def multiple_optima(gene_number=937, resolution=80, model_restarts=10, seed=10000, max_iters=300, optimize=True, plot=True):
"""
Show an example of a multimodal error surface for Gaussian process
regression. Gene 939 has bimodal behaviour where the noisy mode is
higher.
"""
# Contour over a range of length scales and signal/noise ratios.
length_scales = np.linspace(0.1, 60., resolution)
log_SNRs = np.linspace(-3., 4., resolution)
try:import pods
except ImportError:
print 'pods unavailable, see https://github.com/sods/ods for example datasets'
return
data = pods.datasets.della_gatta_TRP63_gene_expression(data_set='della_gatta',gene_number=gene_number)
# data['Y'] = data['Y'][0::2, :]
# data['X'] = data['X'][0::2, :]
data['Y'] = data['Y'] - np.mean(data['Y'])
lls = GPy.examples.regression._contour_data(data, length_scales, log_SNRs, GPy.kern.RBF)
if plot:
pb.contour(length_scales, log_SNRs, np.exp(lls), 20, cmap=pb.cm.jet)
ax = pb.gca()
pb.xlabel('length scale')
pb.ylabel('log_10 SNR')
xlim = ax.get_xlim()
ylim = ax.get_ylim()
# Now run a few optimizations
models = []
optim_point_x = np.empty(2)
optim_point_y = np.empty(2)
np.random.seed(seed=seed)
for i in range(0, model_restarts):
# kern = GPy.kern.RBF(1, variance=np.random.exponential(1.), lengthscale=np.random.exponential(50.))
kern = GPy.kern.RBF(1, variance=np.random.uniform(1e-3, 1), lengthscale=np.random.uniform(5, 50))
m = GPy.models.GPRegression(data['X'], data['Y'], kernel=kern)
m.likelihood.variance = np.random.uniform(1e-3, 1)
optim_point_x[0] = m.rbf.lengthscale
optim_point_y[0] = np.log10(m.rbf.variance) - np.log10(m.likelihood.variance);
# optimize
if optimize:
m.optimize('scg', xtol=1e-6, ftol=1e-6, max_iters=max_iters)
optim_point_x[1] = m.rbf.lengthscale
optim_point_y[1] = np.log10(m.rbf.variance) - np.log10(m.likelihood.variance);
if plot:
pb.arrow(optim_point_x[0], optim_point_y[0], optim_point_x[1] - optim_point_x[0], optim_point_y[1] - optim_point_y[0], label=str(i), head_length=1, head_width=0.5, fc='k', ec='k')
models.append(m)
if plot:
ax.set_xlim(xlim)
ax.set_ylim(ylim)
return m # (models, lls)
def draw_bar(xs, y, dat):
global scale
for ix in range(len(xs)):
if dat[ix] > 0: color = "red"
else: color = "blue"
pl.arrow(xs[ix], y/2., scale*dat[ix], 0, color=color)
def plot_profile(self):
self.logger.debug('Plotting Profile curves')
try:
xnew = np.linspace(self.time[0], self.time[-1], num=50)
#Function handle for generating plot interpolate points
f1 = lambda (tck): interpolate.splev(xnew, tck)
ynew = np.array(map(f1, self.tcks)).T
ax = pl.gca()
color_list = ['r', 'g', 'b', 'c', 'y']
ax.set_color_cycle(color_list)
pl.plot(self.time, self.var, 'x', xnew, ynew)
# plot arrows
arrow_scale = 40.0
dx = (self.time[-1] - self.time[0]) / arrow_scale
dy = self.slopes.T * dx # transpose operation here
for ii in range(self.n_sample):
t = self.time[ii]
X = self.var[ii, :]
DY = dy[:, ii]
for jj in range(self.n_var):
pl.arrow(t, X[jj], dx, DY[jj], linewidth=1)
pl.title('Plot of spline fitted biochem profile vs time')
pl.xlabel('time')
pl.ylabel('profile')
pl.axis('tight')
pl.show()
except AttributeError:
sys.stderr.writelines("Define Profile before trying to plot..!")
raise
def arc(xx, yy, index, draw_dots=True):
A = array([xx[0], yy[0]])
B = array([xx[1], yy[1]])
if draw_dots:
plot(A[0], A[1], "ko")
plot(B[0], B[1], "ko")
AB = B-A
AB_len = sqrt(sum(AB**2))
AB = AB / AB_len
pAB = array([AB[1], -AB[0]])
AB_mid = (A+B)/2.
if index == 1:
R = AB_mid + pAB * AB_len/1.5
else:
R = AB_mid + pAB * AB_len/4.
r = sqrt(sum((A-R)**2))
P_arrow = R - pAB * r
# Draw the arc from A to B centered at R
phi1 = atan2((A-R)[1], (A-R)[0])
phi2 = atan2((B-R)[1], (B-R)[0])
n = 100 # number of divisions
phi = linspace(phi1, phi2, n)
xx = r*cos(phi)+R[0]
yy = r*sin(phi)+R[1]
plot(xx, yy, "k-", lw=2)
x, x2 = xx[n/2-1:n/2+1]
y, y2 = yy[n/2-1:n/2+1]
dx = x2-x
dy = y2-y
arrow(x, y, dx/2, dy/2, fc="black", head_width=0.05)
def get_cov_ev(cov, plot=False):
import numpy as np
import pandas as pd
cov = np.mat(cov)
eig_vals, eig_vecs = np.linalg.eig(cov)
df = pd.DataFrame()
df['ev_x'] = eig_vecs[0, :].tolist()[0]
df['ev_y'] = eig_vecs[1, :].tolist()[0]
df['e_values'] = eig_vals
df['e_values_sqrt'] = df.e_values.apply(np.sqrt)
df.fillna(0, inplace=True)
df = df.sort_values(by='e_values', ascending=False).reset_index()
main_axis=df.ev_x[0] * df.e_values_sqrt[0], df.ev_y[0] * df.e_values_sqrt[0]
angle = vector_to_angle(main_axis[0], main_axis[1]) # from -135 to 45 degrees
angle = angle if angle >= -90 else 180+angle # to make it from -90 to 90
if plot:
print('cov\n\t' + str(cov).replace('\n', '\n\t'))
import pylab as plt
samples = 100
df_original_multi_samples = pd.DataFrame(np.random.multivariate_normal([0, 0], cov, samples), columns=['X', 'Y'])
df_original_multi_samples.plot.scatter(x='X', y='Y', alpha=0.1)
m = df_original_multi_samples.max().max()
plt.axis([-m, m, -m, m])
for i in [0, 1]: # 0 is the main eigenvector
if df.ev_x[i] * df.e_values_sqrt[i] + df.ev_y[i] * df.e_values_sqrt[i]: # cannot plot 0 size vector
plt.arrow(0, 0,
df.ev_x[i] * df.e_values_sqrt[i], df.ev_y[i] * df.e_values_sqrt[i],
head_width=0.15, head_length=0.15,
length_includes_head=True, fc='k', ec='k')
else:
print('zero length eigenvector, skipping')
plt.show()
return df, angle
def plot_profile(self) :
self.logger.debug('Plotting Profile curves')
try :
xnew = np.linspace(self.time[0],self.time[-1],num=50)
#Function handle for generating plot interpolate points
f1 = lambda(tck) : interpolate.splev(xnew,tck)
ynew = np.array(map(f1,self.tcks)).T
ax = pl.gca()
color_list = ['r','g','b','c','y']
ax.set_color_cycle(color_list)
pl.plot(self.time,self.var,'x',xnew,ynew);
# plot arrows
arrow_scale = 40.0
dx = (self.time[-1]-self.time[0])/arrow_scale;
dy = self.slopes.T * dx # transpose operation here
for ii in range(self.n_sample) :
t = self.time[ii]
X = self.var[ii,:]
DY = dy[:,ii]
for jj in range(self.n_var) :
pl.arrow(t,X[jj],dx,DY[jj],linewidth=1)
pl.title('Plot of spline fitted biochem profile vs time')
pl.xlabel('time')
pl.ylabel('profile')
pl.axis('tight')
pl.show()
except AttributeError :
sys.stderr.writelines(
"Define Profile before trying to plot..!")
