def _hinton(W, error=None, vmax=None, square=True):
"""
Draws a Hinton diagram for visualizing a weight matrix.
Temporarily disables matplotlib interactive mode if it is on,
otherwise this takes forever.
Originally copied from
http://wiki.scipy.org/Cookbook/Matplotlib/HintonDiagrams
"""
reenable = False
if plt.isinteractive():
plt.ioff()
reenable = True
#P.clf()
W = misc.atleast_nd(W, 2)
(height, width) = W.shape
if not vmax:
#vmax = 2**np.ceil(np.log(np.max(np.abs(W)))/np.log(2))
if error is not None:
vmax = np.max(np.abs(W) + error)
else:
vmax = np.max(np.abs(W))
plt.fill(0.5+np.array([0,width,width,0]),
0.5+np.array([0,0,height,height]),
'gray')
plt.axis('off')
if square:
plt.axis('equal')
plt.gca().invert_yaxis()
for x in range(width):
for y in range(height):
_x = x+1
_y = y+1
w = W[y,x]
_w = np.abs(w)
if w > 0:
_c = 'white'
else:
_c = 'black'
if error is not None:
e = error[y,x]
if e < 0:
print(e, _w, vmax)
raise Exception("BUG? Negative error")
if _w + e > vmax:
print(e, _w, vmax)
raise Exception("BUG? Value+error greater than max")
_rectangle(_x,
_y,
min(1, np.sqrt((_w+e)/vmax)),
min(1, np.sqrt((_w+e)/vmax)),
edgecolor=_c,
fill=False)
_blob(_x, _y, min(1, _w/vmax), _c)
if reenable:
plt.ion()
def plot_Nhden(elem,N,hcol,hden,bounds=False):
for i in to_plot[elem]:
plt.clf()
x = np.array(hden,dtype=np.float)
y = np.array(N[i])
#x,y,hcol = trim(x,y,hcol)
y = hcol[0] - y
xlims=[0.75*np.amin(x), 1.25*np.amax(x)]
ylims=[0.75*np.amin(y), 1.25*np.amax(y)]
try:
if bounds:
l = minNHI - observed[elem][i]["column"][2]
if observed[elem][i]["column"][0]==-30.:
u=maxNHI
else:
u = maxNHI - observed[elem][i]["column"][0]
plt.fill([-30.,30., 30., -30.], [l,l,u,u], '0.50', alpha=0.2, edgecolor='b')
#plt.fill_between(np.arange(xlims[0],xlims[1]),lower,upper,color='0.50')
except KeyError:
pass
plt.plot(x, y, color_map[i],label=ion_state(i,elem))
plt.ylabel(r"log $N_{HI}/N_{%s}$"%(str(elem)+str(roman[i])))
plt.xlabel("log $n_{H}$")
plt.minorticks_on()
makedir('hden')
f=os.path.join(paths["plot_path"],"hden", elem+roman[i]+"N_Nhden.png")
plt.xlim([-3.,0.])
#plt.ylim(ylims)
plt.savefig(f)
plt.show()
plt.close()
def hinton(W, maxweight=None, fig=None):
"""
Draws a Hinton diagram for visualizing a weight matrix.
Temporarily disables matplotlib interactive mode if it is on,
otherwise this takes forever.
"""
if fig is None:
fig = plt.gcf()
reenable = False
height, width = W.shape
if not maxweight:
maxweight = 2**np.ceil(np.log(np.max(np.abs(W)))/np.log(2))
ax = fig.add_subplot(111)
plt.fill(np.array([0, width, width, 0]),
np.array([0, 0, height, height]),
'gray')
ax.axis('off')
ax.axis('equal')
for x in xrange(width):
for y in xrange(height):
_x = x+1
_y = y+1
w = W[y, x]
if w > 0:
_blob(_x - 0.5,
height - _y + 0.5,
min(1, w/maxweight),
'green')
elif w < 0:
_blob(_x - 0.5,
height - _y + 0.5,
min(1, -w/maxweight),
'red')
def standard_process():
"""
standard process from scikit learn
"""
X = np.atleast_2d([1., 3., 5., 6., 7., 8.]).T
y = f(X).ravel()
x = np.atleast_2d(np.linspace(0, 10, 1000)).T
gp = gaussian_process.GaussianProcess(theta0=1e-2, thetaL=1e-4, thetaU=1e-1)
gp.fit(X, y)
y_pred, MSE = gp.predict(x, eval_MSE=True)
sigma = np.sqrt(MSE)
# Plot the function, the prediction and the 95% confidence interval based on
# the MSE
fig = plt.figure()
plt.plot(x, f(x), 'r:', label=u'$f(x) = x\,\sin(x)$')
plt.plot(X, y, 'r.', markersize=10, label=u'Observations')
plt.plot(x, y_pred, 'b-', label=u'Prediction')
plt.fill(np.concatenate([x, x[::-1]]),
np.concatenate([y_pred - 1.9600 * sigma,
(y_pred + 1.9600 * sigma)[::-1]]),
alpha=.5, fc='b', ec='None', label='95% confidence interval')
plt.xlabel('$x$')
plt.ylabel('$f(x)$')
plt.ylim(-10, 20)
plt.legend(loc='upper left')
plt.show()
def plot_triangle(x, y, color=None, draw_lines=True, fill=False):
"""plot an rgb triangle in xy
Args:
x,y (numpy.array): [r, g, b] coords
kwargs:
color (str): if none, 1st point--> red, 2nd --> green, 3rd -> blue
drawLines (bool): draw outline
fill (bool): fill triangle
"""
if fill:
plt.fill(x, y, color='grey', alpha='0.5')
if draw_lines:
indexVal = np.hstack([np.arange(x.size), 0])
plt.plot(x[indexVal], y[indexVal], '-k')
if color:
plt.plot(x[0], y[0], 'o', x[1], y[1], 'o', x[2], y[2], 'o',
color=color)
else:
plt.plot(x[0], y[0], 'or', x[1], y[1], 'og', x[2], y[2], 'ob')
def plot_2_lines(y_pred,y_reco,name0,chain0,path0='/home/stanford/rbaltman/users/bchen45/data/MCL_data/ig_specific/variable_region_plots/'):
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
import subprocess
import os
#y_axis scaling
ratio0 = 1.3
#main
matplotlib.use('Agg')
#example name0 = MCL001_H_chain
if not os.path.isdir(path0+chain0):
cmd_line = 'mkdir '+path0+chain0
cmd0 = subprocess.Popen(cmd_line,shell=True)
cmd0.wait()
len0 = len(y_pred) #len y1 = y2
x = np.linspace(0, len0+1, len0+2)
#print(x)
y_pred = np.array([0]+y_pred+[0])
#print(y_pred)
y_reco = np.array([0]+y_reco+[0])
max0 = ratio0*max(max(y_pred),max(y_reco))
#print(y_reco)
ax = plt.gca()
alpha0 = 0.3
pred0, = plt.fill(x,y_pred,'b',alpha=alpha0,label='MARIA Predicted')
reco0, = plt.fill(x,y_reco,'r',alpha=alpha0,label='MHCII Peptide Recovered')
plt.legend(handles=[pred0,reco0,])
#plt.fill(x,y_pred,'b*',alphax,y_reco,'r*',alpha=0.2)
ax.set_xlabel(name0+' Amino Acid Sequence')
ax.set_ylabel('Peptides recovered/Predicted scores')
ax.set_title(name0+' Peptide Recovered vs. MARIA Prediction Scores')
ax.set_ylim([0,max0])
plt.savefig(path0+chain0+'/'+name0+'_pred_vs_recovered.png', bbox_inches='tight')
plt.close()
def plot_data_and_line(w1,w2):
w1,w2 = float(w1),float(w2)
if w2 != 0 :
y1,y2 = (-w1*(xl1))/w2, (-w1*(xl2))/w2
vx1,vy1 = [xl1,xl2,xl2,xl1,xl1], [y1,y2,yl2,yl2,y1]
vx2,vy2 = [xl1,xl2,xl2,xl1,xl1], [y1,y2,yl1,yl1,y1]
elif w1 != 0:
vx1,vy1 = [xl2,0,0,xl2,xl2], [yl1,yl1,yl2,yl2,yl1]
vx2,vy2 = [xl1,0,0,xl1,xl1], [yl1,yl1,yl2,yl2,yl1]
else:
print "ERROR, Invalid w1 and w2."
return;
if w2 > 0 or ( w2 == 0 and w1 > 0):
c1,c2 = 'b','r'
else:
c1,c2 = 'r','b'
fig = plt.figure()
ax = fig.add_subplot(111)
plt.scatter(X1[Y > 0], X2[Y > 0], s = 80, c = 'b', marker = "o")
plt.scatter(X1[Y<= 0], X2[Y<= 0], s = 80, c = 'r', marker = "^")
plt.fill(vx1, vy1, c1, alpha = 0.25)
plt.fill(vx2, vy2, c2, alpha = 0.25)
ax.set_title(("w1 = %s, w2 = %s")%( w1, w2))
ax.set_xlim(xl1, xl2)
ax.set_ylim(yl1, yl2)
fig.set_size_inches(6, 6)
plt.show()
def point_load():
# point load shear
x = np.linspace(0,L,100)
y = np.ones(len(x))*P/2
y[x>Ploc] = y[x>Ploc]-P
x[0]=0
x[-1]=0
plt.subplot(3,1,2)
plt.ylabel('Shear, V')
plt.title('Shear Diagram')
plt.fill(x, y, 'b', alpha=0.25)
plt.grid(True)
plt.xlim([-1, L+1])
# point load bending
x = np.linspace(-L/2,L/2,100)
y = -(x**2)+(np.max(x**2))
x = np.linspace(0,L,100)
plt.subplot(3,1,3)
plt.title('Bending Diagram')
plt.ylabel('Moment, M')
plt.fill(x, y, 'b', alpha=0.25)
plt.grid(True)
plt.xlim([-1, L+1])
# add point load
plt.subplot(3,1,1)
plt.annotate('P=%i'%P, ha = 'center', va = 'bottom',
xytext = (Ploc, 15), xy = (Ploc,7.5),
arrowprops = { 'facecolor' : 'black', 'shrink' : 0.05 })
plt.title('Free Body Diagram')
plt.axis('off') # removes axis and labels
def dist_load():
# add distributed load
plt.subplot(3,1,1)
for k in np.linspace(0,L,20):
ax1.arrow(k, 11+L/10, 0, -3, head_width=L*0.01, head_length=L*0.1, fc='k', ec='k')
plt.title('Free Body Diagram')
plt.axis('off') # removes axis and labels
#ax1.set_yticklabels('')
# dist load shear
x = [0,0,L,L]
y = [0,5,-5,0]
plt.subplot(3,1,2)
plt.ylabel('Shear, V')
plt.title('Shear Diagram')
plt.fill(x, y, 'b', alpha=0.25)
plt.grid(True)
plt.xlim([-1, L+1])
# dist load bending
x = np.linspace(-L/2,L/2,100)
y = -(x**2)+(np.max(x**2))
x = np.linspace(0,L,100)
plt.subplot(3,1,3)
plt.title('Bending Diagram')
plt.ylabel('Moment, M')
plt.fill(x, y, 'b', alpha=0.25)
plt.grid(True)
plt.xlim([-1, L+1])
def plot_interval_f(fun, x, pow2=0, num_points=101):
"""
Plots the interval extension of a function `fun` over the interval `x`,
which is divided into num=1, 2, 4, ..., 2**pow2 uniform subintervals.
