def display_coeff(data=None):
betaAll,betaErrAll, R2adjAll = measure_stamp_coeff(data = data, zernike_max_order=20)
ind = np.arange(len(betaAll[0]))
momname = ('M20','M22.Real','M22.imag','M31.real','M31.imag','M33.real','M33.imag')
fmtarr = ['bo-','ro-','go-','co-','mo-','yo-','ko-']
pl.figure(figsize=(17,13))
for i in range(7):
pl.subplot(7,1,i+1)
pl.errorbar(ind,betaAll[i],yerr = betaErrAll[i],fmt=fmtarr[i])
pl.grid()
pl.xlim(-1,21)
if i ==0:
pl.ylim(-10,65)
elif i ==1:
pl.ylim(-5,6)
elif i ==2:
pl.ylim(-5,6)
elif i == 3:
pl.ylim(-0.1,0.1)
elif i == 4:
pl.ylim(-0.1,0.1)
elif i ==5:
pl.ylim(-100,100)
elif i == 6:
pl.ylim(-100,100)
pl.xticks(ind,('','','','','','','','','','','','','','','','','','','',''))
pl.ylabel(momname[i])
pl.xticks(ind,('0','1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19'))
pl.xlabel('Zernike Coefficients')
return '--- done ! ----'
def time_delays_plot(env, **kwargs):
models = kwargs.pop('models', env.models)
obj_index = kwargs.pop('obj_index', 0)
src_index = kwargs.pop('src_index', 0)
key = kwargs.pop('key', 'accepted')
d = defaultdict(list)
for m in models:
obj,data = m['obj,data'][obj_index]
t0 = data['arrival times'][src_index][0]
for i,t in enumerate(data['arrival times'][src_index][1:]):
d[i].append( float('%0.6f'%convert('arcsec^2 to days', t-t0, obj.dL, obj.z, data['nu'])) )
t0 = t
s = product(range(1,1+len(d)), ['solid', 'dashed', 'dashdot', 'dotted'])
for k,v in d.iteritems():
#print 'td plot', k, len(v)
#print v
lw,ls = s.next()
pl.hist(v, bins=25, histtype='step', color='k', ls=ls, lw=lw, label='%s - %s' % (str(k+1),str(k+2)), **kwargs)
#pl.xlim(xmin=0)
pl.ylim(ymin=0)
pl.xlim(xmin=pl.xlim()[0] - 0.01*(pl.xlim()[1] - pl.xlim()[0]))
pl.legend()
pl.xlabel(_time_delays_xlabel)
pl.ylabel(r'Count')
def simulation1(numTrials, numSteps, loc):
results = {'UsualDrunk': [], 'ColdDrunk': [], 'EDrunk': [], 'PhotoDrunk': [], 'DDrunk': []}
drunken_types = {'UsualDrunk': UsualDrunk, 'ColdDrunk': ColdDrunk, 'EDrunk': EDrunk, 'PhotoDrunk': PhotoDrunk,
'DDrunk': DDrunk}
for drunken in drunken_types.keys():
#Create field
initial_loc = Location(loc[0], loc[1])
field = Field()
print "Simu", drunken
drunk = Drunk(drunken)
drunk_man = drunken_types[drunken](drunk)
field.addDrunk(drunk_man, initial_loc)
#print drunk_man
for trial in range(numTrials):
distance = walkVector(field, drunk_man, numSteps)
results[drunken].append((round(distance[0], 1), round(distance[1], 1)))
print drunken, "=", results[drunken]
for result in results.keys():
# x, y = zip(*results[result])
# print "x", x
# print "y", y
pylab.plot(*zip(*results[result]), marker='o', color='r', ls='')
pylab.title(result)
pylab.xlabel('X coordinateds')
pylab.ylabel('Y coordinateds')
pylab.xlim(-100, 100)
pylab.ylim(-100, 100)
pylab.figure()
pylab.show
def plot_frontier(self,frontier_only=False,plot_samples=True) :
""" Plot the frontier"""
frontier = self.frontier
frontier_energy = self.frontier_energy
feat1,feat2 = self.feats
pl.figure()
if not frontier_only :
ll_list1,ll_list2 = zip(*self.all_seq_energy)
pl.plot(ll_list1,ll_list2,'b*')
if plot_samples :
ll_list1,ll_list2 = zip(*self.sample_seq_energy)
pl.plot(ll_list1,ll_list2,'g*')
pl.plot(*zip(*sorted(frontier_energy)),color='magenta',\
marker='*', linestyle='dashed')
ctr = dict(zip(set(frontier_energy),[0]*
len(set(frontier_energy))))
for i,e in enumerate(frontier_energy) :
ctr[e] += 1
pl.text(e[0],e[1]+0.1*ctr[e],str(i),fontsize=10)
pl.text(e[0]+0.4,e[1]+0.1*ctr[e],frontier[i],fontsize=9)
pl.xlabel('Energy:'+feat1)
pl.ylabel('Energy:'+feat2)
pl.title('Energy Plot')
xmin,xmax = pl.xlim()
ymin,ymax = pl.ylim()
pl.xlim(xmin,xmax)
pl.ylim(ymin,ymax)
pic_dir = '../docs/tex/pics/'
pl.savefig(pic_dir+self.name+'.pdf')
pl.savefig(pic_dir+self.name+'.png')
def geweke_plot(data, name, format='png', suffix='-diagnostic', path='./', fontmap = None,
verbose=1):
# Generate Geweke (1992) diagnostic plots
if fontmap is None: fontmap = {1:10, 2:8, 3:6, 4:5, 5:4}
# Generate new scatter plot
figure()
x, y = transpose(data)
scatter(x.tolist(), y.tolist())
# Plot options
xlabel('First iteration', fontsize='x-small')
ylabel('Z-score for %s' % name, fontsize='x-small')
# Plot lines at +/- 2 sd from zero
pyplot((nmin(x), nmax(x)), (2, 2), '--')
pyplot((nmin(x), nmax(x)), (-2, -2), '--')
# Set plot bound
ylim(min(-2.5, nmin(y)), max(2.5, nmax(y)))
xlim(0, nmax(x))
# Save to file
if not os.path.exists(path):
os.mkdir(path)
if not path.endswith('/'):
path += '/'
savefig("%s%s%s.%s" % (path, name, suffix, format))
def plotForce():
figure(size=3,aspect=0.5)
subplot(1,2,1)
from EvalTraj import plotFF
plotFF(vp=351,t=28,f=900,cm=0.6,foffset=8)
subplot_annotate()
subplot(1,2,2)
for i in [1,2,3,4]:
R=np.squeeze(np.load('Rdpse%d.npy'%i))
R=stats.nanmedian(R,axis=2)[:,1:,:]
dps=np.linspace(-1,1,201)[1:]
plt.plot(dps,R[:,:,2].mean(0));
plt.legend([0,0.1,0.2,0.3],loc=3)
i=2
R=np.squeeze(np.load('Rdpse%d.npy'%i))
R=stats.nanmedian(R,axis=2)[:,1:,:]
mn=np.argmin(R,axis=1)
y=np.random.randn(mn.shape[0])*0.00002+0.0438
plt.plot(np.sort(dps[mn[:,2]]),y,'+',mew=1,ms=6,mec=[ 0.39 , 0.76, 0.64])
plt.xlabel('Displacement of Force Origin')
plt.ylabel('Average Net Force Magnitude')
hh=dps[mn[:,2]]
err=np.std(hh)/np.sqrt(hh.shape[0])*stats.t.ppf(0.975,hh.shape[0])
err2=np.std(hh)/np.sqrt(hh.shape[0])*stats.t.ppf(0.75,hh.shape[0])
m=np.mean(hh)
print m, m-err,m+err
np.save('force',[m, m-err,m+err,m-err2,m+err2])
plt.xlim([-0.5,0.5])
plt.ylim([0.0435,0.046])
plt.grid(b=True,axis='x')
subplot_annotate()
def plot_sphere_x( s, fname ):
""" put plot of ionization fractions from sphere `s` into fname """
plt.figure()
s.Edges.units = 'kpc'
s.r_c.units = 'kpc'
xx = s.r_c
L = s.Edges[-1]
plt.plot( xx, np.log10( s.xHe1 ),
color='green', ls='-', label = r'$x_{\rm HeI}$' )
plt.plot( xx, np.log10( s.xHe2 ),
color='green', ls='--', label = r'$x_{\rm HeII}$' )
plt.plot( xx, np.log10( s.xHe3 ),
color='green', ls=':', label = r'$x_{\rm HeIII}$' )
plt.plot( xx, np.log10( s.xH1 ),
color='red', ls='-', label = r'$x_{\rm HI}$' )
plt.plot( xx, np.log10( s.xH2 ),
color='red', ls='--', label = r'$x_{\rm HII}$' )
plt.xlim( -L/20, L+L/20 )
plt.xlabel( 'r_c [kpc]' )
plt.ylim( -4.5, 0.2 )
plt.ylabel( 'log 10 ( x )' )
plt.grid()
plt.legend(loc='best', ncol=2)
plt.tight_layout()
plt.savefig( 'doc/img/x_' + fname )
def plotB2reg(prefix=''):
w=loadStanFit(prefix+'revE2B2LHregCa.fit')
px=np.array(np.linspace(-0.5,0.5,101),ndmin=2)
a1=np.array(w['ma'][:,4],ndmin=2).T+1
a0=np.array(w['ma'][:,3],ndmin=2).T
printCI(w,'ma')
y=np.concatenate([sap(a0+a1*px,97.5,axis=0),sap(a0+a1*px[:,::-1],2.5,axis=0)])
x=np.squeeze(np.concatenate([px,px[:,::-1]],axis=1))
man=np.array([-0.4,-0.2,0,0.2,0.4])
plt.plot(px[0,:],np.median(a0)+np.median(a1)*px[0,:],'red')
#plt.plot([-1,1],[0.5,0.5],'grey')
ax=plt.gca()
ax.set_aspect(1)
ax.add_patch(plt.Polygon(np.array([x,y]).T,alpha=0.2,fill=True,fc='red',ec='w'))
y=np.concatenate([sap(a0+a1*px,75,axis=0),sap(a0+a1*px[:,::-1],25,axis=0)])
ax.add_patch(plt.Polygon(np.array([x,y]).T,alpha=0.2,fill=True,fc='red',ec='w'))
mus=[]
for m in range(len(man)):
mus.append(loadStanFit(prefix+'revE2B2LHC%d.fit'%m)['ma4']+man[m])
mus=np.array(mus).T
errorbar(mus,x=man)
ax.set_xticks(man)
plt.xlim([-0.5,0.5])
plt.ylim([-0.6,0.8])
plt.xlabel('Pivot Displacement')