raise
def plot_ROC_Risk(w,
x,
y,
best_operating_point,
risk,
fname,
title,
TH=None,
NoTH=None):
from matplotlib import rc
from numpy import ones
import pylab
rc('font', family='serif', size=20)
fig = pylab.figure(1, figsize=(8, 8), dpi=100, facecolor='w')
ax = fig.add_subplot(111)
fig.hold(True)
m = w[0] / w[1]
line_x = arange(0, 1, 0.001)
line_y = ones(1000) - m * line_x
pylab.fill_between(x, ones(len(y)), y, facecolor='#D0D0D0')
pylab.plot(x, y, 'r', linewidth=3)
best = [x[best_operating_point], y[best_operating_point]]
pylab.plot(best[0],
best[1],
'*k',
markersize=20,
label='Risk$^*$ ={0:.3f}'.format(risk))
pylab.plot(line_x, line_y, 'k', linewidth=3)
midline = len(line_x) / 2
arrow_x, arrow_y = line_x[midline], line_y[midline]
pylab.arrow(arrow_x,
arrow_y,
-w[0] * 0.15,
-w[1] * 0.15,
head_length=.02,
head_width=.02,
linewidth=2,
color='black')
pylab.axis([-0.005, 1.001, -0.005, 1.001])
pylab.xlabel('$FPR$')
pylab.ylabel('$FNR$')
pylab.title(title)
if TH != None:
pylab.plot(TH['fpr'],
TH['fnr'],
'ob',
markersize=12,
label='TH Risk={0:.3f}'.format(TH['risk']))
if NoTH != None:
pylab.plot(NoTH['fpr'],
NoTH['fnr'],
'sc',
markersize=12,
label='BM Risk={0:.3f}'.format(NoTH['risk']))
pyplot.legend(numpoints=1, prop={'size': 16})
pylab.savefig(fname)
pylab.grid()
ax.set_aspect('equal')
pylab.show()
pylab.close()
def plotAssignment(idx, coords, centroids, warehouseCoord, output):
V = max(idx) + 1
cmap = plt.cm.get_cmap('Dark2')
customerColors = [cmap(1.0 * idx[i] / V) for i in range(len(idx))]
centroidColors = [cmap(1.0 * i / V) for i in range(V)]
xy = coords
pylab.scatter([warehouseCoord[0]], [warehouseCoord[1]])
pylab.scatter(centroids[:,0], centroids[:,1], marker='o', s=500, linewidths=2, c='none')
pylab.scatter(centroids[:,0], centroids[:,1], marker='x', s=500, linewidths=2, c=centroidColors)
pylab.scatter(xy[:,0], xy[:,1], s=100, c=customerColors)
for cluster in range(V):
customerIndices = indices(cluster, idx)
clusterCustomersCoords = [warehouseCoord] + [list(coords[i]) for i in customerIndices]
N = len(clusterCustomersCoords)
for i in range(N):
j = (i+1) % N
x = clusterCustomersCoords[i][0]
y = clusterCustomersCoords[i][1]
dx = clusterCustomersCoords[j][0] - clusterCustomersCoords[i][0]
dy = clusterCustomersCoords[j][1] - clusterCustomersCoords[i][1]
pylab.arrow(x, y, dx, dy, color=centroidColors[cluster], fc="k",
head_width=1.0, head_length=2.5, length_includes_head=True)
pylab.savefig(output)
pylab.close()
def fig_spec(po, pos, sig_loc, typ=0):
ax1 = py.subplot(gs[pos[2]:pos[3], pos[0]:pos[1]])
set_axis(ax1, -0.05, 1.05, letter= po)
freq, time_spec, spec_mtrx = spectrogram(sig_loc, Fs, nperseg=2*Fs)
im = py.pcolormesh(time_spec/60, freq, spec_mtrx,
norm = LogNorm(vmin = 1e1, vmax=5e2), vmax=400, cmap= 'Greens')
py.ylim(0,150)
# cbar=py.colorbar()
# cbar.ax.set_title('power ($mV^2$)', fontsize = 12)
times = [2.9, 3.4, 6.3, 6.8]
if typ=='naris':
for time in times:
py.axvline(time, color='grey', ls='--', lw=1)
py.text(2.6, 160, 'naris block', color='black', fontsize=15)
py.text(6, 160, 'naris block', color='black', fontsize=15)
else:
py.axvline(1.45, color='grey', ls='--', lw=4)
py.text(1.45, 170, 'KX injection', color='black', fontsize=15)
py.arrow(1.45, 165, 0, -10, length_includes_head=True, clip_on = False,
head_width=0.1, head_length=4)
# py.axvline(105, color='red', ls='--', lw=2)
ax1.spines['right'].set_visible(False)
ax1.spines['top'].set_visible(False)
py.xlabel('Time (min)')
py.ylabel('Frequency (Hz)')
cax2 = make_axes_locatable(ax1).append_axes("right", size="5%", pad=0)
cbar = py.colorbar(im, cax = cax2)#, format=mpl.ticker.FuncFormatter(fmt))
cbar.ax.set_title('$mV^2$', fontsize = 12)
cbar.ax.tick_params(labelsize=12)
def triangle_vector_space(S,T,r, steps = 21): """ This draws the phase space in term of the triangular description of phase space, given a game specified by S, T and r. Steps defines the number ofdecrete steps to take in each axis. Note ==== This was a mostly experimental idea, it is not currently in use """ ##Initialise a population at a certain point, with small frequencies of mutants around it M = GP_evo3(S,T,r=r, steps = steps) pl.figure() pl.plot( [0,.5],[0,1], color = 'black', linewidth = 1 ) pl.plot( [0.5,1],[1,0], color = 'black', linewidth = 1 ) xa_s = np.linspace(0,1,101) pl.plot( xa_s, map(M.phi_R,xa_s), '--', color = 'black', linewidth = 2.5 ) pl.xlabel( '$x_A$', fontsize = 30 ) pl.ylabel( '$\\varphi$', fontsize = 30 ) for i in xrange(steps): for j in xrange(steps): arrow = delta_x(i,j,M) #print arrow pl.arrow( *arrow ) pl.show()
def plot_match_displacement(im1, locs1, locs2, matchscores, numMatches=-1):
""" show a figure with lines where feats in im1 moved to in im2
input: im1 (image as array), locs1,locs2 (location of features),
matchscores (as output from 'match'), numMatches (number of matches to plot) """
if numMatches == -1:
numMatches = len(matchscores)
pylab.gray()
pylab.imshow(im1)
cols1 = im1.shape[1]
for i in range(numMatches):
if matchscores[i] > 0:
pylab.arrow(locs1[i, 1],
locs1[i, 0],
locs2[int(matchscores[i]), 1] - locs1[i, 1],
locs2[int(matchscores[i]), 0] - locs1[i, 0],
head_width=1.0,
head_length=2.0,
linewidth=0.5,
fc='r',
ec='r')
pylab.axis('off')
pylab.show()
def plot(self,plot_frame,**kwargs):
import pylab as plb
default_args = {'draw_frame':True,
'frame_head_width':20,
'contour_kwargs':{'edgecolor': 'none',
'linewidth': 0.0,
'facecolor': 'none'}}
from pylab import plot,arrow
lines = self.model.coords_from_frame(plot_frame)
self.curves = list()
#plot_args = kwargs.pop('plot_args',default_args)
for line_key in lines.keys():
try:
element_args = kwargs['contour_kwargs'][line_key]
except KeyError:
element_args = default_args['contour_kwargs']
line = lines[line_key]
from matplotlib.patches import Polygon
poly = Polygon(zip(line[0,:],line[1,:]),**element_args)
#plb.plot([1,2,3,4])
plb.gca().add_patch(poly,)
if 'draw_frame' in kwargs.keys():
if kwargs['draw_frame']:
frame_args = dict()
p = plot_frame['p']
a1 = plot_frame['a1']
a2 = plot_frame['a2']
frame_args['color'] = 'g'
frame_args['head_width'] = kwargs['frame_head_width']
arrow(p[0],p[1],a1[0],a1[1],**frame_args)
frame_args['color'] = 'b'
frame_args['head_width'] = kwargs['frame_head_width']
arrow(p[0],p[1],a2[0],a2[1],**frame_args)
def plot_ch():
for job in jobs_orig:
print "plane of", job.path
pylab.clf()
x_center = int((job.position(0)[0] + job.position(1)[0])/2)
x_final = 50 + x_center
#plane = np.concatenate((job.plane(y=50)[:, x_final:],
# job.plane(y=50)[:, :x_final]), axis=1)
plane = job.plane(y=50)
myplane = plane[plane < 0.0]
p0 = myplane.min()
p12 = np.median(myplane)
p14 = np.median(myplane[myplane<p12])
p34 = np.median(myplane[myplane>p12])
p1 = myplane.max()
contour_values = (p0, p14, p12, p34, p1)
pylab.title(r'$u=%.4f,\ D=%.4f,\ Q=%i$ ' %
((job.u_x**2+job.u_y**2)**0.5, job.D_minus, job.ch_objects))
car = pylab.imshow(plane, vmin=-0.001, vmax=0.0,
interpolation='nearest')
pylab.contour(plane, contour_values, linestyles='dashed',
colors='white')
print job.u_x, job.u_y
pylab.grid(True)
pylab.colorbar(car)
pylab.arrow(1, 1, 2*job.u_x/(job.u_x if job.u_x else 1.0), 2*job.u_y/(job.u_y if job.u_y else 1.0), width=0.5)
#imgfilename = 'plane_r20-y50-u_x%.4fD%.4fch%03i.png' % \
# (job.u_x, job.D_minus, job.ch_objects)
imgfilename = 'plane_%s.png' % job.job_id
pylab.savefig(imgfilename)
def add_point(event): x, y = event.xdata, event.ydata points.append((x, y)) pylab.cla() pylab.scatter(*zip(*points)) pylab.xlim(-10, 10) pylab.ylim(-10, 10) pylab.draw() if len(points) < 3: return c, r = three_point_circle(*points) cir = pylab.Circle(c, r) pylab.gca().add_patch(cir) for p in points: angle = angle_at_point(c, p) if angle < 0: angle += 2*np.pi if angle >= np.pi: angle = angle - np.pi print np.degrees(angle) dx, dy = np.array((np.cos(angle), np.sin(angle))) pylab.text(p[0], p[1], "%.2f"%np.degrees(angle)) pylab.arrow(p[0], p[1], dx, dy) pylab.show()
def arc(xx, yy, index):
A = array([xx[0], yy[0]])
B = array([xx[1], yy[1]])
plot(A[0], A[1], "ko")
plot(B[0], B[1], "ko")
AB = B - A
AB_len = sqrt(sum(AB**2))
AB = AB / AB_len
pAB = array([AB[1], -AB[0]])
AB_mid = (A + B) / 2.
if index == 1:
R = AB_mid + pAB * AB_len / 1.5
else:
R = AB_mid + pAB * AB_len / 4.
r = sqrt(sum((A - R)**2))
P_arrow = R - pAB * r
# Draw the arc from A to B centered at R
phi1 = atan2((A - R)[1], (A - R)[0])
phi2 = atan2((B - R)[1], (B - R)[0])
n = 100 # number of divisions
phi = linspace(phi1, phi2, n)
xx = r * cos(phi) + R[0]
yy = r * sin(phi) + R[1]
plot(xx, yy, "k-", lw=2)
x, x2 = xx[n / 2 - 1:n / 2 + 1]
y, y2 = yy[n / 2 - 1:n / 2 + 1]
dx = x2 - x
dy = y2 - y
arrow(x, y, dx / 2, dy / 2, fc="black", head_width=0.05)
def multiple_optima(gene_number=937, resolution=80, model_restarts=10, seed=10000, optim_iters=300):
"""Show an example of a multimodal error surface for Gaussian process regression. Gene 939 has bimodal behaviour where the noisey mode is higher."""