The original function is plotted at num_points points
"""
num_intervals = [2 ** p for p in range(pow2 + 1)]
# plt.figure()
# plt.subplot(1, 1, 1)
for num in num_intervals:
fact_alfa = num * 1.0 / num_intervals[-1] # for plotting
subdivided_intervals = split_interval(x, num)
total_range = range_interval_f(fun, subdivided_intervals)
print "Total range (N={}) = {}".format(num, total_range)
# Draw each subinterval and its range:
for x1 in subdivided_intervals:
low = float(x1.lo)
high = float(x1.hi)
Ffun = fun(x1)
# draw a block of the correct size:
xa1 = np.array([low, low, high, high])
ya1 = np.array([float(Ffun.lo), float(Ffun.hi), float(Ffun.hi), float(Ffun.lo)])
plt.fill(xa1, ya1, "b", alpha=fact_alfa)
# plot the graph of the function:
low = float(x.lo)
high = float(x.hi)
xx = np.linspace(low, high, num_points)
yy = [fun(x) for x in xx]
plt.plot(xx, yy, "red")
def wiggle (traces, skipt=1,scale=1.,lwidth=.1,offsets=None,redvel=0., manthifts=None, tshift=0.,sampr=1.,clip=10., dx=1., color='black',fill=True,line=True, ax=None):
ns = traces.shape[1]
ntr = traces.shape[0]
t = np.arange(ns)*sampr
timereduce = lambda offsets, redvel, shift: [float(offset) / redvel + shift for offset in offsets]
if (offsets is not None):
shifts = timereduce(offsets, redvel, tshift)
elif (manthifts is not None):
shifts = manthifts
else:
shifts = np.zeros((ntr,))
for i in range(0, ntr, skipt):
trace = traces[i].copy()
trace[0] = 0
trace[-1] = 0
if ax == None:
if (line):
plt.plot(i*dx + clipsign(trace / scale, clip), t - shifts[i], color=color, linewidth=lwidth)
if (fill):
for j in range(ns):
if (trace[j] < 0):
trace[j] = 0
plt.fill(i*dx + clipsign(trace / scale, clip), t - shifts[i], color=color, linewidth=0)
else:
if (line):
ax.plot(i*dx + clipsign(trace / scale, clip), t - shifts[i], color=color, linewidth=lwidth)
if (fill):
for j in range(ns):
if (trace[j] < 0):
trace[j] = 0
ax.fill(i*dx + clipsign(trace / scale, clip), t - shifts[i], color=color, linewidth=0)
def main():
axes = lsst.afw.geom.ellipses.Axes(4, 3, 1)
ellipse = lsst.afw.geom.ellipses.Ellipse(
axes, lsst.geom.Point2D(0.25338, 0.76032))
region = lsst.afw.geom.ellipses.PixelRegion(ellipse)
for bbox in [ellipse.computeBBox(), lsst.geom.Box2D(region.getBBox())]:
corners = bbox.getCorners()
pyplot.fill([p.getX() for p in corners], [p.getY()
for p in corners], alpha=0.2)
envelope = region.getBBox()
envelope.grow(2)
ellipse.plot(alpha=0.2)
ellX = []
ellY = []
allX, allY = numpy.meshgrid(
numpy.arange(envelope.getBeginX(), envelope.getEndX()),
numpy.arange(envelope.getBeginY(), envelope.getEndY())
)
gt = ellipse.getGridTransform()
mgt = gt.getMatrix()
transX = mgt[0, 0] * allX + mgt[0, 1] * allY + mgt[0, 2]
transY = mgt[1, 0] * allX + mgt[1, 1] * allY + mgt[1, 2]
allR = (transX**2 + transY**2)**0.5
pyplot.plot(ellX, ellY, 'ro', markeredgewidth=0, alpha=0.5)
pyplot.plot(allX[allR < 1], allY[allR < 1], '+')
pyplot.plot(allX[allR > 1], allY[allR > 1], 'x')
def hinton(W, max_weight=None):
""" Draws a Hinton diagram for visualizing a weight matrix.
"""
if max_weight is None:
max_weight = 2 ** np.ceil(np.log2(np.max(np.abs(W))))
# Temporarily disable matplotlib interactive mode if it is on,
# otherwise this takes forever.
isinteractive = plt.isinteractive()
if isinteractive:
plt.ioff()
height, width = W.shape
plt.clf()
plt.fill(np.array([0, width, width, 0]), np.array([0, 0, height, height]), "gray")
plt.axis("off")
plt.axis("equal")
for (y, x), w in np.ndenumerate(W):
if w != 0:
color = "white" if w > 0 else "black"
area = min(1, np.abs(w) / max_weight)
_blob(x + 0.5, height - y - 0.5, area, color)
if isinteractive:
plt.ion()
def plot_kde_overlap(self, terms, color1='#0067a2', color2='#e8a945', overlap_color='#dddddd', **kwargs):
term1 = terms[0]
term2 = terms[1]
t1 = self.stem(term1)
t2 = self.stem(term2)
bc = self.score_braycurtis(t1, t2, **kwargs)
kde1 = self.kde(t1, **kwargs)
kde2 = self.kde(t2, **kwargs)
plt.plot(kde1, color=color1, label=term1)
plt.plot(kde2, color=color2, label=term2)
overlap = np.minimum(kde1, kde2)
plt.fill(overlap, color=overlap_color)
plt.title(term1+', '+term2+' - '+str(round(bc, 4)))
plt.xlabel('Word Offset')
plt.ylabel('Number of Occurrences')
plt.legend(loc='upper right')
fig = plt.gcf()
fig.set_size_inches(10, 4)
fig.tight_layout()
return plt
def radar_plot():
"""
radar plot
"""
# 生成测试数据
labels = np.array(["A组", "B组", "C组", "D组", "E组", "F组"])
data = np.array([68, 83, 90, 77, 89, 73])
theta = np.linspace(0, 2*np.pi, len(data), endpoint=False)
# 数据预处理
data = np.concatenate((data, [data[0]]))
theta = np.concatenate((theta, [theta[0]]))
# 画图方式
plt.subplot(111, polar=True)
plt.title("雷达图", fontproperties=myfont)
# 设置"theta grid"/"radar grid"
plt.thetagrids(theta*(180/np.pi), labels=labels, fontproperties=myfont)
plt.rgrids(np.arange(20, 100, 20), labels=np.arange(20, 100, 20), angle=0)
plt.ylim(0, 100)
# 画雷达图,并填充雷达图内部区域
plt.plot(theta, data, "bo-", linewidth=2)
plt.fill(theta, data, color="red", alpha=0.25)
# 图形显示
plt.show()
return
def pretty_rho3(meanr, rho, sig, sqrtn):
import matplotlib.patches as mp
t1 = 0.5
t2 = 300.
y_sv = 1.1e-2**2
y_y5 = 2.2e-3**2
sv_req = plt.fill( [t1, t1, t2, t2], [0., y_sv, y_sv, 0.],
color = '#FFFF82')
y5_req = plt.fill( [t1, t1, t2, t2], [0., y_y5, y_y5, 0.],
color = '#BAFFA4')
plt.plot(meanr, rho, color='blue')
plt.plot(meanr, -rho, color='blue', ls=':')
plt.errorbar(meanr[rho>0], rho[rho>0], yerr=sig[rho>0]/sqrtn, color='blue', ls='')
plt.errorbar(meanr[rho<0], -rho[rho<0], yerr=sig[rho<0]/sqrtn, color='blue', ls='')
rho1_line = plt.errorbar(-meanr, rho, yerr=sig, color='blue')
sv_req = mp.Patch(color='#FFFF82')
y5_req = mp.Patch(color='#BAFFA4')
plt.legend([rho1_line, sv_req, y5_req],
[r'$\rho_1(\theta)$', 'SV Requirements', 'Y5 Requirements'])
plt.xlim( [t1,t2] )
plt.ylim( [1.e-6, 3.e-4] )
plt.xlabel(r'$\theta$ (arcmin)')
plt.ylabel(r'$\rho_3$')
plt.xscale('log')
plt.yscale('log', nonposy='clip')
def test_voronoi(self):
# make up data points
np.random.seed(1234)
points = np.random.rand(15, 2)
# compute Voronoi tesselation
vor = Voronoi(points)
# plot
regions, vertices = self.voronoi_finite_polygons_2d(vor)
print "--"
print regions
print "--"
print vertices
# colorize
for region in regions:
polygon = vertices[region]
plt.fill(*zip(*polygon), alpha=0.4)
plt.plot(points[:, 0], points[:, 1], "ko")
plt.xlim(vor.min_bound[0] - 0.1, vor.max_bound[0] + 0.1)
plt.ylim(vor.min_bound[1] - 0.1, vor.max_bound[1] + 0.1)
plt.show()
def funk_graph_boot_naive_beta(beta, seuil ,n,estimateur,type_name, plot_save=False):
# graph de convergence pour le beta
# beta : float, seuil : float, n : integer, plot_save : Boolean
l=[]
x_r = range(1,n)
for esc in x_r:
echantillon = funk_pareto(beta,esc,seuil,plot_boolean=False)
l.append(funk_bootstrap_naive_beta(echantillon,seuil,esc,estimateur,rep=True))
# graphique
y = np.repeat(beta,len(l))
echa = [funk_sig_beta_emp(funk_pareto(beta,x,seuil),seuil) for x in range(len(l))]
test1 = ([l[x] - 1.96*echa[x]*(1/np.sqrt(x)) for x in range(len(l))]) # il faudra mettre les var de la loie normale
test2 = ([l[x] + 1.96*echa[x]*(1/np.sqrt(x)) for x in range(len(l))])
plt.figure()
plt.title(r'Estimation du $\beta$ par methode bootstrap naive par '+type_name+
'\n'+r' $\beta$='+str(beta)+', seuil = '+str(seuil),fontsize=16)
plt.plot(x_r, l, 'r', label=r' Estimation des $\theta_{(n,B)}$')
plt.fill(np.concatenate([x_r, x_r[::-1]]), np.concatenate([test1,test2[::-1]]), alpha=.5, fc='b', ec='None', label='95% confidence interval')
plt.xlabel('Taille de l\'echantillon')
plt.legend(loc='upper left')
if(plot_save==True):
plt.savefig("plot\\conv_beta_boot"+type_name+"_n="+str(n)+".png",bbox_inches="tight")
return([l,test1,test2])
def funk_theta_graph_conv(beta,seuil,a_i,n,perce,estimateur,typename,plot_save=False):
# pour faire les courbes de convergences vers theta
# beta: float, seuil:float, a_i : float, perce : float,
# estimateur : fonction, typename : string, plot_save: boolean
l_test=[]
l1=[]
l2=[]
l_r=[]
thetta = (seuil/a_i)**beta
for esc in range(1,n):
echantillon = funk_pareto(beta,esc,seuil,plot_boolean=False)
[test,test1,test2] = funk_IC_theta(echantillon,seuil,beta,a_i,perce)
#l_r.append(funk_theta_moment(echantillon,seuil,a_i))
l_r.append(funk_theta_mle(echantillon,seuil,a_i))
l_test.append(test)
l1.append(test1)
l2.append(test2)
plt.figure()
plt.title(r'Aprroximation du $\theta$ avec methode empirique',fontsize=16)
plt.plot(range(1,100),l_r,'r',label=r'$\theta$ estime')
plt.fill(np.concatenate([range(1,100), range(1,100)[::-1]]), np.concatenate([[thetta - l_test[x] for x in range(len(l_r))],#l_r[x]
[thetta + l_test[x] for x in range(len(l_r))][::-1]]), \
alpha=.5, fc='b', ec='None', label=str(perce*100)+'% confidence interval')
plt.xlabel('Taille de l\'echantillon')
plt.legend(loc='lower right')
if(plot_save==True):
plt.savefig('plot\conv_thet_IC_'+typename+'.png',bbox_inches="tight")
return([l_r,l1,l2,l_test])
def load_world():
shpRecords = shpUtils.loadShapefile('world_borders/world_borders.shp')['features']
colors = load_color_map()
plt.figure(figsize=(16, 9))
last = ''
for i in range(0,len(shpRecords)):
if shpRecords[i]['info']['CNTRY_NAME'] != last:
print shpRecords[i]['info']['CNTRY_NAME']
last = shpRecords[i]['info']['CNTRY_NAME']
# x and y are empty lists to be populated with the coords of each geometry.
x = []
y = []
#print shpRecords[i]
for j in range(0,len(shpRecords[i]['shape']['parts'][0]['points'])):
tempx = float(shpRecords[i]['shape']['parts'][0]['points'][j][0])
tempy = float(shpRecords[i]['shape']['parts'][0]['points'][j][1])
x.append(tempx)
y.append(tempy) # Populate the lists
# Creates a polygon in matplotlib for each geometry in the shapefile
if shpRecords[i]['info']['CNTRY_NAME'] in colors:
if shpRecords[i]['info']['CNTRY_NAME'] == 'Congo' or shpRecords[i]['info']['CNTRY_NAME'] == 'Zaire':
plt.fill(x,y, facecolor=colors['Democratic Republic of the Congo'])
plt.fill(x,y, facecolor=colors[shpRecords[i]['info']['CNTRY_NAME']])
plt.axis('equal')
plt.savefig('world_calls.png', dpi=100, format='png')
plt.show()
def plotting(DIR, z_name, opos):
colours = ['#313695', '#4575b4', '#74add1',\
'#abd9e9', '#fdae61', '#f46d43', '#d73027', '#a50026',\
'#313695', '#4575b4', '#74add1',\
'#abd9e9', '#fdae61', '#f46d43', '#d73027', '#a50026',\
'#313695', '#4575b4', '#74add1',\
'#abd9e9', '#fdae61', '#f46d43', '#d73027', '#a50026']
xlo, xhi, ylo, yhi, zlo, zhi = coords(DIR, z_name)
vor = Voronoi(opos)
fig = voronoi_plot_2d(vor, show_vertices=False, point_size=0.1)
# add colours
for region in vor.regions:
if not -1 in region:
polygon = [vor.vertices[i] for i in region]
plt.fill(*zip(*polygon), c=colours[2*len(region)+1])
#plt.fill
plt.xlim(0, xhi)
plt.ylim(ylo, yhi)
plt.xlabel('$x$ (\AA)')
plt.ylabel('$y$ (\AA)')
plt.savefig('PLOTS_C/{}/voronoi_2d_{}.pdf'.format(DIR,z_name),
bbox_inches='tight')
#plt.show()
return
def histogram_gdal_direct(bag_file, patch_name,verbose):
# This is the one
'Plot the depth histogram. Use the tif until gdal 1.7.0 comes out'
patch = osgeo.gdal.Open(bag_file)
band = patch.GetRasterBand(1)
bandmin,bandmax = band.ComputeRasterMinMax()
hist = band.GetDefaultHistogram()
#print hist
#print '----------------------------------------------------------------------'
#print hist[3]
hist_vals = hist[3][:-1]
while hist_vals[-1] == 0:
hist_vals.pop()
xticks = ['%02.1f' % depth for depth in np.arange(hist[0],hist[1],(hist[1]-hist[0])/5)]
xticks.append('%.1f' % hist[1])
if verbose:
print (xticks) # Why is the 0.0 tick not showing?
