tricontourf(triang, f, levels=levels, cmap='RdBu')
plt.tricontour(triang,
f,
levels=levels,
linestyles='solid',
colors='k',
linewidths=0.5)
plt.colorbar(cntf)
def contour(*arguments, **kwargs):
"""Call signatures::
contour(X, Y, C, N, **kwargs)
contour(X, Y, C, V, **kwargs)
Create a contour plot of a 2-D llc array (with tricontour).
*C* is the array of color values.
*N* is the number of levels
*V* is a list of levels
*X* and *Y*, specify the (*x*, *y*) coordinates of
the grid points
**kwargs are passed to tricontour.
"""
arglen = len(arguments)
h = []
if arglen >= 3:
data = arguments[2].flatten()
x = arguments[0].flatten()
y = arguments[1].flatten()
# Create the Triangulation;
# no triangles so Delaunay triangulation created.
triang = tri.Triangulation(x, y)
ntri = triang.triangles.shape[0]
# Mask off unwanted triangles.
mask = np.where(data[triang.triangles].prod(axis=1)==0., 1, 0)
triang.set_mask(mask)
if arglen == 3:
h = plt.tricontour(triang, data, **kwargs)
elif arglen == 4:
h = plt.tricontour(triang, data, arguments[3], **kwargs)
else:
print("wrong number of arguments")
print("need at least 3 or 4 arguments")
sys.exit(__doc__)
# show the triangles for debugging
#plt.triplot(triang, color='0.7')
else:
print("wrong number of arguments")
print("need at least x,y,fld")
sys.exit(__doc__)
return h
def contour(*arguments, **kwargs):
"""Call signatures::
contour(X, Y, C, N, **kwargs)
contour(X, Y, C, V, **kwargs)
Create a contour plot of a 2-D llc array (with tricontour).
*C* is the array of color values.
*N* is the number of levels
*V* is a list of levels
*X* and *Y*, specify the (*x*, *y*) coordinates of
the grid points
**kwargs are passed to tricontour.
"""
arglen = len(arguments)
h = []
if arglen >= 3:
data = arguments[2].flatten()
x = arguments[0].flatten()
y = arguments[1].flatten()
# Create the Triangulation;
# no triangles so Delaunay triangulation created.
triang = tri.Triangulation(x, y)
ntri = triang.triangles.shape[0]
# Mask off unwanted triangles.
mask = np.where(data[triang.triangles].prod(axis=1) == 0., 1, 0)
triang.set_mask(mask)
if arglen == 3:
h = plt.tricontour(triang, data, **kwargs)
elif arglen == 4:
h = plt.tricontour(triang, data, arguments[3], **kwargs)
else:
print("wrong number of arguments")
print("need at least 3 or 4 arguments")
sys.exit(__doc__)
# show the triangles for debugging
#plt.triplot(triang, color='0.7')
else:
print("wrong number of arguments")
print("need at least x,y,fld")
sys.exit(__doc__)
return h
def CreateFig(dt_output=0.1):
from tables import open_file
archive = open_file('dambreak.h5','r')
import dambreak
dambreak.outputStepping.dt_output=dt_output
dambreak.outputStepping.nDTout=None
dambreak.outputStepping.setOutputStepping()
dambreak.myTpFlowProblem.initializeAll()
import matplotlib.tri as mtri
from matplotlib import pyplot as plt
import numpy as np
domain = dambreak.domain
domain.L = dambreak.tank_dim
domain.x = (0.,0.,0.)
nodes = archive.get_node("/nodesSpatial_Domain0")
x=nodes[:,0]
y=nodes[:,1]
elements = archive.get_node("/elementsSpatial_Domain0")
triang = mtri.Triangulation(x, y, elements)
xg = np.linspace(0, domain.L[0], 20)
yg = np.linspace(0, domain.L[1], 20)
xi, yi = np.meshgrid(xg,yg)
plt.figure()
for it,t in enumerate(dambreak.myTpFlowProblem.so.tnList[:]):
phi = archive.get_node("/phi_t{0:d}".format(it))
vof = archive.get_node("/vof_t{0:d}".format(it))
wvof = np.ones(vof.shape,'d')
wvof -= vof
u = archive.get_node("/u_t{0:d}".format(it))
v = archive.get_node("/v_t{0:d}".format(it))
plt.clf()
plt.xlabel(r'z[m]')
plt.ylabel(r'x[m]')
colors = ['w','b', 'g','r','c','m','y','k']*(max(domain.segmentFlags)//8 + 1)
plt.xlim(domain.x[0]-0.1*domain.L[0],domain.x[0]+domain.L[0]+0.1*domain.L[0])
for si,s in enumerate(domain.segments):
plt.plot([domain.vertices[s[0]][0],
domain.vertices[s[1]][0]],
[domain.vertices[s[0]][1],
domain.vertices[s[1]][1]],
color=colors[domain.segmentFlags[si]-1],
linewidth=2,
marker='o')
plt.tricontourf(x,y,elements,wvof*np.sqrt(u[:]**2 + v[:]**2))
plt.tricontour(x,y,elements,phi,[0], linewidths=4)
u_interp_lin = mtri.LinearTriInterpolator(triang, u[:])
v_interp_lin = mtri.LinearTriInterpolator(triang, v[:])
u_lin = u_interp_lin(xi, yi)
v_lin = v_interp_lin(xi, yi)
plt.streamplot(xg, yg, u_lin, v_lin,color='k')
plt.title('T={0:2.2f}'.format(t))
plt.axis('equal')
plt.xlim((0,domain.L[0]))
plt.savefig('phi{0:04d}.png'.format(it))
def contour(self, *args, **kwargs):
""" Show contours of values."""