# Contour over a range of length scales and signal/noise ratios.
length_scales = np.linspace(0.1, 60.0, resolution)
log_SNRs = np.linspace(-3.0, 4.0, resolution)
data = GPy.util.datasets.della_gatta_TRP63_gene_expression(gene_number)
# data['Y'] = data['Y'][0::2, :]
# data['X'] = data['X'][0::2, :]
data["Y"] = data["Y"] - np.mean(data["Y"])
lls = GPy.examples.regression._contour_data(data, length_scales, log_SNRs, GPy.kern.rbf)
pb.contour(length_scales, log_SNRs, np.exp(lls), 20, cmap=pb.cm.jet)
ax = pb.gca()
pb.xlabel("length scale")
pb.ylabel("log_10 SNR")
xlim = ax.get_xlim()
ylim = ax.get_ylim()
# Now run a few optimizations
models = []
optim_point_x = np.empty(2)
optim_point_y = np.empty(2)
np.random.seed(seed=seed)
for i in range(0, model_restarts):
# kern = GPy.kern.rbf(1, variance=np.random.exponential(1.), lengthscale=np.random.exponential(50.))
kern = GPy.kern.rbf(1, variance=np.random.uniform(1e-3, 1), lengthscale=np.random.uniform(5, 50))
m = GPy.models.GPRegression(data["X"], data["Y"], kernel=kern)
m["noise_variance"] = np.random.uniform(1e-3, 1)
optim_point_x[0] = m["rbf_lengthscale"]
optim_point_y[0] = np.log10(m["rbf_variance"]) - np.log10(m["noise_variance"])
# optimize
m.optimize("scg", xtol=1e-6, ftol=1e-6, max_f_eval=optim_iters)
optim_point_x[1] = m["rbf_lengthscale"]
optim_point_y[1] = np.log10(m["rbf_variance"]) - np.log10(m["noise_variance"])
pb.arrow(
optim_point_x[0],
optim_point_y[0],
optim_point_x[1] - optim_point_x[0],
optim_point_y[1] - optim_point_y[0],
label=str(i),
head_length=1,
head_width=0.5,
fc="k",
ec="k",
)
models.append(m)
ax.set_xlim(xlim)
ax.set_ylim(ylim)
return m # (models, lls)
def arrows(points_from,
points_to,
color='k',
width=None,
width_ratio=0.002,
label=None,
label_kw={},
margin_ratio=None,
**kw):
"""draw arrows from each point_from to each point_to.
- points_from, points_to: each is a seq of xy pairs.
- color or c: arrow color(s).
- width: arrow width(s), default to auto adjust with width_ratio.
- width_ratio: set width to minimal_axisrange * width_ratio.
- label=None: a list of strs to label the arrow heads.
- label_kw: pass to pylab.text(x,y,txt,...)
- margin_ratio: if provided as a number, canvas margins will be set to
axisrange * margin_ratio.
**kw: params pass to pylab.arrow(,...)
"""
# convert and valid check of the points
points_from = asarray(points_from, float)
points_to = asarray(points_to, float)
num_points = len(points_from)
if len(points_to) != num_points:
raise ValueError('Length of two group of points unmatched')
if not width: #auto adjust arrow widt
min_range = min(asarray(xlim()).ptp(), asarray(ylim()).ptp())
width = min_range * width_ratio
#vectorize colors and width if necessary
color = kw.pop('c', color)
if isscalar(color): color = [color] * num_points
if isscalar(width): width = [width] * num_points
#draw each arrow
#?? length_include_head=True will break??
default = {'length_includes_head': False, 'alpha': 0.75}
kw = dict(default, **kw)
for (x0, y0), (x1, y1), w, c in zip(points_from, points_to, width, color):
pylab.arrow(x0,
y0,
x1 - x0,
y1 - y0,
edgecolor=c,
facecolor=c,
width=w,
**kw)
if label: #label the arrow heads
text_points(points_to, label, **label_kw)
#hack fix of axis limits, otherwise some of the arrows will be invisible
#not neccessary if the points were also scattered
if margin_ratio is not None:
x, y = concatenate((points_from, points_to)).T #all the points
xmargin = x.ptp() * margin_ratio
ymargin = y.ptp() * margin_ratio
xlim(x.min() - xmargin, x.max() + xmargin)
ylim(y.min() - ymargin, y.max() + xmargin)
return
def scatter_particles(self, state): for particle in state["particles"]: x, y = particle["x"] vx, vy = particle["v"] if particle["id"] == state["best_id"]: pl.scatter(x, y, c='y', s=35) else: pl.scatter(particle["x"][0], particle["x"][1], c='k') pl.arrow(x, y, vx, vy, shape="full", head_width=0.03, width=0.00001, alpha=0.3)
def draw_edges(graph, arrow_width=.1, color=(.7, .7, .7)):
"""Draw the edges of a networkx graph"""
for i in graph.edges():
pylab.arrow(i[0][1],
i[0][0],
.5 * (i[1][1] - i[0][1]),
.5 * (i[1][0] - i[0][0]),
width=arrow_width,
color=color)
def Finish(self):
import matplotlib
matplotlib.use('agg')
import pylab
fig = pylab.figure(figsize=(10, 4))
fig.subplots_adjust(wspace=0.3, bottom=0.15)
ax = pylab.subplot(1, 2, 1)
for track in self.tracks[:50]:
l = inner.intersection(track.pos, track.dir).first
pylab.arrow(track.pos.x,
track.pos.y,
l * track.dir.x,
l * track.dir.y,
edgecolor='k',
head_width=10,
width=1e-2)
pylab.scatter([track.pos.x], [track.pos.y])
ax.add_artist(
self.cylinder_patch(outer, 'top', facecolor="None", edgecolor='r'))
ax.add_artist(
self.cylinder_patch(inner, 'top', facecolor="None", edgecolor='r'))
ax.set_aspect('equal')
ax.set_xlabel('x [m]')
ax.set_ylabel('y [m]')
ax.set_ylim((-1000, 1000))
ax.set_xlim((-1000, 1000))
ax = pylab.subplot(1, 2, 2)
for track in self.tracks:
if abs(track.pos.y) < 20:
l = inner.intersection(track.pos, track.dir).first
pylab.arrow(track.pos.x,
track.pos.z,
l * track.dir.x,
l * track.dir.z,
edgecolor='k',
head_width=10,
width=1e-2)
pylab.scatter([track.pos.x], [track.pos.z])
ax.add_artist(
self.cylinder_patch(outer, 'side', facecolor="None",
edgecolor='r'))
ax.add_artist(
self.cylinder_patch(inner, 'side', facecolor="None",
edgecolor='r'))
ax.set_aspect('equal')
ax.set_xlabel('x [m]')
ax.set_ylabel('z [m]')
ax.set_ylim((-1000, 1000))
ax.set_xlim((-1000, 1000))
pylab.savefig(args.outfile)
def test_optimal_angle_filter(): image = pylab.imread(sys.argv[1]) image = np.mean(image, axis=2) image = image[::-1] pylab.gray() f = AngleFilter((7, 7)) components = f.get_component_values(image, mode='same') angles = np.radians(range(0, 180, 1)) def best_angle_value(c): values = f.basis.response_at_angle(c, angles) return angles[np.argmax(values)], np.max(values) for y, x in np.ndindex(components.shape[:2]): if y%4 != 0: continue if x%4 != 0: continue maxval = f.basis.max_response_value(components[y,x]) if maxval < 2: continue maxang_an = f.basis.max_response_angle(components[y,x]) maxang, maxval = best_angle_value(components[y,x]) pylab.scatter(x, y) dy = -5.0 dx, dy = np.array((np.cos(maxang), np.sin(maxang)))*10 #dx = np.tan(maxang_an)*dy #d = d/np.linalg.norm(d)*3 pylab.arrow(x, y, dx, dy, color='blue') #d = np.array((-np.sin(maxang_an), -np.cos(maxang_an))) #d = d/np.linalg.norm(d)*3 #pylab.arrow(x, y, d[0], d[1], color='green') #pylab.plot(x, y, '.') pylab.imshow(image, origin="lower") #pylab.xlim(0, components.shape[1]) #pylab.ylim(components.shape[0], 0) pylab.show() return #pylab.subplot(1,2,1) #pylab.imshow(image) #pylab.subplot(1,2,2) filtered = np.zeros(image.shape) for y, x in np.ndindex(components.shape[:2]): maxval = f.basis.max_response_value(components[y,x]) minval = f.basis.min_response_value(components[y,x]) #print maxval, minval filtered[y,x] = maxval #filtered[y, x] = best_angle_value(components[y,x]) #pylab.hist(filtered.flatten()) pylab.imshow(filtered > 3) pylab.show()
def drawScaledEigenvectors(X,Y, eigVectors, eigVals, theColor='k'):
""" Draw scaled eigenvectors starting at (X,Y)"""
# For each eigenvector
for col in xrange(eigVectors.shape[1]):
# Draw it from (X,Y) to the eigenvector length
# scaled by the respective eigenvalue
pylab.arrow(X,Y,eigVectors[0,col]*eigVals[col],
eigVectors[1,col]*eigVals[col],
width=0.01, color=theColor)
def imshow_cube_image(image, header=None, compass=True, blackhole=True,
cmap=None):
"""
Call imshow() to plot a cube image. Make sure it is already
masked. Also pass in the header to do the compass rose calculations.