plt.xticks([val * len(hist_vals)/5 for val in range(len(xticks))],xticks) # Yuck!
plt.fill(range(len(hist_vals)),hist_vals)
plt.grid(True)
plt.savefig(patch_name+'-hist.png') #,dpi=50)
with file(patch_name+'.hist','w') as o:
o.write('\n'.join([str(v) for v in hist_vals]))
def hist_with_peak(x, bins=None, range=None, ax=None, orientation='vertical',
histtype=None, **kwargs):
if ax is None:
ax = plt.gca()
hist, bin_edges = np.histogram(x, bins=bins, range=range)
hist_n = hist * 1.0/hist.max()
width = bin_edges[1] - bin_edges[0]
x = np.ravel(zip(bin_edges[:-1], bin_edges[:-1]+width))
y = np.ravel(zip(hist_n, hist_n))
if histtype == 'step':
if orientation == 'vertical':
plt.plot(x, y, **kwargs)
elif orientation == 'horizontal':
plt.plot(y, x, **kwargs)
else:
raise ValueError
elif histtype == 'stepfilled':
if orientation == 'vertical':
plt.fill(x, y, **kwargs)
elif orientation == 'horizontal':
plt.fill(y, x, **kwargs)
else:
raise ValueError
else:
raise ValueError
def GPVisualize1D(self, locations, measurements, predict_range = (0, 1), num_samples = 1000):
"""
Visualize posterior in graphical form
NOTE: very ineffecient since we are using the weight space view to vizualize this
"""
# Grid points
x = np.atleast_2d(np.linspace(predict_range[0], predict_range[1], num_samples, endpoint=False)).T
# Compute predictions - very inefficient because we are using the weight space view
predicted_mean = [0.0] * num_samples
predicted_variance = [0.0] * num_samples
for i in xrange(num_samples):
predicted_mean[i] = self.GPMean(locations, measurements, x[i])[0]
predicted_variance[i] = self.GPVariance2(locations, x[i])[0]
# Plot posterior mean and variances
pl.plot(x, self.GPRegressionTestEnvironment(x), 'r:', label=u'$f(x)$')
pl.plot(locations, measurements, 'r.', markersize=10, label=u'Observations')
pl.plot(x, predicted_mean, 'b-', label=u'Prediction')
pl.fill(np.concatenate([x, x[::-1]]),
np.concatenate([predicted_mean - 1.9600 * np.sqrt(predicted_variance),
(predicted_mean + 1.9600 * np.sqrt(predicted_variance))[::-1]]),
alpha=.5, fc='b', ec='None', label='95% confidence interval')
pl.xlabel('$x$')
pl.ylabel('$f(x)$')
pl.legend(loc='upper left')
pl.show()
def hinton(W, maxWeight=None):
"""
Draws a Hinton diagram for visualizing a weight matrix.
Temporarily disables matplotlib interactive mode if it is on,
otherwise this takes forever.
"""
reenable = False
if plt.isinteractive():
plt.ioff()
plt.clf()
height, width = W.shape
if not maxWeight:
maxWeight = 2**np.ceil(np.log(np.max(np.abs(W)))/np.log(2))
plt.fill(np.array([0, width, width, 0]), np.array([0, 0, height, height]),
'gray')
plt.axis('off')
plt.axis('equal')
for x in xrange(width):
for y in xrange(height):
_x = x+1
_y = y+1
w = W[y, x]
if w > 0:
_blob(_x - 0.5, height - _y + 0.5,
min(1, w/maxWeight), 'white')
elif w < 0:
_blob(_x - 0.5, height - _y + 0.5,
min(1, -w/maxWeight), 'black')
if reenable:
plt.ion()
plt.show()
def convexview(linearcombination):
# draw K
plt.plot([1.0, 2.0, 20.0, 3.0, 1.0],[2.0, 4.0, 0.0, 1.0, 2.0],'b',lw=2.0)
plt.fill([1.0, 2.0, 20.0, 3.0, 1.0],[2.0, 4.0, 0.0, 1.0, 2.0],
facecolor='b', alpha=0.2, edgecolor='none')
plt.text(3.5,1.2,r'$K$',fontsize=28,color='b')
# draw axes
plt.plot([0.5, 0.5],[-0.5, 4.5],'k',lw=1.0)
plt.plot([0.0, 4.0],[0.5, 0.5],'k',lw=1.0)
# plot u, v
u = np.array([1.6,1.7])
v = np.array([3.0,3.0])
plt.plot(u[0],u[1],'.',markersize=14,color='k')
plt.text(u[0]-0.3,u[1]-0.3,r'$u$',fontsize=24,color='k')
plt.plot(v[0],v[1],'.',markersize=14,color='k')
plt.text(v[0]+0.1,v[1]+0.1,r'$v$',fontsize=24,color='k')
# show either interpretation
eps = 0.6
z = (1.0 - eps) * u + eps * v
plt.plot(z[0],z[1],'.',markersize=14,color='k')
if linearcombination:
# lin-comb : (1 - eps) u + eps v
plt.plot([u[0],v[0]], [u[1],v[1]],'k',lw=2.0)
plt.text(z[0],z[1]-0.3,r'$(1-\varepsilon) u + \varepsilon v$',fontsize=24,color='k')
else:
# intoK : u + eps (v - u)
ax = plt.axes()
w = eps * (v - u)
ax.arrow(u[0],u[1],w[0],w[1],
head_width=0.1, head_length=0.2, length_includes_head=True, fc='k', ec='k')
plt.text(z[0],z[1]-0.3,r'$u + \varepsilon (v - u)$',fontsize=24,color='k')
plt.axis([-1.0,4.0,0.0,5.0],'k',lw=2.0)
plt.axis('off')
def main():
x = linspace(0, 1, 200)
y = sin(4 * pi * x) * exp(-5 * x)
fill(x, y, 'r')
grid(True)
show()
def noiseless():
X = np.atleast_2d([1.,3.,5.,6.,7.,8.,]).T
# observations
y = f(X).ravel() # reshape to 1-D
# mesh the input space to cover all points to predict f(x) and the MSE
x = np.atleast_2d(np.linspace(0,10,1000)).T # and flatten
# instantiate gauss process
gp = GaussianProcess(corr='cubic', theta0=1e-2, thetaL=1e-4,
thetaU=1e-1, random_start=100)
# fit to data using maximum likelihood estimation of params
gp.fit(X,y)
# make predictions on meshed x-axis, also return MSE
y_pred, MSE = gp.predict(x, eval_MSE=True)
sigma = np.sqrt(MSE)
# plot
fig = plt.figure()
plt.plot(x, f(x), 'r:', label=u'$f(x) = x\,\sin(x)$')
plt.plot(X, y, 'r.', markersize=10, label=u'Observations')
plt.plot(x, y_pred, 'b-', label=u'Prediction')
# fill the space between the +/-MSE
plt.fill(np.concatenate([x, x[::-1]]), # reverse order of x
np.concatenate([y_pred - 1.9600 * sigma,
(y_pred + 1.9600 * sigma)[::-1]]),
alpha=0.5, fc='b', ec='None', label='95% confidence interval')
# shade, fill color, edge color
plt.title('Noiseless case')
plt.xlabel('$x$')
plt.ylabel('$f(x)$')
plt.ylim(-10, 20)
plt.legend(loc='upper left')
return
def __main__():
'''test code'''
# make up data points
#np.random.seed(1234)
points = np.random.rand(3, 2)
# compute Voronoi tesselation
vor = Voronoi(points)
# plot
regions, vertices = voronoi_finite_polygons_2d(vor,radius=100000)
print("--")
print(regions)
print("--")
print(vertices)
# colorize
for region in regions:
polygon = vertices[region]
plt.fill(*zip(*polygon), alpha=0.4)
plt.plot(points[:,0], points[:,1], 'ko')
plt.axis('equal')
plt.xlim(vor.min_bound[0] - 0.1, vor.max_bound[0] + 0.1)
plt.ylim(vor.min_bound[1] - 0.1, vor.max_bound[1] + 0.1)
#plt.savefig('voro.png')
plt.show()
def display(self): length = self.length width = self.width base_x = self.x - .5*length base_y = self.y - .5*width xs = [base_x, base_x + length, base_x+length, base_x, base_x] ys = [base_y, base_y, base_y+width, base_y+width, base_y] plt.plot(xs, ys, 'k') if not self.flyable: plt.fill(xs, ys, 'r') for letter in self.exitnodelist: if letter == 'C': x = base_x + .5*length y = base_y +.5*width if letter == 'N': x = base_x + .5*length y = base_y + width if letter == 'S': x = base_x + .5*length y = base_y if letter == 'E': x = base_x + length y = base_y + .5*width if letter == 'W': x = base_x y = base_y + .5*width plt.plot([x, base_x+.5*length],[y, base_y +.5*width], 'g') plt.plot([x, base_x+.5*length],[y, base_y +.5*width], 'go')
# loop thru years
i = 0
for minmag in minmags:
fig, ax = plt.subplots(1, figsize=(14, 8))
width = 0.35
# first plot filled box between 1986 & 1992
if minmag == 5.0:
fy = 7
else:
fy = 13
fx1 = 1986 - width
fx2 = 1992 + width
plt.fill([fx1, fx2, fx2, fx1, fx1], [0, 0, fy, fy, 0],
'0.8',
edgecolor='0.8')
plt.text(1989,
8.1,
' Australian $\mathregular{M_L}$\n' + 'equations developed',
rotation=90.,
ha='center',
va='bottom',
fontsize=13)
for pm in pltmean:
i += 1
plt_years = arange(1960, 2019)
n_origML = []
D = elphmod.dispersion.sample(ph.D, q)
ph2 = copy.copy(ph)
elphmod.ph.q2r(ph2, D, q, nq, apply_asr_simple=True)
plt.figure()
for subplot, D in enumerate([ph.D, ph2.D]):
plt.subplot(121 + subplot)
w2, e, order = elphmod.dispersion.dispersion(D,
q_path,
vectors=True,
order=True,
broadcast=False)
if comm.rank == 0:
w = elphmod.ph.sgnsqrt(w2) * elphmod.misc.Ry * 1e3
pol = elphmod.ph.polarization(e, q_path)
for i in range(w.shape[1]):
fatbands = elphmod.plot.compline(x, w[:, i], pol[:, i])
for j, fatband in enumerate(fatbands):
plt.fill(*fatband, color=colors[j], linewidth=0.0)
if comm.rank == 0:
plt.show()
def process(file, name, trueFile):
scores = []
trueScores = []
sampleRate = 3
c = 0
X_samps = []
for line in file:
c = c + sampleRate
if float(line) not in scores:
scores.append(float(line))
X_samps.append(c)
scores = (np.array(scores) * sampleRate).T
for line in trueFile:
trueScores.append(float(line))
fig = plt.figure()
#plt.plot(scores, markersize=10)
#X = np.atleast_2d([x for x in range(0, len(scores))]).T
scores2 = scores
#scores2 = scores[::sampleRate]
scores2 = np.array(scores2).reshape(len(scores2), 1)
#scores2 = list(itertools.chain.from_iterable(itertools.repeat(q, x) for q in scores2))
trueScores = np.array(trueScores).reshape(len(trueScores), 1)
X = np.atleast_2d(np.linspace(0, len(scores2), len(scores))).T
# for i in range(len(scores2), len(scores)):
# scores2.append(scores2[len(scores2) - 1])
#plt.plot(scores2, '--')
x = np.atleast_2d([x for x in range(0, len(scores2))]).T
X = np.atleast_2d(np.linspace(0, len(scores2), len(scores))).T
#X = np.atleast_2d([x for x in range(0, len(scores2))]).T
#X = np.atleast_2d(X).T
x_val_true = findIn(int(round(max(trueScores)[0] * 0.7)),
trueScores) / sampleRate
dy = 0.5 + 1.0 * np.random.random(np.array(scores2).shape)
gp = GP()
gp.create(x, scores2)
y_pred, sigma = gp.predict(X)
_X = np.atleast_2d([x for x in range(0, len(scores))]).T
#x_val_gp = findIn(int(round(max(scores) * 0.7)), scores2)
#plt.plot(scores, markersize=10)
#plt.errorbar(X.ravel(), scores2, dy, fmt='r.', label=u'Observations')
"""
resultScoreFile = open('true_document_rates/' + name + ".csv", "w")
resultScoreFile.write("% of Docs Looked at" + "," + "% of Docs Returned" + "," + "Number of Documents" + "," + "Total Number of Documents" + "\t" + "Sample Rate:" + str(sampleRate) + "\n")
percentages = [x for x in range(1, 100)]
for per in percentages:
ind = (len(X) / 100) * per
score = ((scores[int(ind)] / scores[-1]) * 100)
resultScoreFile.write(str(per) + "," + str(score) + "," + str(int(ind)) + "," + str(len(scores)) + "\n")
resultScoreFile.close()
"""
p0 = (0.3, 5) # starting search coefs
opt, pcov = curve_fit(model_func, X_samps, scores2, p0)
#a, k = opt
#y2 = model_func(x, a, k)
# plt.plot(X_samps, y2, label='Fit. func: f(x) = %.3f e^{-%.3f x}' % (a,k))
p1 = plt.plot(X_samps, scores2, c='C1', label=u'True')
# y_pred = np.array([ '%.2f' % elem for elem in y_pred ])
# y_pred_u = {}
# for i, item in enumerate(y_pred):
# if item not in y_pred_u:
# y_pred_u[item] = i
# _X = np.array(list(y_pred_u.values()))
# y_pred = np.array(list(y_pred_u.keys()))
p2 = plt.plot(X_samps, y_pred, c='b', label='Prediction GP')
#p3 =plt.plot([x for x in range(0, len(trueScores[::sampleRate]))], trueScores[::sampleRate], c='C2', label=u'All Values')
p3 = plt.plot([x for x in range(0, len(trueScores))],
trueScores,
c='C2',
label=u'All Values')
plt.fill(np.concatenate([X_samps, X_samps[::-1]]),
np.concatenate(
[y_pred - 1.9600 * sigma, (y_pred + 1.9600 * sigma)[::-1]]),
alpha=.1,
fc='g',
ec='None',
label='95% confidence interval')
plt.xlabel('Number of Documents')
plt.ylabel('Return Rate')
#plt.xlim(0, len(scores))
# plt.title(str())
plt.title("Sample Rate: " + str(sampleRate) + " 70% Recall: " +
str(x_val_true))
plt.legend(loc='upper right')
plt.show()
plt.plot(X, y, 'r+', markersize=20, lw=2.0, label='observations')
plt.errorbar(X.ravel(),
y,
dy,
fmt='r.',
markersize=10,
label='Observations')
plt.plot(Xt,
y_pred,
color='g',
linestyle='--',
lw=1.5,
label='GP prediction')
plt.fill(np.concatenate([Xt, Xt[::-1]]),
np.concatenate(
[y_pred - 1.96 * sigma, (y_pred + 1.96 * sigma)[::-1]]),
alpha=0.5,
label='95% conf interval')
plt.title('GP regression')
plt.xlabel('X1')
plt.ylabel('X2')
plt.grid(True)
plt.legend()
plt.show()
#fit a GP to market data
#load data
start = datetime(2015, 1, 1, 0, 0, 0, 0, pytz.utc)
end = datetime(2016, 1, 1, 0, 0, 0, 0, pytz.utc)
spy = data.DataReader("SPY", 'google', start, end)
import sys
sys.path.append('../scraper')
import location_sampler
states_file = 'states.xml'
borders = np.asarray(location_sampler.get_borders(states_file))
labels = location_sampler.get_labels(states_file)
nLabels = len(borders)
state_center = np.zeros([nLabels, 2])
for i in range(0, nLabels):
plt.fill(borders[i][:, 0], borders[i][:, 1], 'r-')
border_A = map(float, borders[i][:, 0])
border_B = map(float, borders[i][:, 1])
#pdb.set_trace()
state_center[i, 1] = np.mean(border_A)
state_center[i, 0] = np.mean(border_B)
plt.plot(state_center[i, 1], state_center[i, 0], 'b.')
np.save("state_center.npy", state_center)
plt.show()
plt.hold(True)
juneau_ak = (58.3019, 134.4197)
honolulu_hi = (21.3069, 157.8583)
print(great_circle(juneau_ak, honolulu_hi).kilometers)
matplotlib.rcParams['font.family']='Arial Unicode MS'
matplotlib.rcParams['font.sans-serif']=['Arial Unicode MS']
radar_labels = np.array(['爆发力','技巧熟练度','气势',\
'稳定性','速度'])
nAttr = 5
data = np.array([[0.8,0.9,0.9,0.75],
[0.85,0.87,0.9,0.9],
[0.9,0.6,1.0,0.6],
[0.8,0.7,0.7,0.9],
[0.6,0.9,0.9,0.92]]
)
data_labels = ('马龙','张继科','马琳',\
'王励勤')
angles = np.linspace(0, 2*np.pi, nAttr, endpoint = False)
data = np.concatenate((data, [data[0]]))
angles = np.concatenate((angles, [angles[0]]))
fig = plt.figure(facecolor = 'white')
plt.subplot(111, polar = True)
plt.plot(angles, data, 'o-', linewidth = 1.5, alpha = 0.9)
plt.fill(angles, data, alpha = 0.2)
plt.thetagrids(angles*180/np.pi, radar_labels)
plt.figtext(0.05, 0.97, '中国国家队乒乓球运动员参数雷达图',ha =
'left', size = 15)
legend = plt.legend(data_labels, loc = (0.9,0.92), labelspacing= 0.1)
#plt.setp(legend.get_texts(), fontsize = 'small')
#plt.grid(True)
plt.savefig('9.5PingPong_holland_radar.jpg')
plt.show()
def generate_cover(title, subtitle, file_name):
sha = hashlib.sha3_512()
sha.update((title + subtitle).encode("utf8"))
rem = int.from_bytes(sha.digest(), "little")
rg = np.random.default_rng(rem)
r = np.sqrt(1 - 0.5**2)
x = [0, 0, r, 2 * r, 2 * r, r, 0]
y = [1, 0, -0.5, 0, 1, 1.5, 1]
x_data = np.array(x)
y_data = np.array(y)
fig = plt.figure(figsize=(66, 36))
x_orig = x_data.copy()
width = 37
height = 25
for j in range(height):
x_data = x_orig.copy()
shift = (j % 2) == 0
x_data += shift * r
for i in range(width):
plt.fill(x_data, y_data, color=color[rg.integers(0, len(color))])
x_data += 2 * r
y_data -= 1 + 0.5
fig.savefig(f"{file_name}-back.png",
pad_inches=0,
bbox_inches="tight",
dpi=108)
ax = fig.axes[0]
ylim = ax.get_ylim()
h = ylim[1] - ylim[0]
img = Image.open(f"{file_name}-back.png")
vadj = int(img.size[1] / h // 1)
px = img.size[0] // (width + 1)
box = [px // 2, vadj, img.size[0] - px // 2, img.size[1] - vadj]
crop = img.crop(box)
sz = crop.size
if sz[0] / sz[1] > 16 / 9:
new_width = int(np.ceil(sz[0] * (16 / 9) / (sz[0] / sz[1])))
loss = sz[0] - new_width
box = [loss // 2, 0, sz[0] - loss // 2, crop.size[1]]
crop = crop.crop(box)
crop.save(f"{file_name}-back.png")
plt.fill(
[0, (width + r / 2) * 2 * r, (width + r / 2) * 2 * r, 0],
[-3 + 0.5 - 1.5, -3 + 0.5 - 1.5, -8 - 2 - 1.5, -8 - 2 - 1.5],
color="#ffffff",
)
plt.subplots_adjust(0, 0, 1, 1, 0, 0)
for ax in fig.axes:
ax.set_axis_off()
ax.axis("off")
ax.margins(0, 0)
ax.xaxis.set_major_locator(plt.NullLocator())
ax.yaxis.set_major_locator(plt.NullLocator())
ax.text(
5 * r,
-6 - 1.5,
title.replace("`", ""),
fontsize=3 * 60,
color=color[1],
fontweight="normal",
fontname="Roboto Condensed",
)
if subtitle:
ax.text(
5 * r,
-8.5 - 1.5,
subtitle.replace("`", ""),
fontsize=3 * 40,
color=color[3],
fontname="Roboto Condensed",
fontweight="light",
)
fig.savefig(f"{file_name}-cover.png",
pad_inches=0,
bbox_inches="tight",
dpi=108)
ylim = ax.get_ylim()
h = ylim[1] - ylim[0]
img = Image.open(f"{file_name}-cover.png")
vadj = int(img.size[1] / h // 1)
px = img.size[0] // (width + 1)
box = [px // 2, vadj, img.size[0] - px // 2, img.size[1] - vadj]
crop = img.crop(box)
sz = crop.size
if sz[0] / sz[1] > 16 / 9:
new_width = int(np.ceil(sz[0] * (16 / 9) / (sz[0] / sz[1])))
loss = sz[0] - new_width
box = [loss // 2, 0, sz[0] - loss // 2, crop.size[1]]
crop = crop.crop(box)
crop.save(f"{file_name}-cover.png")
def wiggle(traces,
skipt=1,
scale=1.,
lwidth=.1,
offsets=None,
redvel=0.,
manthifts=None,
tshift=0.,
sampr=1.,
clip=10.,
dx=1.,
color='black',
fill=True,
line=True,
ax=None):
ns = traces.shape[1]
ntr = traces.shape[0]
t = np.arange(ns) * sampr
timereduce = lambda offsets, redvel, shift: [
float(offset) / redvel + shift for offset in offsets
]
if (offsets is not None):
shifts = timereduce(offsets, redvel, tshift)
elif (manthifts is not None):
shifts = manthifts
else:
shifts = np.zeros((ntr, ))
for i in range(0, ntr, skipt):
trace = traces[i].copy()
trace[0] = 0
trace[-1] = 0
if ax == None:
if (line):
plt.plot(i * dx + clipsign(trace / scale, clip),
t - shifts[i],
color=color,
linewidth=lwidth)
if (fill):
for j in range(ns):
if (trace[j] < 0):
trace[j] = 0
plt.fill(i * dx + clipsign(trace / scale, clip),
t - shifts[i],
color=color,
linewidth=0)
else:
if (line):
ax.plot(i * dx + clipsign(trace / scale, clip),
t - shifts[i],
color=color,
linewidth=lwidth)
if (fill):
for j in range(ns):
if (trace[j] < 0):
trace[j] = 0
ax.fill(i * dx + clipsign(trace / scale, clip),
t - shifts[i],
color=color,
linewidth=0)
for i in range(xx.size):
if (srad < np.sqrt(xx[i]**2 + yy[i]**2) < rmax * 0.97 * np.sqrt(3) / 2.):
# if (10.7 * srad < np.sqrt(xx[i]**2 + yy[i]**2) < rmax*0.97*np.sqrt(3)/2.):
xs = np.append(xs, xx[i])
ys = np.append(ys, yy[i])
# plot segments
# -------------
r0 = srad / sqrt(3)
th = 2 * np.pi * np.arange(6) / 6. + np.pi / 6.
for i in range(xs.size):
hx = xs[i] + r0 * np.cos(th)
hy = ys[i] + r0 * np.sin(th)
plt.fill(hx, hy, fc='none', linewidth=1)
plt.plot(xs, ys, 'r.')
# plot spider arms
# ----------------
#r0 = rmax
#x0, x1, y0, y1 = -r0, r0, 0, 0
#plt.plot([x0, x1], [y0, y1], color='gray', linewidth=5)
#x0, y0 = r0 * np.cos(np.pi/3), r0 * np.sin(np.pi/3)
#x1, y1 = -x0, -y0
#plt.plot([x0, x1], [y0, y1], color='gray', linewidth=5)
#x0, y0 = r0 * np.cos(2*np.pi/3), r0 * np.sin(2*np.pi/3)
#x1, y1 = -x0, -y0
#plt.plot([x0, x1], [y0, y1], color='gray', linewidth=5)
# plot sample points
# -*- coding: utf-8 -*-
"""
Created on Sun Sep 27 02:05:03 2015
@author: antalcides
"""
import matplotlib.pyplot as plt
n = 16
m = 6
plt.figure(figsize=(n * 0.2, m * 0.2))
plt.gca().axison = False
x = 8
y = 4
plt.fill((x, x + 1, x + 1, x), (y, y, y + 1, y + 1), 'r', linewidth=0)
for i in range(0, n + 1):
ii = (i, i)
jj = (0, m)
plt.plot(ii, jj, '0.4', linewidth=0.2)
for j in range(0, m + 1):
ii = (0, n)
jj = (j, j)
plt.plot(ii, jj, '0.4', linewidth=0.2)
plt.savefig('myplot.pdf', bbox_inches='tight')
def plot_regions(model,
X,
y,
num_ticks=100,
cmap='rainbow',
fig_size=None,
legend=True,
close=True,
display=True,
path=None,
keras=False):
# Convert X to numpy array
X = np.array(X)
y = np.array(y)
# Check to see if there are exactly 2 features
if X.shape[1] != 2:
raise Exception('Training set must contain exactly ' + 'two features.')
# Find min and max points for grid axes
minx, maxx = min(X[:, 0]), max(X[:, 0])
marginx = (maxx - minx) / 20
x0, x1 = minx - marginx, maxx + marginx
miny, maxy = min(X[:, 1]), max(X[:, 1])
marginy = (maxy - miny) / 20
y0, y1 = miny - marginy, maxy + marginy
# Create grid tick marks
xticks = np.linspace(x0, x1, num_ticks)
yticks = np.linspace(y0, y1, num_ticks)
# Create array of grid points
# tile stacks copies of xticks end creating a size num_ticks^2 array
# repeat repeats each elt of yticks to create a size num_ticks^2 array
# They are combined into an array of shape (2, num_ticks^2)
# transpose creates array of pts with shape (num_ticks^2, 2).
grid_pts = np.transpose(
[np.tile(xticks, len(yticks)),
np.repeat(yticks, len(xticks))])
# Feed grid points to model to generate 1D array of classes
if (keras == True):
class_pts = model.predict_classes(grid_pts)
class_pts = class_pts.reshape((len(class_pts), ))
else:
class_pts = model.predict(grid_pts)
# Get list of classes. This could, in theory, contain text labels.
classes = np.unique(y)
k = len(classes)
# create new list with numerical classes
class_pts_2 = np.zeros(class_pts.shape)
for i in range(len(classes)):
sel = class_pts == classes[i]
class_pts_2[sel] = i
# reshape classification array into 2D array corresponding to grid
class_grid = class_pts_2.reshape(len(xticks), len(yticks))
# Set a color map
my_cmap = plt.get_cmap(cmap)
# Close any open figures and set plot size.
if (close):
plt.close()
if (not fig_size is None):
plt.figure(figsize=fig_size)
# Add color mesh
plt.pcolormesh(xticks,
yticks,
class_grid,
cmap=my_cmap,
zorder=1,
vmin=0,
vmax=k - 1)
# Add transparency layer to lighten the colors
plt.fill([x0, x0, x1, x1], [y0, y1, y1, y0], 'white', alpha=0.5, zorder=2)
# Select discrete cuts for color map
cuts = np.arange(k) / (k - 1)
# Add scatter plot for each class, with seperate colors and labels
for i in range(k):
sel = y == classes[i]
my_c = mplc.rgb2hex(my_cmap(cuts[i]))
plt.scatter(X[sel, 0],
X[sel, 1],
c=my_c,
edgecolor='k',
zorder=3,
label=classes[i])
if (legend):
plt.legend()
if (not path is None):
plt.savefig(path, format='png')
if (display):
plt.show()
import numpy as np
import matplotlib
matplotlib.use('TkAgg')
import matplotlib.pyplot as plt
x = np.linspace(0, 5*np.pi, 1000)
y1 = np.sin(x)
y2 = np.sin(2*x)
# plt.plot(x, y1)
# plt.plot(x, y2)
# fill range between x axis and curve
plt.fill(x, y1, 'b', alpha=0.3)
plt.fill(x, y2, 'r', alpha=0.3)
plt.show()
def draw_roles(p,z,roles,background=False,marker=".",size=1):
c = [ROLE_COLORS[x] for x in roles]
plt.scatter(p,z,color=c,marker=marker,s=size)
if background:
ylim = plt.ylim()
plt.hlines(2.5,0,1)
plt.vlines(0.05,ylim[0],2.5)
plt.vlines(0.625,ylim[0],2.5)
plt.vlines(0.8,ylim[0],2.5)
plt.vlines(0.3,2.5,ylim[1])
plt.vlines(0.75,2.5,ylim[1])
plt.fill([0,0.3,0.3,0],[ylim[1],ylim[1],2.5,2.5],color=ROLE_COLORS["R5"],alpha=.2)
plt.fill([0.75,0.3,0.3,0.75],[ylim[1],ylim[1],2.5,2.5],color=ROLE_COLORS["R6"],alpha=.2)
plt.fill([0.75,1,1,.75],[ylim[1],ylim[1],2.5,2.5],color=ROLE_COLORS["R7"],alpha=.2)
plt.fill([0,.05,.05,0],[ylim[0],ylim[0],2.5,2.5],color=ROLE_COLORS["R1"],alpha=.2)
plt.fill([.625,.05,.05,.625],[ylim[0],ylim[0],2.5,2.5],color=ROLE_COLORS["R2"],alpha=.2)
plt.fill([.625,.8,.8,.625],[ylim[0],ylim[0],2.5,2.5],color=ROLE_COLORS["R3"],alpha=.2)
plt.fill([1,.8,.8,1],[ylim[0],ylim[0],2.5,2.5],color=ROLE_COLORS["R4"],alpha=.2)
plt.ylim(ylim)
plt.xlim((-0.01,1))
plt.xlabel("Participation coefficient")
plt.ylabel("z-score of within-module degree")
a=random.uniform(0,1000)
b=random.uniform(0,1000)
w=random.uniform(0,100)
h=random.uniform(0,100)
f=box(a,b,a+w,b+h)
print(f.area);
if f.contains(pnt2):
print("Covered");
else:
print("Not Covered");
plt.figure()
x,y=c1.exterior.coords.xy;
plt.fill(x,y,edgecolor='black', linewidth=2.1)
x,y=f.exterior.coords.xy;
plt.fill(x,y,edgecolor='black', linewidth=2.1)
plt.plot(pnt2.x,pnt2.y,'r',marker = 'o');
#plt.plot(x,y)
plt.show()
"""poly = Polygon([(2.2, 4.2), (7.2, -25.1), (9.26, -2.456)])
x,y=poly.exterior.coords.xy;
plt.fill(x,y,edgecolor='black', linewidth=2.1)
"""
'''p1 = Point(10,10);
c1= p1.buffer(20);
x,y=c1.exterior.coords.xy;
}, {
'name': 'r_state',
'bits': 2
}, {
'name': 'r_closed',
'bits': 1
}]
path_location = os.path.dirname(os.path.realpath(__file__))
dreamer_file = os.path.join(path_location, 'two_player', 'ctrl.json')
# dreamer_file = '/home/formal/cyberphysical_systems/hw5/two_player/ctrl.json'
dreamer_sim = Controller(dreamer_lookup, dreamer_file)
node_init = '0'
var_list = dreamer_sim.simulate(node_init, 40)
plt.fill([0, 1, 1, 0], [0, 0, 1, 1], 'b', alpha=0.2, edgecolor='r')
plt.fill([1, 2, 2, 1], [0, 0, 1, 1], 'y', alpha=0.2, edgecolor='r')
plt.fill([2, 3, 3, 2], [0, 0, 1, 1], 'b', alpha=0.2, edgecolor='r')
plt.fill([3, 4, 4, 3], [0, 0, 1, 1], 'y', alpha=0.2, edgecolor='r')
plt.grid()
l = len(var_list)
anim = animation.FuncAnimation(fig,
animate,
init_func=init(),
frames=l,
interval=1000,
blit=True,
repeat=False)
def plot_multipoles(data,
main_harmonic_order=2,
r0=17.5 / 1000,
plot_label='',
harmonics=None,
directory=None,
filename=None,
max_multipole=None,
ymin=1e-6,
colors=None,
alpha_blending=0.6,
legend=None,
reference_data_idx=0,
display_plot=True):
""" plots mutipole data comparisons """
''' processes input parameters '''
if colors == None:
colors = colors_redline
if filename == None:
filename = 'multipoles.ps'
if max_multipole is None:
max_multipole = max(data[reference_data_idx].harmonics)
if harmonics is None:
harmonics = []
for i in data[reference_data_idx].harmonics:
if i <= max_multipole:
harmonics.append(i)
''' defines main multipole '''
nr_bars = len(data)
#main_idx = data[reference_data_idx].harmonics.index(main_multipole_order)
#main_multipole = abs(data[reference_data_idx].LNn_avg[main_idx]*(r0**(data[reference_data_idx].harmonics[main_idx]-1)))
''' main loop for normal component '''
fig = plt.figure(figsize=(8, 8))
ax = fig.add_subplot(1, 1, 1)
ax.set_yscale('log')
dx = 1 #0.4/nr_bars
xticks = []
for j in range(nr_bars):
main_idx = data[j].harmonics.index(main_harmonic_order)
main_multipole = abs(data[j].LNn_avg[main_idx] *
(r0**(data[j].harmonics[main_idx] - 1)))
#main_multipole_error = abs(data[j].LNn_std[main_idx]*(r0**(data[j].harmonics[main_idx]-1)))
x, y, n = [], [], 1
for i in range(len(harmonics)):
idx = data[j].harmonics.index(harmonics[i])
alpha = r0**(data[j].harmonics[idx] -
1) / (r0**(data[j].harmonics[main_idx] - 1))
error = alpha * math.sqrt(
(data[j].LNn_std[idx] / data[j].LNn_avg[main_idx])**2 +
(data[j].LNn_avg[idx] * data[j].LNn_std[main_idx] /
data[j].LNn_avg[main_idx])**2)
multipole_0 = alpha * abs(
data[j].LNn_avg[idx] / data[j].LNn_avg[main_idx])
multipole_p = multipole_0 + error
multipole_n = multipole_0 - error
if multipole_n < 0:
multipole_n = ymin
x0 = n * (nr_bars + 2) + j
if j == nr_bars / 2:
xticks.append(x0)
x.append(x0 - 0.5 * dx), y.append(ymin)
x.append(x0 - 0.5 * dx), y.append(multipole_0)
x.append(x0 + 0.5 * dx), y.append(multipole_0)
x.append(x0 + 0.5 * dx), y.append(ymin)
if (multipole_n != 0) or (multipole_p != 0):
plt.plot([x0, x0], [multipole_n, multipole_p],
color=(0, 0, 0)) #colors[j])
plt.plot([x0 - 0.25 * dx, x0 + 0.25 * dx],
[multipole_n, multipole_n],
color=(0, 0, 0)) #colors[j])
plt.plot([x0 - 0.25 * dx, x0 + 0.25 * dx],
[multipole_p, multipole_p],
color=(0, 0, 0)) #colors[j])
n += 1
plt.fill(x,
y,
color=RotatingCoilMeasurement.alpha_blending(
colors[j % len(colors)], alpha_blending))
''' creates plots '''
ax.grid(True)
ax.xaxis.set_ticks(xticks)
ax.xaxis.set_ticklabels(['{0:d}'.format(i) for i in harmonics])
plt.ylim(ymin=ymin)
plt.xlabel('harmonic order')
plt.ylabel('relative normal multipole strengths (r$_0$ = ' +
str(r0 * 1000) + ' mm)')
if legend is not None:
plt.legend(legend)
plt.title(plot_label + ': normal components')
if directory is not None:
fname = os.path.join(directory, filename + '_normal.ps')
else:
fname = filename + '_normal.ps'
plt.savefig(fname)
if display_plot:
plt.show()
plt.close()
fig = plt.figure(figsize=(8, 8))
ax = fig.add_subplot(1, 1, 1)
ax.set_yscale('log')
dx = 1 #0.4/nr_bars
xticks = []
for j in range(nr_bars):
x, y, n = [], [], 1
for i in range(len(harmonics)):
idx = data[j].harmonics.index(harmonics[i])
multipole_0 = abs(data[j].LSn_avg[idx]) * (r0**(
data[j].harmonics[idx] - 1)) / main_multipole
multipole_p = (abs(data[j].LSn_avg[idx]) +
data[j].LSn_std[idx]) * (r0**(
data[j].harmonics[idx] - 1)) / main_multipole
multipole_n = (abs(data[j].LSn_avg[idx]) -
data[j].LSn_std[idx]) * (r0**(
data[j].harmonics[idx] - 1)) / main_multipole
if multipole_n < 0:
multipole_n = ymin
x0 = n * (nr_bars + 2) + j
if j == nr_bars / 2:
xticks.append(x0)
x.append(x0 - 0.5 * dx), y.append(ymin)
x.append(x0 - 0.5 * dx), y.append(multipole_0)
x.append(x0 + 0.5 * dx), y.append(multipole_0)
x.append(x0 + 0.5 * dx), y.append(ymin)
if (multipole_n != 0) or (multipole_p != 0):
plt.plot([x0, x0], [multipole_n, multipole_p],
color=(0, 0, 0)) #colors[j])
plt.plot([x0 - 0.25 * dx, x0 + 0.25 * dx],
[multipole_n, multipole_n],
color=(0, 0, 0)) #colors[j])
plt.plot([x0 - 0.25 * dx, x0 + 0.25 * dx],
[multipole_p, multipole_p],
color=(0, 0, 0)) #colors[j])
n += 1
plt.fill(x,
y,
color=RotatingCoilMeasurement.alpha_blending(
colors[j % len(colors)], alpha_blending))
ax.grid(True)
ax.xaxis.set_ticks(xticks)
ax.xaxis.set_ticklabels(['{0:d}'.format(i) for i in harmonics])
plt.xlabel('harmonic order')
plt.ylabel('relative skew multipole strengths (r$_0$ = ' + str(r0 * 1000) +
' mm)')
if legend is not None:
plt.legend(legend)
plt.title(plot_label + ': skew components')
if directory is not None:
fname = os.path.join(directory, filename + '_skew.ps')
else:
fname = filename + '_skew.ps'
plt.savefig(fname)
if display_plot:
plt.show()
plt.close()
def display_obstacle(self):
obstacle_x, obstacle_y = self.obstacle.exterior.xy #this method is defined in class Polygon
plt.fill(obstacle_x, obstacle_y)
'weight': 'bold',
})
# Set the font used for MathJax - more on thiprint(images)
rc('mathtext', **{'default': 'regular'})
plt.rc('font', family='serif')
plt.figure()
ax = plt.axes(xlim=(0, 12), ylim=(0, 9))
plt.plot(CV, fes, zorder=5)
plt.plot(CV, fes_biased, zorder=5)
# Plot N circles to represent N walkers
for j in range(N):
# prevent crossing of each other
plt.plot(rx[j], ry[j], color='black', zorder=10 + j)
plt.fill(rx[j], ry[j], color='yellow', zorder=10 + j)
if N > 1:
plt.text(cx[j],
cy[j],
'%s' % str(j + 1),
zorder=10 + j,
fontsize='8')
plt.fill_between(CV, 0, fes, color='steelblue')
plt.fill_between(CV, fes, fes_biased, color='palegreen')
plt.xlabel('Centers of mass separation distance (nm)',
fontsize='12',
fontweight='bold')
plt.ylabel('Free energy ($k_{B} T$)', fontsize='12', fontweight='bold')
if N == 1:
def plot(self):
fig = plt.figure(figsize=(15, 5))
plt.subplot(2, 3, 1).set_title("Koch Line (iterations = 0)")
points = self.koch(a=np.array([0, 0]),
b=np.array([1, 0]),
iterations=0)
ptsx = []
ptsy = []
for i in range(len(points)):
ptsx.append(points[i][0])
ptsy.append(points[i][1])
plt.plot(ptsx, ptsy, '-')
plt.axis('equal')
plt.axis('off')
plt.subplot(2, 3, 2).set_title("Koch Line (iterations = 1)")
points = self.koch(a=np.array([0, 0]),
b=np.array([1, 0]),
iterations=1)
ptsx = []
ptsy = []
for i in range(len(points)):
ptsx.append(points[i][0])
ptsy.append(points[i][1])
plt.plot(ptsx, ptsy, '-')
plt.axis('equal')
plt.axis('off')
plt.subplot(2, 3, 3).set_title("Koch Line (iterations = 2)")
points = self.koch(a=np.array([0, 0]),
b=np.array([1, 0]),
iterations=2)
ptsx = []
ptsy = []
for i in range(len(points)):
ptsx.append(points[i][0])
ptsy.append(points[i][1])
plt.plot(ptsx, ptsy, '-')
plt.axis('equal')
plt.axis('off')
plt.subplot(2, 3, 4).set_title("Koch Line (iterations = 3)")
points = self.koch(a=np.array([0, 0]),
b=np.array([1, 0]),
iterations=3)
ptsx = []
ptsy = []
for i in range(len(points)):
ptsx.append(points[i][0])
ptsy.append(points[i][1])
plt.plot(ptsx, ptsy, '-')
plt.axis('equal')
plt.axis('off')
plt.subplot(2, 3, 5).set_title("Koch Line (iterations = 4)")
points = self.koch(a=np.array([0, 0]),
b=np.array([1, 0]),
iterations=4)
ptsx = []
ptsy = []
for i in range(len(points)):
ptsx.append(points[i][0])
ptsy.append(points[i][1])
plt.plot(ptsx, ptsy, '-')
plt.axis('equal')
plt.axis('off')
plt.subplot(2, 3, 6).set_title("Koch Line (iterations = 5)")
points = self.koch(a=np.array([0, 0]),
b=np.array([1, 0]),
iterations=5)
ptsx = []
ptsy = []
for i in range(len(points)):
ptsx.append(points[i][0])
ptsy.append(points[i][1])
plt.plot(ptsx, ptsy, '-')
plt.axis('equal')
plt.axis('off')
h = np.sqrt(3) / 2.
a = np.array([0, 0])
b = np.array([1, 0])
c = np.array([0.5, h])
iterations = 7
points1 = self.koch(a=np.array([0, 0]),
b=np.array([1, 0]),
iterations=iterations)
points2 = self.koch(a=np.array([1, 0]),
b=np.array([0.5, -h]),
iterations=iterations)
points3 = self.koch(a=np.array([0.5, -h]),
b=np.array([0, 0]),
iterations=iterations)
points = []
for i in range(len(points1)):
points.append(np.array(points1[i]))
for i in range(len(points2)):
points.append(np.array(points2[i]))
for i in range(len(points3)):
points.append(np.array(points3[i]))
ptsx = []
ptsy = []
for i in range(len(points)):
ptsx.append(points[i][0])
ptsy.append(points[i][1])
plt.figure(figsize=(25, 25))
plt.title("Koch Triangle (iterations = 7)")
plt.plot(ptsx, ptsy, '-')
plt.fill(ptsx, ptsy, color='lightcyan', alpha=0.7)
plt.axis('equal')
plt.axis('off')
plt.show()
flat = list(
itertools.chain(
*[point for point in adj if point is not "removed"]))
# this works only if order is not a concern...........
#flat_no_duplicates = list(set(map(tuple, flat)))
#print(flat)
flat_no_duplicates = [
e for i, e in enumerate(flat) if e not in flat[:i]
]
polygons[i] = flat_no_duplicates
#print(flat)
return polygons
if __name__ == '__main__':
polygons_fixed = fix_polygons(polygons[:])
#polygons_fixed = list(filter(None, polygons_fixed))
#print(polygons_fixed)
#print(polygons_fixed)
for i in range(len(polygons)):
plt.fill(*zip(*polygons[i]), "r")
#try: # polygon may get removed in fixed which would result in index error since we are looping unfixed
plt.fill(*zip(*polygons_fixed[i]), "b")
# except:
# pass
plt.xlim([0, 1]), plt.ylim([0, 1])
plt.show()
def kepflatten(infile,
outfile=None,
datacol='PDCSAP_FLUX',
errcol='PDCSAP_FLUX_ERR',
nsig=3.,
stepsize=0.5,
winsize=5.0,
npoly=3,
niter=1,
ranges='0,0',
plot=False,
overwrite=False,
verbose=False,
logfile='kepflatten.log'):
"""
kepflatten -- Remove low frequency variability from time-series, preserve
transits and flares
kepflatten detrends data for low-frequency photometric structure by
dividing by the mean of best-fit sliding polynomials over a sequential
series of small time ranges across the data. For example, a typical
timestamp is fit three times of ``stepsize=1.0`` and ``winsize=3.0``. The
adopted fit to the timestamp will be the mean of the three values. Outliers
are iteratively-clipped from the fit, therefore structure in e.g.
short-lived transits or flares are better preserved compared to e.g.
bandpass filtering methods (``kepfilter``). Optionally, input data, best
fits, fit outliers and output data are rendered to a plot window. In many
respects kepflatten performs the opposite task to kepoutlier which removes
statistical outliers while preserving low-frequency structure in light
curves.
Parameters
----------
infile : str
The name of a MAST standard format FITS file containing a Kepler light
curve within the first data extension.
outfile : str
The name of the output FITS file. outfile will be a direct copy of
infile but with NaN timestamps removed and two new columns in the 1st
extension - DETSAP_FLUX (a flattened or detrended for low-frequency
variations version of the data) and DETSAP_FLUX_ERR (the associated
1-:math:`\sigma` error).
datacol : str
The column name containing data stored within extension 1 of infile.
Typically this name is SAP_FLUX (Simple Aperture Photometry fluxes),
PDCSAP_FLUX (Pre-search Data Conditioning fluxes) or CBVSAP_FLUX
(SAP_FLUX corrected for systematic artifacts by the PyKE tool
kepcotrend).
errcol : str
The column name containing photometric 1-:math:`\sigma` errors
stored within extension 1 of infile. Typically this name is
SAP_FLUX_ERR (Simple Aperture Photometry fluxes), PDCSAP_FLUX_ERR
(Pre-search Data Conditioning fluxes). The error column coupled to
CBVSAP_FLUX data is SAP_FLUX_ERR. kepflatten normalizes datacol and
errcol consistently using a series of best fit polynomials.
nsig : float
The sigma clipping threshold in units of standard deviation. Data
deviating from a best fit function by more than the threshold will
ignored during subsequent fit iterations.
stepsize : float
The data within datacol is unlikely to be well represented by a single
polynomial function. stepsize splits the data up into a series of time
blocks, each is fit independently by a separate function. The user can
provide an informed choice of stepsize after inspecting the data with
the kepdraw tool. Units are days.
winsize : float
The size of the window to be fit during each step. Units are days.
winsize must be greater or equal to stepsize. winsize >> stepsize is
recommended.
npoly : integer
The order of each piecemeal polynomial function.
niter : integer
If outliers outside of nsig are found in a particular data section,
that data will be removed temporarily and the time series fit again.
This will be iterated niter times before freezing upon the best current
fit.
ranges : str
The user can choose specific time ranges of data on which to work. This
could, for example, avoid removing known stellar flares from a dataset.
Time ranges are supplied as comma-separated pairs of Barycentric Julian
Dates (BJDs). Multiple ranges are separated by a semi-colon. An example
containing two time ranges is:
``2455012.48517,2455014.50072;2455022.63487,2455025.08231``.
If the user wants to correct the entire time series then providing
``ranges='0,0'`` will tell the task to operate on the whole time
series.
plot : bool
Plot the data, fit, outliers and result?
overwrite : bool
Overwrite the output file?
verbose : bool
Print informative messages and warnings to the shell and logfile?
logfile : str
Name of the logfile containing error and warning messages.
Examples
--------
.. code-block:: bash
$ kepflatten kplr012557548-2011177032512_llc.fits
--nsig 3 --stepsize 1.0 --winsize 3.0 --npoly 3 --niter 10 --plot
--overwrite --verbose
.. image:: ../_static/images/api/kepflatten.png
:align: center
"""
if outfile is None:
outfile = infile.split('.')[0] + "-{}.fits".format(__all__[0])
# log the call
hashline = '--------------------------------------------------------------'
kepmsg.log(logfile, hashline, verbose)
call = ('KEPFLATTEN -- ' + ' infile={}'.format(infile) +
' outfile={}'.format(outfile) + ' datacol={}'.format(datacol) +
' errcol={}'.format(errcol) + ' nsig={}'.format(nsig) +
' stepsize={}'.format(stepsize) + ' winsize={}'.format(winsize) +
' npoly={}'.format(npoly) + ' niter={}'.format(niter) +
' ranges={}'.format(ranges) + ' plot={}'.format(plot) +
' overwrite={}'.format(overwrite) + ' verbose={}'.format(verbose) +
' logfile={}'.format(logfile))
kepmsg.log(logfile, call + '\n', verbose)
# start time
kepmsg.clock('KEPFLATTEN started at', logfile, verbose)
# test winsize > stepsize
if winsize < stepsize:
errmsg = 'ERROR -- KEPFLATTEN: winsize must be greater than stepsize'
kepmsg.err(logfile, errmsg, verbose)
# overwrite output file
if overwrite:
kepio.overwrite(outfile, logfile, verbose)
if kepio.fileexists(outfile):
errmsg = ('ERROR -- KEPFLATTEN: {} exists. Use overwrite=True'.format(
outfile))
kepmsg.err(logfile, errmsg, verbose)
# open input file
instr = pyfits.open(infile, 'readonly')
tstart, tstop, bjdref, cadence = kepio.timekeys(instr, infile, logfile,
verbose)
try:
work = instr[0].header['FILEVER']
cadenom = 1.0
except:
cadenom = cadence
# fudge non-compliant FITS keywords with no values
instr = kepkey.emptykeys(instr, infile, logfile, verbose)
# read table structure
table = kepio.readfitstab(infile, instr[1], logfile, verbose)
# filter input data table
try:
datac = table.field(datacol)
except:
errmsg = ('ERROR -- KEPFLATTEN: cannot find or read data column {}'.
format(datacol))
kepmsg.err(logfile, message, verbose)
try:
err = table.field(errcol)
except:
errmsg = ('WARNING -- KEPFLATTEN: cannot find or read error column {}'.
format(errcol))
kepmsg.warn(logfile, errmsg, verbose)
errcol = 'None'
if errcol.lower() == 'none' or errcol == 'PSF_FLUX_ERR':
err = datac * cadence
err = np.sqrt(np.abs(err)) / cadence
work1 = np.array([table.field('time'), datac, err])
else:
work1 = np.array([table.field('time'), datac, err])
work1 = np.rot90(work1, 3)
work1 = work1[~np.isnan(work1).any(1)]
# read table columns
intime = work1[:, 2] + bjdref
indata = work1[:, 1]
inerr = work1[:, 0]
if len(intime) == 0:
message = 'ERROR -- KEPFLATTEN: one of the input arrays is all NaN'
kepmsg.err(logfile, message, verbose)
# time ranges for region to be corrected
t1, t2 = kepio.timeranges(ranges, logfile, verbose)
cadencelis = kepstat.filterOnRange(intime, t1, t2)
# find limits of each time step
tstep1, tstep2 = [], []
work = intime[0]
while work <= intime[-1]:
tstep1.append(work)
tstep2.append(
np.array([work + winsize, intime[-1]], dtype='float64').min())
work += stepsize
# find cadence limits of each time step
cstep1, cstep2 = [], []
for n in range(len(tstep1)):
for i in range(len(intime) - 1):
if intime[i] <= tstep1[n] and intime[i + 1] > tstep1[n]:
for j in range(i, len(intime) - 1):
if intime[j] < tstep2[n] and intime[j + 1] >= tstep2[n]:
cstep1.append(i)
cstep2.append(j + 1)
# comment keyword in output file
kepkey.history(call, instr[0], outfile, logfile, verbose)
# clean up x-axis unit
intime0 = tstart // 100 * 100.0
ptime = intime - intime0
xlab = 'BJD $-$ {}'.format(intime0)
# clean up y-axis units
pout = copy(indata)
nrm = len(str(int(pout.max()))) - 1
pout = pout / 10**nrm
ylab = '10$^{}$'.format(nrm) + 'e$^-$ s$^{-1}$'
# data limits
xmin = ptime.min()
xmax = ptime.max()
ymin = pout.min()
ymax = pout.max()
xr = xmax - xmin
yr = ymax - ymin
ptime = np.insert(ptime, [0], [ptime[0]])
ptime = np.append(ptime, [ptime[-1]])
pout = np.insert(pout, [0], [0.0])
pout = np.append(pout, 0.0)
if plot:
plt.figure()
plt.clf()
# plot data
ax = plt.axes([0.06, 0.54, 0.93, 0.43])
# force tick labels to be absolute rather than relative
plt.gca().xaxis.set_major_formatter(
plt.ScalarFormatter(useOffset=False))
plt.gca().yaxis.set_major_formatter(
plt.ScalarFormatter(useOffset=False))
# rotate y labels by 90 deg
labels = ax.get_yticklabels()
plt.setp(plt.gca(), xticklabels=[])
plt.plot(ptime[1:-1],
pout[1:-1],
color='#363636',
linestyle='-',
linewidth=1.0)
plt.fill(ptime, pout, color='#a8a7a7', linewidth=0.0, alpha=0.2)
plt.ylabel(ylab, {'color': 'k'})
plt.grid()
# loop over each time step, fit data, determine rms
fitarray = np.zeros((len(indata), len(cstep1)), dtype='float32')
sigarray = np.zeros((len(indata), len(cstep1)), dtype='float32')
fitarray[:, :] = np.nan
sigarray[:, :] = np.nan
masterfit = indata * 0.0
mastersigma = np.zeros(len(masterfit))
functype = getattr(kepfunc, 'poly' + str(npoly))
for i in tqdm(range(len(cstep1))):
timeSeries = intime[cstep1[i]:cstep2[i] + 1] - intime[cstep1[i]]
dataSeries = indata[cstep1[i]:cstep2[i] + 1]
fitTimeSeries = np.array([], dtype='float32')
fitDataSeries = np.array([], dtype='float32')
pinit = [dataSeries.mean()]
if npoly > 0:
for j in range(npoly):
pinit.append(0.0)
pinit = np.array(pinit, dtype='float32')
try:
if len(fitarray[cstep1[i]:cstep2[i] + 1, i]) > len(pinit):
coeffs, errors, covar, iiter, sigma, chi2, dof, fit, plotx, ploty = \
kepfit.lsqclip(functype, pinit, timeSeries, dataSeries,
None, nsig, nsig, niter, logfile, verbose)
fitarray[cstep1[i]:cstep2[i] + 1, i] = 0.0
sigarray[cstep1[i]:cstep2[i] + 1, i] = sigma
for j in range(len(coeffs)):
fitarray[cstep1[i]:cstep2[i] + 1,
i] += coeffs[j] * timeSeries**j
except:
message = ('WARNING -- KEPFLATTEN: could not fit range ' +
str(intime[cstep1[i]]) + '-' + str(intime[cstep2[i]]))
kepmsg.warn(logfile, message, verbose)
# find mean fit for each timestamp
for i in range(len(indata)):
masterfit[i] = np.nanmean(fitarray[i, :])
mastersigma[i] = np.nanmean(sigarray[i, :])
masterfit[-1] = masterfit[-4] #fudge
masterfit[-2] = masterfit[-4] #fudge
masterfit[-3] = masterfit[-4] #fudge
if plot:
plt.plot(intime - intime0, masterfit / 10**nrm, 'b')
# reject outliers
rejtime, rejdata = [], []
naxis2 = 0
for i in range(len(masterfit)):
if (abs(indata[i] - masterfit[i]) > nsig * mastersigma[i]
and i in cadencelis):
rejtime.append(intime[i])
rejdata.append(indata[i])
rejtime = np.array(rejtime, dtype='float64')
rejdata = np.array(rejdata, dtype='float32')
if plot:
plt.plot(rejtime - intime0, rejdata / 10**nrm, 'ro', markersize=2)
# new data for output file
outdata = indata / masterfit
outerr = inerr / masterfit
pout = copy(outdata)
ylab = 'Normalized Flux'
# plot ranges
if plot:
plt.xlim(xmin - xr * 0.01, xmax + xr * 0.01)
if ymin >= 0.0:
plt.ylim(ymin - yr * 0.01, ymax + yr * 0.01)
else:
plt.ylim(1.0e-10, ymax + yr * 0.01)
# plot residual data
ax = plt.axes([0.06, 0.09, 0.93, 0.43])
plt.gca().xaxis.set_major_formatter(
plt.ScalarFormatter(useOffset=False))
plt.gca().yaxis.set_major_formatter(
plt.ScalarFormatter(useOffset=False))
# rotate y labels by 90 deg
labels = ax.get_yticklabels()
ymin = pout.min()
ymax = pout.max()
yr = ymax - ymin
pout = np.insert(pout, [0], [0.0])
pout = np.append(pout, 0.0)
plt.plot(ptime[1:-1],
pout[1:-1],
color='#363636',
linestyle='-',
linewidth=1.0)
plt.fill(ptime, pout, color='#a8a7a7', linewidth=0.0, alpha=0.2)
plt.xlabel(xlab, {'color': 'k'})
plt.ylabel(ylab, {'color': 'k'})
plt.grid()
# plot ranges
plt.xlim(xmin - xr * 0.01, xmax + xr * 0.01)
if ymin >= 0.0:
plt.ylim(ymin - yr * 0.01, ymax + yr * 0.01)
else:
plt.ylim(1.0e-10, ymax + yr * 0.01)
# render plot
plt.savefig(re.sub('.fits', '.png', outfile))
plt.show()
# add NaNs back into data
n = 0
work1 = np.array([], dtype='float32')
work2 = np.array([], dtype='float32')
instr = pyfits.open(infile, 'readonly')
table = kepio.readfitstab(infile, instr[1], logfile, verbose)
tn = table.field('time')
dn = table.field(datacol)
for i in range(len(table.field(0))):
if np.isfinite(tn[i]) and np.isfinite(dn[i]) and np.isfinite(err[i]):
try:
work1 = np.append(work1, outdata[n])
work2 = np.append(work2, outerr[n])
n += 1
except:
pass
else:
work1 = np.append(work1, np.nan)
work2 = np.append(work2, np.nan)
# history keyword in output file
kepkey.history(call, instr[0], outfile, logfile, verbose)
# write output file
try:
print("Writing output file {}...".format(outfile))
col1 = pyfits.Column(name='DETSAP_FLUX', format='E13.7', array=work1)
col2 = pyfits.Column(name='DETSAP_FLUX_ERR',
format='E13.7',
array=work2)
cols = instr[1].data.columns + col1 + col2
instr[1] = pyfits.BinTableHDU.from_columns(cols,
header=instr[1].header)
instr.writeto(outfile)
except ValueError:
try:
instr[1].data.field('DETSAP_FLUX')[:] = work1
instr[1].data.field('DETSAP_FLUX_ERR')[:] = work2
instr.writeto(outfile)
except:
message = ('ERROR -- KEPFLATTEN: cannot add DETSAP_FLUX data to '
'FITS file')
kepmsg.err(logfile, message, verbose)
# close input file
instr.close()
## end time
kepmsg.clock('KEPFLATTEN completed at', logfile, verbose)
y_args = logaritmetic_spira_coridnates(y, r)
draw(x_args, y_args)
x_args = aritmetic_spiral_codinates(x, r)
y_args = aritmetic_spiral_codinates(y, r)
draw(x_args, y_args)
draw(r, [y(i) for i in r])
theta = np.arange(0, 8 * np.pi, 0.1)
a = 1
b = .2
for dt in np.arange(0, 2 * np.pi, np.pi / 2.0):
x = a * np.cos(theta + dt) * np.exp(b * theta)
y = a * np.sin(theta + dt) * np.exp(b * theta)
dt = dt + np.pi / 4.0
x2 = a * np.cos(theta + dt) * np.exp(b * theta)
y2 = a * np.sin(theta + dt) * np.exp(b * theta)
xf = np.concatenate((x, x2[::-1]))
yf = np.concatenate((y, y2[::-1]))
p1 = plt.fill(xf, yf)
plt.show()
def fill_one_square(self, position, color):
x, y = self.get_xy_coordinate(position)
plt.fill(x,y, color)
def vicsek(self, a, b, c, d, iterations, offset=np.array([0, 0])):
ab = (a + b) / 3.
ba = 2 * (a + b) / 3.
bc = (2 * b + c) / 3.
cb = (b + 2 * c) / 3.
dc = (c + 2 * d) / 3.
cd = (2 * c + d) / 3.
ad = (d + a) / 3.
da = 2 * (d + a) / 3.
abd = 2 * a / 3. + (b + d) / 3.
bac = a + (2 * b + d) / 3.
cbd = 4 * a / 3. + 2 * (b + d) / 3.
dac = a + (b + 2 * d) / 3.
if iterations == 0:
plt.fill([
ab[0] + offset[0], ba[0] + offset[0], bac[0] + offset[0],
bc[0] + offset[0], cb[0] + offset[0], cbd[0] + offset[0],
cd[0] + offset[0], dc[0] + offset[0], dac[0] + offset[0],
da[0] + offset[0], ad[0] + offset[0], abd[0] + offset[0]
], [
ab[1] + offset[1], ba[1] + offset[1], bac[1] + offset[1],
bc[1] + offset[1], cb[1] + offset[1], cbd[1] + offset[1],
cd[1] + offset[1], dc[1] + offset[1], dac[1] + offset[1],
da[1] + offset[1], ad[1] + offset[1], abd[1] + offset[1]
], 'saddlebrown')
#plt.hold(True)
else:
abd_m = np.array([0, 0])
bac_m = bac - abd
cbd_m = cbd - abd
dac_m = dac - abd
offset1 = offset + abd
self.vicsek(abd_m, bac_m, cbd_m, dac_m, iterations - 1, offset1)
ab_m = np.array([0, 0])
ba_m = ba - ab
bac_m = bac - ab
abd_m = abd - ab
offset2 = offset + ab
self.vicsek(ab_m, ba_m, bac_m, abd_m, iterations - 1, offset2)
bac_m = np.array([0, 0])
bc_m = bc - bac
cb_m = cb - bac
cbd_m = cbd - bac
offset4 = offset + bac
self.vicsek(bac_m, bc_m, cb_m, cbd_m, iterations - 1, offset4)
dac_m = np.array([0, 0])
cbd_m = cbd - dac
cd_m = cd - dac
dc_m = dc - dac
offset6 = offset + dac
self.vicsek(dac_m, cbd_m, cd_m, dc_m, iterations - 1, offset6)
ad_m = np.array([0, 0])
abd_m = abd - ad
dac_m = dac - ad
da_m = da - ad
offset8 = offset + ad
self.vicsek(ad_m, abd_m, dac_m, da_m, iterations - 1, offset8)
m2.drawmapboundary(fill_color='0.8')
m2.fillcontinents(color='w', lake_color='0.8') #, zorder=0)
m2.drawcoastlines()
m2.drawcountries()
m2.drawstates()
# fill main area
xv = mean([llcrnrlon, urcrnrlon])
yv = mean([llcrnrlat, urcrnrlat])
xv = [llcrnrlon, urcrnrlon, urcrnrlon, llcrnrlon, llcrnrlon]
yv = [llcrnrlat, llcrnrlat, urcrnrlat, urcrnrlat, llcrnrlat]
x, y = m2(xv, yv)
#plt.plot(x, y, 'rs',ms=6)
plt.fill(x, y, facecolor='none', edgecolor='r', linewidth=2)
##########################################################################################
# label states
##########################################################################################
'''
state = ['WA', 'NT', 'SA', 'QLD', 'NSW', 'VIC', 'TAS']
slat = [-26, -21.0, -29.5, -23.0, -32.5, -37.1, -42.]
