def plot_contour(mesh,
field,
plot_boundary=False,
plot_fill=False,
plot_patch=False):
if plot_fill:
plt.subplot(2, 1, 1)
x1 = np.min(mesh[:, :, 0])
x2 = np.max(mesh[:, :, 0])
y1 = np.min(mesh[:, :, 1])
y2 = np.max(mesh[:, :, 1])
plt.imshow(field.T, cmap='Greys', extent=[x1, x2, y1,
y2]) #, zorder=2)
if plot_boundary:
length_x = mesh[-1, 0, 0]
length_y = mesh[0, -1, 1]
plt.subplot(2, 1, 2)
plt.contour(mesh[:, ::-1, 0], mesh[:, ::-1, 1], field,
levels=[0]) #, zorder=3)
plt.plot([0] * 2, [0, length_y], 'k', linewidth=0.4) #, zorder=1)
plt.plot([length_x] * 2, [0, length_y], 'k',
linewidth=0.4) #, zorder=1)
plt.plot([0, length_x], [0] * 2, 'k', linewidth=0.4) #, zorder=1)
plt.plot([0, length_x], [length_y] * 2, 'k',
linewidth=0.4) #, zorder=1)
plt.axis('equal')
if plot_patch:
pass
def zsview(im, cmap=pl.cm.gray, figsize=(8,5), contours=False, ccolor='r'):
z1, z2 = zscale(im)
pl.figure(figsize=figsize)
pl.imshow(im, vmin=z1, vmax=z2, origin='lower', cmap=cmap, interpolation='none')
if contours:
pl.contour(im, levels=[z2], origin='lower', colors=ccolor)
pl.tight_layout()
def plot_svc(X, y, mysvc, bounds=None, grid=50):
if bounds is None:
xmin = np.min(X[:, 0], 0)
xmax = np.max(X[:, 0], 0)
ymin = np.min(X[:, 1], 0)
ymax = np.max(X[:, 1], 0)
else:
xmin, ymin = bounds[0], bounds[0]
xmax, ymax = bounds[1], bounds[1]
aspect_ratio = (xmax - xmin) / (ymax - ymin)
xgrid, ygrid = np.meshgrid(np.linspace(xmin, xmax, grid),
np.linspace(ymin, ymax, grid))
plt.gca(aspect=aspect_ratio)
plt.xlim(xmin, xmax)
plt.ylim(ymin, ymax)
plt.xticks([])
plt.yticks([])
plt.hold(True)
plt.plot(X[y == 1, 0], X[y == 1, 1], 'bo')
plt.plot(X[y == -1, 0], X[y == -1, 1], 'ro')
box_xy = np.append(xgrid.reshape(xgrid.size, 1), ygrid.reshape(ygrid.size, 1), 1)
if mysvc is not None:
scores = mysvc.decision_function(box_xy)
else:
print 'You must have a valid SVC object.'
return None;
CS=plt.contourf(xgrid, ygrid, scores.reshape(xgrid.shape), alpha=0.5, cmap='jet_r')
plt.contour(xgrid, ygrid, scores.reshape(xgrid.shape), levels=[0], colors='k', linestyles='solid', linewidths=1.5)
plt.contour(xgrid, ygrid, scores.reshape(xgrid.shape), levels=[-1,1], colors='k', linestyles='dashed', linewidths=1)
plt.plot(mysvc.support_vectors_[:,0], mysvc.support_vectors_[:,1], 'ko', markerfacecolor='none', markersize=10)
CB = plt.colorbar(CS)
def plot_svc(X, y, mysvc, bounds=None, grid=50):
if bounds is None:
xmin = np.min(X[:, 0], 0)
xmax = np.max(X[:, 0], 0)
ymin = np.min(X[:, 1], 0)
ymax = np.max(X[:, 1], 0)
else:
xmin, ymin = bounds[0], bounds[0]
xmax, ymax = bounds[1], bounds[1]
aspect_ratio = (xmax - xmin) / (ymax - ymin)
xgrid, ygrid = np.meshgrid(np.linspace(xmin, xmax, grid),
np.linspace(ymin, ymax, grid))
plt.gca(aspect=aspect_ratio)
plt.xlim(xmin, xmax)
plt.ylim(ymin, ymax)
plt.xticks([])
plt.yticks([])
plt.hold(True)
plt.plot(X[y == 1, 0], X[y == 1, 1], 'bo')
plt.plot(X[y == -1, 0], X[y == -1, 1], 'ro')
box_xy = np.append(xgrid.reshape(xgrid.size, 1), ygrid.reshape(ygrid.size, 1), 1)
if mysvc is not None:
scores = mysvc.decision_function(box_xy)
else:
print 'You must have a valid SVC object.'
return None;
CS=plt.contourf(xgrid, ygrid, scores.reshape(xgrid.shape), alpha=0.5, cmap='jet_r')
plt.contour(xgrid, ygrid, scores.reshape(xgrid.shape), levels=[0], colors='k', linestyles='solid', linewidths=1.5)
plt.contour(xgrid, ygrid, scores.reshape(xgrid.shape), levels=[-1,1], colors='k', linestyles='dashed', linewidths=1)
plt.plot(mysvc.support_vectors_[:,0], mysvc.support_vectors_[:,1], 'ko', markerfacecolor='none', markersize=10)
CB = plt.colorbar(CS)
def plot_solution(problem_data, solution):
from numpy import linspace
from matplotlib.pylab import contour, colorbar, contourf, xlabel, ylabel, title, show
from matplotlib.mlab import griddata
print(" * Preparing for plotting...")
NN = problem_data["NN"]
# Extract node coordinates seperately for plotting
x, y = [0] * NN, [0] * NN
for i, node in enumerate(problem_data["nodes"]):
x[i] = node[0]
y[i] = node[1]
# Refine the contour plot mesh for a "smoother" image, by generating a
# 200*200 grid
xi = linspace(min(x), max(x), 200)
yi = linspace(min(y), max(y), 200)
# Approximate the mid values from neighbors
zi = griddata(x, y, solution, xi, yi)
print(" * Plotting...")