"""
# Setup axis info (x is the 2nd axis)
xcube = (np.arange(image.shape[1]) - m31pos[0]) * 0.05
ycube = (np.arange(image.shape[0]) - m31pos[1]) * 0.05
xtickLoc = py.MultipleLocator(0.4)
if cmap is None:
cmap = py.cm.jet
# Plot the image.
py.imshow(image,
extent=[xcube[0], xcube[-1], ycube[0], ycube[-1]],
cmap=cmap)
py.gca().get_xaxis().set_major_locator(xtickLoc)
py.xlabel('X (arcsec)')
py.ylabel('Y (arcsec)')
# Get the spectrograph position angle for compass rose
if compass is True:
if header is None:
pa = paSpec
else:
pa = header['PA_SPEC']
# Make a compass rose
cosSin = np.array([ math.cos(math.radians(pa)),
math.sin(math.radians(pa)) ])
arr_base = np.array([ xcube[-1]-0.5, ycube[-1]-0.6 ])
arr_n = cosSin * 0.2
arr_w = cosSin[::-1] * 0.2
py.arrow(arr_base[0], arr_base[1], arr_n[0], arr_n[1],
edgecolor='w', facecolor='w', width=0.03, head_width=0.08)
py.arrow(arr_base[0], arr_base[1], -arr_w[0], arr_w[1],
edgecolor='w', facecolor='w', width=0.03, head_width=0.08)
py.text(arr_base[0]+arr_n[0]+0.1, arr_base[1]+arr_n[1]+0.1, 'N',
color='white',
horizontalalignment='left', verticalalignment='bottom')
py.text(arr_base[0]-arr_w[0]-0.15, arr_base[1]+arr_w[1]+0.1, 'E',
color='white',
horizontalalignment='right', verticalalignment='center')
if blackhole is True:
py.plot([0], [0], 'ko')
py.xlim([-0.5, 0.6])
py.ylim([-2.0, 1.8])
def imshow_cube_image(image, header=None, compass=True, blackhole=True,
cmap=None):
"""
Call imshow() to plot a cube image. Make sure it is already
masked. Also pass in the header to do the compass rose calculations.
"""
# Setup axis info (x is the 2nd axis)
xcube = (np.arange(image.shape[1]) - m31pos[0]) * 0.05
ycube = (np.arange(image.shape[0]) - m31pos[1]) * 0.05
xtickLoc = py.MultipleLocator(0.4)
if cmap is None:
cmap = py.cm.jet
# Plot the image.
py.imshow(image,
extent=[xcube[0], xcube[-1], ycube[0], ycube[-1]],
cmap=cmap)
py.gca().get_xaxis().set_major_locator(xtickLoc)
py.xlabel('X (arcsec)')
py.ylabel('Y (arcsec)')
# Get the spectrograph position angle for compass rose
if compass is True:
if header is None:
pa = paSpec
else:
pa = header['PA_SPEC']
# Make a compass rose
cosSin = np.array([ math.cos(math.radians(pa)),
math.sin(math.radians(pa)) ])
arr_base = np.array([ xcube[-1]-0.5, ycube[-1]-0.6 ])
arr_n = cosSin * 0.2
arr_w = cosSin[::-1] * 0.2
py.arrow(arr_base[0], arr_base[1], arr_n[0], arr_n[1],
edgecolor='w', facecolor='w', width=0.03, head_width=0.08)
py.arrow(arr_base[0], arr_base[1], -arr_w[0], arr_w[1],
edgecolor='w', facecolor='w', width=0.03, head_width=0.08)
py.text(arr_base[0]+arr_n[0]+0.1, arr_base[1]+arr_n[1]+0.1, 'N',
color='white',
horizontalalignment='left', verticalalignment='bottom')
py.text(arr_base[0]-arr_w[0]-0.15, arr_base[1]+arr_w[1]+0.1, 'E',
color='white',
horizontalalignment='right', verticalalignment='center')
if blackhole is True:
py.plot([0], [0], 'ko')
py.xlim([-0.5, 0.6])
py.ylim([-2.0, 1.8])
def arrow(start=(0, 0), vel=(0, (0, 0)), color='b'):
if vel == (0, (0, 0)):
xr, yr = 0.1, 0.1
else:
if vel[0] == 0:
sp = 0.1
else:
sp = vel[0]
x = vel[1][0]
y = vel[1][1]
xr = sp * x * qq(x, y)
yr = sp * y * qq(x, y)
pylab.arrow(start[0], start[1], xr, yr, head_width=0.05, head_length=0.1, color=color)
def show_angle(angle,power):
ARROW_STEP = 40
kernel = np.ones((ARROW_STEP,ARROW_STEP))
rowFilter = gaussian(ARROW_STEP,ARROW_STEP/5)
colFilter = rowFilter
gb180 = cmt.get_cmap('gb180')
#X = np.arange(0,angle.shape(-1),ARROW_STEP)
#Y = np.arange(0,angle.shape(-2),ARROW_STEP)
x = np.matrix(np.arange(ARROW_STEP/2,angle.shape[-1],ARROW_STEP))
y = np.transpose(np.matrix(np.arange(ARROW_STEP/2,angle.shape[-2],ARROW_STEP)))
X = np.array((0*y+1)*x)
Y = np.array(y*(0*x+1))
#u = convolve2d(sin(angle),kernel,mode='same')
#v = convolve2d(cos(angle),kernel,mode='same')
#p = convolve2d(power,kernel,mode='same')
u = sepfir2d(np.sin(angle),rowFilter,colFilter)
v = sepfir2d(np.cos(angle),rowFilter,colFilter)
p = sepfir2d(power,rowFilter,colFilter)
U = u[ARROW_STEP/2::ARROW_STEP,ARROW_STEP/2::ARROW_STEP]*p[ARROW_STEP/2::ARROW_STEP,ARROW_STEP/2::ARROW_STEP]
V = v[ARROW_STEP/2::ARROW_STEP,ARROW_STEP/2::ARROW_STEP]*p[ARROW_STEP/2::ARROW_STEP,ARROW_STEP/2::ARROW_STEP]
#U = sin(angle[ARROW_STEP/2::ARROW_STEP,ARROW_STEP/2::ARROW_STEP])*(power[ARROW_STEP/2::ARROW_STEP,ARROW_STEP/2::ARROW_STEP])
#V = cos(angle[ARROW_STEP/2::ARROW_STEP,ARROW_STEP/2::ARROW_STEP])*(power[ARROW_STEP/2::ARROW_STEP,ARROW_STEP/2::ARROW_STEP])
#X = X[(power[::ARROW_STEP,::ARROW_STEP]>.016)]
#Y = Y[(power[::ARROW_STEP,::ARROW_STEP]>.016)]
#U = U[(power[::ARROW_STEP,::ARROW_STEP]>.016)]
#V = V[(power[::ARROW_STEP,::ARROW_STEP]>.016)]
ua = ARROW_STEP/1.5*np.nansum(np.sin(angle)*power)/np.nansum(power)
va = -ARROW_STEP/1.5*np.nansum(np.cos(angle)*power)/np.nansum(power)
xc, yc = angle.shape[-1]/2, angle.shape[-2]/2
pylab.imshow(angle,cmap=gb180)
#pylab.imshow(angle,cmap='hsv')
pylab.quiver(X,Y,U,V,pivot='middle',color='w',headwidth=1,headlength=0)
pylab.arrow(xc,yc,ua,va,color='w',linewidth=2)
pylab.arrow(xc,yc,-ua,-va,color='w',linewidth=2)
ax=pylab.gca()
ax.set_axis_off()
pylab.show()
A = np.arctan2(-ua,va)
return A
def snapshot(t, pos, vel, colors, arrow_scale=.2):
global img
pylab.cla()
pylab.axis([0, 1, 0, 1])
pylab.setp(pylab.gca(), xticks=[0, 1], yticks=[0, 1])
for (x, y), (dx, dy), c in zip(pos, vel, colors):
dx *= arrow_scale
dy *= arrow_scale
circle = pylab.Circle((x, y), radius=sigma, fc=c)
pylab.gca().add_patch(circle)
pylab.arrow( x, y, dx, dy, fc="k", ec="k", head_width=0.05, head_length=0.05 )
pylab.text(.5, 1.03, 't = %.2f' % t, ha='center')
pylab.savefig(os.path.join(output_dir, '%04i.png' % img))
img += 1
def snapshot(t, pos, vel, colors, arrow_scale=0.2):
global img
pylab.cla()
pylab.axis([0, 1, 0, 1])
pylab.setp(pylab.gca(), xticks=[0, 1], yticks=[0, 1])
for (x, y), (dx, dy), c in zip(pos, vel, colors):
dx *= arrow_scale
dy *= arrow_scale
circle = pylab.Circle((x, y), radius=sigma, fc=c)
pylab.gca().add_patch(circle)
pylab.arrow(x, y, dx, dy, fc="k", ec="k", head_width=0.05, head_length=0.05)
pylab.text(0.5, 1.03, "t = %.2f" % t, ha="center")
pylab.savefig(os.path.join(output_dir, "%d.png" % img))
img += 1
def riemann():
# grid info
xmin = 0.0
xmax = 1.0
nzones = 1
ng = 0
gr = gpu.grid(nzones, xmin=xmin, xmax=xmax)
#------------------------------------------------------------------------
# plot a domain without ghostcells
gpu.drawGrid(gr)
gpu.labelCenter(gr, 0, r"$i$")
gpu.labelCellCenter(gr, 0, r"$q_i$")
gpu.markCellLeftState(gr, 0, r"$q_{i-1/2,R}^{n+1/2}$", color="r")
gpu.markCellRightState(gr, 0, r"$q_{i+1/2,L}^{n+1/2}$", color="r")
pylab.arrow(gr.xc[0]-0.05*gr.dx, 0.5, -0.13*gr.dx, 0,
shape='full', head_width=0.075, head_length=0.05,
lw=1, width=0.01,
edgecolor="none", facecolor="r",
length_includes_head=True, zorder=100)
pylab.arrow(gr.xc[0]+0.05*gr.dx, 0.5, 0.13*gr.dx, 0,
shape='full', head_width=0.075, head_length=0.05,
lw=1, width=0.01,
edgecolor="none", facecolor="r",
length_includes_head=True, zorder=100)
pylab.xlim(gr.xl[0]-0.25*gr.dx,gr.xr[2*ng+nzones-1]+0.25*gr.dx)
# pylab.ylim(-0.25, 0.75)
pylab.axis("off")
pylab.subplots_adjust(left=0.05,right=0.95,bottom=0.05,top=0.95)
f = pylab.gcf()
f.set_size_inches(4.0,2.5)
pylab.savefig("states.png")
pylab.savefig("states.eps")
def drawScaledEigenvectors(X, Y, eigVectors, eigVals, theColor='k'):
""" Draw scaled eigenvectors starting at (X,Y)"""
# For each eigenvector
for col in xrange(eigVectors.shape[1]):
# Draw it from (X,Y) to the eigenvector length
# scaled by the respective eigenvalue
pylab.arrow(X,
Y,
eigVectors[0, col] * eigVals[col],
eigVectors[1, col] * eigVals[col],
width=0.01,
color=theColor)
def multiple_optima(gene_number=937,resolution=80, model_restarts=10, seed=10000):
"""Show an example of a multimodal error surface for Gaussian process regression. Gene 939 has bimodal behaviour where the noisey mode is higher."""