fig, ax = plt.subplots(figsize=settings["figsize"])
# Projection circle
ax.text(0, 1.02, "N", ha="center", va="baseline", fontsize=16)
ax.add_artist(plt.Circle((0, 0), 1, color="w", zorder=0))
ax.add_artist(plt.Circle((0, 0), 1, color="None", ec="k", zorder=3))
ax.set_aspect("equal")
plt.tricontour(self.triang, self.values, *args, **kwargs)
plt.colorbar()
plt.axis('off')
plt.show()
def CreateFig():
from tables import openFile
archive = openFile('linear_waves.h5','r')
import linear_waves
import linear_waves_so
import matplotlib.tri as mtri
from matplotlib import pyplot as plt
import numpy as np
domain = linear_waves.domain
nodes = archive.getNode("/nodesSpatial_Domain0")
x=nodes[:,0]
y=nodes[:,1]
elements = archive.getNode("/elementsSpatial_Domain0")
triang = mtri.Triangulation(x, y, elements)
domain.L=linear_waves.tank_dim
domain.x=[0.,0.]
xg = np.linspace(0, domain.L[0], 20)
yg = np.linspace(0, domain.L[1], 20)
xi, yi = np.meshgrid(xg,yg)
plt.figure()
for it,t in enumerate(linear_waves_so.tnList[:]):
phi = archive.getNode("/phi_t"+`it`)
vof = archive.getNode("/vof_t"+`it`)
wvof = np.ones(vof.shape,'d')
wvof -= vof
u = archive.getNode("/u_t"+`it`)
v = archive.getNode("/v_t"+`it`)
plt.clf()
plt.xlabel(r'z[m]')
plt.ylabel(r'x[m]')
colors = ['b','g','r','c','m','y','k','w']
plt.xlim(domain.x[0]-0.1*domain.L[0],domain.x[0]+domain.L[0]+0.1*domain.L[0])
for si,s in enumerate(domain.segments):
plt.plot([domain.vertices[s[0]][0],
domain.vertices[s[1]][0]],
[domain.vertices[s[0]][1],
domain.vertices[s[1]][1]],
color=colors[domain.segmentFlags[si]-1],
linewidth=2,
marker='o')
plt.tricontourf(x,y,elements,wvof*np.sqrt(u[:]**2 + v[:]**2))
plt.tricontour(x,y,elements,phi,[0], linewidth=4)
u_interp_lin = mtri.LinearTriInterpolator(triang, u[:])
v_interp_lin = mtri.LinearTriInterpolator(triang, v[:])
u_lin = u_interp_lin(xi, yi)
v_lin = v_interp_lin(xi, yi)
plt.streamplot(xg, yg, u_lin, v_lin,color='k')
plt.title('T=%2.2f' % (t,))
plt.xlim((0,domain.L[0]))
plt.ylim(0,domain.L[1])
plt.savefig('phi%4.4d.png' % (it,))
def stab_plot(self):
x = self.x
y = self.y
z = self.z
# initialize the delauney triangulation:
triang = tri.Triangulation(x, y)
# do the plots:
plt.tricontourf(triang, z, colors=self.color, alpha=0.3, levels=[1.0, 2.0])
plt.tricontour(triang, z, colors=self.color, levels=[1.0, 2.0])
# title of the plot
plt.title("Stability of " + self.model_name, fontsize=16)
# labels
plt.xlabel(self.param_names[0], fontsize=18)
plt.ylabel(self.param_names[1], fontsize=18)
def plotResult(self, **k):
x = []
y = []
z = []
for n in self.nodes:
x.append(n.x)
y.append(n.y)
z.append(k['r'][n.i-1])
t = tri.Triangulation(x, y)
plt.tricontour(t, z, 15, linewidths=0.5)
#plt.tricontourf(t, z, 15, cmap=plt.cm.rainbow)
plt.colorbar()
#plt.plot(x, y, 'ko', ms=3)
def plotcontour(md, par, **kwargs):
if hasattr(md.results, 'TransientSolution'):
if hasattr(md.results.TransientSolution[-1], 'catch_mesh'):
lens = []
for q in range(len(md.results.TransientSolution[-1].catch_mesh)):
lens.append(
len(md.results.TransientSolution[-1].catch_mesh[q][0]))
try:
tricontour(md.mesh.x, md.mesh.y, np.squeeze(par), **kwargs)
except:
right_index = int(
np.nonzero(lens == np.intersect1d(lens, len(par)))[0])
tricontour(md.results.TransientSolution[-1].catch_mesh[right_index][0],
md.results.TransientSolution[-1].catch_mesh[right_index][1],
np.squeeze(par), **kwargs)
def splineContourPlot(self,
cmap='twilight_shifted',
save=False,
axis=False,
showLift=False,
lvs=40):
# Visualizza curve di livello su grafico 2D della superficie B-spline.
# showLift: se true mostra i triangoli di sollevamento utilizzati nella costruzione della superficie;
# lvs: numero di livelli da mostrare.
if not axis:
plt.axis('off')
plt.axis('equal')
# Settaggio dei livelli.
(mn, mx) = (min(self.plotHeights), max(self.plotHeights))
tol = 6e-3
if mn < -tol:
lvs = int(lvs / 2)
levels = np.block(
[np.linspace(mn, -tol, lvs),
np.linspace(tol, mx, lvs)])
else:
levels = np.linspace(tol, mx, lvs)
# Visualizzazione delle curve di livello.
plt.tricontour(self.plotTriangulation,
self.plotHeights,
levels=levels,
cmap=cmap,
linewidths=0.4)
# Visualizzazione del dominio e dei triangoli di sollevamento, se richiesti.
self.domain.domainPlot(labels=False,
legend=False,
showExecute=False,
color='#000000',
colorPS='#000000')
if showLift:
self.lift_triangles.liftPlot(onlyLifts=True,
legend=False,
labels=False,
showExecute=False)
# Salvo l'immagine, se richiesto.
if save:
name = input('Nome del file?\n')
plt.savefig(name, dpi=600)
plt.show()
def computeContours(self):
extend = self.uExtend.itemText(self.uExtend.currentIndex())
data = self.getData()
if not data:
return
x, y, z = data
levels = self.getLevels()
if not levels:
return
try:
if self._isMPLOk(
) == True: # If so, we can use the tricontour function
try:
cs = plt.tricontour(x, y, z, levels, extend=extend)
except:
raise ContourGenerationError()
else:
gx = x.reshape(self._nr, self._nc)
gy = y.reshape(self._nr, self._nc)
gz = z.reshape(self._nr, self._nc)
cs = plt.contour(gx, gy, gz, levels, extend=extend)
except:
raise
lines = list()
levels = [float(l) for l in cs.levels]
for i, line in enumerate(cs.collections):
linestrings = []
for path in line.get_paths():
if len(path.vertices) > 1:
linestrings.append(path.vertices)
lines.append([i, levels[i], linestrings])
self.progressBar.setValue(i + 1)
return lines
def chi_sq_contour(analysis_dict):
plt.figure()
cnorm = mpl.colors.Normalize(vmin=0., vmax=20.) #40.)