# Plot the contour lines with black
contour(xi, yi, zi, 15, linewidths=0.5, colors='k')
# Plot the filled contour plot
plot = contourf(xi, yi, zi, 15, antialiased=True)
colorbar(plot, format="%.3f").set_label("T")
xlabel('X')
ylabel('Y')
title("Contour plot of T values for {0}".format(problem_data["title"]))
show()
def plot_hyperplane(X, Y, model, K, plot_id, d=500):
I0 = np.where(Y == -1)[0]
I1 = np.where(Y == 1)[0]
plt.subplot(plot_id)
plt.plot(X[I1, 0], X[I1, 1], 'og')
plt.plot(X[I0, 0], X[I0, 1], 'xb')
min_val = np.min(X, 0)
max_val = np.max(X, 0)
clf = model()
clf.train(X, Y, K)
x0_plot = np.linspace(min_val[0, 0], max_val[0, 0], d)
x1_plot = np.linspace(min_val[0, 1], max_val[0, 1], d)
[x0, x1] = plt.meshgrid(x0_plot, x1_plot)
Y_all = np.matrix(np.zeros([d, d]))
for i in range(d):
X_all = np.matrix(np.zeros([d, 2]))
X_all[:, 0] = np.matrix(x0[:, i]).T
X_all[:, 1] = np.matrix(x1[:, i]).T
Y_all[:, i] = clf.predict(X_all)
plt.contour(np.array(x0),
np.array(x1),
np.array(Y_all),
levels=[0.0],
colors='red')
def make_2d_surface_contours(x,
y,
z,
title='',
x_axis_name='',
y_axis_name='',
z_axis_name='',
extra_contour_line=None):
fig = plt.figure()
ax = plt.axes()
X, Y, Z = grid(x, y, z, resX=187, resY=187)
if extra_contour_line != None:
contours2 = plt.contour(X,
Y,
Z,
levels=[extra_contour_line],
colors='blue',
linestyles=':')
# plt.plot([0], [0], ls=':',c='blue', label=entry['label'])
ax.scatter(x, y, c='red', s=2, zorder=5)
contours = plt.contour(X, Y, Z, colors='black', vmin=0.5, vmax=max(z))
plt.contourf(X, Y, Z, 100)
ax.set_xlim([min(x), max(x)])
ax.set_ylim([min(y), max(y)])
plt.title(title)
plt.xlabel(x_axis_name)
plt.ylabel(y_axis_name)
cbar = plt.colorbar()
cbar.ax.set_ylabel(z_axis_name)
plt.tight_layout()
plt.show()
plt.savefig('plot.png')
def plot(func, dataset, x1s, x1e, x2s, x2e, delta, levels, title=None, track=None, f_val=None):
# t, a, b, c = dataset
k1 = np.arange(x1s, x1e, delta)
k2 = np.arange(x2s, x2e, delta)
K1, K2 = np.meshgrid(k1, k2)
FX = np.zeros(K1.shape)
row, col = K1.shape
for i in xrange(row):
for j in xrange(col):
FX[i, j] = func(array([K1[i, j], K2[i, j]]), *dataset)
fig = plt.figure(title)
subfig1 = fig.add_subplot(1, 2, 1)
surf1 = plt.contour(K1, K2, FX, levels=levels, stride=0.001)
if track:
track = array(track)
plt.plot(track[:, 0], track[:, 1])
plt.xlabel("k1")
plt.ylabel("k2")
subfig2 = fig.add_subplot(1, 2, 2, projection='3d')
surf2 = subfig2.plot_wireframe(K1, K2, FX, rstride=10, cstride=10, color='y')
plt.contour(K1, K2, FX, stride=1, levels=levels)
if track != None and f_val != None:
f_val = array(f_val)
subfig2.scatter(track[:, 0], track[:, 1], f_val)
plt.show()
def backGroundB(xk, Nk, w):
prob = np.ones((100, 100))
A = np.linspace(0, 100, 100)
B = np.linspace(0, 100, 100)
A, B = np.meshgrid(A, B)
x = []
for j in range(len(xk)):
for k in range(Nk[j]):
x.append(xk[j])
plt.figure(figsize=(12, 4))
plt.subplot(121)
plt.hist(x, bins=len(xk))
plt.ylabel('Number of counts N')
plt.xlabel('Measurement variable x')
for i in range(len(xk)):
Dk = (A * np.exp(-1 * (xk[i]**2) / (2 * w**2)) + B)
prob *= (Nk[i] * np.log(Dk) - Dk)
plt.subplot(122)
plt.contour(A, B, prob)
plt.ylabel('Background B')
plt.xlabel('Amplitude A')
plt.savefig('Background.png')
def plot_hyperplane(X, Y, model, K, plot_id, d = 500):
I0 = np.where(Y==-1)[0]
I1 = np.where(Y==1)[0]
plt.subplot(plot_id)
plt.plot(X[I1, 0], X[I1, 1], 'og')
plt.plot(X[I0, 0], X[I0, 1], 'xb')
min_val = np.min(X, 0)
max_val = np.max(X, 0)
clf = model()
clf.train(X, Y, K)
x0_plot = np.linspace(min_val[0, 0], max_val[0, 0], d)
x1_plot = np.linspace(min_val[0, 1], max_val[0, 1], d)
[x0, x1] = plt.meshgrid(x0_plot, x1_plot);
Y_all = np.matrix(np.zeros([d, d]))
for i in range(d):
X_all = np.matrix(np.zeros([d, 2]))
X_all[:, 0] = np.matrix(x0[:, i]).T
X_all[:, 1] = np.matrix(x1[:, i]).T
Y_all[:, i] = clf.predict(X_all)
plt.contour(np.array(x0), np.array(x1), np.array(Y_all), levels = [0.0], colors = 'red')
def plot(m):
col1 = '#0172B2'
col2 = '#CC6600'
mins, maxs, xx, yy, Xplot = gridParams()
mf, vf = m.predict_f(Xplot)
plt.figure()
plt.plot(Xtrain[:, 0][Ytrain[:, 0] == 1],
Xtrain[:, 1][Ytrain[:, 0] == 1],
'o',
color=col1,
mew=0,
alpha=0.5)
plt.plot(Xtrain[:, 0][Ytrain[:, 0] == -1],
Xtrain[:, 1][Ytrain[:, 0] == -1],
'o',
color=col2,
mew=0,
alpha=0.5)
zu = m.sgp_layer.zu
plt.plot(zu[:, 0], zu[:, 1], 'ro', mew=0, ms=4)
plt.contour(xx,
yy,
mf.reshape(*xx.shape), [0],
colors='k',
linewidths=1.8,
zorder=100)
def run_xor():
from operator import xor
from scipy import special
# create dataset
print "generating dataset..."
n = 25
Y = np.zeros((0, 3))
for i in [0, 1]:
for j in [0, 1]:
a = i * np.ones((n, 1))
b = j * np.ones((n, 1))
c = xor(bool(i), bool(j)) * np.ones((n, 1))
Y_ij = np.hstack((a, b, c))
Y = np.vstack((Y, Y_ij))
Y = 2 * Y - 1
# inference
print "inference ..."
M = 10
D = 2
lvm = aep.SGPLVM(Y, D, M, lik='Probit')
lvm.optimise(method='L-BFGS-B', alpha=0.1, maxiter=200)
# predict given inputs
mx, vx = lvm.get_posterior_x()
lims = [-1.5, 1.5]
x = np.linspace(*lims, num=101)
y = np.linspace(*lims, num=101)
X, Y = np.meshgrid(x, y)
X_ravel = X.ravel()
Y_ravel = Y.ravel()
inputs = np.vstack((X_ravel, Y_ravel)).T
my, vy = lvm.predict_f(inputs)
t = my / np.sqrt(1 + vy)
Z = 0.5 * (1 + special.erf(t / np.sqrt(2)))
for d in range(3):
plt.figure()
plt.scatter(mx[:, 0], mx[:, 1])
zu = lvm.sgp_layer.zu
plt.plot(zu[:, 0], zu[:, 1], 'ko')
plt.contour(X, Y, np.log(Z[:, d] + 1e-16).reshape(X.shape))
plt.xlim(*lims)
plt.ylim(*lims)
# Y_test = np.array([[1, -1, 1], [-1, 1, 1], [-1, -1, -1], [1, 1, -1]])
# # impute missing data
# for k in range(3):
# Y_test_k = Y_test
# missing_mask = np.ones_like(Y_test_k)
# missing_mask[:, k] = 0
# my_pred, vy_pred = lvm.impute_missing(
# Y_test_k, missing_mask,
# alpha=0.1, no_iters=100, add_noise=False)
# print k, my_pred, vy_pred, Y_test_k
plt.show()
def _plot_nullclines(self, resolution):
"""
Plot nullclines.
Arguments
resolution
Resolution of plot
"""
x_mesh, y_mesh, ode_x, ode_y = self._get_ode_values(resolution)
plt.contour(
x_mesh, y_mesh, ode_x,
levels=[0], linewidths=2, colors='black')
plt.contour(
x_mesh, y_mesh, ode_y,
levels=[0], linewidths=2, colors='black',
linestyles='dashed')
lblx = mlines.Line2D(
[], [],
color='black',
marker='', markersize=15,
label=r'$\dot\varphi_0=0$')
lbly = mlines.Line2D(
[], [],
color='black', linestyle='dashed',
marker='', markersize=15,
label=r'$\dot\varphi_1=0$')
plt.legend(handles=[lblx, lbly], loc='best')
def plot(x,y,field,filename,c=200):
plt.figure()
# define grid.
xi = np.linspace(min(x),max(x),100)
yi = np.linspace(min(y),max(y),100)
# grid the data.
si_lin = griddata((x, y), field, (xi[None,:], yi[:,None]), method='linear')
si_cub = griddata((x, y), field, (xi[None,:], yi[:,None]), method='linear')
print np.min(field)
print np.max(field)
plt.subplot(211)
# contour the gridded data, plotting dots at the randomly spaced data points.
CS = plt.contour(xi,yi,si_lin,c,linewidths=0.5,colors='k')
CS = plt.contourf(xi,yi,si_lin,c,cmap=plt.cm.jet)
plt.colorbar() # draw colorbar
# plot data points.
# plt.scatter(x,y,marker='o',c='b',s=5)
plt.xlim(min(x),max(x))
plt.ylim(min(y),max(y))
plt.title('Lineaarinen interpolointi')
#plt.tight_layout()
plt.subplot(212)