plt.ylabel('Perceived Displacemet')
def plotB3reg():
w=loadStanFit('revE2B3BHreg.fit')
printCI(w,'mmu')
printCI(w,'mr')
for b in range(2):
subplot(1,2,b+1)
plt.title('')
px=np.array(np.linspace(-0.5,0.5,101),ndmin=2)
a0=np.array(w['mmu'][:,b],ndmin=2).T
a1=np.array(w['mr'][:,b],ndmin=2).T
y=np.concatenate([sap(a0+a1*px,97.5,axis=0),sap(a0+a1*px[:,::-1],2.5,axis=0)])
x=np.squeeze(np.concatenate([px,px[:,::-1]],axis=1))
plt.plot(px[0,:],np.median(a0)+np.median(a1)*px[0,:],'red')
#plt.plot([-1,1],[0.5,0.5],'grey')
ax=plt.gca()
ax.set_aspect(1)
ax.add_patch(plt.Polygon(np.array([x,y]).T,alpha=0.2,fill=True,fc='red',ec='w'))
y=np.concatenate([sap(a0+a1*px,75,axis=0),sap(a0+a1*px[:,::-1],25,axis=0)])
ax.add_patch(plt.Polygon(np.array([x,y]).T,alpha=0.2,fill=True,fc='red',ec='w'))
man=np.array([-0.4,-0.2,0,0.2,0.4])
mus=[]
for m in range(len(man)):
mus.append(loadStanFit('revE2B3BH%d.fit'%m)['mmu'][:,b])
mus=np.array(mus).T
errorbar(mus,x=man)
ax.set_xticks(man)
plt.xlim([-0.5,0.5])
plt.ylim([-0.4,0.8])
#plt.xlabel('Manipulated Displacement')
if b==0:
plt.ylabel('Perceived Displacemet')
plt.gca().set_yticklabels([])
subplot_annotate()
plt.text(-1.1,-0.6,'Pivot Displacement',fontsize=8);
def plot_roc(self, roc=None):
"""Plot ROC curves
.. plot::
:include-source:
:width: 80%
from dreamtools import rocs
r = rocs.ROC()
r.scores = [.9,.5,.6,.7,.1,.2,.6,.4,.7,.9, .2]
r.classes = [1,0,1,0,0,1,1,0,0,1,1]
r.plot_roc()
"""
if roc == None:
roc = self.get_roc()
from pylab import plot, xlim, ylim ,grid, title, xlabel, ylabel
x = roc['fpr']
plot(x, roc['tpr'], '-o')
plot([0,1], [0,1],'r')
ylim([0, 1])
xlim([0, 1])
grid(True)
title("ROC curve (AUC=%s)" % self.compute_auc(roc))
xlabel("FPR")
ylabel("TPR")
def rmsdSpreadSubplot(multiplier=1.0, layout=(-1, -1)):
rmsd_data = dict( (e, rad_data[e]['innov'][quant]) for e in rad_data.iterkeys() )
spread_data = dict( (e, rad_data[e]['spread'][quant]) for e in rad_data.iterkeys() )
times = temp.getTimes()
n_t = len(times)
for exp, exp_name in exp_names.iteritems():
pylab.plot(sawtooth(times, times)[:(n_t + 1)], rmsd_data[exp][:(n_t + 1)], color=colors[exp], linestyle='-')
pylab.plot(times[(n_t / 2):], rmsd_data[exp][n_t::2], color=colors[exp], linestyle='-')
for exp, exp_name in exp_names.iteritems():
pylab.plot(sawtooth(times, times)[:(n_t + 1)], spread_data[exp][:(n_t + 1)], color=colors[exp], linestyle='--')
pylab.plot(times[(n_t / 2):], spread_data[exp][n_t::2], color=colors[exp], linestyle='--')
ylim = pylab.ylim()
pylab.plot(times, -1 * np.ones((len(times),)), color='#999999', linestyle='-', label="RMS Innovation")
pylab.plot(times, -1 * np.ones((len(times),)), color='#999999', linestyle='--', label="Spread")
pylab.axhline(y=7, color='k', linestyle=':')
pylab.axvline(x=14400, color='k', linestyle=':')
pylab.ylabel("RMS Innovation/Spread (dBZ)", size='large')
pylab.xlim(times[0], times[-1])
pylab.ylim(ylim)
pylab.legend(loc=4)
pylab.xticks(times[::2], [ "" for t in times[::2] ])
pylab.yticks(size='x-large')
return
def correlation_matrix(data, size=8.0):
""" Calculates and shows the correlation matrix of the pandas data frame
'data' as a heat map.
Only the correlations between numerical variables are calculated!
"""
# calculate the correlation matrix
corr = data.corr()
#print corr
lc = len(corr.columns)
# set some settings for plottin'
pl.pcolor(corr, vmin = -1, vmax = 1, edgecolor = "black")
pl.colorbar()
pl.xlim([-5,lc])
pl.ylim([0,lc+5])
pl.axis('off')
# anotate the rows and columns with their corresponding variables
ax = pl.gca()
for i in range(0,lc):
ax.annotate(corr.columns[i], (-0.5, i+0.5), \
size='large', horizontalalignment='right', verticalalignment='center')
ax.annotate(corr.columns[i], (i+0.5, lc+0.5),\
size='large', rotation='vertical',\
horizontalalignment='center', verticalalignment='right')
# change the size of the image
fig = pl.figure(num=1)
fig.set_size_inches(size+(size/4), size)
pl.show()
def InitializePlot(self, goal_config):
self.fig = pl.figure()
lower_limits, upper_limits = self.boundary_limits
pl.xlim([lower_limits[0], upper_limits[0]])
pl.ylim([lower_limits[1], upper_limits[1]])
pl.plot(goal_config[0], goal_config[1], 'gx')
# Show all obstacles in environment
for b in self.robot.GetEnv().GetBodies():
if b.GetName() == self.robot.GetName():
continue
bb = b.ComputeAABB()
pl.plot([bb.pos()[0] - bb.extents()[0],
bb.pos()[0] + bb.extents()[0],
bb.pos()[0] + bb.extents()[0],
bb.pos()[0] - bb.extents()[0],
bb.pos()[0] - bb.extents()[0]],
[bb.pos()[1] - bb.extents()[1],
bb.pos()[1] - bb.extents()[1],
bb.pos()[1] + bb.extents()[1],
bb.pos()[1] + bb.extents()[1],
bb.pos()[1] - bb.extents()[1]], 'r')
pl.ion()
pl.show()
def run(steps=10): for i in range(steps): Q.time_step() #Q.plot_links() py.xlim((0,config['XSIZE'])) py.ylim((0,config['YSIZE'])) py.draw()
def plotFeatureImportance(featureImportance, title, originalImage=None, lim=0.06, colorate=None):
"""
originalImage : the index of the original image. If None, ignore
"""
indices = featureImportanceIndices(len(featureImportance), originalImage)
pl.figure()
pl.title(title)
if colorate is not None:
nbType = len(colorate)
X = [[] for i in range(nbType)]
Y = [[] for i in range(nbType)]
for j, f in enumerate(featureImportance):
X[j % nbType].append(j)
Y[j % nbType].append(f)
for i in range(nbType):
pl.bar(X[i], Y[i], align="center", label=colorate[i][0], color=colorate[i][1])
pl.legend()
else:
pl.bar(range(len(featureImportance)), featureImportance, align="center")
#pl.xticks(pl.arange(len(indices)), indices, rotation=-90)
pl.xlim([-1, len(indices)])
pl.ylabel("Feature importance")
pl.xlabel("Filter indices")
pl.ylim(0, lim)
pl.show()
def whiskerplot(shear,dRA=1.,dDEC=1.,scale=5, combine=1, offset=(0,0) ):
if combine>1:
s = (combine*int(shear.shape[0]/combine),
combine*int(shear.shape[1]/combine))
shear = shear[0:s[0]:combine, 0:s[1]:combine] \
+ shear[1:s[0]:combine, 0:s[1]:combine] \
+ shear[0:s[0]:combine, 1:s[1]:combine] \
+ shear[1:s[0]:combine, 1:s[1]:combine]
shear *= 0.25
dRA *= combine
dDEC *= combine
theta = shear**0.5
RA = offset[0] + np.arange(shear.shape[0])*dRA
DEC = offset[1] + np.arange(shear.shape[1])*dDEC
pylab.quiver(RA,DEC,
theta.real.T,theta.imag.T,
pivot = 'middle',
headwidth = 0,
headlength = 0,
headaxislength = 0,
scale=scale)
pylab.xlim(0,shear.shape[0]*dRA)
pylab.ylim(0,shear.shape[1]*dDEC)
pylab.xlabel('RA (arcmin)')
pylab.ylabel('DEC (arcmin)')
def drunkTest(numTrials = 1000):
#stepsTaken = [10, 100, 1000, 10000]
stepsTaken = 1000
for dClass in (UsualDrunk, ColdDrunk, EDrunk, PhotoDrunk, DDrunk):
#initialize field
field = Field()
origin = Location(0, 0)
# initialize drunk
drunk = dClass('Drunk')
field.addDrunk(drunk, origin)
x_pos, y_pos = [], [] # initialize to empty
x, y = 0.0, 0.0
for trial in range(numTrials): # trials
x, y = walkVector(field, drunk, stepsTaken)
x_pos.append(x)
y_pos.append(y)
#pylab.plot(x_pos, y_pos, 'ro', s=5,
# label = dClass.__name__)
pylab.scatter(x_pos, y_pos,s=5, color='red')
pylab.title(str(dClass))
pylab.xlabel('x')
pylab.grid()
pylab.xlim(-100, 100)
pylab.ylim(-100,100)
pylab.ylabel('y')
pylab.show()
def plotMean(self, Channel, listPops, colors = [], ylabel = "Fluorescence (a.u.)"):
"""
missing doc
"""
if type(listPops) != type([]): listPops = [listPops]
maxf = 0.
minf = 1.e10
maxx = 0.0
minx = -1.0
for pop in listPops:
F = np.array( self.getFluorescence(pop, Channel).mean(axis=1) )
plot.simplePlot( F, fillcolor=self.colors[pop], label = pop )
if maxf < F.max().max() : maxf = F.max().max()
if minf > F.min().min() : minf = F.min().min()
maxx = max(maxx, F.shape[0])
# setting labels and axes
pl.xlabel('Time (h)')
pl.ylabel(ylabel)
pl.ylim(0.3*minf, 1.2*maxf)
pl.xlim(minx, maxx)
#pl.tight_layout()
return
def makeimg(wav):
global callpath
global imgpath
fs, frames = wavfile.read(os.path.join(callpath, wav))
pylab.ion()
# generate specgram
pylab.figure(1)
# generate specgram
pylab.specgram(
frames,
NFFT=256,
Fs=22050,
detrend=pylab.detrend_none,
window=numpy.hamming(256),
noverlap=192,
cmap=pylab.get_cmap('Greys'))
x_width = len(frames)/fs
pylab.ylim([0,11025])
pylab.xlim([0,round(x_width,3)-0.006])
img_path = os.path.join(imgpath, wav.replace(".wav",".png"))
pylab.savefig(img_path)
return img_path
def plot_importances(imp, clfName, obj):
imp=np.vstack(imp)
print imp
mean_importance = np.mean(imp,axis=0)
std_importance = np.std(imp,axis=0)
indices = np.argsort(mean_importance)[::-1]
print indices
print featureNames
featureList = []
# num_features = len(featureNames)
print("Feature ranking:")
for f in range(num_features):
featureList.append(featureNames[indices[f]])
print("%d. feature %s (%.2f)" % (f, featureNames[indices[f]], mean_importance[indices[f]]))
fig = pl.figure(figsize=(8,6),dpi=150)
pl.title("Feature importances",fontsize=30)
pl.bar(range(num_features), mean_importance[indices],
yerr = std_importance[indices], color=paired[0], align="center",
edgecolor=paired[0],ecolor=paired[1])
pl.xticks(range(num_features), featureList, size=15,rotation=90)
pl.ylabel("Importance",size=30)
pl.yticks(size=20)
pl.xlim([-1, num_features])
# fix_axes()
pl.tight_layout()
save_path = 'plots/'+obj+'/'+clfName+'_feature_importances.pdf'
fig.savefig(save_path)
def plotCoeff(X, y, obj, featureNames, whichReg):
""" Plot Regression's Coeff
"""
clf = classifiers[whichReg]
clf,_,_ = fitAlgo(clf, X,y, opt= True, param_dict = param_dist_dict[whichReg])
if whichReg == "LogisticRegression":
coeff = np.absolute(clf.coef_[0])
else:
coeff = np.absolute(clf.coef_)
print coeff
indices = np.argsort(coeff)[::-1]
print indices
print featureNames
featureList = []
# num_features = len(featureNames)
print("Feature ranking:")
for f in range(num_features):
featureList.append(featureNames[indices[f]])
print("%d. feature %s (%.2f)" % (f, featureNames[indices[f]], coeff[indices[f]]))
fig = pl.figure(figsize=(8,6),dpi=150)
pl.title("Feature importances",fontsize=30)
# pl.bar(range(num_features), coeff[indices],
# yerr = std_importance[indices], color=paired[0], align="center",
# edgecolor=paired[0],ecolor=paired[1])
pl.bar(range(num_features), coeff[indices], color=paired[0], align="center",
edgecolor=paired[0],ecolor=paired[1])
pl.xticks(range(num_features), featureList, size=15,rotation=90)
pl.ylabel("Importance",size=30)
pl.yticks(size=20)
pl.xlim([-1, num_features])
# fix_axes()
pl.tight_layout()
save_path = 'plots/'+obj+'/'+whichReg+'_feature_importances.pdf'
fig.savefig(save_path)
def InitializePlot(self, goal_config): # default
self.fig = pl.figure()
pl.xlim([self.lower_limits[0], self.upper_limits[0]])
pl.ylim([self.lower_limits[1], self.upper_limits[1]])
pl.plot(goal_config[0], goal_config[1], "gx")
# Show all obstacles in environment
for b in self.robot.GetEnv().GetBodies():
if b.GetName() == self.robot.GetName():
continue
bb = b.ComputeAABB()
pl.plot(
[
bb.pos()[0] - bb.extents()[0],
bb.pos()[0] + bb.extents()[0],
bb.pos()[0] + bb.extents()[0],
bb.pos()[0] - bb.extents()[0],
bb.pos()[0] - bb.extents()[0],
],
[
bb.pos()[1] - bb.extents()[1],
bb.pos()[1] - bb.extents()[1],
bb.pos()[1] + bb.extents()[1],
bb.pos()[1] + bb.extents()[1],
bb.pos()[1] - bb.extents()[1],
],
"r",
)
pl.ion()
pl.show()
def updatePlot(self):
""" Updates the antenna config plot"""
self.sp_ax.clear()
self.sp_fig.clear()
row = self.slider.value()
self.spinner.setValue(row)
data_x = self.fits_data[row,0,0,0,:]
data_y = self.fits_data[row,0,0,1,:]
flagged_x = self.fits_flagged[row,0,0,0,:]
flagged_y = self.fits_flagged[row,0,0,1,:]
freqs = self.fits_freqs
tsys = self.fits_tsys[row,:]
#plt.plot(freqs, data_x)
plt.plot(freqs[flagged_x == 0], data_x[flagged_x == 0], color='#333333', label='Pol A [%2.1f Jy]'%tsys[0])
plt.plot(freqs[flagged_y == 0], data_y[flagged_y == 0], color='#CC0000', label='Pol B [%2.1f Jy]'%tsys[1])
plt.ylabel('%s [%s]'%(self.fits_data_name, self.fits_data_unit))
plt.xlabel('%s [%s]'%(self.fits_freq_type, self.fits_freq_unit))
plt.title('Beam %s: %s %s'%(self.fits_beam[row], self.fits_date[row], self.fits_time[row]))
plt.xlim(np.min(freqs[flagged_x == 0]), np.max(freqs[flagged_x == 0]))
plt.legend()
plt.show()
self.sp_fig.canvas.draw()
self.lab_info.setText(self.fits_filename)
def plot_file_color(base, thin=True, start=0, size=14, save=False):
conf, track, pegs = load(base)
fig = pl.figure(figsize=(size,size*conf['top']/conf['wall']))
track = track[start:]
x = track[:,0]; y = track[:,1]
t = np.linspace(0,1,x.shape[0])
points = np.array([x,y]).transpose().reshape(-1,1,2)
segs = np.concatenate([points[:-1],points[1:]],axis=1)
lc = LineCollection(segs, linewidths=0.25, cmap=pl.cm.coolwarm)
lc.set_array(t)
pl.gca().add_collection(lc)
#pl.scatter(x, y, c=np.arange(len(x)),linestyle='-',cmap=pl.cm.coolwarm)
#pl.plot(track[-1000000:,0], track[-1000000:,1], '-', linewidth=0.0125, alpha=0.8)
for peg in pegs:
pl.gca().add_artist(pl.Circle(peg, conf['radius'], color='k', alpha=0.3))
pl.xlim(0, conf['wall'])
pl.ylim(0, conf['top'])
pl.xticks([])
pl.yticks([])
pl.tight_layout()
pl.show()
if save:
pl.savefig(base+".png", dpi=200)
def tracks_movie(base, skip=1, frames=500, size=10):
"""
A movie of each particle as a point
"""
conf, track, pegs = load(base)
fig = pl.figure(figsize=(size,size*conf['top']/conf['wall']))
plot = None
for t in xrange(1,max(frames, track.shape[1]/skip)):
tmp = track[:,t*skip,:]
if not ((tmp[:,0] > 0) & (tmp[:,1] > 0) & (tmp[:,0] < conf['wall']) & (tmp[:,1] < conf['top'])).any():
continue
if plot is None:
plot = pl.plot(tmp[:,0], tmp[:,1], 'k,', alpha=1.0, ms=0.1)[0]
pl.xticks([])
pl.yticks([])
pl.xlim(0,conf['wall'])
pl.ylim(0,conf['top'])
pl.tight_layout()
else:
plot.set_xdata(tmp[:,0])
plot.set_ydata(tmp[:,1])
pl.draw()
pl.savefig(base+'-movie-%05d.png' % (t-1))
def plotVOI(self,n,points,L,data,kern,temp1,temp2,a,m,path):
z=np.zeros(m)
for i in xrange(m):
z[i]=self.VOIfunc(n,points[i,:],L,data,kern,temp1,temp2,False,a,False)
fig=plt.figure()
fig.set_size_inches(21, 21)
plt.plot(points,z,'-')
plt.xlabel('x',fontsize=60)
Xp=data.Xhist[0:self._numberTraining,0]
pylab.plot(Xp,np.zeros(len(Xp))+0.00009,'o',color='red',markersize=40,label="Training point")
if n>0:
Xp=data.Xhist[self._numberTraining:self._numberTraining+n,0]
pylab.plot(Xp,np.zeros(len(Xp))+0.00009,'o',color='firebrick',markersize=40,label="Chosen point")
ax = plt.subplot(111)
box = ax.get_position()
ax.set_position([box.x0, box.y0+box.height*0.1, box.width, box.height*0.9])
# Put a legend to the right of the current axis
ax.legend(loc='upper center', bbox_to_anchor=(0.5, -0.09),ncol=2,fontsize=50)
pylab.xlim([-0.5,0.5])
# plt.legend()
plt.savefig(os.path.join(path,'%d'%n+"VOI_n.pdf"))
plt.close(fig)
def plotFreqVsGoodTuring(counts, confidence=1.96, loglog=False):
"""
Draws a scatterplot of the empirical frequencies of the counted species
versus their Simple Good Turing smoothed values, in rank order. Depends on
pylab and matplotlib.
"""
import pylab
from matplotlib import rc
tot = float(sum(counts.values()))
freqs = dict([(species, cnt/tot) for species, cnt in counts.iteritems()])
sgt, p0 = simpleGoodTuringProbs(counts, confidence)
if loglog:
plotFunc = pylab.loglog
else:
plotFunc = pylab.plot
plotFunc(sorted(freqs.values(), reverse=True), 'kD', mfc='white',
label="Observed")
plotFunc(sorted(sgt.values(), reverse=True), 'k+',
label="Simple Good-Turing Estimate")
pylab.xlim(-0.5, len(freqs)+0.5)
pylab.xlabel("Rank")
pylab.ylabel("Frequency")
pylab.legend(numpoints=1)
def draw(self):
print self.edgeno
pos = 0
dy = 8
edgeno = self.edgeno
edge = self.edges[edgeno]
edgeprev = self.edges[edgeno-1]
p = np.round(edge["top"](1024))
top = min(p+2*dy, 2048)
bot = min(p-2*dy, 2048)
self.cutout = self.flat[1][bot:top,:].copy()
pl.figure(1)
pl.clf()
start = 0
dy = 512
for i in xrange(2048/dy):
pl.subplot(2048/dy,1,i+1)
pl.xlim(start, start+dy)
if i == 0: pl.title("edge %i] %s|%s" % (edgeno,
edgeprev["Target_Name"], edge["Target_Name"]))
pl.subplots_adjust(left=.07,right=.99,bottom=.05,top=.95)
pl.imshow(self.flat[1][bot:top,start:start+dy], extent=(start,
start+dy, bot, top), cmap='Greys', vmin=2000, vmax=6000)
pix = np.arange(start, start+dy)
pl.plot(pix, edge["top"](pix), 'r', linewidth=1)
pl.plot(pix, edgeprev["bottom"](pix), 'r', linewidth=1)
pl.plot(edge["xposs_top"], edge["yposs_top"], 'o')
pl.plot(edgeprev["xposs_bot"], edgeprev["yposs_bot"], 'o')
hpp = edge["hpps"]
pl.axvline(hpp[0],ymax=.5, color='blue', linewidth=5)
pl.axvline(hpp[1],ymax=.5, color='red', linewidth=5)
hpp = edgeprev["hpps"]
pl.axvline(hpp[0],ymin=.5,color='blue', linewidth=5)
pl.axvline(hpp[1],ymin=.5,color='red', linewidth=5)
if False:
L = top-bot
Lx = len(edge["xposs"])
for i in xrange(Lx):
xp = edge["xposs"][i]
frac1 = (edge["top"](xp)-bot-1)/L
pl.axvline(xp,ymin=frac1)
for xp in edgeprev["xposs"]:
frac2 = (edgeprev["bottom"](xp)-bot)/L
pl.axvline(xp,ymax=frac2)
start += dy
def plot_prob_effector(sens, fpr, xmax=1, baserate=0.1):
"""Plots a line graph of P(effector|positive test) against
the baserate of effectors in the input set to the classifier.
The baserate argument draws an annotation arrow
indicating P(pos|+ve) at that baserate
"""
assert 0.1 <= xmax <= 1, "Max x axis value must be in range [0,1]"
assert 0.01 <= baserate <= 1, "Baserate annotation must be in range [0,1]"
baserates = pylab.arange(0, 1.05, xmax * 0.005)
probs = [p_correct_given_pos(sens, fpr, b) for b in baserates]
pylab.plot(baserates, probs, 'r')
pylab.title("P(eff|pos) vs baserate; sens: %.2f, fpr: %.2f" % (sens, fpr))
pylab.ylabel("P(effector|positive)")
pylab.xlabel("effector baserate")
pylab.xlim(0, xmax)
pylab.ylim(0, 1)
# Add annotation arrow
xpos, ypos = (baserate, p_correct_given_pos(sens, fpr, baserate))
if baserate < xmax:
if xpos > 0.7 * xmax:
xtextpos = 0.05 * xmax
else:
xtextpos = xpos + (xmax-xpos)/5.
if ypos > 0.5:
ytextpos = ypos - 0.05
else:
ytextpos = ypos + 0.05
pylab.annotate('baserate: %.2f, P(pos|+ve): %.3f' % (xpos, ypos),
xy=(xpos, ypos),
xytext=(xtextpos, ytextpos),
arrowprops=dict(facecolor='black', shrink=0.05))
else:
pylab.text(0.05 * xmax, 0.95, 'baserate: %.2f, P(pos|+ve): %.3f' % \
(xpos, ypos))
def plot_spectrum():
#get the data...
a_0=struct.unpack('>1024l',fpga.read('even',1024*4,0))
a_1=struct.unpack('>1024l',fpga.read('odd',1024*4,0))
interleave_a=[]
for i in range(1024):
interleave_a.append(a_0[i])
interleave_a.append(a_1[i])
pylab.figure(num=1,figsize=(10,10))
pylab.ioff()
pylab.plot(interleave_a)
#pylab.semilogy(interleave_a)
pylab.title('Integration number %i.'%prev_integration)
pylab.ylabel('Power (arbitrary units)')
pylab.grid()
pylab.xlabel('Channel')
pylab.xlim(0,2048)
pylab.ioff()
pylab.hold(False)
pylab.show()
pylab.draw()
NETarr_sus140 / NETarr_sus140[0],
'-',
label='140GHz')
py.plot(hwp_temperature_arr,
NETarr_sus166 / NETarr_sus166[0],
'-',
label='166GHz')
py.plot(hwp_temperature_arr,
NETarr_sus195 / NETarr_sus195[0],
'-',
label='195GHz')
py.plot(hwp_temperature_arr,
NETarr_sus235 / NETarr_sus235[0],
'-',
label='235GHz')
py.xlim([1, 35])
py.ylim([0.9, 2])
#py.xlabel('Temperature [K]',fontsize=17)
py.ylabel('$NET_{\\nu}(T)/NET(5K)$', fontsize=17)
py.xticks(color='k', size=17)
py.yticks(color='k', size=17)
#py.legend(loc='best')
py.subplot(212)
py.plot(hwp_temperature_arr,
NETarr_sus280 / NETarr_sus280[0],
'-',
label='280GHz')
py.plot(hwp_temperature_arr,
NETarr_sus337 / NETarr_sus337[0],
'-',
def derive_wifes_calibration(cube_fn_list,
calib_out_fn,
stdstar_name_list=None,
extract_in_list=None,
airmass_list=None,
ref_dir=metadata_dir,
ref_fname_list=None,
plot_stars=False,
plot_sensf=False,
norm_stars=False,
method='poly',
polydeg=30,
excise_cut=0.5,
wave_min=None,
wave_max=None,
extinction_fn=None,
ytrim=5):
if plot_stars or plot_sensf:
import pylab
# get extinction curve
if extinction_fn == None:
extinct_interp = sso_extinct_interp
else:
ext_data = numpy.loadtxt(extinction_fn)
extinct_interp = scipy.interpolate.interp1d(ext_data[:, 0],
ext_data[:, 1],
bounds_error=False,
fill_value=numpy.nan)
# first extract stdstar spectra and compare to reference
fratio_results = []
for i in range(len(cube_fn_list)):
f = pyfits.open(cube_fn_list[i])
cube_hdr = f[1].header
f.close()
#------------------------------------
# figure out which star it is
# NEW VERSION 0.7.0: smart star name lookup!
#
# top priority: user forces the name
if stdstar_name_list != None:
star_name = stdstar_name_list[i]
# if you forced an unknown star name, reset name to None
if star_name not in ref_fname_lookup.keys():
star_name = None
else:
star_name = None
# try to find the nearest standard in the list
if star_name == None:
try:
star_name, dist = find_nearest_stdstar(cube_fn_list[i])
if dist > 200.0:
star_name = None
except:
# last resort: use the object name from the fits header
# and pray it's correct
star_name = cube_hdr['OBJECT']
#------------------------------------
#print star_name
if airmass_list != None:
secz = airmass_list[i]
else:
try:
secz = cube_hdr['AIRMASS']
except:
print 'AIRMASS header missing for %s' % cube_fn_list[i].split(
'/')[-1]
secz = 1.0
# check if there is a calib spectrum...
if ref_fname_list != None:
ref_fname = ref_name_list[i]
elif star_name in ref_fname_lookup.keys():
ref_fname = ref_fname_lookup[star_name]
else:
continue
# get observed data
if extract_in_list == None:
obs_wave, obs_flux = extract_wifes_stdstar(cube_fn_list[i],
ytrim=ytrim)
else:
ex_data = numpy.loadtxt(extract_in_list[i])
obs_wave = ex_data[:, 0]
obs_flux = ex_data[:, 1]
if wave_min == None:
wave_min = numpy.min(obs_wave)
if wave_max == None:
wave_max = numpy.max(obs_wave)
# get reference data
ref_data = numpy.loadtxt(ref_dir + ref_fname)
ref_interp = scipy.interpolate.interp1d(ref_data[:, 0],
ref_data[:, 1],
bounds_error=False,
fill_value=numpy.nan)
ref_flux = ref_interp(obs_wave)
std_ext = extinct_interp(obs_wave)
good_inds = numpy.nonzero(
(ref_flux == ref_flux) * (std_ext == std_ext) *
(obs_wave >= wave_min) * (obs_wave <= wave_max) *
(obs_flux > 0.0))[0]
init_flux_ratio = -2.5 * numpy.log10(
obs_flux[good_inds] / ref_flux[good_inds])
flux_ratio = init_flux_ratio + (secz - 1.0) * std_ext[good_inds]
fratio_results.append([obs_wave[good_inds], init_flux_ratio])
if plot_stars:
scaled_flux = obs_flux[good_inds] / numpy.mean(
10.0**(-0.4 * flux_ratio))
pylab.figure()
pylab.plot(obs_wave,
ref_flux,
color='b',
label='Reference star flux')
pylab.plot(obs_wave[good_inds],
scaled_flux,
color='r',
label='Scaled observed flux')
pylab.title(star_name)
pylab.xlabel(r'Wavelength [$\AA$]')
pylab.legend(loc='lower right', fancybox=True, shadow=True)
# from all comparisons, derive a calibration solution
# EVENTUALLY WILL FIT AN EXTINCTION TERM TOO
if norm_stars:
i_mid = len(fratio_results[0][0]) / 2
fscale_max = min([x[1][i_mid] for x in fratio_results])
init_full_y = numpy.concatenate(
[x[1] - x[1][i_mid] + fscale_max for x in fratio_results])
else:
init_full_y = numpy.concatenate([x[1] for x in fratio_results])
init_full_x = numpy.concatenate([x[0] for x in fratio_results])
init_good_inds = numpy.nonzero(
(init_full_y == init_full_y) *
(init_full_y < numpy.median(init_full_y) + 20.0) *
(strong_telluric_mask(init_full_x)) * (halpha_mask(init_full_x)))[0]
# do a first fit
next_full_y = init_full_y[init_good_inds]
next_full_x = init_full_x[init_good_inds]
sort_order = next_full_x.argsort()
temp_full_x = next_full_x[sort_order]
temp_full_y = next_full_y[sort_order]
# ----------- Fred's update 3 -------------------
if method == 'smooth_SG':
# Savitzky-Golay requires continuous data. ->need to fill the 'holes'
# It is a problem for red spectra (at this point at least)
# Check if there are gaps (telluric, Halpha, etc ...)
init_bad_inds = \
numpy.nonzero(1-
((init_full_y == init_full_y)*
(init_full_y < numpy.median(init_full_y)+20.0)*
(telluric_mask(init_full_x))*
(halpha_mask(init_full_x))))[0]
if len(init_bad_inds) > 0:
# if yes, first fit a polynomial, then use it to 'fill the gaps.
temp_calib = numpy.polyfit(temp_full_x, temp_full_y, polydeg)
temp_fvals = numpy.polyval(temp_calib, init_full_x)
init_full_y[init_bad_inds] = temp_fvals[init_bad_inds]
temp_full_y = init_full_y # to ensure this case is then compatible
temp_full_x = init_full_x
# Fails if multiple stars ... need to order the array !
this_sort_order = temp_full_x.argsort()
temp_full_x = temp_full_x[this_sort_order]
temp_full_y = temp_full_y[this_sort_order]
# Then fit SG normally
temp_fvals = savitzky_golay(temp_full_y, 101, 1, 0)
excise_cut = 0.003
else:
temp_best_calib = numpy.polyfit(temp_full_x, temp_full_y, polydeg)
temp_fvals = numpy.polyval(temp_best_calib, temp_full_x)
# excise outliers
final_good_inds = numpy.nonzero(
numpy.abs(temp_fvals - temp_full_y) /
numpy.abs(temp_fvals) < excise_cut)[0]
full_x = temp_full_x[final_good_inds]
full_y = temp_full_y[final_good_inds]
# ------------ Fred's update 3 ----------------
if method == 'smooth_SG': # Fails if multiple stars ... need to order the array !