x = analysis_dict['r_eff']
y = analysis_dict['COT']
z = analysis_dict['difference']
b = plt.tricontour(x, y, z, 70, norm=cnorm) #70)
plt.xlabel('Cloud Particle Effective Radius (r_eff) (um)', fontsize=18)
plt.ylabel('Cloud Optical Thickness (COT)', fontsize=18)
plt.title(analysis_dict['phase'] +
' Cloud {} Wavelength Retrieval Values'.format(
str(analysis_dict['num_retrieval_wavelengths'])),
fontsize=20)
plt.clabel(b, inline=1, fontsize=15)
reff_best = analysis_dict['best_reff']
COT_best = analysis_dict['best_COT']
label = 'COT: ' + str(round(COT_best,
2)) + ', r_eff: ' + str(reff_best) + 'um'
bbox = dict(boxstyle="round", fc="0.8", alpha=1)
arrow = dict(facecolor='black', shrink=0.05)
plt.annotate(label,[reff_best,COT_best],xytext=(reff_best+2,COT_best+0.5),\
bbox=bbox,fontsize=15,arrowprops=arrow)
plt.scatter(reff_best, COT_best, marker="X", c='k', s=70)
return
def along_width(md, par, **kwargs):
cont = tricontour(md.mesh.x, md.mesh.y, par, **kwargs)
lines = cont.__dict__['allsegs'][0]
if len(lines) == 2:
upper = np.transpose(lines[0])[:, :len(lines[1])]
lower = np.transpose(list(reversed(lines[1])))[:, :len(lines[0])]
width = [(np.array(upper[1]) - np.array(lower[1])), upper[0]]
else:
x_coords = np.transpose(lines)[0]
x_coords = x_coords[:int(len(x_coords) / 2)]
w = np.transpose(lines)[1]
width = [
w[:int(ceil(len(w) / 2))] - w[int(len(w) / 2):len(w)], x_coords
]
width[0] = width[0][:len(width[1])]
width[1] = width[1][:len(width[0])]
return width
def plot_mesh(mesh,
dims=2,
node_labels=False,
vals=None,
with_colorbar=False,
levels=None,
border=None):
if not isinstance(mesh.points, np.ndarray):
mesh.points = np.array(mesh.points)
nodes_x = mesh.points[:, 0]
nodes_y = mesh.points[:, 1]
if dims == 2:
elements_tris = [c for c in mesh.cells if c.type == "triangle"][0].data
#plt.figure(figsize=(8, 8))
if vals is None:
plt.triplot(nodes_x, nodes_y, elements_tris, alpha=0.9, color='r')
else:
triangulation = tri.Triangulation(nodes_x, nodes_y, elements_tris)
p = plt.tricontourf(triangulation, vals, 30)
if with_colorbar: plt.colorbar()
if levels:
cn = plt.tricontour(triangulation, vals, levels, colors='w')
plt.clabel(cn, fmt='%0.2f', colors='k', fontsize=10)
if border:
plt.hlines(1 - border, -1 + border, 1 - border, 'r')
plt.hlines(-1 + border, -1 + border, 1 - border, 'r')
plt.vlines(1 - border, -1 + border, 1 - border, 'r')
plt.vlines(-1 + border, -1 + border, 1 - border, 'r')
if node_labels:
for i, (x, y) in enumerate(zip(nodes_x, nodes_y)):
plt.text(x, y, i)
if vals is not None:
return p
def contour(data, x, y, label=None, log=False):
tri=Triangulation(x,y)
plt.close('all')
plt.figure()
ax=plt.subplot(111)
ax.minorticks_on()
if(log):
ax.set_xscale("log",nonposx='clip')
ax.set_yscale("log",nonposy='clip')
ax.set_xlim([min(x.min(),y.min()),max(x.max(),y.max())])
ax.set_ylim([min(x.min(),y.min()),max(x.max(),y.max())])
plt.xlabel('r [AU]')
plt.ylabel('z [AU]')
nmax=data.max()
nmin=data.min()
levels=np.logspace(np.log10(nmin),np.log10(nmax),num=12)
plt.tricontourf(tri, data, levels, norm=colors.LogNorm(vmin=nmin, vmax=nmax))
cbar=plt.colorbar(format='%.2e')
cbar.set_label(label)
CS=plt.tricontour(tri, data, levels, colors='black', linewidths=1.5)
plt.clabel(CS, fontsize=8, inline=1)
cbar.add_lines(CS)
plt.triplot(tri, color='black', alpha=0.2)
plt.show(block=False)
def plotiso_SubTh2simp2D(q, me, u, **kwargs):
plane = kwargs.pop('plane', True)
niso = kwargs.pop('niso', 15)
isorange = kwargs.pop('isorange', None)
color = check_color(kwargs.pop('color', None))
cmap = kwargs.pop('cmap', plt.cm.get_cmap(name='viridis'))
if isorange is None and niso > 1:
isorange = np.linspace(min(u), max(u), num=niso)
else:
if np.isscalar(isorange):
isorange = np.array([isorange])
else:
isorange = np.sort(isorange)
if color is not None:
kwargs['colors'] = np.tile(color, (len(isorange), 1))
else:
kwargs['cmap'] = cmap
#kwargs['vmin']=kwargs.get('vmin',np.min(u))
#kwargs['vmax']=kwargs.get('vmax',np.max(u))
fig = plt.gcf()
if plane:
return plt.tricontour(
q[:, 0], q[:, 1], me, u, isorange,
**kwargs) #vmin=vmin,vmax=vmax, shading=shading,**kwargs)
nq = q.shape[0]