# contour the gridded data, plotting dots at the randomly spaced data points.
CS = plt.contour(xi,yi,si_cub,c,linewidths=0.5,colors='k')
CS = plt.contourf(xi,yi,si_cub,c,cmap=plt.cm.jet)
plt.colorbar() # draw colorbar
# plot data points.
# plt.scatter(x,y,marker='o',c='b',s=5)
plt.xlim(min(x),max(x))
plt.ylim(min(y),max(y))
plt.title('Kuubinen interpolointi')
plt.savefig(filename)
def draw_decision_boundary(X, y, model, title):
resolution = 0.01
markers = ('o', 's', '^')
colors = ('lightgreen', 'red', 'blue')
cmap = mpl.colors.ListedColormap(colors)
x1_min, x1_max = X[:, 0].min() - 1, X[:, 0].max() + 1
x2_min, x2_max = X[:, 1].min() - 1, X[:, 1].max() + 1
xx1, xx2 = np.meshgrid(np.arange(x1_min, x1_max, resolution),
np.arange(x2_min, x2_max, resolution))
mpd = model.predict(np.array([xx1.ravel(),
xx2.ravel()]).T).reshape(xx1.shape)
plt.contour(xx1, xx2, mpd, cmap=mpl.colors.ListedColormap(['k']))
plt.contourf(xx1, xx2, mpd, alpha=0.4, cmap=cmap)
plt.xlim(xx1.min(), xx1.max())
plt.ylim(xx2.min(), xx2.max())
for idx, cl in enumerate(np.unique(y)):
plt.scatter(x=X[y == cl, 0],
y=X[y == cl, 1],
alpha=0.8,
c=[cmap(idx)],
marker=markers[idx],
s=80,
label=cl)
plt.xlabel(iris.feature_names[2])
plt.ylabel(iris.feature_names[3])
plt.legend(loc='upper left')
plt.title(title)
return mpd
def plot_cost_function(data): x = data[:, 0] y = data[:, 1] theta_0_mesh, theta_1_mesh = np.meshgrid(np.arange(-10, 10, 0.01), np.arange(-1, 4, 0.01)) cost_all_points = np.zeros(theta_0_mesh.shape) cost_all_points = compute_costs_thetas(theta_0_mesh, theta_1_mesh, x, y) plt.contour(theta_0_mesh, theta_1_mesh, cost_all_points, 100) plt.show()
def contour(image):
"""
contour plot
"""
plt.figure()
image = image.convert('L')
plt.gray()
plt.contour(image, origin='image')
plt.axis('equal')
def visualFit(x, mu, sigma2):
temp = np.arange(0, 35, 0.5)
x1, x2 = np.meshgrid(temp, temp)
z = multivariateGaussian(
np.vstack((x1.flatten(), x2.flatten())).T, mu, sigma2)
z = z.reshape(x1.shape)
plt.plot(x[:, 0], x[:, 1], 'bx')
plt.contour(x1, x2, z, np.power(10.0, np.arange(-20, 0, 3)))
plt.xlabel('Latency (ms)')
plt.ylabel('Throughput (mb/s)')
def sanity_steppar2(self):
import numpy as np
import matplotlib.pylab as plt
from PyAstronomy import funcFit as fuf
# Set up a Gaussian model
# and create some "data"
x = np.linspace(0,2,100)
gf = fuf.GaussFit1d()
gf["A"] = 0.87
gf["mu"] = 1.0
gf["sig"] = 0.2
y = gf.evaluate(x)
y += np.random.normal(0.0, 0.1, len(x))
# Thaw parameters, which are to be fitted ...
gf.thaw(["A", "mu", "sig"])
# ... and "disturb" starting values a little.
gf["A"] = gf["A"] + np.random.normal(0.0, 0.1)
gf["mu"] = gf["mu"] + np.random.normal(0.0, 0.1)
gf["sig"] = gf["sig"] + np.random.normal(0.0, 0.03)
# Find the best fit solution
gf.fit(x, y, yerr=np.ones(len(x))*0.1)
# Step the amplitude (area of the Gaussian) and the
# center ("mu") of the Gaussian through the given
# ranges.
sp = gf.steppar(["A", "mu"], ranges={"A":[0.8, 0.95, 20], \
"mu":[0.96,1.05,15]})
# Get the values for `A`, `mu`, and chi-square
# from the output of steppar.
As = map(lambda x:x[0], sp)
mus = map(lambda x:x[1], sp)
chis = map(lambda x:x[2], sp)
# Create a chi-square array using the
# indices contained in the output.
z = np.zeros((20, 15))
for s in sp:
z[s[3]] = s[2]
# Find minimum chi-square and define levels
# for 68%, 90%, and 99% confidence intervals.
cm = min(chis)
levels = [cm+2.3, cm+4.61, cm+9.21]
# Plot the contours to explore the confidence
# interval and correlation.
plt.xlabel("mu")
plt.ylabel("A")
plt.contour(np.sort(np.unique(mus)), np.sort(np.unique(As)), z, \
levels=levels)
# Plot the input value
plt.plot([1.0], [0.87], 'k+', markersize=20)
def contourplot(objfun, xmin, xmax, ymin, ymax, ncontours=50, fill=True):
x = np.linspace(xmin, xmax, 200)
y = np.linspace(ymin, ymax, 200)
X, Y = np.meshgrid(x,y)
Z = objfun(X,Y)
if fill:
plt.contourf(X,Y,Z,ncontours); # plot the contours
else:
plt.contour(X,Y,Z,ncontours); # plot the contours
plt.scatter(1,1,marker="x",s=50,color="r"); # mark the minimum
def animate(self):
plt.contour(self.X, self.Y, self.Z, colors="gray", levels=[0.4, 3, 15, 50, 150, 500, 1500, 5000])
plt.plot(1, 1, 'ro', markersize=15)
plt.title(self.title, fontsize=20)
plt.xlim(-4, 4)
plt.ylim(-3, 3)
plt.xlabel('x')
plt.ylabel('y')
anim = animation.FuncAnimation(self.fig, self.ani_update, init_func=self.ani_init,
frames=self.frames, interval=self.interval, blit=True)
return anim
def draw_grid_plot():
if not has_plt:
return
plt.imshow(z_sample, cmap=plt.cm.binary, origin='lower',
interpolation='nearest',
extent=(grid_min, grid_max, grid_min, grid_max))
plt.hold(True) # XXX: restore plt state
plt.contour(np.linspace(grid_min, grid_max, grid_n),
np.linspace(grid_min, grid_max, grid_n),
z_actual)
plt.savefig(grid_filename)
plt.close()
def contour_variable(fname, varname, **kwargs):
ncfname = os.path.join(ensemble_base_path, fname)
try:
ncf = nc.Dataset(ncfname, "r")
except IOError as error:
print(ncfname, "not found.")