# Contour over a range of length scales and signal/noise ratios.
length_scales = np.linspace(0.1, 60., resolution)
log_SNRs = np.linspace(-3., 4., resolution)
data = GPy.util.datasets.della_gatta_TRP63_gene_expression(gene_number)
# Sub sample the data to ensure multiple optima
#data['Y'] = data['Y'][0::2, :]
#data['X'] = data['X'][0::2, :]
# Remove the mean (no bias kernel to ensure signal/noise is in RBF/white)
data['Y'] = data['Y'] - np.mean(data['Y'])
lls = GPy.examples.regression._contour_data(data, length_scales, log_SNRs, GPy.kern.rbf)
pb.contour(length_scales, log_SNRs, np.exp(lls), 20)
ax = pb.gca()
pb.xlabel('length scale')
pb.ylabel('log_10 SNR')
xlim = ax.get_xlim()
ylim = ax.get_ylim()
# Now run a few optimizations
models = []
optim_point_x = np.empty(2)
optim_point_y = np.empty(2)
np.random.seed(seed=seed)
for i in range(0, model_restarts):
kern = GPy.kern.rbf(1, variance=np.random.exponential(1.), lengthscale=np.random.exponential(50.)) + GPy.kern.white(1,variance=np.random.exponential(1.))
m = GPy.models.GP_regression(data['X'],data['Y'], kernel=kern)
optim_point_x[0] = m.get('rbf_lengthscale')
optim_point_y[0] = np.log10(m.get('rbf_variance')) - np.log10(m.get('white_variance'));
# optimize
m.ensure_default_constraints()
m.optimize(xtol=1e-6,ftol=1e-6)
optim_point_x[1] = m.get('rbf_lengthscale')
optim_point_y[1] = np.log10(m.get('rbf_variance')) - np.log10(m.get('white_variance'));
pb.arrow(optim_point_x[0], optim_point_y[0], optim_point_x[1]-optim_point_x[0], optim_point_y[1]-optim_point_y[0], label=str(i), head_length=1, head_width=0.5, fc='k', ec='k')
models.append(m)
ax.set_xlim(xlim)
ax.set_ylim(ylim)
return (models, lls)
def snapshot(t, pos, vel, colors, arrow_scale=0.2):
global img
pylab.cla()
pylab.axis([0, 1, 0, 1])
pylab.setp(pylab.gca(), xticks=[0, 1], yticks=[0, 1])
for (x, y), (dx, dy), c in zip(pos, vel, colors): # putting position, velocity, and colors arrays into 3D tuple.
dx *= arrow_scale # rescale vel_x by multiplying w/ arrow_scale
dy *= arrow_scale # rescale vel_y by multiplying w/ arrow_scale
circle = pylab.Circle((x, y), radius=sigma, fc=c) # fc sets color of circle
pylab.gca().add_patch(circle)
pylab.arrow(x, y, dx, dy, fc="k", ec="k", head_width=0.05, head_length=0.05)
pylab.text(
0.5, 1.03, "t = %.2f" % t, ha="center"
) # .5 for middle of box on x-axis, 1.03 is just above box on y-axis
pylab.savefig(os.path.join(output_dir, "%d.png" % img))
img += 1
def plotSystem(boat, plot_time, r, line_th, u0):
fig.canvas.restore_region(background_main)
# gather the X and Y location
boat_x = boat.state[0]
boat_y = boat.state[1]
boat_th = boat.state[4]
axes = [-PLOT_SIZE, PLOT_SIZE, -PLOT_SIZE, PLOT_SIZE]
ax_main.plot([-PLOT_SIZE, PLOT_SIZE], [-PLOT_SIZE, PLOT_SIZE],
'x', markersize=1, markerfacecolor='white', markeredgecolor='white')
ax_main.axis(axes) # requires those invisible 4 corner white markers
boat_arrow = pylab.arrow(boat_x, boat_y,0.05*np.cos(boat_th),0.05*np.sin(boat_th),
fc="g", ec="g", head_width=0.5, head_length=1.0)
ax_main.draw_artist(boat_arrow)
style = 'b-'
if boat.plotData is not None:
ax_main.draw_artist(ax_main.plot(boat.plotData[:, 0], boat.plotData[:, 1], style, linewidth=0.25)[0])
ax_main.draw_artist(ax_main.plot([0, 50.*np.cos(line_th)], [0, 50.*np.sin(line_th)], 'k--', linewidth=0.25)[0])
# rectangle coords
left, width = 0.01, 0.95
bottom, height = 0.0, 0.96
right = left + width
top = bottom + height
time_text = ax_main.text(right, top, "time = {:.2f} s".format(plot_time),
horizontalalignment='right', verticalalignment='bottom',
transform=ax_main.transAxes, size=20)
surge_text = ax_main.text(left, top, "u = {:.2f} m/s".format(boat.state[2]),
horizontalalignment='left', verticalalignment='bottom',
transform=ax_main.transAxes, size=20)
location_text = ax_main.text((left+right)/2., top, "r = {:.2f}, th = {:.2f}, u0 = {:.2f}".format(r, np.rad2deg(line_th), u0),
horizontalalignment='center', verticalalignment='bottom',
transform=ax_main.transAxes, size=20)
ax_main.draw_artist(time_text)
ax_main.draw_artist(surge_text)
ax_main.draw_artist(location_text)
fig.canvas.blit(ax_main.bbox)
def snapshot(self, title, pos, vel, sphere_ind, img_name):
pylab.subplots_adjust(left=0.10, right=0.90, top=0.90, bottom=0.10)
pylab.gcf().set_size_inches(6, 6)
pylab.cla()
pylab.axis([0, 1, 0, 1])
pylab.setp(pylab.gca(), xticks=[0, 1], yticks=[0, 1])
for (x, y), c in zip(pos, self.colors):
circle = pylab.Circle((x, y), radius=self.sigma, fc=c)
pylab.gca().add_patch(circle)
(dx, dy) = vel
dx *= self.arrow_scale
dy *= self.arrow_scale
pylab.arrow(pos[sphere_ind][0], pos[sphere_ind][1], dx, dy, fc="k", ec="k",
head_width=0.1*np.linalg.norm(vel), head_length=0.1*np.linalg.norm(vel))
pylab.text(.5, 1.03, title, ha='center')
pylab.savefig(os.path.join(self.output_dir, img_name+".png"))
def showCoulombDirection(ptx, ww, im=None, dd=None, fig=100):
""" Show direction of Coulomb peak in an image """
if dd is None:
pp = ptx
ww = 10 * ww
sigma = 5
else:
ptx = ptx.reshape((1, 2))
ww = ww.reshape((1, 2))
tr = qtt.data.image_transform(dd)
pp = tr.pixel2scan(ptx.T).T
pp2 = tr.pixel2scan((ptx + ww).T).T
ww = (pp2 - pp).flatten()
ww = 40 * ww / np.linalg.norm(ww)
sigma = 5 * 3
if fig is not None:
if im is not None:
plt.figure(fig)
plt.clf()
if dd is None:
plt.imshow(im, interpolation='nearest')
else:
show2Dimage(im, dd, fig=fig)
if fig is not None:
plt.figure(fig)
hh = pylab.arrow(pp[0, 0], pp[0, 1], ww[0], ww[
1], linewidth=4, fc="k", ec="k", head_width=sigma / 2, head_length=sigma / 2)
hh.set_alpha(0.8)
plt.axis('image')
def plot_F(self, scale=1):
for i, (X, dx, dy) in enumerate(zip(self.X, self.D['x'], self.D['y'])):
j = i * self.ndof
if self.frame == '1D':
F = [0, self.Fo[j]]
else:
F = [self.Fo[j], self.Fo[j + 1]]
nF = np.linalg.norm(F)
if nF != 0:
pl.arrow(X[0] + self.scale * dx,
X[1] + self.scale * dy,
scale * F[0],
scale * F[1],
head_width=scale * 0.2 * nF,
head_length=scale * 0.3 * nF,
color=color[1])
def arrows(
points_from, points_to, color="k", width=None, width_ratio=0.002, label=None, label_kw={}, margin_ratio=None, **kw
):
"""draw arrows from each point_from to each point_to.
- points_from, points_to: each is a seq of xy pairs.
- color or c: arrow color(s).
- width: arrow width(s), default to auto adjust with width_ratio.
- width_ratio: set width to minimal_axisrange * width_ratio.
- label=None: a list of strs to label the arrow heads.
- label_kw: pass to pylab.text(x,y,txt,...)
- margin_ratio: if provided as a number, canvas margins will be set to
axisrange * margin_ratio.