assert isinstance(u, np.ndarray) and u.shape[0] == nq
Q = np.concatenate((q, u.reshape((nq, 1))), axis=1)
assert False, "Not yet implemented"
return plotiso_SubTh2simp3D(Q, me, u, isorange=isorange, **kwargs)
def update(step_i):
t_step = trajectory[step_i]
t_x = t_step[:, 0]
t_y = t_step[:, 1]
t = np.multiply(t_x, t_y)
cont = plt.tricontour(nodes_x, nodes_y, t)
return cont
def plot_quantity(filename_bin, filename_non, plotnum, qty='vel', limits=[-20, 20]):
hdu_v = fits.open(filename_bin)
hdu = fits.open(filename_non)
data_v = hdu_v[1].data
data = hdu[2].data
if qty == 'vel':
v = data_v['VPXF'] - np.mean(data_v['VPXF'])
elif qty == 'sigma':
v = data_v['SPXF']
elif qty == 'h3':
v = data_v['H3PXF']
else:
v = data_v['H4PXF']
plt.subplot(220 + plotnum)
img = display_bins_generators(data_v['YS'], data_v['XS'], v, data['D'], data['A'], vmin=limits[0], vmax=limits[1], pixelsize=None)
plt.tricontour(data_v['YS'], data_v['XS'], -2.5*np.log10(data_v['FLUX']/np.max(data_v['FLUX'])), levels=np.arange(20), colors='k', linewidths=contourthickness)
if plotnum == 1:
plt.title("$ \langle V \\rangle $ [km/s]", fontsize=titlesize, y=1.04)
plt.ylabel("arcsec", fontsize=textsize)
if plotnum == 2:
plt.title("$\sigma$ [km/s]", fontsize=titlesize, y=1.04)
if plotnum == 3:
plt.title("$h_3$", fontsize=titlesize, y=1.04)
plt.ylabel("arcsec", fontsize=textsize)
plt.xlabel("arcsec", fontsize=textsize)
if plotnum == 4:
plt.title("$h_4$", fontsize=titlesize, y=1.04)
plt.xlabel("arcsec", fontsize=textsize)
ax = plt.gca()
divider = mplax.make_axes_locatable(ax)
cax = divider.append_axes("right", size="5%", pad=0.05)
cticks = np.array([limits[0], np.sum(limits)/2, limits[1]])
cb = plt.colorbar(img, cax = cax, ticks = cticks)
ax.tick_params(direction = 'in', which='both', right=True, top=True, labelleft=False, labelsize=digitsize)
ax.set_aspect('equal')
cax.tick_params(direction = 'in', labelsize=digitsize*1.05)
def contour_paths(self, epsilon):
'''Extract the polygon patches for the provided epsilon'''
figure = pyplot.figure()
contours = pyplot.tricontour(self.triang, self.vals, levels=[epsilon])
paths = Paths()
if len(contours.collections) == 0:
return paths
for path in contours.collections[0].get_paths():
paths.append(Path(path.vertices[:, 0] + 1j*path.vertices[:, 1]))
pyplot.close(figure)
return paths
def plot_contour(self, **kwargs):
"""Contour plot of the xy plane
Parameters
----------
**kwargs
Forwarded to `plt.tricontour()`.
"""
x, y, _ = self.pos
contour = plt.tricontour(x, y, self.data, **kwargs)
self._decorate_plot()
return contour
def test_tri_smooth_contouring():
# Image comparison based on example tricontour_smooth_user.
n_angles = 20
n_radii = 10
min_radius = 0.15
def z(x, y):
r1 = np.sqrt((0.5 - x) ** 2 + (0.5 - y) ** 2)
theta1 = np.arctan2(0.5 - x, 0.5 - y)
r2 = np.sqrt((-x - 0.2) ** 2 + (-y - 0.2) ** 2)
theta2 = np.arctan2(-x - 0.2, -y - 0.2)
z = -(
2 * (np.exp((r1 / 10) ** 2) - 1) * 30.0 * np.cos(7.0 * theta1)
+ (np.exp((r2 / 10) ** 2) - 1) * 30.0 * np.cos(11.0 * theta2)
+ 0.7 * (x ** 2 + y ** 2)
)
return (np.max(z) - z) / (np.max(z) - np.min(z))
# First create the x and y coordinates of the points.
radii = np.linspace(min_radius, 0.95, n_radii)
angles = np.linspace(0 + n_angles, 2 * np.pi + n_angles, n_angles, endpoint=False)
angles = np.repeat(angles[..., np.newaxis], n_radii, axis=1)
angles[:, 1::2] += np.pi / n_angles
x0 = (radii * np.cos(angles)).flatten()
y0 = (radii * np.sin(angles)).flatten()
triang0 = mtri.Triangulation(x0, y0) # Delaunay triangulation
z0 = z(x0, y0)
xmid = x0[triang0.triangles].mean(axis=1)
ymid = y0[triang0.triangles].mean(axis=1)
mask = np.where(xmid * xmid + ymid * ymid < min_radius * min_radius, 1, 0)
triang0.set_mask(mask)
# Then the plot
refiner = mtri.UniformTriRefiner(triang0)
tri_refi, z_test_refi = refiner.refine_field(z0, subdiv=4)
levels = np.arange(0.0, 1.0, 0.025)
plt.triplot(triang0, lw=0.5, color="0.5")
plt.tricontour(tri_refi, z_test_refi, levels=levels, colors="black")
def tricontourf_deformed(a, mesh, d, name, cmap, dpi, magf):
"""Plot contour with the tricoutour function and the boundary line with
the boundary node.