raise error
plt.contour(np.squeeze(ncf.variables[varname][0:150, 0:150]),
origin="lower",
interpolation="nearest",
**kwargs)
def plotDecisionBoundary(theta_p):
u = np.linspace(-1, 1.5, 50)
v = np.linspace(-1, 1.5, 50)
z = np.zeros((np.size(u), np.size(v)))
for i in range(np.size(u)):
for j in range(np.size(v)):
z[i][j] = np.dot(mapFeature(u[i], v[j]), theta_p)
z = z.T
plt.contour(u, v, z, [0, 0.0000001])
return
def backward():
x = tf.placeholder(tf.float32, shape=(None, 2))
y_ = tf.placeholder(tf.float32, shape=(None, 1))
X, Y_, Y_c = generateds.generateds()
y = forward.forward(x, REGULARIZER)
global_step = tf.Variable(0, trainable=False)
learning_rate = tf.train.exponential_decay(LEARNING_RATE_BASE,
global_step,
300 / BATCH_SIZE,
LEARNING_RATE_DECAY,
staircase=True)
#定义损失函数
loss_mse = tf.reduce_mean(tf.square(y - y_))
loss_total = loss_mse + tf.add_n(tf.get_collection('losses'))
#反向传播方法 包含正则化
train_step = tf.train.AdamOptimizer(learning_rate).minimize(loss_total)
#生成会话，训练STEPS轮
with tf.Session() as sess:
init_op = tf.global_variables_initializer()
sess.run(init_op)
for i in range(STEPS):
start = (i * BATCH_SIZE) % 300
end = start + BATCH_SIZE
sess.run(train_step,
feed_dict={
x: X[start:end],
y_: Y_[start:end]
})
if i % 2000 == 0:
loss_V = sess.run(loss_total, feed_dict={x: X, y_: Y_})
print("After %d step(s), loss is: %g" % (i, loss_V))
#xx在-3到3之间以步长为0.01，yy在-3到3之间以步长0.01，生成二维网格坐标点
xx, yy = np.mgrid[-3:3:.01, -3:3:.01]
#将xx，yy拉直，并合成一个2列的矩阵，得到一个网格坐标点的集合
grid = np.c_[xx.ravel(), yy.ravel()]
#将网格坐标点喂入神经网络，probs为输出
probs = sess.run(y, feed_dict={x: grid})
#probs的shape调整成xx的样子
probs = probs.reshape(xx.shape)
plt.scatter(X[:, 0], X[:, 1], c=np.squeeze(Y_c))
plt.contour(xx, yy, probs, levels=[.5])
plt.show()
def draw_grid_plot():
if not has_plt:
return
plt.imshow(z_sample,
cmap=plt.cm.binary,
origin='lower',
interpolation='nearest',
extent=(grid_min, grid_max, grid_min, grid_max))
plt.hold(True) # XXX: restore plt state
plt.contour(np.linspace(grid_min, grid_max, grid_n),
np.linspace(grid_min, grid_max, grid_n), z_actual)
plt.savefig(grid_filename)
plt.close()
def chkimg(p, sub, title):
import matplotlib.pylab as plt
from numpy import mgrid
plt.imshow(sub)
y, x = mgrid[:60, :60]
plt.contour(p(x, y))
plt.title(title)
plt.show()
ans = raw_input('Image Okay [y/n] ?')
plt.clf()
if ans.upper() == 'N':
return False
else:
return True
def __call__(self, **params):
p = ParamOverrides(self, params)
name = p.plot_template.keys().pop(0)
plot = make_template_plot(p.plot_template,
p.sheet.views.Maps,
p.sheet.xdensity,
p.sheet.bounds,
p.normalize,
name=p.plot_template[name])
fig = plt.figure(figsize=(5, 5))
if plot:
bitmap = plot.bitmap
isint = plt.isinteractive(
) # Temporarily make non-interactive for plotting
plt.ioff() # Turn interactive mode off
plt.imshow(bitmap.image, origin='lower', interpolation='nearest')
plt.axis('off')
for (t, pref, sel, c) in p.overlay:
v = plt.flipud(p.sheet.views.Maps[pref].view()[0])
if (t == 'contours'):
plt.contour(v, [sel, sel], colors=c, linewidths=2)
if (t == 'arrows'):
s = plt.flipud(p.sheet.views.Maps[sel].view()[0])
scale = int(np.ceil(np.log10(len(v))))
X = np.array([x for x in xrange(len(v) / scale)])
v_sc = np.zeros((len(v) / scale, len(v) / scale))
s_sc = np.zeros((len(v) / scale, len(v) / scale))
for i in X:
for j in X:
v_sc[i][j] = v[scale * i][scale * j]
s_sc[i][j] = s[scale * i][scale * j]
plt.quiver(scale * X,
scale * X,
-np.cos(2 * np.pi * v_sc) * s_sc,
-np.sin(2 * np.pi * v_sc) * s_sc,
color=c,
edgecolors=c,
minshaft=3,
linewidths=1)
p.title = '%s overlaid with %s at time %s' % (plot.name, pref,
topo.sim.timestr())
if isint: plt.ion()
p.filename_suffix = "_" + p.sheet.name
self._generate_figure(p)
return fig
def boundary(X, y, theta):
y_ = y.reshape(y.size,)
classes = (0., 1.)
colors = ('b', 'r')
marks = ('o', '+')
for i, color, mark in zip(classes, colors, marks):
plt.scatter(np.array(X)[y_ == i, 0], np.array(X)[y_ == i, 1], c=color, marker=mark)
def fn((ui,vj)):
return map_feature(np.array(ui), np.array(vj)).dot(theta)
plt.contour(*calc_contour(X, fn))
plt.legend(['y=%s' % i for i in classes] + ['Decision boundary'])
plt.show()
def show(self, rootFilename):
"""
Plot the solution
@param rootFilename a wild card expression, eg 'XXX_rk%d.txt'
"""
import glob
from matplotlib import pylab
import re
import os
dataWindows = {}
for f in glob.glob(rootFilename):
pe = int(re.search(r'_rk(\d+)\.txt', f).group(1))
dataWindows[pe] = numpy.loadtxt(f, unpack=False)
nBigSizes = (self.decomp[0]*self.n,
self.decomp[1]*self.n)
bigData = numpy.zeros(nBigSizes, numpy.float64)
for j in range(self.decomp[0]):
begJ = j*self.n
endJ = begJ + self.n
for i in range(self.decomp[1]):
pe = j*self.decomp[1] + i
begI = i*self.n
endI = begI + self.n
minVal = min(dataWindows[pe].flat)
maxVal = max(dataWindows[pe].flat)
bigData[begJ:endJ, begI:endI] = dataWindows[pe]
xs = self.x0s[1] + numpy.array([(i + 0.5)*self.hs[1] for i in \
range(1, self.decomp[1]*self.n-1)])
ys = self.x0s[0] + numpy.array([(j + 0.5)*self.hs[0] for j in \
range(1, self.decomp[0]*self.n-1)])
pylab.contour(xs, ys, bigData[1:-1,1:-1], 21)
pylab.colorbar()
# plot the domain decomp
for m in range(1, self.decomp[0]):
yVal = self.x0s[0] + m * self.ls[0] - self.hs[0] / 2.0
pylab.plot([xs[0], xs[-1]], [yVal, yVal], 'k--')
yVal += self.hs[0]
pylab.plot([xs[0], xs[-1]], [yVal, yVal], 'k--')
for n in range(1, self.decomp[1]):
xVal = self.x0s[1] + n * self.ls[1] - self.hs[1] / 2.0
pylab.plot([xVal, xVal], [ys[0], ys[-1]], 'k--')
xVal += self.hs[1]
pylab.plot([xVal, xVal], [ys[0], ys[-1]], 'k--')
pylab.show()
fname = re.sub(r'_rk\*.txt', '', rootFilename) + '.png'
print 'saving colorplot in file ' + fname
pylab.savefig(fname)
def plot(self, func, interp=True, plotter='imshow'):
import matplotlib as mpl
from matplotlib import pylab as pl
if interp:
lpi = self.interpolator(func)
z = lpi[self.yrange[0]:self.yrange[1]:complex(0, self.nrange),
self.xrange[0]:self.xrange[1]:complex(0, self.nrange)]
else:
y, x = np.mgrid[
self.yrange[0]:self.yrange[1]:complex(0, self.nrange),
self.xrange[0]:self.xrange[1]:complex(0, self.nrange)]
z = func(x, y)
z = np.where(np.isinf(z), 0.0, z)
extent = (self.xrange[0], self.xrange[1], self.yrange[0],
self.yrange[1])
pl.ioff()
pl.clf()
pl.hot() # Some like it hot
if plotter == 'imshow':
pl.imshow(np.nan_to_num(z),
interpolation='nearest',
extent=extent,
origin='lower')
elif plotter == 'contour':
Y, X = np.ogrid[
self.yrange[0]:self.yrange[1]:complex(0, self.nrange),
self.xrange[0]:self.xrange[1]:complex(0, self.nrange)]
pl.contour(np.ravel(X), np.ravel(Y), z, 20)
x = self.x
y = self.y
lc = mpl.collections.LineCollection(np.array([
((x[i], y[i]), (x[j], y[j])) for i, j in self.tri.edge_db
]),
colors=[(0, 0, 0, 0.2)])
ax = pl.gca()
ax.add_collection(lc)
if interp:
title = '%s Interpolant' % self.name
else:
title = 'Reference'
if hasattr(func, 'title'):
pl.title('%s: %s' % (func.title, title))
else:
pl.title(title)
pl.show()
pl.ion()
def plot_model(data_array, mixture, axis=(0, 1), samples=20, contour_lines=20):
""" Plot the scaterplot of data_array and the contour lines of the
probability for the mixture.
"""
import matplotlib
import matplotlib.pylab as plt
import matplotlib.cm as cm
axis = list(axis)
if isinstance(mixture, GMClusterModel):
mixture = mixture.norm_model
if isinstance(data_array, Orange.data.Table):
data_array, _, _ = data_array.to_numpy_MA()
array = data_array[:, axis]
weights = mixture.weights
means = mixture.means[:, axis]
covariances = [cov[axis, :][:, axis] for cov in mixture.covariances
] # TODO: Need the whole marginal distribution.
gmm = GMModel(weights, means, covariances)
min = numpy.min(array, 0)
max = numpy.max(array, 0)
extent = (min[0], max[0], min[1], max[1])
X = numpy.linspace(min[0], max[0], samples)
Y = numpy.linspace(min[1], max[1], samples)
Z = numpy.zeros((X.shape[0], Y.shape[0]))
for i, x in enumerate(X):
for j, y in enumerate(Y):
Z[i, j] = gmm([x, y])
plt.plot(array[:, 0], array[:, 1], "ro")
plt.contour(X, Y, Z.T, contour_lines, extent=extent)
im = plt.imshow(Z.T,
interpolation='bilinear',
origin='lower',
cmap=cm.gray,
extent=extent)
plt.plot(means[:, 0], means[:, 1], "b+")
plt.show()
def show(self, rootFilename):
"""
Plot the solution
@param rootFilename a wild card expression, eg 'XXX_rk%d.txt'
"""
import glob
from matplotlib import pylab
import re
import os
dataWindows = {}
for f in glob.glob(rootFilename):
pe = int(re.search(r'_rk(\d+)\.txt', f).group(1))
dataWindows[pe] = numpy.loadtxt(f, unpack=False)
nBigSizes = (self.decomp[0] * self.n, self.decomp[1] * self.n)
bigData = numpy.zeros(nBigSizes, numpy.float64)
for j in range(self.decomp[0]):
begJ = j * self.n
endJ = begJ + self.n
for i in range(self.decomp[1]):
pe = j * self.decomp[1] + i
begI = i * self.n
endI = begI + self.n
minVal = min(dataWindows[pe].flat)
maxVal = max(dataWindows[pe].flat)
bigData[begJ:endJ, begI:endI] = dataWindows[pe]
xs = self.x0s[1] + numpy.array([(i + 0.5)*self.hs[1] for i in \
range(1, self.decomp[1]*self.n-1)])
ys = self.x0s[0] + numpy.array([(j + 0.5)*self.hs[0] for j in \
range(1, self.decomp[0]*self.n-1)])
pylab.contour(xs, ys, bigData[1:-1, 1:-1], 21)
pylab.colorbar()
# plot the domain decomp
for m in range(1, self.decomp[0]):
yVal = self.x0s[0] + m * self.ls[0] - self.hs[0] / 2.0
pylab.plot([xs[0], xs[-1]], [yVal, yVal], 'k--')
yVal += self.hs[0]
pylab.plot([xs[0], xs[-1]], [yVal, yVal], 'k--')
for n in range(1, self.decomp[1]):
xVal = self.x0s[1] + n * self.ls[1] - self.hs[1] / 2.0
pylab.plot([xVal, xVal], [ys[0], ys[-1]], 'k--')
xVal += self.hs[1]
pylab.plot([xVal, xVal], [ys[0], ys[-1]], 'k--')
pylab.show()
fname = re.sub(r'_rk\*.txt', '', rootFilename) + '.png'
print 'saving colorplot in file ' + fname
pylab.savefig(fname)
def plot_non_linear_boundary(theta, Xlabel='X', Ylabel='Y', plot_title='plot'):
u = np.linspace(-1, 1.5, 50)
v = np.linspace(-1, 1.5, 50)
z = np.zeros((len(u), len(v)))
for i in range(len(u)):
for j in range(len(v)):
z[i, j] = (map_feature(np.array(u[i]), np.array(v[j])).dot(np.array(theta)))
z = z.T
contour(u, v, z)
title(plot_title)
xlabel(Xlabel)
ylabel(Ylabel)
show()
def plot(self, func, interp=True, plotter='imshow'):
import matplotlib as mpl
from matplotlib import pylab as pl
if interp:
lpi = self.interpolator(func)
z = lpi[self.yrange[0]:self.yrange[1]:complex(0, self.nrange),
self.xrange[0]:self.xrange[1]:complex(0, self.nrange)]
else:
y, x = np.mgrid[
self.yrange[0]:self.yrange[1]:complex(0, self.nrange),
self.xrange[0]:self.xrange[1]:complex(0, self.nrange)]
z = func(x, y)
z = np.where(np.isinf(z), 0.0, z)
extent = (self.xrange[0], self.xrange[1],
self.yrange[0], self.yrange[1])
pl.ioff()
pl.clf()
pl.hot() # Some like it hot
if plotter == 'imshow':
pl.imshow(np.nan_to_num(z), interpolation='nearest', extent=extent,
origin='lower')
elif plotter == 'contour':
Y, X = np.ogrid[
self.yrange[0]:self.yrange[1]:complex(0, self.nrange),
self.xrange[0]:self.xrange[1]:complex(0, self.nrange)]
pl.contour(np.ravel(X), np.ravel(Y), z, 20)
x = self.x
y = self.y
lc = mpl.collections.LineCollection(
np.array([((x[i], y[i]), (x[j], y[j]))
for i, j in self.tri.edge_db]),
colors=[(0, 0, 0, 0.2)])
ax = pl.gca()
ax.add_collection(lc)
if interp:
title = '%s Interpolant' % self.name
else:
title = 'Reference'
if hasattr(func, 'title'):
pl.title('%s: %s' % (func.title, title))
else:
pl.title(title)
pl.show()
pl.ion()
def diffDensity(fig, F2, F3, Trange):
T1 = copy.deepcopy(Trange)
T2 = copy.deepcopy(Trange)
X, Y = numpy.meshgrid(T1, T2)
p2 = []
p3 = []
for tau in Trange:
p2.append(F2.pdf(tau))
p3.append(F3.pdf(tau))
p2mat = numpy.matrix(p2)
p3mat = numpy.matrix(p3)
pp2 = p2mat.T * p2mat
pp3 = p3mat.T * p3mat
PXP = numpy.array(numpy.log(pp3) - numpy.log(pp2))
# norm = plt.cm.colors.Normalize(vmin=-0.8,vmax=0.8)
levels = numpy.arange(-2.0, .1, .1)
cmap = plt.cm.get_cmap("PiYG")
cmap.set_under(color='red', alpha=0.3)
cmap.set_over(color='red', alpha=0.3)
cset = plt.contourf(X,
Y,
PXP,
levels=numpy.array([-10.0, 0, .8]),
colors=('r', 'g'),
alpha=.3) #plt.cm.get_cmap(cmap,2))
matplotlib.rcParams['contour.negative_linestyle'] = 'solid'
levels = numpy.arange(-10, .8, .1)
cs2 = plt.contour(X, Y, PXP, levels=levels, colors='k', alpha=.2)
plt.clabel(cs2, levels[91:], fontsize=9, inline=1)
# plt.colorbar(cset)
plt.xlabel("First Opening Time $\\tau_1$")
plt.ylabel("Second Opening Time $\\tau_2$")
plt.title(
"Test Statistic Comparing Models as a Function of Two Observations")
plt.show()
def __hist2d(self,
x,
y,
contour=False,
bins=(200, 200),
cmap="Purples",
interpolation='nearest',
origin="lower",
colors="k"):
"""
Parameters
----------
bins : tuple of two ints
"""
H, xedges, yedges = np.histogram2d(x, y, bins)
extent = [xedges.min(), xedges.max(), yedges.min(), yedges.max()]
if not contour:
plt.imshow(H,
extent=extent,
interpolation=interpolation,
origin=origin,
cmap=cmap,
aspect="auto")
# plt.colorbar(fontsize=4)
else:
CS = plt.contour(H, extent=extent, origin=origin, colors=colors)
plt.clabel(CS, inline=1, fontsize=10)
def contour(X,Y,Z,
extent=None, vrange=None, levels=None, extend='both',
inaxis=None,
cmap=None, addcolorbar=True, clabel=None,
smooth=True, smoothlen=None):
'''Build a super fancy contour image'''
# Build up some nice ranges and levels to be plotted
XX, YY = _getmesh(X,Y,Z)
extent = _getextent(extent, XX, YY)
vrange = _getvrange(vrange, XX,YY,Z, inaxis=inaxis)
levels = _getlevels(levels, vrange)
cmap = _getcmap(cmap)
# Smooth if needed
if smooth:
X,Y,Z = _smooth(X,Y,Z, smoothlen)
cs = pylab.contourf(X, Y, Z, levels,
vmin=vrange[0], vmax=vrange[1],
extent=extent, extend='both',
cmap=cmap)
ccs = pylab.contour(X, Y, Z, levels, vmin=vrange[0], vmax=vrange[1],
cmap=cmap)
# setup a colorbar, add in the lines, and then return it all out.
if addcolorbar:
cb = colorbar(cs, ccs, levels=levels, clabel=clabel)
return cs, ccs, cb
return cs, ccs
def viz_data(X, mu, sigma_sq):
X1, X2 = np.meshgrid(np.arange(0,35,0.5), np.arange(0,35,0.5))
X1_flattened = X1.flatten()
X2_flattened = X2.flatten()
new_X = np.empty((X1_flattened.size,2))
new_X[:, 0] = X1_flattened
new_X[:, 1] = X2_flattened
Z = multivariate_gaussian(new_X, mu, sigma_sq)
Z = Z.reshape(X1.shape)
plt.hold()
plt.plot(X[:,0], X[:,1], 'bx')
plt.contour(X1, X2, Z, levels=10.0**(np.arange(-20.0,0,3)))
plt.axis([0, 30, 0, 30])
plt.xlabel('Latency ms')
plt.ylabel('Tput Mbps')
plt.hold()
def plots(saliency_map):
"""
Positive/Negative values mean that when occluding that pixel the prediction went down/up.
Parameters
----------
saliency_map : np.array. shape(x,y)
Saliency map to be plotted
"""
# Plot mask and original image
fig, ax = plt.subplots(1,2, figsize=(12, 4))
cf = ax[0].imshow(saliency_map, clim=[np.amin(saliency_map), np.amax(saliency_map)])
fig.colorbar(cf, ax=ax[0], fraction=0.046, pad=0.04)
ax[0].set_title('Saliency map')
x,y = saliency_map.shape
ori_patch = np.array(ori)[(X-x)/2:(X+x)/2, (Y-y)/2:(Y+y)/2] #central patch
ax[1].imshow(ori_patch)
ax[1].set_title('Original image')
# Plot contour plots of the mask over the image
plt.figure()
plt.imshow(ori_patch)
CS = plt.contour(np.arange(saliency_map.shape[0]), np.arange(saliency_map.shape[1]), saliency_map)
plt.clabel(CS, inline=1, fontsize=10)
plt.title('Contour plot')
# Plot RGBA image (soft mask)
plt.figure()
saliency_map -= np.amin(saliency_map)
saliency_map /= np.amax(saliency_map)
alpha_channel = np.round(saliency_map*255)
rgba_arr = np.dstack((ori_patch, alpha_channel)).astype(np.uint8)
plt.imshow(rgba_arr)
plt.title('RGBA image')
def plot_contour(z,x,y,title="TITLE",xtitle="",ytitle="",xrange=None,yrange=None,plot_points=0,contour_levels=20,
cmap=None,cbar=True,fill=False,cbar_title="",show=1):
fig = plt.figure()
if fill:
fig = plt.contourf(x, y, z.T, contour_levels, cmap=cmap, origin='lower')
else:
fig = plt.contour( x, y, z.T, contour_levels, cmap=cmap, origin='lower')
if cbar:
cbar = plt.colorbar(fig)
cbar.ax.set_ylabel(cbar_title)
plt.title(title)
plt.xlabel(xtitle)
plt.ylabel(ytitle)
# the scatter plot:
if plot_points:
axScatter = plt.subplot(111)
axScatter.scatter( np.outer(x,np.ones_like(y)), np.outer(np.ones_like(x),y))
# set axes range
plt.xlim(xrange)
plt.ylim(yrange)
if show:
plt.show()
return fig
def draw_boundary(classifier):
dim = np.linspace(-1, 1.5, 1000)
dx, dy = np.meshgrid(dim, dim)
v = map_features(dx.flatten(), dy.flatten(), order=6)
z = (np.dot(classifier.coef_, v) + classifier.intercept_).reshape(
1000, 1000)
CS = plt.contour(dx, dy, z, levels=[0], colors=['r'])
def plot_model(data_array, mixture, axis=(0, 1), samples=20, contour_lines=20):
""" Plot the scaterplot of data_array and the contour lines of the
probability for the mixture.
"""
import matplotlib
import matplotlib.pylab as plt
import matplotlib.cm as cm
axis = list(axis)
if isinstance(mixture, GMClusterModel):
mixture = mixture.norm_model
if isinstance(data_array, Orange.data.Table):
data_array, _, _ = data_array.to_numpy_MA()
array = data_array[:, axis]
weights = mixture.weights
means = mixture.means[:, axis]
covariances = [cov[axis,:][:, axis] for cov in mixture.covariances] # TODO: Need the whole marginal distribution.
gmm = GMModel(weights, means, covariances)
min = numpy.min(array, 0)
max = numpy.max(array, 0)
extent = (min[0], max[0], min[1], max[1])
X = numpy.linspace(min[0], max[0], samples)
Y = numpy.linspace(min[1], max[1], samples)
Z = numpy.zeros((X.shape[0], Y.shape[0]))
for i, x in enumerate(X):
for j, y in enumerate(Y):
Z[i, j] = gmm([x, y])
plt.plot(array[:,0], array[:,1], "ro")
plt.contour(X, Y, Z.T, contour_lines,
extent=extent)
im = plt.imshow(Z.T, interpolation='bilinear', origin='lower',
cmap=cm.gray, extent=extent)
plt.plot(means[:, 0], means[:, 1], "b+")
plt.show()
def plot_interpolated(self):
plt.contourf(self.get_Xinterpolated_mesh(),
self.get_Yinterpolated_mesh(),
self.Z_INTERPOLATED,
50,
cmap=mpl.cm.jet)
plt.colorbar()
plt.contour(self.get_Xinterpolated_mesh(),
self.get_Yinterpolated_mesh(),
self.Z_INTERPOLATED,
20,
colors="k")
plt.plot(self.Xdeformed(), self.Ydeformed(), "or", label="Data")
plt.legend()