slon = [122, 133.5, 135.0, 144.5, 146.5, 143.6, 147.0]
for i, st in enumerate(state):
x, y = m(slon[i], slat[i])
plt.text(x, y, st, size=11, horizontalalignment='center', verticalalignment='center', weight='normal')
'''
##########################################################################################
# add colourbar
##########################################################################################
color='0.99',
linewidth=0.0)
##########################################################################################
# get land & lake polygons for masking
##########################################################################################
polys = get_map_polygons(m)
mask_outside_polygons(polys, 'lightskyblue', plt)
# get lake ploygons and mask
polygons = []
for polygon in m.lakepolygons:
poly = polygon.get_coords()
plt.fill(poly[:, 0], poly[:, 1], 'lightskyblue')
polygons.append(poly)
###############################################################################
# make 50-km grid the ugly way
###############################################################################
cell_size = 30.
min_nresp = 2
grd_lons = []
grd_lats = []
grd_geom = []
grd_mmi = []
grd_count = []
lon_grd = minlon
# with shaded regions of potential
#plot_isw_state(L = 2)
#plt.ylabel("$\psi(x)$", fontsize = 15)
#plt.xlabel("$x$", fontsize = 15)
#plt.axis([-.5, 2.5, 0, 2])
#plt.fill([-.5, 0, 0, -.5], [0, 0, 2, 2], 'b', [2.0, 2.5, 2.5, 2.0], [0, 0, 2, 2], 'b', alpha=0.2)
#plt.text(.6, 1.7, "$L = 2$", fontsize = 14)
# Single spin arrows, centered on psi
# plt.arrow(.5, 1.4-.05, 0, .18) # Spin up arrow
# plt.arrow(.5, 1.4+.13, 0, -.18) # Spin down arrow
# Double spin arrows
#plt.arrow(1-.03, 1.0-.05, 0, .18) # Spin up arrow
#plt.arrow(1+.03, 1.0+.13, 0, -.18) # Spin down arrow
# Plotting ISW probability distribution with L = 1
# on x = [-.5, 1.5] and y = [0, 2.5]
# with shaded regions of potential
plot_isw_prob()
plt.ylabel("$P(x)$", fontsize=18)
plt.xlabel("$x$", fontsize=18)
plt.axis([-.5, 1.5, 0, 2.5])
plt.fill([-.5, 0, 0, -.5], [0, 0, 2.5, 2.5],
'b', [1.0, 1.5, 1.5, 1.0], [0, 0, 2.5, 2.5],
'b',
alpha=0.2)
plt.text(.75, 1.7, "$L = 1$", fontsize=18)
plt.show()
y_pred, MSE = gp.predict(x, eval_MSE=True)
sigma = np.sqrt(MSE)
x_true = np.array(map(f, timePts))
# Plot the function, the prediction and the 95% confidence interval based on
# the MSE
fig = pl.figure()
dXdT_true = np.array(map(df, timePts))
print "dXdT_true", dXdT_true
pl.plot(x_true, dXdT_true, 'g', label=u'$df(x)$', linewidth=5.0)
pl.errorbar(X.ravel(), y, dy, fmt='r.', markersize=10, label=u'Observations')
pl.plot(x, y_pred, 'b-', label=u'Prediction')
pl.fill(np.concatenate([x, x[::-1]]),
np.concatenate(
[y_pred - 1.9600 * sigma, (y_pred + 1.9600 * sigma)[::-1]]),
alpha=.5,
fc='b',
ec='None',
label='95% confidence interval')
pl.xlabel('$x$')
pl.ylabel('$dx/dt$')
pl.ylim(-0.5, 4)
pl.legend(bbox_to_anchor=(0, 1), loc='upper left', ncol=2)
savefig('figures/test/diffEqPlot.png')
def integrateTraj(xs, dXdT_pred):
dXdT_pred = np.matrix(dXdT_pred)
xs = np.matrix(xs)
indices = np.array(range(len(xs)))
def evaluate_A(predA,system_params, print_results=True,show_plots=False, proportion_of_max=0.9):
'''
evaluate_A(predA,system_params, print_results,show_plots):
compute results for adjacency matrix estimation
Inputs:
predA: predicted adjacency matrix (no threshold)
system_params: dictionary with:
'w': scalar or (n,1)
'A': (n,n)
'K': scalar
'Gamma': vectorized function
print_results: boolean to determine if results should be displayed
show_plots: boolean to determine if result should be plotted
Outputs:
A_res: series with labeled results
'''
#print("predA:",predA,type(predA))
FS=16 # fontsize
correctA=system_params['A']
pos_label=1.0 # determines which label is considered a positive.
fpr, tpr, thresholds = roc_curve(remove_diagonal(correctA,1),
remove_diagonal(predA,1),
pos_label=pos_label,
drop_intermediate=False)
roc_auc = auc(fpr, tpr)
#print("roc_auc:",roc_auc,type(roc_auc))
warnings.filterwarnings('ignore')
f1_scores=np.array([f1_score(remove_diagonal(correctA,1),1*(remove_diagonal(predA,1)>thr)) for thr in thresholds])
warnings.filterwarnings('default')
optimal_f1=np.max(f1_scores)
optimal_threshold=thresholds[np.argmax(f1_scores)]
inds=list(np.where(f1_scores>= proportion_of_max*optimal_f1)[0])
threshold_range=[np.min(thresholds[inds]),np.max(thresholds[inds])]
if show_plots:
plt.figure()
plt.plot(thresholds,f1_scores,color='black')
plt.xlim(0,1)
plt.ylim(0,1)
plt.xlabel('threshold',fontsize=FS)
plt.ylabel('F1 score',fontsize=FS)
plt.fill(np.append(thresholds[inds],[threshold_range[0],threshold_range[1]]),
np.append(f1_scores[inds],[0.0,0.0]),color='red',alpha=0.2)
plt.text(0.5,0.5,'>%.1f %% of peak f1 score' %(100*proportion_of_max),fontsize=FS,ha='center')
n_errors=np.sum(np.sum(abs((predA>optimal_threshold).astype(int)-correctA)))/2
num_osc=correctA.shape[0]
if print_results:
print('')
print('Evaluating adjacency matrix:')
print('')
print('Errors: %d out of %d' % (n_errors,(num_osc*(num_osc-1)/2)))
print('Error rate: %.5f%%' % (n_errors/(num_osc*(num_osc-1.0)/2.0)*100.0))
print('Area under ROC curve: %.5f' % (roc_auc))
print('Best f1 score: %.5f' %(optimal_f1))
print('Threshold for best f1 score: %.5f' %(optimal_threshold))
print('Threshold range for >%.1f%% of best f1 score: [%.5f,%.5f]' % (100*proportion_of_max,threshold_range[0],threshold_range[1]))
print('')
A_res=pd.Series()
A_res['Number of errors']=n_errors
A_res['Error rate']=n_errors/(num_osc*(num_osc-1)/2)*100
A_res['Area under ROC curve']=roc_auc
A_res['Best f1 score']=optimal_f1
A_res['Threshold for best f1 score']=optimal_threshold
A_res['Threshold range for >%.1f%% of best f1 score'% (100*proportion_of_max)]=threshold_range
return A_res
def visualize(self,
scene,
trajector,
head_on,
sampled_landmark=None,
sampled_relation=None,
description='',
step=0.02):
relation = sampled_relation
print relation
if hasattr(relation, 'measurement'):
print relation.measurement, relation.measurement.best_distance_class, relation.measurement.best_degree_class
# plt.figure( figsize=(6,8) )
#plt.subplot(1,2,1)
scene_bb = scene.get_bounding_box()
scene_bb = scene_bb.inflate(
Vec2(scene_bb.width * 0.5, scene_bb.height * 0.5))
if relation:
probabilities, points = self.get_probabilities_box(
scene_bb, relation, head_on, sampled_landmark, step)
# xs, ys = points[:,0], points[:,1]
xs = arange(scene_bb.min_point.x, scene_bb.max_point.x, step)
ys = arange(scene_bb.min_point.y, scene_bb.max_point.y, step)
# probabilities = zeros( ( len(ys),len(xs) ) )
# for i,x in enumerate(xs):
# for j,y in enumerate(ys):
# rel = relation( head_on, sampled_landmark, Landmark('', PointRepresentation(Vec2(x,y)), None, None) )
# if hasattr(rel, 'measurement'):
# rel.measurement.best_degree_class = sampled_relation.measurement.best_degree_class
# rel.measurement.best_distance_class = sampled_relation.measurement.best_distance_class
# probabilities[j,i] = rel.is_applicable()
# # print rel.distance, probabilities[j,i]
set_printoptions(threshold='nan')
#print probabilities
x = array([list(xs - step * 0.5)] * len(ys))
y = array([list(ys - step * 0.5)] * len(xs)).T
probabilities = probabilities.reshape((len(xs), len(ys))).T
# print probabilities
#print self.get_entropy(probabilities)
plt.pcolor(x,
y,
probabilities,
cmap='jet',
edgecolors='none',
alpha=0.7)
plt.colorbar()
for lmk in scene.landmarks.values():
if isinstance(lmk.representation, GroupLineRepresentation):
xs = [
lmk.representation.line.start.x,
lmk.representation.line.end.x
]
ys = [
lmk.representation.line.start.y,
lmk.representation.line.end.y
]
plt.fill(xs, ys, facecolor='none', linewidth=2)
elif isinstance(lmk.representation, RectangleRepresentation):
rect = lmk.representation.rect
xs = [
rect.min_point.x, rect.min_point.x, rect.max_point.x,
rect.max_point.x
]
ys = [
rect.min_point.y, rect.max_point.y, rect.max_point.y,
rect.min_point.y
]
plt.fill(xs, ys, facecolor='none', linewidth=2)
plt.text(rect.min_point.x + 0.01, rect.max_point.y + 0.02,
lmk.name)
plt.plot(self.location.x, self.location.y, 'bx', markeredgewidth=2)
traj_rep = trajector.representation
if isinstance(traj_rep, GroupLineRepresentation):
xs = [traj_rep.line.start.x, traj_rep.line.end.x]
ys = [traj_rep.line.start.y, traj_rep.line.end.y]
plt.fill(xs, ys, facecolor='none', linewidth=2)
elif isinstance(traj_rep, RectangleRepresentation):
rect = traj_rep.rect
xs = [
rect.min_point.x, rect.min_point.x, rect.max_point.x,
rect.max_point.x
]
ys = [
rect.min_point.y, rect.max_point.y, rect.max_point.y,
rect.min_point.y
]
plt.fill(xs, ys, facecolor='none', linewidth=2)
elif isinstance(traj_rep, PointRepresentation):
plt.plot(traj_rep.location.x,
traj_rep.location.y,
'bo',
markeredgewidth=2)
plt.text(traj_rep.middle.x + 0.01, traj_rep.middle.y + 0.02,
'trajector')
'''
plt.plot(poi.x,poi.y,'rx',markeredgewidth=2)
plt.text(poi.x+0.01,
poi.y+0.02,'POI')
'''
plt.plot(head_on.x, head_on.y, 'ro', markeredgewidth=2)
plt.text(head_on.x + 0.02, head_on.y + 0.01, 'perspective')
if sampled_landmark:
lwidth = 3
lcolor = (0, 1, 0)
if isinstance(sampled_landmark.representation,
PointRepresentation):
plt.plot(sampled_landmark.representation.location.x,
sampled_landmark.representation.location.y,
'.',
markeredgewidth=lwidth,
color=lcolor)
elif isinstance(sampled_landmark.representation,
LineRepresentation):
xs = [
sampled_landmark.representation.line.start.x,
sampled_landmark.representation.line.end.x
]
ys = [
sampled_landmark.representation.line.start.y,
sampled_landmark.representation.line.end.y
]
plt.fill(xs,
ys,
facecolor='none',
edgecolor=lcolor,
linewidth=lwidth)
elif isinstance(sampled_landmark.representation,
RectangleRepresentation):
rect = sampled_landmark.representation.rect
xs = [
rect.min_point.x, rect.min_point.x, rect.max_point.x,
rect.max_point.x
]
ys = [
rect.min_point.y, rect.max_point.y, rect.max_point.y,
rect.min_point.y
]
plt.fill(xs,
ys,
facecolor='none',
edgecolor=lcolor,
linewidth=lwidth)
# rel_scores = []
# for relation in relations:
# rel_scores.append( relation.probability(poi, sampled_landmark) )
# rel_scores = array(rel_scores)
# rel_probabilities = rel_scores/sum(rel_scores)
# index = rel_probabilities.cumsum().searchsorted( random.sample(1) )[0]
# sampled_relation = relations[index]
# toprint = str(poi)+' ; '+sampled_relation.get_description() + " " + sampled_landmark.get_description()
# print toprint
plt.axis('scaled')
plt.axis([
scene_bb.min_point.x, scene_bb.max_point.x, scene_bb.min_point.y,
scene_bb.max_point.y
])
title = "Probability of location given description:\n" + description
# plt.suptitle('\n'.join(wrap(title,50)))
plt.suptitle(title)
# plt.subplot(2,2,2)
# plt.axis([0,1.5,-0.1,1.1])
# xs = arange(0,3,0.01)
# ys = {}
# for relation in relations:
# name = relation.__class__.__name__
# plt.plot( xs, relation.distance_probability(xs) )
# plt.axvline(x=distance,linewidth=2)
# print distance
plt.show()