"""
fig = plt.figure(name, dpi=dpi)
ax1 = fig.add_subplot(1, 1, 1, aspect='equal')
c = mesh.nodes_coord
bn = mesh.boundary_nodes
xx, yy, zz = c[:, 0]+d[::2]*magf, c[:, 1]+d[1::2]*magf, a
dx = d[::2]*magf
dy = d[1::2]*magf
ccx = np.append(c[bn[:, 1], 0]+dx[bn[:, 1]], c[bn[0, 1], 0]+dx[bn[0, 1]])
ccy = np.append(c[bn[:, 1], 1]+dy[bn[:, 1]], c[bn[0, 1], 1]+dy[bn[0, 1]])
plt.plot(ccx, ccy, '-k')
triangles = []
for n1, n2, n3, n4 in mesh.ele_conn:
triangles.append([n1, n2, n3])
triangles.append([n1, n3, n4])
triangles = np.asarray(triangles)
CS2 = plt.tricontourf(xx, yy, triangles, zz, N=10, origin='lower',
cmap=cmap)
CS3 = plt.tricontour(xx, yy, triangles, zz, N=10, origin='lower',colors='k')
plt.xlabel(r'$x$', fontsize=14)
plt.ylabel(r'$y$', fontsize=14)
divider = make_axes_locatable(ax1)
cax = divider.append_axes("right", size=0.3, pad=0.1)
cbar = plt.colorbar(CS2, cax=cax)
cbar.ax.set_label(name, fontsize=12)
plt.clabel(CS3, fontsize=8, colors='k', fmt='%1.1f')
limits=plt.axis('off')
# plt.savefig('1.png', transparent=True, dpi=300)
#plt.axes().set_aspect('equal')
#plt.axes().autoscale_view(True, True, True)
plt.draw()
def plot(self, epsilons, **kwargs):
epsilons = list(numpy.sort(epsilons))
padepsilons = [epsilons[0]*0.9] + epsilons + [epsilons[-1]*1.1]
X = []
Y = []
Z = []
for epsilon in padepsilons:
paths = self.contour_paths(epsilon)
for path in paths:
X += list(numpy.real(path.vertices[:-1]))
Y += list(numpy.imag(path.vertices[:-1]))
Z += [epsilon] * (len(path.vertices) - 1)
contours = pyplot.tricontour(X, Y, Z, levels=epsilons,
colors=pyplot.rcParams['axes.color_cycle']
)
plot_finish(contours, **kwargs)
return contours
def contour(self, prop=None):
if(prop=='Tdust'):
data=self.T[0:len(self.x)]['1']
label="Dust temperature [K]"
elif(prop=='rho'):
data=np.log(self.rho[0:len(self.x)]['1'])
label="Log some density [?]"
else:
try:
data=self.prop
label='Unknown property'
except:
print "Please specify property to plot. Valid properties are [Tdust, rho]"
return
x_au = self.x/1.49e13
y_au = self.y/1.49e13
tri=Triangulation(x_au,y_au)
plt.close('all')
plt.figure()
ax=plt.subplot(111)
ax.set_xscale("log",nonposx='clip')
ax.set_yscale("log",nonposy='clip')
ax.set_xlim([0.1,200])
ax.set_ylim([0.1,200])
plt.xlabel('r [AU]')
plt.ylabel('z [AU]')
nmax=data.max()
nmin=data.min()
levels=np.arange(12) * (nmax-nmin)/12. + nmin
plt.tricontourf(tri, data, levels)
cbar=plt.colorbar()
cbar.set_label(label)
CS=plt.tricontour(tri, data, levels, colors='black', linewidths=1.5)
plt.clabel(CS, fontsize=8, inline=1)
cbar.add_lines(CS)
plt.triplot(tri, color='black', alpha=0.2)
def computeContours(self):
extend = str(self.uExtend.itemText(self.uExtend.currentIndex()))
x, y, z = self._data
levels = self.getLevels()
if self._isMPLOk()==True: # If so, we can use the new tricontour fonction
cs = plt.tricontour(x, y, z, levels, extend=extend)
else:
gx = x.reshape(self._nr,self._nc)
gy = y.reshape(self._nr,self._nc)
gz = z.reshape(self._nr,self._nc)
cs = plt.contour(gx, gy, gz, levels, extend=extend)
lines = list()
levels = [float(l) for l in cs.levels]
self.progressBar.setRange(0, len(cs.collections))
for i, line in enumerate(cs.collections):
linestrings = []
for path in line.get_paths():
if len(path.vertices) > 1:
linestrings.append(path.vertices)
lines.append([ i, levels[i], linestrings])
self.progressBar.setValue(i+1)
self.progressBar.setValue(0)
return lines
def lineContourFeatures(self):
x,y,z=self.data()
levels = self.levels()
usegrid=self.isGridded() and self._useGrid
try:
if usegrid:
gx,gy,gz=self.gridContourData()
cs = contour(gx, gy, gz, levels )
else:
trig,z=self.trigContourData()
cs = tricontour(trig, z, levels )
except:
raise ContourGenerationError.fromException(sys.exc_info())
fields = self.fields()
zfield=self.zFieldName()
dx,dy=self._origin
for i, line in enumerate(cs.collections):
level=float(cs.levels[i])
glines = []
try:
for path in line.get_paths():
if len(path.vertices) > 1:
points=[QgsPointXY(x,y) for x,y in path.vertices]
glines.append(points)
geom=QgsGeometry.fromMultiPolylineXY(glines)
geom.translate(dx,dy)
feat = QgsFeature(fields)
feat.setGeometry(geom)
feat['index']=i
feat[zfield]=level
feat['label']=self._levelLabel(level)
yield feat
except:
message=sys.exc_info()[1]
self._feedback.reportError(message)
Xmax, Ymax = X[area_max].flat[amax], Y[area_max].flat[amax]
lsteps_ = int(max(refi_magU[area_max])/lmax*lsteps)
lx = Xmin + np.sign(Xmax-Xmin)*np.linspace(0, abs(Xmax-Xmin)**(1./args.lpow), 1 + lsteps_)**args.lpow
ly = Ymin + np.sign(Ymax-Ymin)*np.linspace(0, abs(Ymax-Ymin)**(1./args.lpow), 1 + lsteps_)**args.lpow
#plt.plot(lx, ly, '*')
lx, ly = (lx[1:] + lx[:-1])/2, (ly[1:] + ly[:-1])/2
#plt.plot(lx, ly, 'D')
labelpos = tuple(map(tuple, np.vstack((lx,ly)).T))
linewidth, fontsize = .5, 6
### Plot detailed contours
refi_magU = np.maximum(refi_magU, lmin)
dl, ds = ((lmax-lmin)/lsteps/2,1) if np.max(magU) > lmax else (0,0)
levels = np.linspace(lmin, lmax + dl, 1 + 2*lsteps + ds)
if grayscale:
plt.tricontour(refi_triang, refi_magU, levels=levels, colors='lightgray', linewidths=0.05)
else:
cmap = cm.get_cmap('coolwarm')
plt.tricontourf(refi_triang, refi_magU, cmap=cmap, levels=levels)
### Plot black contours with labels
levels = np.linspace(lmin, lmax, 1 + lsteps)
CS = plt.tricontour(refi_triang, refi_magU, levels=levels, colors='k', linewidths=.3)
clabels = plt.clabel(CS, levels,
inline=True,
use_clabeltext=True,
fmt='%g',
manual=labelpos,
fontsize=6)
[ txt.set_backgroundcolor('white') for txt in clabels ]
[ txt.set_bbox(dict(facecolor='white', edgecolor='none', pad=0.5)) for txt in clabels ]