this_sort_order = full_x.argsort()
full_x = full_x[this_sort_order]
full_y = full_y[this_sort_order]
final_fvals = savitzky_golay(full_y, 101, 1, 0)
this_f = scipy.interpolate.interp1d(full_x,
final_fvals,
bounds_error=False,
kind='linear')
all_final_fvals = this_f(init_full_x)
final_x = full_x
final_y = full_y
else:
best_calib = numpy.polyfit(full_x, full_y, polydeg)
final_fvals = numpy.polyval(best_calib, full_x)
final_x = numpy.arange(
numpy.min(full_x), 1.000001 * numpy.max(full_x),
0.0001 * (numpy.max(full_x) - numpy.min(full_x)))
final_y = numpy.polyval(best_calib, final_x)
# plot if requested
if plot_sensf:
pylab.figure()
# MC update - raw fit on top
pylab.axes([0.10, 0.35, 0.85, 0.60])
pylab.plot(temp_full_x,
temp_full_y,
'r.',
markerfacecolor='none',
markeredgecolor='r',
label='Raw sensitivity (initial regions)')
pylab.plot(full_x,
full_y,
color='b',
label='Raw sensitivity (valid regions)')
pylab.plot(temp_full_x,
temp_fvals,
color=r'#FF6103',
lw=2,
label='Initial fit')
if method == 'smooth_SG':
pylab.plot(init_full_x,
all_final_fvals,
color=r'#00FF00',
lw=2,
label='Final fit')
else:
pylab.plot(full_x,
final_fvals,
color=r'#00FF00',
lw=2,
label='Final fit')
#pylab.hlines(-37.5,numpy.min(full_x),numpy.max(full_x), 'k')
pylab.xlim([numpy.min(full_x), numpy.max(full_x)])
curr_ylim = pylab.ylim()
curr_xlim = pylab.xlim()
pylab.ylim(curr_ylim[::-1])
pylab.title('Derived sensitivity function')
pylab.legend(loc='lower right', fancybox=True, shadow=True)
# lower plot - residuals!
pylab.axes([0.10, 0.10, 0.85, 0.25])
pylab.plot(full_x,
full_y - final_fvals,
'k.',
mec=r'#666666',
markerfacecolor='none',
label='Residuals')
pylab.axhline(0.0, color='k')
pylab.xlim(curr_xlim)
pylab.ylim([-0.2, 0.2])
pylab.xlabel(r'Wavelength [$\AA$]')
pylab.ylabel('Residuals')
if plot_stars or plot_sensf:
pylab.show()
# Fred's update ... now, careful, because that's dirty ...
# the function does not always return the same thing !
# SAVE IN THE PICKLE FILE THE WAVELENGTH AND CALIB FVAL ARRAYS
save_calib = {'wave': final_x, 'cal': final_y}
f1 = open(calib_out_fn, 'w')
pickle.dump(save_calib, f1)
f1.close()
return
fp.close()
layers=['l23','l4']
colors={'pyr':'r','pv':'b'}
celltypes=['pyr','pv']
sub_fig_num=len(layers)
pylab.figure(1)
for xi, xin in enumerate(layers):
pylab.subplot(sub_fig_num,1,xi+1)
if xi==0:
pylab.title('V1_1')
for yin in celltypes:
spks=spikes['V1_1'+xin+yin]
pylab.scatter(spks[0],spks[1],c=colors[yin], s=5, edgecolors='none')
pylab.xlim([0.0,simtime])
pylab.ylabel(xin)
pylab.savefig('../figs/zoom_raster_pref'+str(top_down_pyr)+'_'+str(top_down_pv)+'_'+str(msd)+'_'+str(fraction)+'_'+sim_len+'.eps')
pylab.figure(2)
for xi, xin in enumerate(layers):
pylab.subplot(sub_fig_num,1,xi+1)
if xi==0:
pylab.title('V1_2')
for yin in celltypes:
spks=spikes['V1_2'+xin+yin]
pylab.scatter(spks[0],spks[1],c=colors[yin], s=5, edgecolors='none')
pylab.xlim([0.0,simtime])
pylab.ylabel(xin)
import pylab as plt
from roadprofile import *
from scipy.signal import periodogram
testprofile = RoadProfile()
profile = testprofile.get_profile_by_class("A", 100, 0.1)
plt.loglog(*periodogram(profile[1], fs=10))
plt.xlabel("Spatial frequency")
plt.ylabel("PSD")
plt.grid("on")
plt.ylim([1E-8, 0.01])
plt.xlim([0.01, 5])
plt.show()
pylab.loglog(cl[:, 0], cl[:, 1 + i], spec[i], lw=2, label=str(label[i]))
for i in range(len(cl)):
covariance = linalg.inv(inverse[i * 6:(i + 1) * 6, :])
# print linalg.eigh(covariance*1e25,eigvals_only=True)
delta = numpy.random.multivariate_normal(cl[i, 1:7], covariance)
cl[i, 1:7] = delta
# print i,cl[i,1:7]
numpy.savetxt(filename2, cl)
#c1 = 'cp %s %s'%(filename1,filename1+'temp')
#c2 = 'cp %s %s'%(filename2,filename2+'temp')
#c3 = 'mv %s %s'%(filename2+'temp',filename1)
#c4 = 'mv %s %s'%(filename1+'temp',filename2)
#subprocess.call(c1,shell=True)
#subprocess.call(c2,shell=True)
#subprocess.call(c3,shell=True)
#subprocess.call(c4,shell=True)
for i in range(6):
pylab.loglog(cl[:, 0], cl[:, 1 + i], '--' + spec[i], lw=2)
pylab.legend(loc=3, fontsize=18)
pylab.xlabel('$\mathtt{\ell}$', fontsize=22)
pylab.ylabel('$\mathtt{C_{\ell}}$', fontsize=22)
pylab.xlim(min(cl[:, 0]), max(cl[:, 0]))
pylab.ylim(ymax=2e-7)
pylab.savefig(filename2.replace('txt', 'eps'))
pylab.show()
def plotAgainstTime(self, pend=-1):
plt.figure()
plt.xlim([-0.05, self.t])
plt.plot(self.allCoords[pend, :, -1], self.allCoords[pend, :, 0])
plt.show()
def J(m, x):
s = f(m, x, a) + f(m, x, b)
for i in range(1, N):
theta = a + i * h
if i % 2 == 1:
s += 4 * f(m, x, theta)
else:
s += 2 * f(m, x, theta)
return (s*h/3)
xpoints = []
ypoints0 = []
ypoints1 = []
ypoints2 = []
for x in linspace(0,20,1000):
xpoints.append(x)
ypoints0.append(J(0,x))
ypoints1.append(J(1,x))
ypoints2.append(J(2,x))
xlim(0,20)
ylim(-1,1)
plot(xpoints,ypoints0,"k-",label="m=0")
plot(xpoints,ypoints1,"k--",label="m=1")
plot(xpoints,ypoints2,"ko",label="m=2")
legend(loc = 'best')
xlabel('x')
ylabel('J(m,x)')
title('Plot of Bessel functions')
show()
print("Input S.dtype: " + str(S.dtype))
# Prepare and run EMD
emd = EMD()
emd.FIXE_H = 5
emd.nbsym = 2
emd.spline_kind = 'cubic'
emd.DTYPE = DTYPE
nIMF = emd.emd(S, T, max_imf)
imfNo = nIMF.shape[0]
# Plot results
c = 1
r = np.ceil((imfNo + 1) / c)
plt.ioff()
plt.subplot(r, c, 1)
plt.plot(T, S, 'r')
plt.xlim((tMin, tMax))
plt.title("Original signal")
for num in range(imfNo):
plt.subplot(r, c, num + 2)
plt.plot(T, nIMF[num], 'g')
plt.xlim((tMin, tMax))
plt.ylabel("Imf " + str(num + 1))
plt.tight_layout()
plt.show()
# did the user request an x-axis limit below the maximum death value found in the input?
if xLimit < maxDeath:
print 'Requested xLimit (' + str(
xLimit) + ') value is lower than max death value (' + str(
maxDeath) + ')...aborting'
sys.exit()
# are there more dimensions in the data then we have colors for?
if len(colorPalette) < np.max(rawData[:, 0]):
print 'The current colormap has insufficient colors to represent all the dimensions in the data...aborting'
sys.exit()
# build barcode plot
pylab.grid(True, which='both')
pylab.xlim(-.025, xLimit + .025)
pylab.xlabel('Time')
pylab.ylabel('Index')
for i in range(len(rawData)):
mpl.pyplot.hlines(i + 1,
rawData[i, 1],
rawData[i, 2],
colors=colorPalette[int(rawData[i, 0])])
# build the legend
dimensions = []
for i in range(int(np.max(rawData[:, 0])) + 1):
dimensions.append(
mpl.patches.Patch(color=colorPalette[i], label=r'$H_{}$'.format(i)))
# -*- coding: utf-8 -*-
"""
Created on Fri Sep 29 21:03:22 2017
@author: XMKZ
"""
import numpy
import pylab as py
N=1000
delta=0.01
Time=0
a=15
b=0.015
x=[0]
y=[0]
while Time<=0.999:
Time=Time+delta
N=N+(a*N-b*N**2)*delta
x.append(Time)
y.append(N)
else:
plot=py.plot(x,y,'.',label='N')
py.title('model')
py.xlabel('Time')
py.ylabel('N')
py.xlim(0,1)
py.ylim(0,2000)
py.legend(loc='best')
py.show()
threshold = 2.5
T_obs, clusters, cluster_p_values, H0 = \
permutation_cluster_1samp_test(epochs_power,
n_permutations=100, threshold=threshold, tail=0)
###############################################################################
# View time-frequency plots
import pylab as pl
pl.clf()
pl.subplots_adjust(0.12, 0.08, 0.96, 0.94, 0.2, 0.43)
pl.subplot(2, 1, 1)
pl.plot(times, evoked_data.T)
pl.title('Evoked response (%s)' % ch_name)
pl.xlabel('time (ms)')
pl.ylabel('Magnetic Field (fT/cm)')
pl.xlim(times[0], times[-1])
pl.ylim(-100, 250)
pl.subplot(2, 1, 2)
# Create new stats image with only significant clusters
T_obs_plot = np.nan * np.ones_like(T_obs)
for c, p_val in zip(clusters, cluster_p_values):
if p_val <= 0.05:
T_obs_plot[c] = T_obs[c]
vmax = np.max(np.abs(T_obs))
vmin = -vmax
pl.imshow(T_obs,
cmap=pl.cm.gray,
extent=[times[0], times[-1], frequencies[0], frequencies[-1]],
extent=[x_min, x_max, y_min, y_max],
cmap=pl.cm.gnuplot,
origin='lower')
levels[f] = contours.levels
pl.clabel(contours, inline=1, fmt=super_fmt, fontsize=14)
pl.plot(all_x_i, all_y_i, 'b-', linewidth=2)
pl.plot(all_x_i, all_y_i, 'k+')
pl.plot(logging_f.all_x_i, logging_f.all_y_i, 'k.', markersize=2)
pl.plot([0], [0], 'rx', markersize=12)
pl.xticks(())
pl.yticks(())
pl.xlim(x_min, x_max)
pl.ylim(y_min, y_max)
pl.draw()
pl.figure(index + 100, figsize=(4, 3))
pl.clf()
pl.semilogy(np.maximum(np.abs(all_f_i), 1e-30),
linewidth=2,
label='# iterations')
pl.ylabel('Error on f(x)')
pl.semilogy(logging_f.counts,
np.maximum(np.abs(logging_f.all_f_i), 1e-30),
linewidth=2,
color='g',
label='# function calls')
pl.legend(loc='upper right',
plt.hlines(y, vis, ini, lw=3, color=cm.Dark2(y / (maxy + 5)))
if ii > maxy: break
else: ii += 1
labels = ['%s (%2.1f)' % (wt.name, wt.mag) for wt in worthy_targets[0:maxy]]
ax.set_yticklabels(labels)
ax.set_ylim(-0.5, maxy - 0.5)
# convert epoch to matplotlib float format
labels = np.linspace(minute_ini, minute_end + 1,
12) * 60. + const.timestamp_2018_01_01
plt.xlim([minute_ini, minute_end + 1])
ax.xaxis.set_major_locator(MultipleLocator((minute_end - minute_ini + 1) / 11))
# to human readable date
pre = map(time.gmtime, labels)
labels = map(figures.format_second, pre)
ax.set_xticklabels(labels)
fig.autofmt_xdate()
if save:
threshold_obs_time -= t_acquisition
if SAA: note = '_SAA'
else: note = ''
fname = '%svisibility_stars_obs_%d_o_%d_to_%d%s' % (
folder_figures, threshold_obs_time, fo, lo, note)
x4 = gl.addSpecies ('X4', 0, False)
rxa1 = gl.addFirstOrderReaction (x1, 0.1)
gl.addProduct (rxa1, x2, 1)
rxa2 = gl.addFirstOrderReaction (x2, 0.65)
gl.addProduct (rxa2, x3, 1)
rxa3 = gl.addFirstOrderReaction (x3, 0.2)
gl.addProduct (rxa3, x4, 1)
#r = gl.setSeedUsingTime()
gl.setSeed (1503793684)
pylab.figure(figsize=(8,5))
pylab.xlim((0, 200))
m1 = gl.executeOnGrid (0, 100, 100)
gl.setRateConstant (rxa1, 0.2)
m2 = gl.executeOnGrid (100, 200, 100)
m3 = np.vstack ((m1, m2))
pylab.plot (m3[:,0], m3[:,1], color='r', label='$x_2$')
pylab.plot (m3[:,0], m3[:,2], color='b', label='$x_3$')
pylab.xlabel ('Time')
pylab.legend()
pylab.savefig ('eventExample.pdf')
gl.free()
def normalized_plot(what,
alphaGammaName,
N=1000,
stride=50,
aHi=[],
legendAlpha=.5):
'''
Create normalized plot as it appears in :cite:`Maugis1992` including range of axes with normalized quantities. This function is mainly useful for documentation of Woo itself.
:param what: one of ``a(delta)``, ``F(delta)``, ``a(F)``
:param alphaGammaName: list of (alpha,gamma,name) tuples which are passed to the :obj:`SchwarzModel` constructor
:param N: numer of points in linspace for each axis
:param stride: stride for plotting inverse relationships (with points)
:param aHi: with ``what==a(delta)``, show upper bracket for $a$ for i-th model, if *i* appears in the list
'''
assert what in ('a(delta)', 'F(delta)', 'a(F)')
import pylab
invKw = dict(linewidth=4, alpha=.3)
kw = dict(linewidth=2)
pylab.figure()
for i, (alpha, gamma, name) in enumerate(alphaGammaName):
m = SchwarzModel.makeDefault(alpha=alpha, gamma=gamma, name=name)
if what == 'a(delta)':
ddHat = numpy.linspace(-1.3, 2., num=N)
aaHat = numpy.linspace(0, 2.1, num=N)
pylab.plot(m.deltaHat_aHat(aaHat),
aaHat,
label='$\\alpha$=%g %s' % (m.alpha, m.name),
**kw)
ddH = m.deltaHat_aHat(aaHat)
if i in aHi:
pylab.plot(
ddH, [m.aHat(m.aHi(m.deltaUnhat(dh))) for dh in ddH],
label='$\\alpha$=%g $a_{\mathrm{hi}}$' % m.alpha,
linewidth=1,
alpha=.4)
pylab.plot(ddHat[::stride],
m.aHat_deltaHat(ddHat[::stride], loading=True), 'o',
**invKw)
pylab.plot(ddHat[::stride],
m.aHat_deltaHat(ddHat[::stride], loading=False),
'o', **invKw)
elif what == 'F(delta)':
ffHat = numpy.linspace(-2.1, 1.5, num=N)
ddHat = numpy.linspace(-1.3, 2., num=N)
pylab.plot(ddHat,
m.fHat_aHat(m.aHat_deltaHat(ddHat)),
label='$\\alpha$=%g %s' % (m.alpha, m.name),
**kw)
pylab.plot(ddHat,
m.fHat_aHat(m.aHat_deltaHat(ddHat, loading=False)),
**kw)
pylab.plot([
m.deltaHat(m.delta_a(m.a_F(m.fUnhat(fh))[0]))
for fh in ffHat[::stride]
], ffHat[::stride], 'o', **invKw)
pylab.plot([
m.deltaHat(m.delta_a(m.a_F(m.fUnhat(fh))[1]))
for fh in ffHat[::stride]
], ffHat[::stride], 'o', **invKw)
elif what == 'a(F)':
aaHat = numpy.linspace(0, 2.5, num=N)
ffHat = numpy.linspace(-3, 4, num=N)
pylab.plot(ffHat, [a[0] for a in m.aHat_fHat(ffHat)],
label='$\\alpha$=%g %s' % (m.alpha, m.name),
**kw)
pylab.plot(ffHat, [a[1] for a in m.aHat_fHat(ffHat)], **kw)
pylab.plot(m.fHat_aHat(aaHat[::stride]),
aaHat[::stride],
'o',
label=None,
**invKw)
if what == 'a(delta)':
ddH = [
m.deltaHat(HertzModel.delta_a(m, m.aUnhat(a))) for a in aaHat
]
pylab.plot(ddH, aaHat, label='Hertz', **kw)
pylab.xlabel('$\hat\delta$')
pylab.ylabel('$\hat a$')
pylab.ylim(ymax=2.1)
pylab.xlim(xmax=2.)
elif what == 'F(delta)':
pylab.plot(ddHat, [
m.fHat(HertzModel.F_delta(m, m.deltaUnhat(d))) for d in ddHat
],
label='Hertz',
**kw)
pylab.xlabel('$\hat\delta$')
pylab.ylabel('$\hat P$')
pylab.xlim(-1.3, 2)
pylab.ylim(-2.1, 2)
pylab.axhline(color='k')
pylab.axvline(color='k')
elif what == 'a(F)':
pylab.plot(ffHat,
[m.aHat(HertzModel.a_F(m, m.fUnhat(f))) for f in ffHat],
label='Hertz',
**kw)
pylab.xlabel('$\hat P$')
pylab.ylabel('$\hat a$')
pylab.xlim(xmax=4)
pylab.grid(True)
try:
pylab.legend(loc='best', framealpha=legendAlpha)
except:
pylab.legend(loc='best')
with open("results/avg_clustering.txt", "w+") as f:
f.write("Average Clustering: {}\n".format(clustering_sum / 2394385))
f.write("Number of nodes with Clustering Coefficient of 0 {}\n".format(
hist[0]))
f.write("Number of nodes with Clustering Coefficient of 1 {}\n".format(
hist[-1]))
width = 0.7 * (bins[2] - bins[1])
center = (bins[:-1] + bins[1:]) / 2
plt.figure()
plt.grid(True)
plt.bar(center[1:-1], hist[1:-1], align='center', width=width)
plt.xlabel('Clustering Coefficient')
plt.xlim([0, 1])
plt.ylabel('Number of Nodes')
plt.savefig('results/figures/clustering_hist.pdf')
plt.close()
log_hist = list()
for n in hist:
if n == 0:
log_hist.append(0)
else:
log_hist.append(log10(n))
plt.figure()
plt.grid(True)
plt.bar(center, log_hist, align='center', width=width)
plt.xlabel('Clustering Coefficient')
Tstim=1.0
# Tstim=0.2
nTimeSteps = len(stmframes)
# letters = ['A','B','E']
letters=['A']
dims = numpy.r_[dim, nTimeSteps]
stim = generateLetterStim(dims, stmframes, letters)
lgn = LGN(dt=Tstim/60.0)
lgn.processStimulus(stim, Tstim=Tstim)
ind = numpy.arange(0, 60, 2)
plotResults(lgn, stim, ind)
pylab.xticks([pylab.xlim()[0], pylab.xlim()[1]/2.0, pylab.xlim()[1]], ['0.0', str(Tstim/2.0), str(Tstim)+' s'])
# Example with spot stimulus
#===============================================================================
# Tsim=0.2xxx
# stmframes = numpy.r_[numpy.zeros(1), numpy.ones(15), numpy.zeros(39)]
# nTimeSteps = len(stmframes)
#
# ret = Retina()
# spot = numpy.ones(ret.k.shape)*(ret.k>0)
#
# nBitmaps = 1
# bitmaps = numpy.zeros((ret.k.shape[0], ret.k.shape[1], nBitmaps))
# bitmaps[:,:,0]=spot
#
# stim = generateBitmapStim(bitmaps, stmframes)
#
x1_ = glob_cent_centroid[1] - patch_size
y1_ = glob_cent_centroid[0] - patch_size
x2_ = x1_ + 2 * patch_size
y2_ = y1_ + 2 * patch_size
plt.text(x1_ - 1,
y1_ - 2,
str(i + 1).zfill(3),
fontsize=1.2,
color='w')
plt.plot([x1_, x2_, x2_, x1_, x1_],
[y1_, y1_, y2_, y2_, y1_],
lw=0.2,
color='w')
plt.xlim([0, ncols])
plt.ylim([nrows, 0])
"""
saving out the global file too.
"""
plt.savefig(os.path.join(
saveimgfolder,
basename.replace('.pkl',
'_full-image-cnn-detections.svg')),
dpi=height)
plt.close()
"""
save out the global mask.
"""
fig = plt.figure()
fig.set_size_inches(width / height, 1, forward=False)
layer1 = reflectivity.Epitaxial_Layer(struct2, thickness)
layer1.calc_orientation(v_par, v_perp)
crystal = reflectivity.Sample(Sub, layer1)
crystal.set_Miller(R)
crystal.calc_g0_gH(Energy)
thBragg = float(Sub.calc_Bragg_angle(Energy).subs(Sub.structure.subs).evalf())
angle = pl.linspace(0.975, 1.006, 501) * thBragg
# XRl = layer1.calc_reflection_amplitude(angle, Energy)
#XRs = Sub.calc_reflection_amplitude(angle, Energy)
#
# XT = layer1.calc_transmission_amplitude(angle, Energy)
XR = crystal.calc_reflectivity(angle, Energy)
crystal.print_values(angle, Energy)
pl.plot(*data.T, label='GID_sl', color='red')
#pl.plot(angle-thBragg,abs(XT)**2)
pl.plot(pl.degrees(angle - thBragg), abs(XR)**2, label='dynXRD', color='black')
#pl.plot(pl.degrees(angle-thBragg),abs(Sub.XR)**2, label='dynXRD', color='blue')
#pl.plot(angle-thBragg,1 - abs(XT)**2 - abs(XRl)**2)
pl.yscale('log')
pl.xlabel('Angle (degrees)')
pl.ylabel('Reflectivity')
pl.xlim(-0.25, 0.1)
pl.rc('font', size=18)
pl.legend(loc="upper left", prop={'size': 19})
pl.savefig('pics/test12.eps')
pl.show()
import pylab as pl
import numpy as np
x = np.arange(-10, 10, 0.1)
f1 = (x - 1)**2
f2 = np.exp(-(x - 1)**2) * 50
pl.plot(x, f1, label='f1: Behavioral feature 1')
pl.plot(x, f2, label='f2: Behavioral feature 2')
pl.xlabel("x")
pl.ylabel("Error function value")
pl.legend()
pl.ylim(0, 120)
pl.savefig("Example1.png")
pl.figure()
f2 = np.exp(-(np.sqrt(f1) + 1 - 1)**2) * 50
pl.plot(f1, f2, label='Pareto front')
pl.xlabel("f1")
pl.ylabel("f2")
pl.legend()
pl.xlim(0, 20)
pl.ylim(0, 20)
pl.savefig("Example_pareto.png")
xs = np.linspace(0, length, 101)
plt.figure(1)
plt.clf()
ax1 = plt.subplot(2, 1, 1)
c = plt.scatter(xp[:, 0],
xp[:, 1],
s=0.1,
c=np.log10(np.maximum(pstrain, 1e-16)),
vmin=-4,
vmax=1)
cbar1 = plt.colorbar(c)
cbar1.set_ticks([-4, 1])
plt.axis('equal')
plt.title(title_str)
plt.xlim([0, max_length])
ax2 = plt.subplot(2, 1, 2)
c = plt.scatter(xp[:, 0],
xp[:, 1],
s=0.1,
c=np.log10(pepsII / material.time_factor + 1e-16),
vmin=-8,
vmax=-5)
cbar2 = plt.colorbar(c)
plt.axis('equal')
#plt.plot(xx,bed_fun_np(xx),'--k',linewidth=2)
#plt.plot(xs,surf_fun(xs),'--',color='gray')
cbar2.set_ticks([-8, -5])
#plt.title(title_str)
plt.xlim([0, max_length])
plt.xlabel('Distance (km)')
volume, flooded = x_iterate(t=times[i])
volume *= M0
if flooded:
z_array[i:] = zmax
z_covered[i:] = zmax
break
else:
z, c = get_z(volume)
z_array[i] = z
if c:
z_covered[i] = z
else:
z_uncovered[i] = z
c_array[i] = 0
# Set up plot
pylab.semilogx(t_array, [zmax] * N,
color='k',
linestyle="dashed",
label="top of vessel")
pylab.semilogx(t_array, z_covered, color='b', marker="o", label="water level")
pylab.semilogx(t_array, z_uncovered, color='r', marker="x")
pylab.semilogx(t_array, [ztop] * N, color='g', label="top of core")
pylab.legend(loc="center right")
pylab.xlabel("t (hours)")
pylab.ylabel("z (m)")
pylab.xlim([0, TIME / 3600])
pylab.ylim([R_VESSEL, zmax + 1])
pylab.title("Height of water in core", {"fontsize": 16, "fontweight": "bold"})
pylab.show()
v[1] -= alpha * u[0]
v[N-1] -= gamma * u[N]
#forward sweep
u[1] = v[1] / beta
v[1] = gamma / beta
for j in range(2,N):
den = beta - alpha*v[j-1]
u[j] = (v[j] - alpha*u[j-1])/den
v[j] = gamma / den
#backward sweep
for j in reversed(range(1,N-1)):
u[j] -= u[j+1] * v[j]
t += dt
if t >= p*tstep:
pylab.plot(x, [z for z in u], label='t (s)='+str(round(t,4)) )
pylab.xlim(-L/2,L/2)
pylab.xlabel('x(m)')
pylab.ylabel('Temperature (Celcius)')
pylab.legend(loc=(1.03,0.2))
p += 1
pylab.show()
def plot_results(pilot_dir, subj, channel, alpha_band=(9, 14), theta_band=(3, 6), drop_channels=None, dc=False,
reject_alpha=True, normalize_by='opened'):
drop_channels = drop_channels or []
cm = get_colors()
fg = plt.figure(figsize=(30, 6))
for j_s, experiment in enumerate(subj):
with h5py.File('{}\\{}\\{}'.format(pilot_dir, experiment, 'experiment_data.h5')) as f:
rejections, top_alpha, top_ica = load_rejections(f, reject_alpha=reject_alpha)
fs, channels, p_names = get_info(f, drop_channels)
ch = channels.index(channel)
#plt.plot(fft_filter(f['protocol6/raw_data'][:, ch], fs, band=(3, 35)))
#plt.plot(fft_filter(np.dot(f['protocol6/raw_data'], rejections)[:, ch], fs, band=(3, 35)))
#plt.show()
#from scipy.signal import welch
#plt.plot(*welch(f['protocol1/raw_data'][:60*500//2, channels.index('C3')], fs, nperseg=1000))
#plt.plot(*welch(f['protocol1/raw_data'][60*500//2:, channels.index('C3')], fs, nperseg=1000))
#plt.plot(*welch(f['protocol2/raw_data'][:30*500//2, channels.index('C3')], fs, nperseg=1000))
#plt.plot(*welch(f['protocol2/raw_data'][30*500//2:, channels.index('C3')], fs, nperseg=1000))
#plt.legend(['Close', 'Open', 'Left', 'Right'])
#plt.show()
# collect powers
powers = OrderedDict()
raw = OrderedDict()
alpha = OrderedDict()
pow_theta = []
for j, name in enumerate(p_names):
pow, alpha_x, x = get_protocol_power(f, j, fs, rejections, ch, alpha_band, dc=dc)
if 'FB' in name:
pow_theta.append(get_protocol_power(f, j, fs, rejections, ch, theta_band, dc=dc)[0].mean())
powers = add_data(powers, name, pow, j)
raw = add_data(raw, name, x, j)
alpha = add_data(alpha, name, alpha_x, j)
# plot rejections
n_tops = top_ica.shape[1] + top_alpha.shape[1]
for j_t in range(top_ica.shape[1]):
ax = fg.add_subplot(4, n_tops * len(subj), n_tops * len(subj) * 3 + n_tops * j_s + j_t + 1)
ax.set_xlabel('ICA{}'.format(j_t + 1))
labels, fs = get_lsl_info_from_xml(f['stream_info.xml'][0])
channels = [label for label in labels if label not in drop_channels]
pos = ch_names_to_2d_pos(channels)
plot_topomap(data=top_ica[:, j_t], pos=pos, axes=ax, show=False)
for j_t in range(top_alpha.shape[1]):
ax = fg.add_subplot(4, n_tops * len(subj),
n_tops * len(subj) * 3 + n_tops * j_s + j_t + 1 + top_ica.shape[1])
ax.set_xlabel('CSP{}'.format(j_t + 1))
labels, fs = get_lsl_info_from_xml(f['stream_info.xml'][0])
channels = [label for label in labels if label not in drop_channels]
pos = ch_names_to_2d_pos(channels)
plot_topomap(data=top_alpha[:, j_t], pos=pos, axes=ax, show=False)
# plot powers
if normalize_by == 'opened':
norm = powers['1. Opened'].mean()
elif normalize_by == 'beta':
norm = np.mean(pow_theta)
else:
print('WARNING: norm = 1')
print('norm', norm)
ax1 = fg.add_subplot(3, len(subj), j_s + 1)
ax = fg.add_subplot(3, len(subj), j_s + len(subj) + 1)
t = 0
for j_p, ((name, pow), (name, x)) in enumerate(zip(powers.items(), raw.items())):
if name == '2228. FB':
from scipy.signal import periodogram
fff = plt.figure()
fff.gca().plot(*periodogram(x, fs, nfft=fs * 3), c=cm[name.split()[1]])
plt.xlim(0, 80)
plt.ylim(0, 3e-11)
plt.show()
print(name)
time = np.arange(t, t + len(x)) / fs
color = cm[''.join([i for i in name.split()[1] if not i.isdigit()])]
ax1.plot(time, fft_filter(x, fs, (2, 45)), c=color, alpha=0.4)
ax1.plot(time, alpha[name], c=color)
t += len(x)
ax.plot([j_p], [pow.mean() / norm], 'o', c=color, markersize=10)
ax.errorbar([j_p], [pow.mean() / norm], yerr=pow.std() / norm, c=color, ecolor=color)
fb_x = np.hstack([[j] * len(pows) for j, (key, pows) in enumerate(powers.items()) if 'FB' in key])
fb_y = np.hstack([pows for key, pows in powers.items() if 'FB' in key]) / norm
sns.regplot(x=fb_x, y=fb_y, ax=ax, color=cm['FB'], scatter=False, truncate=True)
ax1.set_xlim(0, t / fs)
ax1.set_ylim(-40, 40)
plt.setp(ax.xaxis.get_majorticklabels(), rotation=70)
ax.set_xticks(range(len(powers)))
ax.set_xticklabels(powers.keys())
ax.set_ylim(0, 3)
ax.set_xlim(-1, len(powers))
ax1.set_title('Day {}'.format(j_s + 1))
return fg
MX_c = MX - MX_m[:, None] U, S, V = numpy.linalg.svd(MX_c, full_matrices=0) #determine value along principal axis UMX = numpy.dot(U, MX_c) #scatterplot, color-coded by principal axis value pylab.scatter(MX[0], MX[1], c=UMX[0], s=9, lw=0) pylab.colorbar() #plot principal axis x = numpy.linspace(min(MX[0]), max(MX[0]), 10) y = MX_m[1] + (x - MX_m[0]) * U[0, 1] / U[0, 0] pylab.plot(x, y, '-k') #set axes limits so x and y scales are equal xlim = pylab.xlim() ylim = pylab.ylim() x0 = numpy.mean(xlim) y0 = numpy.mean(ylim) xr = xlim[1] - xlim[0] yr = ylim[1] - ylim[0] d = 0.5 * max(xr, yr) pylab.xlim(x0 - d, x0 + d) pylab.ylim(y0 - d, y0 + d) pylab.show()
# plot
print("data range: " + str(min) + " - " + str(max))
if options.verbose:
print("Plotting...")
if options.time_coloring:
scatter(xs, ys, color=c, s=1)
else:
plot(xs, ys, ',k')
# set axes
if options.xticks != "":
(xb, xe, xd, xs) = options.xticks.split(",")
xticks(arange(xb, xe, xd), size=xs)
if options.yticks != "":
(yb, ye, yd, ys) = options.yticks.split(",")
yticks(arange(yb, ye, yd), size=ys)
if options.xlim != "":
(xb, xe) = options.xlim.split(",")
xlim(int(xb), int(xe))
else:
xlim(min, max)
if options.ylim != "":
(yb, ye) = options.ylim.split(",")
ylim(int(yb), int(ye))
else:
ylim(min, max)
# show/save
if options.show:
show()
if options.output:
savefig(options.output)
# Plot filters in color with a single spectrum
pl.figure()
pl.plot(Xref[:, 0], Xref[:, 1], '-k', lw=2)
for f, c in zip('ugriz', 'bgrmk'):
X = fetch_filter(f)
pl.fill(X[:, 0], X[:, 1], ec=c, fc=c, alpha=0.4)
kwargs = dict(fontsize=20, ha='center', va='center', alpha=0.5)
pl.text(3500, 0.02, 'u', color='b', **kwargs)
pl.text(4600, 0.02, 'g', color='g', **kwargs)
pl.text(6100, 0.02, 'r', color='r', **kwargs)
pl.text(7500, 0.02, 'i', color='m', **kwargs)
pl.text(8800, 0.02, 'z', color='k', **kwargs)
pl.xlim(3000, 11000)
pl.title('SDSS Filters and Reference Spectrum')
pl.xlabel('Wavelength (Angstroms)')
pl.ylabel('normalized flux / filter transmission')
#----------------------------------------------------------------------
# Plot filters in gray with several redshifted spectra
pl.figure()
redshifts = [0.0, 0.4, 0.8]
colors = 'bgr'
for z, c in zip(redshifts, colors):
pl.plot((1. + z) * Xref[:, 0], Xref[:, 1], color=c)
gnc = evolve(nx, C, tmax, conservative=0, init="rarefaction")
pylab.plot(gc.x, gc.u, color="r", label="conservative")
pylab.plot(gnc.x, gnc.u, color="b", label="non-conservative")
tmax = 0.1
gc = evolve(nx, C, tmax, conservative=1, init="rarefaction")
gnc = evolve(nx, C, tmax, conservative=0, init="rarefaction")
pylab.plot(gc.x, gc.u, color="r", ls="--")
pylab.plot(gnc.x, gnc.u, color="b", ls="--")
pylab.plot(gnc.x, gc.uinit, color="0.5", label="initial conditions")
pylab.xlim(0, 1)
#pylab.legend(loc=3, frameon=False, fontsize="small")
pylab.xlabel("x")
pylab.ylabel("u")
pylab.savefig("burger-rarefaction.png")
#-----------------------------------------------------------------------------
tmax = 0.3
pylab.clf()
gc = evolve(nx, C, tmax, conservative=1, init="shock")
gnc = evolve(nx, C, tmax, conservative=0, init="shock")
def execs_timeit_2vector(exprs, fname=None):
"""
exprs is a list of list of expr to evaluate
The first level of list is put into different graph section in the same graph.
The second level is the expression to put in each section
"""
#exp = [(1,100000),(1e1,100000),(1e2,100000),(1e3,100000), (5e3,50000),
exp = [(1e3,100000),(5e3,50000), \
(1e4,10000),(5e4,5000),(1e5,2000),(1e6,200),(1e7,10)
]
### TO TEST UNCOMMENT THIS LINE
# exp = [(1,1000),(1e1,1000),(1e2,1000),]
times = []
str_expr = []
for g_exprs in exprs:
for expr in g_exprs:
nb_call_scal = 1
if isinstance(expr, tuple):
nb_call_scal = expr[1]
expr = expr[0]
str_expr.append(expr)
time = []
for nb_e, nb_c in exp:
time.append(
timeit_2vector(nb_element=nb_e,
nb_repeat=3,
nb_call=nb_c * nb_call_scal,
expr=expr,
do_amd=False))
times.append(time)
if 'pylab' not in globals():
return
nb_calls = [e[0] for e in exp]
legends = []
colors = ['b', 'r', 'g', 'c', 'm', 'y']
assert len(colors) >= len(times)
fig = pylab.figure()
for idx, (time, expr) in enumerate(zip(times, str_expr)):
###
###
###
# Creating each subplot
###
###
###
###
pylab.subplot(220 + idx + 1)
pylab.subplots_adjust(wspace=0.25, hspace=0.25)
#legend=[]
#plot = fig.add_subplot(1,len(exprs),idx)
speedup = [t["numpy"].min() / t["numexpr"].min() for t in time]
pylab.semilogx(nb_calls, speedup, linewidth=1.0, color='r')
speedup = [t["numpy"].min() / t["theano"].min() for t in time]
pylab.semilogx(nb_calls, speedup, linewidth=1.0, color='b')
pylab.grid(True)
if (idx == 2) or (idx == 3):
pylab.xlabel('Dimension of vectors a and b', fontsize=15)
if (idx == 0) or (idx == 2):
pylab.ylabel('Speed up vs NumPy', fontsize=15)
pylab.axhline(y=1, linewidth=1.0, color='black')
pylab.xlim(1e3, 1e7)
pylab.xticks([1e3, 1e5, 1e7], ['1e3', '1e5', '1e7'])
pylab.title(expr)
if fname:
fig.savefig(fname)
pylab.clf()
else:
pylab.show()
pl.plot(z_after, (100*np.abs((xp_after-xp_before)-(xp[ii+1, :]-xp[0, :]))/np.std(xp[ii+1, :]-xp[0, :])), '.r', markersize = 2)
pl.grid('on')
pl.ylabel('''error($\Delta$x')/$\Delta$x' [%]''')
pl.subplot(2,3,4, sharex=sp1)
pl.plot(z_after, (xp[ii+1, :]-xp[0, :]), '.r', label='HT', markersize = 2)
pl.plot(z_after, (xp_after-xp_before), '.b', label='PyHT', markersize = 2)
ms.sciy()
pl.grid('on')
pl.ylabel("$\Delta$x'")
pl.xlabel('z[m]')
pl.legend(prop = {'size':14})
pl.subplot(2,3,3)
pl.hist((100*np.abs((xp_after-xp_before)-(xp[ii+1, :]-xp[0, :]))/np.std(xp[ii+1, :]-xp[0, :])), bins=100, range=(0,100))
pl.xlabel('Error_x [%]')
pl.ylabel('Occurrences')
pl.xlim(0,100)
rms_err_x = np.std(100*np.abs((xp_after-xp_before)-(xp[ii+1, :]-xp[0, :]))/np.std(xp[ii+1, :]-xp[0, :]))
sp1 = pl.subplot(2,3,2)
pl.plot(z_after, (100*np.abs((yp_after-yp_before)-(yp[ii+1, :]-yp[0, :]))/np.std(yp[ii+1, :]-yp[0, :])), '.r', markersize = 2)
pl.grid('on')
pl.ylabel('''error($\Delta$y')/$\Delta$y' [%]''')
pl.subplot(2,3,5, sharex=sp1)
pl.plot(z_after, (yp[ii+1, :]-yp[0, :]), '.r', label='HT', markersize = 2)
pl.plot(z_after, (yp_after-yp_before), '.b', label='PyHT', markersize = 2)
ms.sciy()
pl.grid('on')
pl.ylabel("$\Delta$y'")
pl.xlabel('z[m]')
pl.legend(prop = {'size':14})
pl.subplot(2,3,6)