**kw: params pass to pylab.arrow(,...)
"""
# convert and valid check of the points
points_from = asarray(points_from, float)
points_to = asarray(points_to, float)
num_points = len(points_from)
if len(points_to) != num_points:
raise ValueError("Length of two group of points unmatched")
if not width: # auto adjust arrow widt
min_range = min(asarray(xlim()).ptp(), asarray(ylim()).ptp())
width = min_range * width_ratio
# vectorize colors and width if necessary
color = kw.pop("c", color)
if isscalar(color):
color = [color] * num_points
if isscalar(width):
width = [width] * num_points
# draw each arrow
# ?? length_include_head=True will break??
default = {"length_includes_head": False, "alpha": 0.75}
kw = dict(default, **kw)
for (x0, y0), (x1, y1), w, c in zip(points_from, points_to, width, color):
pylab.arrow(x0, y0, x1 - x0, y1 - y0, edgecolor=c, facecolor=c, width=w, **kw)
if label: # label the arrow heads
text_points(points_to, label, **label_kw)
# hack fix of axis limits, otherwise some of the arrows will be invisible
# not neccessary if the points were also scattered
if margin_ratio is not None:
x, y = concatenate((points_from, points_to)).T # all the points
xmargin = x.ptp() * margin_ratio
ymargin = y.ptp() * margin_ratio
xlim(x.min() - xmargin, x.max() + xmargin)
ylim(y.min() - ymargin, y.max() + xmargin)
return
def plot_seeing_vs_ao(tint=1200, spec_res=100):
ap_rad_see = 0.4
ap_rad_rao = 0.15
in_file_root = '{0:s}/roboAO_sensitivity_t{1:d}_R{2:d}'.format(work_dir, tint, spec_res)
in_file_see = '{0:s}_ap{1:0.3f}_seeing'.format(in_file_root, ap_rad_see)
in_file_rao = '{0:s}_ap{1:0.3f}'.format(in_file_root, ap_rad_rao)
avg_tab_rao = Table.read(in_file_rao + '_avg_tab.fits')
avg_tab_see = Table.read(in_file_see + '_avg_tab.fits')
# Calculate the band-integrated SNR for each magnitude bin and filter.
mag_rao = avg_tab_rao['mag']
mag_see = avg_tab_see['mag']
hdr1 = '# {0:3s} {1:15s} {2:15s} {3:15s}'
hdr2 = '# {0:3s} {1:7s} {2:7s} {3:7s} {4:7s} {5:7s} {6:7s}'
print hdr1.format('Mag', 'Y SNR (summed)', 'J SNR (summed)', 'H SNR (summed)')
print hdr2.format('', 'Robo-AO', 'Seeing', 'Robo-AO', 'Seeing', 'Robo-AO', 'Seeing')
print hdr2.format('---', '-------', '-------', '-------', '-------', '-------', '-------')
for mm in range(len(mag_rao)):
fmt = ' {0:3d} {1:7.1f} {2:7.1f} {3:7.1f} {4:7.1f} {5:7.1f} {6:7.1f}'
print fmt.format(mag_rao[mm],
avg_tab_rao['snr_sum_y'][mm], avg_tab_see['snr_sum_y'][mm],
avg_tab_rao['snr_sum_j'][mm], avg_tab_see['snr_sum_j'][mm],
avg_tab_rao['snr_sum_h'][mm], avg_tab_see['snr_sum_h'][mm])
py.clf()
py.semilogy(avg_tab_rao['mag'], avg_tab_rao['snr_sum_j'], label='UH Robo-AO',
linewidth=2)
py.semilogy(avg_tab_rao['mag'], avg_tab_see['snr_sum_j'], label='Seeing-Limited',
linewidth=2)
py.xlabel('J-band Magnitude')
py.ylabel('Signal-to-Noise in 1200 sec')
py.xlim(13, 21)
py.ylim(1, 1e4)
py.arrow(16.1, 30, 4.05, 0, color='red', width=2, head_width=10, head_length=0.5,
length_includes_head=True, fc='red', ec='red')
py.text(17.3, 11, '250x More\nSupernovae Ia', color='red',
horizontalalignment='left', fontweight='bold', fontsize=16)
py.legend()
# py.title('Tint={0:d} s, R={1:d}'.format(tint, spec_res))
py.savefig(in_file_rao + '_proposal.png')
return
def plot_match_displacement(im1,locs1,locs2,matchscores, numMatches=-1):
""" show a figure with lines where feats in im1 moved to in im2
input: im1 (image as array), locs1,locs2 (location of features),
matchscores (as output from 'match'), numMatches (number of matches to plot) """
if numMatches == -1 :
numMatches = len(matchscores)
pylab.gray()
pylab.imshow(im1)
cols1 = im1.shape[1]
for i in range(numMatches):
if matchscores[i] > 0:
pylab.arrow(locs1[i,1], locs1[i,0], locs2[int(matchscores[i]),1]-locs1[i,1], locs2[int(matchscores[i]),0]-locs1[i,0], head_width=1.0, head_length=2.0, linewidth=0.5, fc='r', ec='r')
pylab.axis('off')
pylab.show()
def showPerc(perc):
CalSAT = ThreeFourSAT + FourFiveSAT
h3 = sorted(CalSAT)
fit3 = stats.norm.pdf(h3, avg(CalSAT), stanDev(CalSAT))
plt.plot(h3, fit3, '-go')
plt.hist(h3, density=True)
plt.title("California Math SAT Averages 2013-2015")
#arrow from the right
score = calScore(perc, CalSAT)
minusScore = score - 1020
if perc > 0.5:
plt.arrow(1020,
0,
minusScore,
0.01 - perc / 100 + 0.0005,
width=0.0006,
head_width=0.0012,
head_length=30,
length_includes_head=True,
color="blue")
#This arrow was able to start from the right if the percentile was greater than 0.5. The parameter values
#were experimented with for quite a bit, and it took perfecting to actually get the arrow to point exactly at
#at the desired datapoint. "0.01 - perc/100 + 0.0005" represents the change in y from (1020, 0) on the graph.
#The logic behind this is that 0.01 is the max height, and instead of increasing in height, the curve actually
#decreases after the local max, as it's concave down. So it decreases in increments of the percentile as it moves
#to the right. A similar process is completed upon approaching the maximum point, but it involves increasing the
#change in y in increments of percentile instead.
#arrow from the left
else:
plt.arrow(0,
0,
calScore(perc, CalSAT),
perc / 100 + 0.0013,
width=0.0006,
head_width=0.0012,
head_length=30,
length_includes_head=True,
color="red")
SATScore = calScore(perc, CalSAT)
print("SAT Math Score: {}".format(SATScore))
plt.show()
def addArrows(aDict, aColor):
for i in aDict:
x, y = arrowDict[i]
newx, newy = arrowDict[aDict[i]]
dx, dy = newx - x, newy - y
pylab.arrow(
x,
y,
dx,
dy,
head_length=0.3,
head_width=0.20,
color=aColor,
linestyle="dotted",
length_includes_head=True,
)
def plot_graph(classA, classB, wvector, title, b=2):
#fig, axis = plt.sublplot(nrows=2, ncols=2)
yA = []
xA = []
yB = []
xB = []
for instA, instB in zip(classA, classB):
xA.append(instA[0])
yA.append(instA[1])
xB.append(instB[0])
yB.append(instB[1])
#ax = axis[0, 0]
plt.plot(xA, yA, 'ro')
plt.plot(xB, yB, 'bo')
#plt.plot([0, 3], [0, 2], linestyle="dashed", marker="o", color="green")
# plot weight vector
xW = (0, wvector[1])
yW = (0, wvector[2])
# print wvector[1], wvector[2]
# plt.plot(xW, yW, label="weight", linestyle="-", marker="o", color="green")
pl.arrow(0,
0,
wvector[1][0],
wvector[2][0],
fc="g",
ec="g",
head_width=0.15,
head_length=0.2)
# plot hyperplane
#c, a, b = w[0][1], w[1][1], w[2][1]
# find y which is X2, assuming X1=0, 10
y1 = -float((wvector[0][0])) / wvector[2][0]
y2 = -float((wvector[1][0] * 10 + wvector[0][0])) / wvector[2][0]
y1r = float((b - wvector[0][0])) / wvector[2][0]
y2r = float(((b - wvector[0][0]) - wvector[1][0] * 10)) / wvector[2][0]
# plt.plot((0, 10), (y1r, y2r), "c--") # Wtranspose.Y = b
plt.plot((0, 10), (y1, y2), "m--")
plt.axis([0, 15, 0, 15])
plt.title(title)
plt.draw()
plt.show()
def snapshot(t, pos, vel, colors, X, Y, arrow_scale=.2):
""" La routine qui s'occupe des tracés graphiques."""
global img
nbmax = 20
pylab.subplots_adjust(left=0.10, right=0.90, top=0.90, bottom=0.10)
pylab.gcf().set_size_inches(12, 12 * 2 / 3)
# Le premier sous-plot: carré de 2x2
ax1 = pylab.subplot2grid((2, 3), (0, 0), colspan=2, rowspan=2)
pylab.setp(pylab.gca(), xticks=[0, 1], yticks=[0, 1])
pylab.plot(X, Y, 'k') # On y met le trajet de la dernière particule
pylab.xlim((0, 1)) # On doit astreindre les côtés horizontaux
pylab.ylim((0, 1)) # et verticaux
# Boucle sur les points pour rajouter les cercles colorés
for (x, y), c in zip(pos, colors):
circle = pylab.Circle((x, y), radius=sigma, fc=c)
pylab.gca().add_patch(circle)
dx, dy = vel[
-1] * arrow_scale # La dernière particule a droit à son vecteur vitesse
pylab.arrow(x,
y,
dx,
dy,
fc="k",
ec="k",
head_width=0.05,
head_length=0.05)
pylab.text(.5, 1.03, 't = %.2f' % t, ha='center')
# Second sous-plot: histogramme de la projection suivant x des vitesses
ax2 = pylab.subplot2grid((2, 3), (0, 2), colspan=1, rowspan=1)
r = (-2, 2) # Intervalle de vitesses regardé
pylab.hist(vel[:, 0], bins=20, range=r)
pylab.xlim(r)
pylab.ylim((0, nbmax))
pylab.ylabel("Nombre de particules")
pylab.xlabel("$v_x$")
# Troisième sous-plot: histogramme de la norme des vitesses
ax3 = pylab.subplot2grid((2, 3), (1, 2), colspan=1, rowspan=1)
r = (0, 2) # Intervalle de vitesses regardé
pylab.hist(np.sqrt(np.sum(vel**2, axis=1)), bins=20, range=r)
pylab.xlim(r)
pylab.ylim((0, nbmax))
pylab.ylabel("Nombre de particules")
pylab.xlabel("$||\\vec{v}||$")
pylab.savefig(os.path.join(output_dir, '{:04d}.png'.format(img)))
img += 1
def addArrows(k,arrowDeltaX,arrowDeltaY,direction,arrowScale=False): desiredSize = 0.5 * k.zoomedBoxHalfSize currentSize = math.sqrt(arrowDeltaX**2+arrowDeltaY**2) if arrowScale == False: arrowScale = desiredSize / currentSize originX1=k.zoomedBoxHalfSize+k.arrowOffsetX originY1=k.zoomedBoxHalfSize+k.arrowOffsetY deltaX1 =arrowDeltaX*arrowScale deltaY1 =arrowDeltaY*arrowScale labelX1 = k.zoomedBoxHalfSize+k.arrowOffsetX+arrowDeltaX*arrowScale*k.labelLengthScale - 10*k.lengthScale labelY1 = k.zoomedBoxHalfSize+k.arrowOffsetY+arrowDeltaY*arrowScale*k.labelLengthScale - 10*k.lengthScale # print "arrowScale", arrowScale, "origin", originX1+k.extraX, originY1+k.extraY, "delta", deltaX1, deltaY1 pylab.arrow(originX1+k.extraX, originY1+k.extraY, deltaX1, deltaY1, color="white",head_width=8*k.lengthScale,head_length=8*k.lengthScale) pylab.text(labelX1+k.extraX,labelY1+k.extraY,direction,color="white")
def plot_path(path):
pylab.clf()
pylab.xlim(-2, max_size + 1)
pylab.ylim(-2, max_size + 1)
pylab.axis('off')
# Start.
pylab.annotate('start', xy=(0, 0), xytext=(-1, -1), size=10, bbox=dict(boxstyle="round4,pad=.5", fc="0.8"), arrowprops=dict(arrowstyle="->"))
pylab.annotate('stop', xy=(max_size-1, max_size-1), xytext=(max_size, max_size), size=10, bbox=dict(boxstyle="round4,pad=.5", fc="0.8"), arrowprops=dict(arrowstyle="->"))
# Show the food.
for f in food:
pylab.annotate('food', xy=f, size=5, bbox=dict(boxstyle="round4,pad=.5", fc="0.8"), ha='center')
for i in range(len(path) - 1):
pylab.arrow(path[i][0], path[i][1], path[i+1][0] - path[i][0], path[i+1][1] - path[i][1])
def plot_displacements(tab):
t = Table(np.loadtxt(tab),
names=('THING_ID', 'PLATE', 'MJD',
'FIBERID', 'RA', 'DEC', 'Z', 'RA0', 'DEC0'),
dtype=(int, int, int, int, float, float, float, float, float))
rand_ind = np.random.choice(np.arange(len(t)), \
replace=False, size=2000)
P.figure()
for i in rand_ind:
x = t['RA0'][i]
y = t['DEC0'][i]
dx = t['RA'][i]-x
dy = t['DEC'][i]-y
P.arrow(x, y, dx, dy, color='k', width=0.0003)
P.xlim(t['RA'][rand_ind].min(), t['RA'][rand_ind].max())
P.ylim(t['DEC'][rand_ind].min(), t['DEC'][rand_ind].max())
P.show()
def plot(A, title=""):
color = ['g', 'c', 'm', 'y']
label = ['SSP', 'SSPM', 'MR']
x1 = [i[0] for i in w1]
y1 = [i[1] for i in w1]
x2 = [i[0] for i in w2]
y2 = [i[1] for i in w2]
plt.plot(x1, y1, 'ro')
plt.plot(x2, y2, 'bo')
for i, a in enumerate(A):
x = [-3, 10]
y = [-1. * (a[0] + a[1] * j) / a[2] for j in x]
plt.plot(x, y, color[i] + '--', label=label[i])
# Plot Vector
pl.arrow(0, 0, a[1], a[2], fc=color[i], ec=color[i],
head_width=0.15, head_length=0.2)
plt.legend(loc=4, borderaxespad=0.)
plt.title(title)
# plt.axis([-5, 15, -5, 15])
plt.show()
def snapshot(t, pos, vel, colors, arrow_scale=.2):
global img
ax = pylab.cla()
pylab.axis([0, 1, 0, 1], aspect='equal')
pylab.setp(pylab.gca(), xticks=[0, 1], yticks=[0, 1])
for (x, y), (dx, dy), c in zip(pos, vel, colors):
dx *= arrow_scale
dy *= arrow_scale
circle = pylab.Circle((x, y), radius=sigma, fc=c)
pylab.gca().add_patch(circle)
pylab.arrow(x, y, dx, dy, fc="k", ec="k",
head_width=0.05, head_length=0.05)
pylab.text(.5, 1.03, 't = %.2f' % t, ha='center')
img_str = str(img)
pylab.show()
pylab.pause(0.1)
pylab.clf()
img += 1
def fig_power(po, pos, sig_loc, start=400, stop = 405, Title = '', asteriks=[0,0]):
global freq
from mpl_toolkits.axes_grid.inset_locator import inset_axes
ax1 = py.subplot(gs[pos[2]:pos[3], pos[0]:pos[1]])
py.title(Title, fontsize=15)
set_axis(ax1, -0.1, 1.05, letter= po)
labels= ['Olf. bulb', 'Thalamus', 'Visual ctrx']
for i in range(2,-1,-1):
sig_loc[i] = notch_filter(sig_loc[i], Fs, np.arange(50, 450, 50))
freq, sp = welch(sig_loc[i], Fs, nperseg = 1*Fs)
ax1.plot(freq, sp, lw=4, label=labels[i])
# ax1.text(asteriks[0], asteriks[1] , '*', fontsize=20)
py.arrow(asteriks[0], asteriks[1], 0, -12, length_includes_head=True, clip_on = False,
head_width=2, head_length=4)
# py.ylim(.1, 10e4)
py.ylim(0,220)
py.xlim(0, 155)
py.ylabel('power $mV^2$')
ax1.spines['right'].set_visible(False)
ax1.spines['top'].set_visible(False)
py.xlabel('Frequency (Hz)')
if po!='B1':
inset_axes = inset_axes(ax1, width="23%", height=1.0, loc=1)
for n in range(3,sig_loc.shape[0]):
sig_loc[n] = notch_filter(sig_loc[n], Fs, np.arange(50, 450, 50))
freq, sp = welch(sig_loc[n], Fs, nperseg = 1*Fs)
py.plot(freq, sp, lw=2, color='green')
py.ylim(0,220)
py.xlim(0,155)
py.xticks(fontsize=11)
py.yticks(fontsize=11)
# py.ylim(.1, 10e4)
# py.yscale('log')
# py.text(200,100, 'Olf. bulb propofol')
py.xlabel('Frequency (Hz)')
if po=='B1':
ket = mpatches.Patch(color='green', label='Olf. bulb')
kx = mpatches.Patch(color='orange', label='Thalamus LGN')
gam = mpatches.Patch(color='blue', label='Visual cortex')
ax1.legend(loc='lower right', bbox_to_anchor=(1.2, .7), handles=[ket,kx,gam],
ncol=1, frameon = True, fontsize = 15)
def draw_fragment(moves, width=.1):
counter = 0
for fragment in moves:
counter += 1
pylab.hold(True)
def get_color(i):
while i >= len(COLORS):
i -= len(COLORS)
return COLORS[i]
coord1 = None
if fragment['standard_1']:
coord1 = fragment['coord_1']
else:
coord1 = list(fragment['coord_1'][0])
coord2 = None
if fragment['standard_2']:
coord2 = fragment['coord_2']
else:
coord2 = list(fragment['coord_2'][1])
coord2.extend(fragment['coord_2'][0][len(coord2):])
for i in range(len(fragment['rob_id'])):
color = list(get_color(fragment['rob_id'][i]))
if fragment['skipped']:
pylab.plot([coord2[i][0]], [coord2[i][1]],
marker='o',
color=color)
continue
try:
pylab.arrow(coord1[i][0],
coord1[i][1],
coord2[i][0] - coord1[i][0],
coord2[i][1] - coord1[i][1],
length_includes_head=True,
width=width,
head_width=width * 3,
color=color)
except AssertionError:
pass
pylab.hold(False)
def show(self):
fig = pl.figure(figsize=(10,10))
coords = list()
for ii in range(len(self.layers)):
for ij in range(len(self.layers[ii].cells)):
self.layers[ii].cells[ij].coords = (ii, ij)
for ilayer in self.layers:
for icell in ilayer.cells:
pl.scatter(icell.coords[0], icell.coords[1], c='black')
for i in range(len(icell.children)):
pl.arrow(icell.coords[0], icell.coords[1],
icell.children[i].coords[0] - icell.coords[0],
icell.children[i].coords[1] - icell.coords[1],
ec=matplotlib.cm.RdYlBu_r((icell.weights[i] + 1.)/2.))