# Mask off unwanted triangles.
xmid = x[triang.triangles].mean(axis=1)
ymid = y[triang.triangles].mean(axis=1)
mask = np.where(xmid * xmid + ymid * ymid < min_radius * min_radius, 1, 0)
triang.set_mask(mask)
#-----------------------------------------------------------------------------
# Refine data
#-----------------------------------------------------------------------------
refiner = tri.UniformTriRefiner(triang)
tri_refi, z_test_refi = refiner.refine_field(z, subdiv=3)
#-----------------------------------------------------------------------------
# Plot the triangulation and the high-res iso-contours
#-----------------------------------------------------------------------------
plt.figure()
plt.gca().set_aspect('equal')
plt.triplot(triang, lw=0.5, color='white')
levels = np.arange(0., 1., 0.025)
cmap = cm.get_cmap(name='terrain', lut=None)
plt.tricontourf(tri_refi, z_test_refi, levels=levels, cmap=cmap)
plt.tricontour(tri_refi, z_test_refi, levels=levels,
colors=['0.25', '0.5', '0.5', '0.5', '0.5'],
linewidths=[1.0, 0.5, 0.5, 0.5, 0.5])
plt.title("High-resolution tricontouring")
plt.show()
start = time.clock()
plt.subplot(211)
xi = np.linspace(-2.1,2.1,ngridx)
yi = np.linspace(-2.1,2.1,ngridy)
zi = griddata(x,y,z,xi,yi,interp='linear')
plt.contour(xi,yi,zi,15,linewidths=0.5,colors='k')
plt.contourf(xi,yi,zi,15,cmap=plt.cm.rainbow,
norm=plt.normalize(vmax=abs(zi).max(), vmin=-abs(zi).max()))
plt.colorbar() # draw colorbar
plt.plot(x, y, 'ko', ms=3)
plt.xlim(-2,2)
plt.ylim(-2,2)
plt.title('griddata and contour (%d points, %d grid points)' % (npts, ngridx*ngridy))
print ('griddata and contour seconds: %f' % (time.clock() - start))
# tricontour.
start = time.clock()
plt.subplot(212)
triang = tri.Triangulation(x, y)
plt.tricontour(x, y, z, 15, linewidths=0.5, colors='k')
plt.tricontourf(x, y, z, 15, cmap=plt.cm.rainbow,
norm=plt.normalize(vmax=abs(zi).max(), vmin=-abs(zi).max()))
plt.colorbar()
plt.plot(x, y, 'ko', ms=3)
plt.xlim(-2,2)
plt.ylim(-2,2)
plt.title('tricontour (%d points)' % npts)
print ('tricontour seconds: %f' % (time.clock() - start))
plt.show()
plot_masked_tri = True # plot of the excessively flat excluded triangles
plot_refi_tri = False # plot of the refined triangulation
plot_expected = False # plot of the 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()
print min(u), max(u),numpy.mean(u)
if plotvec:
vecx=ux ##/u;
vecy=uy ##/u;
plt.quiver(triang.x, triang.y, vecx, vecy,color='cyan',zorder=100)
# scale=100,headlength=30,headwidth=30)
#units='xy', scale=1000, zorder=1, color='blue',
#width=1, headwidth=0.1, headlength=0.1)
if plotcont:
plt.tricontour(triang, z, levels=[0.25],
#colors=['0.25', '0.5', '0.5', '0.5', '0.5'],
cmap=cmap,
linewidths=[1.0],zorder=50)
if plottri:
aa=1.0
im=plt.tricontourf(triang,z, levels=levels, cmap=cmap,alpha=aa)
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="5%", pad=0.15)
plt.colorbar(im, cax=cax)
plt.title(label)
fig.savefig(pngfile)
fig.savefig(pdffile)
# Create the Triangulation; no triangles so Delaunay triangulation created.
triang = tri.Triangulation(x, y)
# Mask off unwanted triangles.
xmid = x[triang.triangles].mean(axis=1)
ymid = y[triang.triangles].mean(axis=1)
mask = np.where(xmid*xmid + ymid*ymid < min_radius*min_radius, 1, 0)
triang.set_mask(mask)
# pcolor plot.
plt.figure()
plt.gca().set_aspect('equal')
plt.tricontourf(triang, z)
plt.colorbar()
plt.tricontour(triang, z, colors='k')
plt.title('Contour plot of Delaunay triangulation')