# plt.title = "Interpolated" <---- THIS MAKES ERROR IN THE NEXT PLOT!!!!!!!!!!!!!!!!!
plt.grid()
plt.show()
def plot(points, col):
n = 256
x = np.linspace(-100, 100, n)
y = np.linspace(-100, 100, n)
X, Y = np.meshgrid(x, y)
xs = []
ys = []
pl.contourf(X, Y, fun([X, Y]), 8, alpha=.75, cmap='jet')
pl.contour(X, Y, fun([X, Y]), 8, colors='black', linewidth=.5)
for i in range(len(points)):
xs.append(points[i][0])
ys.append(points[i][1])
pl.plot(xs, ys, marker='o', linestyle='--', color=str(col), label='Square')
def plotDecisonBoundary(theta, X, y):
plotData()
zi = np.linspace(-1.5, 1.5, 50)
zj = np.linspace(-1.5, 1.5, 50)
z = np.ones((zi.size, zj.size))
print(np.shape(z))
for i in range(0, zi.size):
for j in range(0, zj.size):
z[i][j] = np.dot(mapFeature(zi[i], zj[j]), theta)
plt.contour(zi,
zj,
z,
levels=[0],
colors='black',
label='Decision Boundary')
plt.show()
def plot_contour_pair(xi, yi, zi):
fig = plt.figure(figsize=(2 * w, golden_mean * w * 2))
ax = fig.add_subplot(1, 2, 1, projection='3d')
cs = plt.contour(xi, yi, zi, 15, linewidths=0.5, color='k')
ax = fig.add_subplot(1, 2, 2, projection='3d')
xig, yig = np.meshgrid(xi, yi)
surf = ax.plot_surface(xig, yig, zi, linewidth=0)
return fig
def conto_plots(Data,DataMHD,**kwargs):
Qu = jana.quantities()
Cur = Qu.Current(Data)
CurMHD = Qu.Current(DataMHD)
Fastsp = Qu.Magspeed(Data)['fast']
Slowsp = Qu.Magspeed(Data)['slow']
Alfvsp = Qu.Magspeed(Data)['alfven']
Vpol = np.sqrt(Data.v1**2 + Data.v2**2)
FastspMHD = Qu.Magspeed(DataMHD)['fast']
SlowspMHD = Qu.Magspeed(DataMHD)['slow']
AlfvspMHD = Qu.Magspeed(DataMHD)['alfven']
VpolMHD = np.sqrt(DataMHD.v1**2 + DataMHD.v2**2)
fastrat = Fastsp/Vpol
slowrat = Slowsp/Vpol
Alfvrat = Alfvsp/Vpol
fastratMHD = FastspMHD/VpolMHD
slowratMHD = SlowspMHD/VpolMHD
AlfvratMHD = AlfvspMHD/VpolMHD
f1 = plt.figure(num=1)
ax1 = f1.add_subplot(121)
currcont=plt.contour(Data.x1,Data.x2,Cur.T,kwargs.get('Currents',[-0.7,-0.6,-0.5,-0.4,-0.3]),colors=kwargs.get('colors','r'),linestyles=kwargs.get('ls','-'),lw=kwargs.get('lw',2.0))
plt.clabel(currcont,manual=True)
currmhdcont = plt.contour(DataMHD.x1,DataMHD.x2,CurMHD.T,kwargs.get('Currents',[-0.7,-0.6,-0.5,-0.4,-0.3]),colors=kwargs.get('colors','k'),linestyles=kwargs.get('ls','-'),lw=kwargs.get('lw',2.0))
plt.clabel(currmhdcont,manual=True)
plt.xlabel(r'r [AU]')
plt.ylabel(r'z [AU]')
plt.title(r'Total Current -- $\int\int J_{z} r dr d\phi$')
ax2 = f1.add_subplot(122)
plt.xlabel(r'r [AU]')
#plt.ylabel(r'$z [AU]$')
plt.title(r'Critical Surfaces')
fcont=plt.contour(Data.x1,Data.x2,fastrat.T,[1.0],colors='r',linestyles='solid')
plt.clabel(fcont,inline=1,fmt=r'Fast')
scont=plt.contour(Data.x1,Data.x2,slowrat.T,[1.0],colors='r',linestyles='dashdot')
plt.clabel(scont,inline=1,fmt=r'Slow')
acont=plt.contour(Data.x1,Data.x2,Alfvrat.T,[1.0],colors='r',linestyles='dashed')
plt.clabel(acont,inline=1,fmt=r'Alfv$\acute{e}$n')
mfcont=plt.contour(DataMHD.x1,DataMHD.x2,fastratMHD.T,[1.0],colors='k',linestyles='solid')
plt.clabel(mfcont,manual=1,fmt=r'Fast')
mscont=plt.contour(DataMHD.x1,DataMHD.x2,slowratMHD.T,[1.0],colors='k',linestyles='dashdot')
plt.clabel(mscont,manual=1,fmt=r'Slow')
macont=plt.contour(DataMHD.x1,DataMHD.x2,AlfvratMHD.T,[1.0],colors='k',linestyles='dashed')
plt.clabel(macont,manual=1,fmt=r'Alfv$\acute{e}$n')
def visualize_GD():
'''
Created on Oct 28, 2010
@author: Peter
'''
import matplotlib
import numpy as np
import matplotlib.cm as cm
import matplotlib.mlab as mlab
import matplotlib.pyplot as plt
leafNode = dict(boxstyle="round4", fc="0.8")
arrow_args = dict(arrowstyle="<-")
matplotlib.rcParams['xtick.direction'] = 'out'
matplotlib.rcParams['ytick.direction'] = 'out'
delta = 0.025
x = np.arange(-2.0, 2.0, delta)
y = np.arange(-2.0, 2.0, delta)
X, Y = np.meshgrid(x, y)
Z1 = -((X-1)**2)
Z2 = -(Y**2)
#Z1 = mlab.bivariate_normal(X, Y, 1.0, 1.0, 0.0, 0.0)
#Z2 = mlab.bivariate_normal(X, Y, 1.5, 0.5, 1, 1)
# difference of Gaussians
Z = 1.0 * (Z2 + Z1)+5.0
# Create a simple contour plot with labels using default colors. The
# inline argument to clabel will control whether the labels are draw
# over the line segments of the contour, removing the lines beneath
# the label
plt.figure()
CS = plt.contour(X, Y, Z)
plt.annotate('', xy=(0.05, 0.05), xycoords='axes fraction',
xytext=(0.2,0.2), textcoords='axes fraction',
va="center", ha="center", bbox=leafNode, arrowprops=arrow_args )
plt.text(-1.9, -1.8, 'P0')
plt.annotate('', xy=(0.2,0.2), xycoords='axes fraction',
xytext=(0.35,0.3), textcoords='axes fraction',
va="center", ha="center", bbox=leafNode, arrowprops=arrow_args )
plt.text(-1.35, -1.23, 'P1')
plt.annotate('', xy=(0.35,0.3), xycoords='axes fraction',
xytext=(0.45,0.35), textcoords='axes fraction',
va="center", ha="center", bbox=leafNode, arrowprops=arrow_args )
plt.text(-0.7, -0.8, 'P2')
plt.text(-0.3, -0.6, 'P3')
plt.clabel(CS, inline=True, fontsize=10)
plt.title('Gradient Ascent')
plt.xlabel('x')
plt.ylabel('y')
plt.show()
def __call__(self, **params):
p=ParamOverrides(self,params)
name=p.plot_template.keys().pop(0)
plot=make_template_plot(p.plot_template,
p.sheet.views.Maps, p.sheet.xdensity,p.sheet.bounds,
p.normalize,name=p.plot_template[name])
fig = plt.figure(figsize=(5,5))
if plot:
bitmap=plot.bitmap
isint=plt.isinteractive() # Temporarily make non-interactive for plotting
plt.ioff() # Turn interactive mode off
plt.imshow(bitmap.image,origin='lower',interpolation='nearest')
plt.axis('off')
for (t,pref,sel,c) in p.overlay:
v = plt.flipud(p.sheet.views.Maps[pref].view()[0])
if (t=='contours'):
plt.contour(v,[sel,sel],colors=c,linewidths=2)
if (t=='arrows'):
s = plt.flipud(p.sheet.views.Maps[sel].view()[0])
scale = int(np.ceil(np.log10(len(v))))
X = np.array([x for x in xrange(len(v)/scale)])
v_sc = np.zeros((len(v)/scale,len(v)/scale))
s_sc = np.zeros((len(v)/scale,len(v)/scale))
for i in X:
for j in X:
v_sc[i][j] = v[scale*i][scale*j]
s_sc[i][j] = s[scale*i][scale*j]
plt.quiver(scale*X, scale*X, -np.cos(2*np.pi*v_sc)*s_sc,
-np.sin(2*np.pi*v_sc)*s_sc, color=c,
edgecolors=c, minshaft=3, linewidths=1)
p.title='%s overlaid with %s at time %s' %(plot.name,pref,topo.sim.timestr())
if isint: plt.ion()
p.filename_suffix="_"+p.sheet.name
self._generate_figure(p)
return fig
def __hist2d(self,x,y,contour=False,bins=(200,200),cmap="Purples",interpolation='nearest',origin="lower", colors="k"):
"""
Parameters
----------
bins : tuple of two ints
"""
H, xedges, yedges = np.histogram2d(x, y, bins)
extent = [xedges.min(), xedges.max(), yedges.min(), yedges.max()]
if not contour:
plt.imshow(H, extent=extent, interpolation=interpolation,origin=origin, cmap=cmap, aspect="auto")
# plt.colorbar(fontsize=4)
else:
CS = plt.contour(H, extent=extent,origin=origin,colors=colors)
plt.clabel(CS, inline=1, fontsize=10)
def scaling_plot(df, zcol, title, zdas=None, xcol='numIsilonNodes', xlabel=None, ycol='numPhysicalComputeNodes', ylabel=None):
if xlabel == None: xlabel = xcol
if ylabel == None: ylabel = ycol
x = df[xcol].values
y = df[ycol].values
z = df[zcol].values
# Set up a regular grid of interpolation points
xi, yi = np.linspace(x.min(), x.max(), 100), np.linspace(y.min(), y.max(), 100)
xi, yi = np.meshgrid(xi, yi)
# Interpolate
zi = scipy.interpolate.griddata((x, y), z, (xi, yi), method='cubic')
fig = plt.figure(title)
fig.clf()
plt.set_cmap(cm.jet)
plt.imshow(zi, vmin=z.min(), vmax=z.max(), origin='lower',
extent=[x.min(), x.max(), y.min(), y.max()], aspect='auto')
# Draw circles on actual measurement points
plt.scatter(x, y, c=z)
plt.colorbar()
CS = plt.contour(xi, yi, zi, colors='k')
plt.clabel(CS, inline=1, fontsize=10, fmt='%1.0f')
if zdas is not None:
dasNodes = np.arange(df.numPhysicalComputeNodes.min(), 2 * df.numPhysicalComputeNodes.max() + 1)
dasZ = zdas * dasNodes
CS = plt.contour(xi, yi, zi, colors='k', linestyles='dashed', levels=dasZ)
fmtdict = {x[1]: 'DAS ' + str(int(x[0])) for x in zip(dasNodes, dasZ)}
plt.clabel(CS, inline=1, fontsize=10, fmt=fmtdict)
plt.title(title)
plt.ylabel(ylabel)
plt.xlabel(xlabel)
plt.show()
def plot(x,y,data,filename):
plt.figure()
# define grid.
xi = np.linspace(min(x),max(x),100)
yi = np.linspace(min(y),max(y),100)
# grid the data.
si = griddata((x, y), data, (xi[None,:], yi[:,None]), method='linear')
# contour the gridded data, plotting dots at the randomly spaced data points.
CS = plt.contour(xi,yi,si,30,linewidths=0.5,colors='k')
CS = plt.contourf(xi,yi,si,30,cmap=plt.cm.jet)
plt.colorbar() # draw colorbar
# plot data points.
# plt.scatter(x,y,marker='o',c='b',s=5)
plt.xlim(min(x),max(x))
plt.ylim(min(y),max(y))
plt.savefig(filename)
def plot(points):
"""
Plotting 2D function and way search
"""
n = 256
x = np.linspace(-12, 12, n)
y = np.linspace(-12, 12, n)
X, Y = np.meshgrid(x, y)
xs = []
ys = []
pl.contourf(X, Y, fun([X, Y]), 8, alpha=0.75, cmap="jet")
C = pl.contour(X, Y, fun([X, Y]), 8, colors="black", linewidth=0.5)
for i in range(len(points)):
xs.append(points[i][0])
ys.append(points[i][1])
pl.plot(xs, ys, marker="o", linestyle="--", color="r", label="Square")
def plot(points):
'''
Plotting 2D function and way search
'''
n = 256
x = np.linspace(-12, 12, n)
y = np.linspace(-12, 12, n)
X, Y = np.meshgrid(x, y)
xs = []
ys = []
pl.contourf(X, Y, fun([X, Y]), 8, alpha=.75, cmap='jet')
C = pl.contour(X, Y, fun([X, Y]), 8, colors='black', linewidth=.5)
for i in range(len(points)):
xs.append(points[i][0])
ys.append(points[i][1])
pl.plot(xs, ys, marker='o', linestyle='--', color='r', label='Square')
def PlotDecisionBoundary(theta, X, y):
if np.shape(X)[1] <= 3:
# 2 points to define a line, so choose two endpoints
plot_x = np.zeros(2)
plot_x[0] = np.min(X[:,1])-2
plot_x[1] = np.max(X[:,1])+2
# Calculate the decision boundary line
plot_y = (-1/theta[2])*(theta[1]*plot_x + theta[0])
plt.figure()
PlotData.PlotData(X[:,1:3], y)
plt.plot(plot_x, plot_y, label = 'Decision Boundary')
plt.legend(bbox_to_anchor=(0.4, 1.35), loc = 1)
plt.xlim(30, 100)
plt.ylim(30, 100)
plt.show()
else:
# grid range
u = np.linspace(-1, 1.5, 50)
v = np.linspace(-1, 1.5, 50)
z = np.zeros((len(u), len(v)))
for i in range(len(u)):
for j in range(len(v)):
z[i,j] = MapFeature.MapFeature(np.array([u[i]]), np.array([v[j]])).dot(theta)
z = z.T
plt.figure()
PlotData.PlotData(X[:,1:3], y)
cs = plt.contour(u, v, z, levels = [0.0, 0.0], colors = 'k')
cs.collections[0].set_label('Decision Boundary')
plt.legend(bbox_to_anchor=(0.4, 1.35), loc = 1)
# plt.xlim(30, 100)
# plt.ylim(30, 100)
plt.show()
def drawPredictionSpace( model ):
#plt.figure()
nGridPoints = 200
predictionPoints = getGrid( nGridPoints, [-6.,6.],[-6.,6.] )[1]
predictions = np.array(model.predict( predictionPoints )[0])
redChannel = predictions[:,0].reshape(nGridPoints,nGridPoints)
greenChannel = predictions[:,1].reshape(nGridPoints,nGridPoints)
blueChannel = predictions[:,2].reshape(nGridPoints,nGridPoints)
#plt.imshow( np.flipud( np.array( [ redChannel, blueChannel, greenChannel ] ).T ) )
plt.figure()
levels = [0.35, 0.97, 0.991]
for level in levels: # loop helps matplotlib2tikz
plt.contour(predictionPoints[:,0].reshape(nGridPoints, nGridPoints), predictionPoints[:,1].reshape(nGridPoints, nGridPoints), redChannel, levels=[level], colors='r', lw=3)
plt.contour(predictionPoints[:,0].reshape(nGridPoints, nGridPoints), predictionPoints[:,1].reshape(nGridPoints, nGridPoints), blueChannel, levels=[level], colors='g', lw=3)
plt.contour(predictionPoints[:,0].reshape(nGridPoints, nGridPoints), predictionPoints[:,1].reshape(nGridPoints, nGridPoints), greenChannel, levels=[level], colors='b', lw=3)
plt.plot(model.Z[:,0], model.Z[:,1], 'ko', mew=0, ms=5)
for i,col in enumerate('rbg'):
ii = model.Y.flat==i
plt.plot(model.X[ii,0], model.X[ii,1],col+'o', mew=0, ms=6, alpha=0.5)
plt.xlim(-6,6)
plt.ylim(-5,5)
pdf_values = np.ndarray(shape)
for ix in range(shape[0]):
for iy in range(shape[1]):
x, y = grid_x[ix, iy], grid_y[ix, iy]
theoretical_pdf = computeTheoriquePDF(x, y)
u = [x, y]
tic = time.time()
pdf_estimate = distribution.computePDF(u)
toc = time.time()
pdf_values[ix, iy] = pdf_estimate
dt.append(toc - tic)
print "dt = %s"%(toc-tic)
delta += abs((pdf_estimate - theoretical_pdf))**2
error = pdf_estimate - theoretical_pdf
abs_error = abs(error) / theoretical_pdf
print "pdf_estimate=%s pdf_theoretical=%s, error=%s, abs_error=%s"%(pdf_estimate, theoretical_pdf, error, abs_error)
# Variation of characteristic function
delta /= (shape[0] * shape[1])
print "delta of pdf=%s" %(np.sqrt(delta))
try :
import matplotlib.pylab as plt
fig = plt.figure()
plt.contour(pdf_values, vmin=np.min(pdf_values), vmax=np.max(pdf_values), origin='lower', extent=[xmin+0.25*dx, xmax-0.25*dx, ymin+0.25*dy, ymax-0.25*dy])
plt.colorbar()
plt.savefig("3Normals2d_pdf.pdf")
plt.close('all')
except ImportError:
ot.log.Warn("Matplotlib not found. Could not create iso values graph of pdf")