pl.text(icell.coords[0] - 0.2, icell.coords[1] + 0.2, ' '.join(['{:.2f}'.format(w) for w in icell.weights]), c='red')
#pl.text(icell.coords[0] - 0.05, icell.coords[1] + 0.2, '{:.2f}'.format(icell.get()), c='green')
fig.colorbar(matplotlib.cm.ScalarMappable(norm=matplotlib.colors.Normalize(vmin=-1, vmax=1), cmap='RdYlBu_r'))
def plot_cdf_from_file(filename):
"""Open file, store cdf to .pdf and .png"""
import numpy as np
import matplotlib.pyplot as plt
import pylab as P
data = np.genfromtxt(filename, delimiter=',')
# SINR data is best presented in dB
from utils import utils
data = utils.WTodB(data)
import cdf_plot
label = ["Iteration %d" % i for i in np.arange(data.shape[0]) + 1]
cdf_plot.cdf_plot(data, '-', label=label)
# plt.xlabel(xlabel)
# plt.ylabel(ylabel)
# plt.title(title)
P.arrow(0, 50, 40, 0, fc="k", ec="k", head_width=3, head_length=5)
plt.savefig(filename + '.pdf', format='pdf')
plt.savefig(filename + '.png', format='png')
def test_disp(disp_x,
disp_y,
rangex=[np.pi / 2 - 1., np.pi / 2 + 1.],
rangey=[0.5, np.pi / 2],
ndots=1000,
factor=1,
seed=1):
''' Test displacements by plotting a set of random points in phi, theta'''
np.random.seed(seed)
nside = hp.npix2nside(disp_x.size)
phi = np.random.uniform(rangex[0], rangex[1], ndots)
theta = np.random.uniform(rangey[0], rangey[1], ndots)
ipix = hp.ang2pix(nside, theta, phi)
dphi = disp_x[ipix]
dtheta = disp_y[ipix]
ra = phi
dec = np.pi / 2 - theta
dd = np.sqrt(dphi**2 + dtheta**2)
alpha = np.arctan2(dphi, dtheta)
## Equation A15 from 0502469
thetap = np.arccos(
np.cos(dd) * np.cos(theta) -
np.sin(dd) * np.sin(theta) * np.cos(alpha))
phip = phi + np.arcsin(np.sin(alpha) * np.sin(dd) / np.sin(thetap))
rap = phip
decp = np.pi / 2 - thetap
plt.figure()
for t, p, t2, p2 in zip(dec, ra, decp, rap):
plt.arrow(p,
t, (p2 - p) * factor, (t2 - t) * factor,
color='k',
width=0.0003)
plt.xlim(rangex[1], rangex[0])
plt.ylim(np.pi / 2 - rangey[1], np.pi / 2 - rangey[0])
def gui_repr(self):
"""Generate a GUI to represent the sentence alignments
"""
if __pylab_loaded__:
fig_width = max(len(self.text_e), len(self.text_f)) + 1
fig_height = 3
pylab.figure(figsize=(fig_width*0.8, fig_height*0.8), facecolor='w')
pylab.box(on=False)
pylab.subplots_adjust(left=0, right=1, bottom=0, top=1)
pylab.xlim(-1, fig_width - 1)
pylab.ylim(0, fig_height)
pylab.xticks([])
pylab.yticks([])
e = [0 for _ in xrange(len(self.text_e))]
f = [0 for _ in xrange(len(self.text_f))]
for (i, j) in self.align:
e[i] = 1
f[j] = 1
# draw the middle line
pylab.arrow(i, 2, j - i, -1, color='r')
for i in xrange(len(e)):
# draw e side line
pylab.text(i, 2.5, self.text_e[i], ha = 'center', va = 'center',
rotation=30)
if e[i] == 1:
pylab.arrow(i, 2.5, 0, -0.5, color='r', alpha=0.3, lw=2)
for i in xrange(len(f)):
# draw f side line
pylab.text(i, 0.5, self.text_f[i], ha = 'center', va = 'center',
rotation=30)
if f[i] == 1:
pylab.arrow(i, 0.5, 0, 0.5, color='r', alpha=0.3, lw=2)
pylab.draw()
def coulomb_barrier():
ax = pylab.subplot(111)
npts = 200
r = numpy.arange(npts, dtype=numpy.float64)/npts
SMALL = 1.e-16
# Coulomb potential
C = 1/(r + SMALL)
# interior, strong potential
V = numpy.zeros(npts) - 2.0
# merge the two
U = numpy.where(C < 10.0, C, V)
pylab.plot(r, U, 'r', linewidth=2)
tlabels = [r"$\lambda_0$"]
tpos = [0.1]
# draw the axes manually
pylab.axis("off")
# y-axis
pylab.arrow(0, 1.1*min(U), 0, 1.1*max(U) - 1.1*min(U),
fc='k', head_width=0.015, head_length=0.18)
pylab.text(-0.05*max(r), 1.1*max(U), r"$U$", color="k", size=15)
# x-axis
pylab.arrow(0, 0, 1.05*max(r), 0,
fc='k', head_width=0.12, head_length=0.02)
pylab.text(1.05*max(r), -0.025*max(U), r"$r$", color="k", size=15, verticalalignment="top")
# draw a line representing a classical particle's energy
E = 0.3*max(U)
pylab.plot([0, max(r)], [E, E], 'b--')
pylab.text(0.75*max(r), 1.05*E, "incoming proton KE", color='b',
horizontalalignment="center")
# find the x-coord of the classical turning point
x = 1.0/E
arrow_params = {'length_includes_head':True}
pylab.arrow(x, 0, 0, E, fc='0.5', ec='0.5', head_width=0.015, head_length=0.25,
**arrow_params)
pylab.text(x, -0.025*max(U), r"$r_0$", color="0.5", size=15,horizontalalignment="center", verticalalignment="top")
f = pylab.gcf()
f.set_size_inches(6.0,6.0)
pylab.savefig("coulomb_barrier.png")
def plot(self, scale=3):
fs = matplotlib.rcParams['legend.fontsize']
if not hasattr(self, 'F'):
self.set_force(self.I)
Fmax = np.max(np.linalg.norm(self.F, axis=1))
index = np.append(self.index['PF']['index'], self.index['CS']['index'])
names = np.append(self.index['PF']['name'], self.index['CS']['name'])
for i, name in zip(index, names):
r, z = self.pf_coil[name]['r'], self.pf_coil[name]['z']
F = self.F[i]
zarrow = scale * F[1] / Fmax
#pl.arrow(r,z,scale*F[0]/Fmax,0, # Fr
# linewidth=2,head_width=0.3,head_length=0.4,
# ec=0.4*np.ones(3),fc=0.7*np.ones(3))
pl.arrow(
r,
z,
0,
zarrow, # Fz
linewidth=2,
head_width=0.12,
head_length=0.1,
ec=0.2 * np.ones(3),
fc=0.2 * np.ones(3))
if name in self.index['PF']['name']:
zarrow += np.sign(zarrow) * 0.5
if abs(zarrow) < self.pf_coil[name]['dz']:
zarrow = np.sign(zarrow) * self.pf_coil[name]['dz']
if zarrow > 0:
va = 'bottom'
else:
va = 'top'
pl.text(r,
z + zarrow,
'{:1.2f}MN'.format(F[1]),
ha='center',
va=va,
fontsize=1.1 * fs,
color=0.1 * np.ones(3),
backgroundcolor=0.9 * np.ones(3))
def main():
points = [(1,0), (0,1), (-1,0), (0,-1)]
plot_shape(points)
polar_points = order_points(points)
# input
in_1 = (1, 0)
plt.plot([in_1[0]], [in_1[1]], marker='o', markersize=10, color="y")
in_2 = (2, 1)
plt.plot([in_2[0]], [in_2[1]], marker='o', markersize=10, color="b")
p.arrow(in_1[0], in_1[1], in_2[0] - in_1[0] - 0.15, in_2[1] - in_1[1] - 0.15, fc="k", ec="k", head_width=0.1, head_length=0.15)
# vec = Y-X
vec = (in_2[0] - in_1[0], in_2[1] - in_1[1])
vec_polar = cartesian_to_polar(vec)
plt.plot([vec[0]], [vec[1]], marker='o', markersize=10, color="g")
p.arrow(0,0, vec[0] - 0.15, vec[1] - 0.15, fc="k", ec="k", head_width=0.1, head_length=0.15)
plt.show()
lamda=0
# extract all the angles of vertices
res_list = [x[1] for x in polar_points]
for idx in range(len(res_list)) :
if vec_polar[1] < res_list[idx] :
A = polar_to_cartesian(polar_points[idx-1])
B = polar_to_cartesian(polar_points[idx])
# the crossing point
cross = cross_point(A, B, vec)
# this is the final lamda
lamda = vec[0]/cross[0]
break
#using for testing: lamda = 2
final_vtx=[]
for pt in points :
final_vtx.append((pt[0]*lamda, pt[1]*lamda))
plot_shape(final_vtx)
plt.show()
def plot(self, plot_frame, **kwargs):
import pylab as plb
default_args = {
'draw_frame': True,
'frame_head_width': 20,
'contour_kwargs': {
'edgecolor': 'none',
'linewidth': 0.0,
'facecolor': 'none'
}
}
from pylab import plot, arrow
lines = self.model.coords_from_frame(plot_frame)
self.curves = list()
#plot_args = kwargs.pop('plot_args',default_args)
for line_key in lines.keys():
try:
element_args = kwargs['contour_kwargs'][line_key]
except KeyError:
element_args = default_args['contour_kwargs']
line = lines[line_key]
from matplotlib.patches import Polygon
poly = Polygon(zip(line[0, :], line[1, :]), **element_args)
#plb.plot([1,2,3,4])
plb.gca().add_patch(poly, )
if 'draw_frame' in kwargs.keys():
if kwargs['draw_frame']:
frame_args = dict()
p = plot_frame['p']
a1 = plot_frame['a1']
a2 = plot_frame['a2']
frame_args['color'] = 'g'
frame_args['head_width'] = kwargs['frame_head_width']
arrow(p[0], p[1], a1[0], a1[1], **frame_args)
frame_args['color'] = 'b'
frame_args['head_width'] = kwargs['frame_head_width']
arrow(p[0], p[1], a2[0], a2[1], **frame_args)