# You can specify your own triangulation rather than perform a Delaunay
# triangulation of the points, where each triangle is given by the indices of
# the three points that make up the triangle, ordered in either a clockwise or
# anticlockwise manner.
xy = np.asarray([
[-0.101, 0.872], [-0.080, 0.883], [-0.069, 0.888], [-0.054, 0.890],
[-0.045, 0.897], [-0.057, 0.895], [-0.073, 0.900], [-0.087, 0.898],
[-0.090, 0.904], [-0.069, 0.907], [-0.069, 0.921], [-0.080, 0.919],
[-0.073, 0.928], [-0.052, 0.930], [-0.048, 0.942], [-0.062, 0.949],
[-0.054, 0.958], [-0.069, 0.954], [-0.087, 0.952], [-0.087, 0.959],
[-0.080, 0.966], [-0.085, 0.973], [-0.087, 0.965], [-0.097, 0.965],
[-0.097, 0.975], [-0.092, 0.984], [-0.101, 0.980], [-0.108, 0.980],
print 'number of time steps:',len(time_var)
itime = netCDF4.date2index(start,time_var,select='nearest')
start_time = netCDF4.num2date(time_var[0],time_var.units)
stop_time = netCDF4.num2date(time_var[-1],time_var.units)
print 'start time:',start_time.strftime('%Y-%b-%d %H:%M')
print 'stop time:',stop_time.strftime('%Y-%b-%d %H:%M')
dtime = netCDF4.num2date(time_var[itime],time_var.units)
daystr = dtime.strftime('%Y-%b-%d %H:%M')
print 'time selected:', daystr
# <codecell>
z = ncv[zvar][itime,:]
# <codecell>
fig = plt.figure(figsize=(12,12))
levs = np.arange(-1,5,.2)
plt.gca().set_aspect(1./np.cos(lat.mean()*np.pi/180))
plt.tricontourf(triang, z,levels=levs)
plt.colorbar()
plt.tricontour(triang, z, colors='k',levels=levs)
plt.title('%s: Elevation (m): %s' % (nc.title,daystr));
# <codecell>
# <codecell>
def contour(time_list, depth_list, dc_list, corr_list, beachball_list,
plot_file):
"""
Plotting contour
"""
# sets figure's dimensions
_fig_x = 60
_fig_y = 40
# creates figure
fig, ax = plt.subplots(figsize=(_fig_x,_fig_y))
# creates a grid on the (main) plot
ax.grid()
# sets labels
plt.xlabel('Time (sec)')
plt.ylabel('Centroid Depth (km)')
# sets font size
plt.rcParams.update({'font.size': 28})
# sets margins on the plot
plt.margins(0.05)
tri.Triangulation(time_list, depth_list)
levels=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
cont = plt.tricontour(time_list, depth_list, corr_list,
len(levels), levels=levels, linewidths=0.5,
colors='k')
plt.tricontourf(time_list, depth_list, corr_list, len(levels),
levels=levels, cmap=plt.cm.cool)
plt.clabel(cont)
cm=plt.cm.copper_r #gia dc
# plotting beachballs on specific x-axis and y-axis
# with a color based on the data_dc values (normalized to 0-1)
_max_corr = max(corr_list)
_index = corr_list.index(_max_corr)
for i in xrange(len(beachball_list)):
if i == _index:
# sets best beachball's color value to red
_color = 'red'
_width = 45 # bigger beachball for best match
else:
# sets beachball's color value
_color = cm(dc_list[i]/100.0)
_width = 35
# draws beachball
b = beach.beach([beachball_list[i][0], beachball_list[i][1],
beachball_list[i][2]], xy=(time_list[i],depth_list[i]),
width=_width, linewidth=1, facecolor=_color)
# holds the aspect but fixes positioning:
b.set_transform(transforms.IdentityTransform())
# brings the all patches to the origin (0, 0).
for p in b._paths:
p.vertices -= [time_list[i], depth_list[i]]
# uses the offset property of the collection to position the patches
b.set_offsets((time_list[i], depth_list[i]))
b._transOffset = ax.transData
# adds beachball to plot
ax.add_collection(b)
# creates a colorbar at the right of main plot
divider = make_axes_locatable(ax)
# makes room for colorbar
cax = divider.append_axes("right", size="1%", pad=0.5)
# set values to colorbar
norm = colors.Normalize(vmin=0.0, vmax=1.0)
# creates colorbar on specific axes, norm, canvas color and orientation
colorbar.ColorbarBase(cax, cmap=plt.cm.cool, norm=norm,
orientation='vertical', label='Correlation')
cax = divider.append_axes("right", size="1%", pad=1.5)
# set values to colorbar
norm = colors.Normalize(vmin=0, vmax=100)
# creates colorbar on specific axes, norm, canvas color and orientation
colorbar.ColorbarBase(cax, cmap=plt.cm.copper_r , norm=norm,
orientation='vertical', label='DC%')
# save plot to file
plt.savefig(plot_file, dpi=fig.dpi)
import matplotlib.pyplot as pt
from mesh import make_mesh
mesh = make_mesh()
# {{{ find connectivity
adjacency = {}
for a, b, c in mesh.elements:
for v1, v2 in [(a,b), (b,c), (c,a)]:
for x, y in [(v1, v2), (v2, v1)]:
adjacency.setdefault(v1, set()).add(v2)
# }}}
from pymetis import part_graph
points = np.array(mesh.points)
elements = np.array(mesh.elements)
vweights = points[:,0]**2
cuts, part_vert = part_graph(2, adjacency,
#vweights=[int(20*x) for x in vweights]
)
pt.triplot(points[:, 0], points[:, 1], elements, color="black", lw=0.1)
pt.tripcolor(points[:, 0], points[:, 1], elements, part_vert)
pt.tricontour(points[:, 0], points[:, 1], elements, part_vert, colors="black", levels=[0])
pt.show()
import numpy as np import math # First create the x and y coordinates of the points. n_angles = 48 n_radii = 8 min_radius = 0.25 radii = np.linspace(min_radius, 0.95, n_radii) angles = np.linspace(0, 2*math.pi, n_angles, endpoint=False) angles = np.repeat(angles[...,np.newaxis], n_radii, axis=1) angles[:,1::2] += math.pi/n_angles x = (radii*np.cos(angles)).flatten() y = (radii*np.sin(angles)).flatten() z = (np.cos(radii)*np.cos(angles*3.0)).flatten() # Create a custom triangulation triang = tri.Triangulation(x, y) # Mask off unwanted triangles. xmid = x[triang.triangles].mean(axis=1) ymid = y[triang.triangles].mean(axis=1) mask = np.where(xmid*xmid + ymid*ymid < min_radius*min_radius, 1, 0) triang.set_mask(mask) plt.figure() plt.gca(projection='3d') plt.tricontour(triang, z) plt.show()
def writeContour(self):
key = "CLsexp"
if self.gridConfig.useDiscovery:
key = "p0exp"
self.writePreHook()
x = np.array([p[self.gridConfig.x] for p in self.contourData.combinedData.values() if p[self.contourData.combineOn] is not None])
y = np.array([p[self.gridConfig.y] for p in self.contourData.combinedData.values() if p[self.contourData.combineOn] is not None])
z = np.array([p[self.contourData.combineOn] for p in self.contourData.combinedData.values() if p[self.contourData.combineOn] is not None])
if x.size == 0 or y.size == 0 or z.size == 0:
print("No data points for for contour")
return
# Set up a regular grid of interpolation points
xMin = 0
yMin = 0
xMax = x.max()
yMax = y.max()
# vertical levels array for the plot
v = np.linspace(0, 1.0, 21, endpoint=True)
plt.ioff()
fig = plt.figure(figsize=(20,6))
ax = plt.subplot(111)
triang = matplotlib.tri.Triangulation(x, y)
CS = plt.tricontour(triang, z, v, linewidths=3.5, colors=('blue'), levels=[0.05])
plt.tricontourf(triang, z, v, cmap=plt.cm.jet_r)
CB = plt.colorbar(ticks=v)
lines = [CS.collections[0]]
labels = ["Combined"]
cmap = get_cmap(len(self.contourData.contributingRegions))
i=0
for f in self.contourData.contributingRegions:
i+=1
rX = np.array([p[self.gridConfig.x] for p in self.contourData.data[f].values() if p[self.contourData.combineOn] is not None])
rY = np.array([p[self.gridConfig.y] for p in self.contourData.data[f].values() if p[self.contourData.combineOn] is not None])
rZ = np.array([p[self.contourData.combineOn] for p in self.contourData.data[f].values() if p[self.contourData.combineOn] is not None])
triang = matplotlib.tri.Triangulation(rX, rY)
# we have exactly 1 contour, so set our tuple to that
rCS = plt.tricontour(triang, rZ, v, linewidths=1.5, colors=(cmap(i),), linestyle='--', levels=[0.05])
label = filterLabel(f, self.gridConfig)
labels.append(label)
lines.append(rCS.collections[0])
plt.title('Optimisation result', weight='bold')
plt.xlabel('%s [GeV]' % (self.gridConfig.x), position=(1,0), horizontalalignment='right', weight='bold')
plt.ylabel('%s [GeV]' % (self.gridConfig.y), position=(0,1), horizontalalignment='right', weight='bold')
(outputFilename, ext) = os.path.splitext(self.outputFilename)
outputFilename = "%s.contour%s" % (outputFilename, ext)
# Shrink current axis by 50%
box = ax.get_position()
ax.set_position([box.x0, box.y0, box.width * 0.5, box.height])
# Put a legend to the right of the current axis
ax.legend(lines, labels, loc='center left', bbox_to_anchor=(1, 0.5), shadow=False, fontsize='x-small')
#legend = plt.legend(lines, labels, loc='upper right', shadow=False, fontsize='x-small')
if not os.path.exists(os.path.dirname(outputFilename)):
print("Creating output dir {0}".format(os.path.dirname(outputFilename)))
os.makedirs(os.path.dirname(outputFilename))
plt.savefig(outputFilename, close=False, verbose=True, bbox_inches='tight')
print("\n=> Wrote contour to {0}".format(outputFilename))
sys.exit()
else:
print 'no valid .soln file'
sys.exit()
x = xy[:, 0]
y = xy[:, 1]
print 'solution has minimum %.6e, maximum %.6e' % (u.min(),u.max())
if (args.contours == np.nan):
NC = 10
print 'plotting with %d automatic contours ...' % NC
du = u.max() - u.min()
C = np.linspace(u.min()+du/(2*NC),u.max()-du/(2*NC),NC)
else:
C = np.array(args.contours)
plt.figure()
plt.gca().set_aspect('equal')
plt.tricontour(x, y, ele, u, C, colors='k', extend='neither', linewidths=0.5, linestyles='solid')
plt.axis('off')
if len(args.o) > 0:
print 'saving contour map in %s ...' % args.o
plt.savefig(args.o,bbox_inches='tight')
else:
print 'plotting to screen (-o not given) ...'
plt.show()
# In[11]:
zcube = cube[itime,klev]
# In[12]:
plt.figure(figsize=(16,6))
ax = plt.axes(projection=ccrs.PlateCarree())
ax.set_extent(bbox)
ax.coastlines(resolution='10m')
plt.tricontourf(triang, zcube.data, levels=levs)
plt.colorbar(fraction=0.046, pad=0.04)
plt.tricontour(triang, zcube.data, colors='k',levels=levs)
tstr = tvar.units.num2date(tvar.points[itime])
gl = ax.gridlines(draw_labels=True)
gl.xlabels_top = False
gl.ylabels_right = False
plt.title('%s: %s: %s' % (var,tstr,zcube.attributes['title']));
# In[13]:
ucube = iris.load_raw(url,'eastward_sea_water_velocity')[0]
vcube = iris.load_raw(url,'northward_sea_water_velocity')[0]
# In[14]:
