def plot_tracks(src, fakewcs, spa=None, **kwargs):
# NOTE -- MAGIC 61 = monthly; this is ASSUMEd below.
tt = np.linspace(2010., 2015., 61)
t0 = TAITime(None, mjd=TAITime.mjd2k + 365.25*10)
#rd0 = src.getPositionAtTime(t0)
#print 'rd0:', rd0
xx,yy = [],[]
rr,dd = [],[]
for t in tt:
#print 'Time', t
rd = src.getPositionAtTime(t0 + (t - 2010.)*365.25*24.*3600.)
ra,dec = rd.ra, rd.dec
rr.append(ra)
dd.append(dec)
ok,x,y = fakewcs.radec2pixelxy(ra,dec)
xx.append(x - 1.)
yy.append(y - 1.)
if spa is None:
spa = [None,None,None]
for rows,cols,sub in spa:
if sub is not None:
plt.subplot(rows,cols,sub)
ax = plt.axis()
plt.plot(xx, yy, 'k-', **kwargs)
plt.axis(ax)
return rr,dd,tt
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 test1():
import numpy as np
import pylab
from scipy import sparse
from regreg.algorithms import FISTA
from regreg.atoms import l1norm
from regreg.container import container
from regreg.smooth import quadratic
Y = np.random.standard_normal(500); Y[100:150] += 7; Y[250:300] += 14
sparsity = l1norm(500, lagrange=1.0)
#Create D
D = (np.identity(500) + np.diag([-1]*499,k=1))[:-1]
D = sparse.csr_matrix(D)
fused = l1norm.linear(D, lagrange=19.5)
loss = quadratic.shift(-Y, lagrange=0.5)
p = container(loss, sparsity, fused)
soln1 = blockwise([sparsity, fused], Y)
solver = FISTA(p)
solver.fit(max_its=800,tol=1e-10)
soln2 = solver.composite.coefs
#plot solution
pylab.figure(num=1)
pylab.clf()
pylab.scatter(np.arange(Y.shape[0]), Y, c='r')
pylab.plot(soln1, c='y', linewidth=6)
pylab.plot(soln2, c='b', linewidth=2)
def simulationWithoutDrugNick(numViruses, maxPop, maxBirthProb, clearProb,
numTrials):
"""
Run the simulation and plot the graph for problem 3 (no drugs are used,
viruses do not have any drug resistance).
For each of numTrials trial, instantiates a patient, runs a simulation
for 300 timesteps, and plots the average virus population size as a
function of time.
numViruses: number of SimpleVirus to create for patient (an integer)
maxPop: maximum virus population for patient (an integer)
maxBirthProb: Maximum reproduction probability (a float between 0-1)
clearProb: Maximum clearance probability (a float between 0-1)
numTrials: number of simulation runs to execute (an integer)
"""
#Instantiate the viruses first, the patient second
viruses= [ SimpleVirus(maxBirthProb, clearProb) for i in range(numViruses) ]
patient = Patient(viruses, maxPop)
#Execute the patient.update method 300 times for 100 trials
steps = 300
countList = [0 for i in range(300)]
for trial in range(numTrials):
for timeStep in range(steps):
countList[timeStep] += patient.update()
avgList = [ countList[i]/float(numTrials) for i in range(steps) ]
#Plot a diagram with xAxis=timeSteps, yAxis=average virus population
xAxis = [ x for x in range(steps) ]
pylab.figure(2)
pylab.plot(xAxis, avgList, 'ro', label='Simple Virus')
pylab.xlabel('Number of elapsed time steps')
pylab.ylabel('Average size of the virus population')
pylab.title('Virus growth in a patient without the aid of any drag')
pylab.legend()
pylab.show()
def testTelescope(self):
import matplotlib
matplotlib.use('AGG')
import matplotlib.mlab as ml
import pylab as pl
import time
w0 = 8.0
k = 2*np.pi/3.0
gb = GaussianBeam(w0, k)
lens = ThinLens(150, 150)
gb2 = lens*gb
self.assertAlmostEqual(gb2._z0, gb._z0 + 2*150.0)
lens2 = ThinLens(300, 600)
gb3 = lens2*gb2
self.assertAlmostEqual(gb3._z0, gb2._z0 + 2*300.0)
self.assertAlmostEqual(gb._w0, gb3._w0/2.0)
z = np.arange(0, 150)
z2 = np.arange(150, 600)
z3 = np.arange(600, 900)
pl.plot(z, gb.w(z, k), z2, gb2.w(z2, k), z3, gb3.w(z3, k))
pl.grid()
pl.xlabel('z')
pl.ylabel('w')
pl.savefig('testTelescope1.png')
time.sleep(0.1)
pl.close('all')
def plot_xc(t_years):
"""Plot the location of the calving front."""
x = x_c(t_years * secpera) / 1000.0 # convert to km
_, _, y_min, y_max = axis()
hold(True)
plot([x, x], [y_min, y_max], '--g')
def plotLists(xList, xLabel=None, eListTitle=None, eList=None, eLabel=None, fListTitle=None, fList=None, fLabel=None):
if h2o.python_username!='kevin':
return
import pylab as plt
print "xList", xList
print "eList", eList
print "fList", fList
font = {'family' : 'normal',
'weight' : 'normal',
'size' : 26}
### plt.rc('font', **font)
plt.rcdefaults()
if eList:
if eListTitle:
plt.title(eListTitle)
plt.figure()
plt.plot (xList, eList)
plt.xlabel(xLabel)
plt.ylabel(eLabel)
plt.draw()
if fList:
if fListTitle:
plt.title(fListTitle)
plt.figure()
plt.plot (xList, fList)
plt.xlabel(xLabel)
plt.ylabel(fLabel)
plt.draw()
if eList or fList:
plt.show()
def check_vpd_ks2_astrometry():
"""
Check the VPD and quiver plots for our KS2-extracted, re-transformed astrometry.
"""
catFile = workDir + '20.KS2_PMA/wd1_catalog.fits'
tab = atpy.Table(catFile)
good = (tab.xe_160 < 0.05) & (tab.ye_160 < 0.05) & \
(tab.xe_814 < 0.05) & (tab.ye_814 < 0.05) & \
(tab.me_814 < 0.05) & (tab.me_160 < 0.05)
tab2 = tab.where(good)
dx = (tab2.x_160 - tab2.x_814) * ast.scale['WFC'] * 1e3
dy = (tab2.y_160 - tab2.y_814) * ast.scale['WFC'] * 1e3
py.clf()
q = py.quiver(tab2.x_814, tab2.y_814, dx, dy, scale=5e2)
py.quiverkey(q, 0.95, 0.85, 5, '5 mas', color='red', labelcolor='red')
py.savefig(workDir + '20.KS2_PMA/vec_diffs_ks2_all.png')
py.clf()
py.plot(dy, dx, 'k.', ms=2)
lim = 30
py.axis([-lim, lim, -lim, lim])
py.xlabel('Y Proper Motion (mas)')
py.ylabel('X Proper Motion (mas)')
py.savefig(workDir + '20.KS2_PMA/vpd_ks2_all.png')
idx = np.where((np.abs(dx) < 10) & (np.abs(dy) < 10))[0]
print('Cluster Members (within dx < 10 mas and dy < 10 mas)')
print((' dx = {dx:6.2f} +/- {dxe:6.2f} mas'.format(dx=dx[idx].mean(),
dxe=dx[idx].std())))
print((' dy = {dy:6.2f} +/- {dye:6.2f} mas'.format(dy=dy[idx].mean(),
dye=dy[idx].std())))
def plot_stress(self, block_ids=None, fignum=0):
block_ids = self.check_block_ids_list(block_ids)
#
plt.figure(fignum)
ax1=plt.gca()
plt.clf()
plt.figure(fignum)
plt.clf()
ax0=plt.gca()
#
for block_id in block_ids:
rws = numpy.core.records.fromarrays(zip(*filter(lambda x: x['block_id']==block_id, self.shear_stress_sequences)), dtype=self.shear_stress_sequences.dtype)
stress_seq = []
for rw in rws:
stress_seq += [[rw['sweep_number'], rw['shear_init']]]
stress_seq += [[rw['sweep_number'], rw['shear_final']]]
X,Y = zip(*stress_seq)
#
ax0.plot(X,Y, '.-', label='block_id: %d' % block_id)
#
plt.figure(fignum+1)
plt.plot(rws['sweep_number'], rws['shear_init'], '.-', label='block_id: %d' % block_id)
plt.plot(rws['sweep_number'], rws['shear_final'], '.-', label='block_id: %d' % block_id)
plt.figure(fignum)
ax0.plot([min(self.shear_stress_sequences['sweep_number']), max(self.shear_stress_sequences['sweep_number'])], [0., 0.], 'k-')
ax0.legend(loc=0, numpoints=1)
plt.figure(fignum)
plt.title('Block shear_stress sequences')
plt.xlabel('sweep number')
plt.ylabel('shear stress')
def plotKerasExperimentcifar10():
index = 5
for experiment_number in range(1,index+1):
outputPath_part_final = os.path.realpath( "/home/jie/docker_folder/random_keras/output_cifar10_mlp/errorFile/hyperopt_experiment_withoutparam_accuracy" + str(experiment_number) + ".txt")
output_plot = os.path.realpath(
"/home/jie/docker_folder/random_keras/output_cifar10_mlp/errorFile/plotErrorCurve" + str(experiment_number) + ".pdf")
df = pd.read_csv(outputPath_part_final,delimiter='\t',header=None)
df.drop(df.columns[[600]], axis=1, inplace=True)
i=1
epochnum = []
while i<=250:
epochnum.append(i)
i = i+1
i=0
while i<10:
df_1=df[df.columns[0:250]].ix[i]
np.reshape(df_1, (1,250))
plt.plot(epochnum,df_1)
i = i+1
# plt.show()
# plt.show()
plt.savefig(output_plot)
plt.close()
def plot_data(x,y,Amp,freq):
"""
Plot the actual data point x,y along with the fit Amp*sin(freq*x)
"""
plb.plot(x,y,'b',linestyle=':')
y_fit = Amp*np.sin(freq*x)
plb.plot(x,y_fit,'r')
def createPlot(dataY, dataX, ticksX, annotations, axisY, axisX, dostep, doannotate):
if not ticksX:
ticksX = dataX
if dostep:
py.step(dataX, dataY, where='post', linestyle='-', label=axisY) # where=post steps after point
else:
py.plot(dataX, dataY, marker='o', ms=5.0, linestyle='-', label=axisY)
if annotations and doannotate:
for note, x, y in zip(annotations, dataX, dataY):
py.annotate(note, (x, y), xytext=(2,2), xycoords='data', textcoords='offset points')
py.xticks(np.arange(1, len(dataX)+1), ticksX, horizontalalignment='left', rotation=30)
leg = py.legend()
leg.draggable()
py.xlabel(axisX)
py.ylabel('time (s)')
# Set X axis tick labels as rungs
#print zip(dataX, dataY)
py.draw()
py.show()
return
def drawPrfastscore(tp,fp,scr,tot,show=True):
tp=numpy.cumsum(tp)
fp=numpy.cumsum(fp)
rec=tp/tot
prec=tp/(fp+tp)
#dif=numpy.abs(prec[1:]-rec[1:])
dif=numpy.abs(prec[::-1]-rec[::-1])
pos=dif.argmin()
pos=len(dif)-pos-1
ap=0
for t in numpy.linspace(0,1,11):
pr=prec[rec>=t]
if pr.size==0:
pr=0
p=numpy.max(pr);
ap=ap+p/11;
if show:
pylab.plot(rec,prec,'-g')
pylab.title("AP=%.3f EPRthr=%.3f"%(ap,scr[pos]))
pylab.xlabel("Recall")
pylab.ylabel("Precision")
pylab.grid()
pylab.show()
pylab.draw()
return rec,prec,scr,ap,scr[pos]
def drawPr(tp,fp,tot,show=True):
"""
draw the precision recall curve
"""
det=numpy.array(sorted(tp+fp))
atp=numpy.array(tp)
afp=numpy.array(fp)
#pylab.figure()
#pylab.clf()
rc=numpy.zeros(len(det))
pr=numpy.zeros(len(det))
#prc=0
#ppr=1
for i,p in enumerate(det):
pr[i]=float(numpy.sum(atp>=p))/numpy.sum(det>=p)
rc[i]=float(numpy.sum(atp>=p))/tot
#print pr,rc,p
ap=0
for c in numpy.linspace(0,1,num=11):
if len(pr[rc>=c])>0:
p=numpy.max(pr[rc>=c])
else:
p=0
ap=ap+p/11
if show:
pylab.plot(rc,pr,'-g')
pylab.title("AP=%.3f"%(ap))
pylab.xlabel("Recall")
pylab.ylabel("Precision")
pylab.grid()
pylab.show()
pylab.draw()
return rc,pr,ap
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 yfromx(self, newtimeaxis, doplot=False, debug=False):
if debug:
print('fastresampler: yfromx called with following parameters')
print(' padvalue:, ', self.padvalue)
print(' initstep, hiresstep:', self.initstep, self.hiresstep)
print(' initial axis limits:', self.initstart, self.initend)
print(' hires axis limits:', self.hiresstart, self.hiresend)
print(' requested axis limits:', newtimeaxis[0], newtimeaxis[-1])
outindices = ((newtimeaxis - self.hiresstart) // self.hiresstep).astype(int)
if debug:
print('len(self.hires_y):', len(self.hires_y))
try:
out_y = self.hires_y[outindices]
except IndexError:
print('')
print('indexing out of bounds in fastresampler')
print(' padvalue:, ', self.padvalue)
print(' initstep, hiresstep:', self.initstep, self.hiresstep)
print(' initial axis limits:', self.initstart, self.initend)
print(' hires axis limits:', self.hiresstart, self.hiresend)
print(' requested axis limits:', newtimeaxis[0], newtimeaxis[-1])
sys.exit()
if doplot:
fig = pl.figure()
ax = fig.add_subplot(111)
ax.set_title('fastresampler timecourses')
pl.plot(self.hires_x, self.hires_y, newtimeaxis, out_y)
pl.legend(('hires', 'output'))
pl.show()
return out_y
def qinit(x,y):
"""
Gaussian hump:
"""
from numpy import where
from pylab import plot,show
nxpoints = 2001
nypoints = 2001
#import sympy
#def sech(x):
#return sympy.cosh(x)**(-1)
zmin = 1000.0
zmin1 = 1000
g = 9.81
A = 10.0 # wave height
k = sqrt(3*A/(4*zmin**3))
z = zeros(shape=shape(y))
u = zeros(shape=shape(y))
hu = zeros(shape=shape(y))
y0 = 180000
c = sqrt(g*(A+zmin))
rho = 1.0e3
for i in range(nxpoints):
for j in range(nypoints):
z[i,j] = A*cosh(k*(y[i,j]-y0))**(-2)
u[i,j] = -sqrt(g/zmin)*z[i,j]
hu[i,j] =(z[i,j]+zmin)*u[i,j]
plot(y,u,'-')
show()
#ze = -((y+0e0)**2)/10.
#z = where(ze>-400000., 400.e0*exp(ze), 0.)
return hu
def plotEventTime(library, num, eventNames, sizes, times, events, filename = None):
from pylab import close, legend, plot, savefig, show, title, xlabel, ylabel
import numpy as np
close()
arches = sizes.keys()
bs = events[arches[0]].keys()[0]
data = []
names = []
for event, color in zip(eventNames, ['b', 'g', 'r', 'y']):
for arch, style in zip(arches, ['-', ':']):
if event in events[arch][bs]:
names.append(arch+'-'+str(bs)+' '+event)
data.append(sizes[arch][bs])
data.append(np.array(events[arch][bs][event])[:,0])
data.append(color+style)
else:
print 'Could not find %s in %s-%d events' % (event, arch, bs)
print data
plot(*data)
title('Performance on '+library+' Example '+str(num))
xlabel('Number of Dof')
ylabel('Time (s)')
legend(names, 'upper left', shadow = True)
if filename is None:
show()
else:
savefig(filename)
return
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 run( self , props , globdat ):
a = []
for i,col in enumerate(self.columndata):
if col.type in globdat.outputNames:
data = globdat.getData( col.type , col.node )
elif hasattr(globdat,col.type):
b = getattr( globdat , col.type )
if type(b) is ndarray:
data = b[globdat.dofs.getForType(col.node,col.dof)]
else:
data = b
else:
data = globdat.getData( col.type , col.node )
data = data * col.factor
a.append(data)
self.outfile.write(str(data)+' ',)
self.outfile.write('\n')
if self.onScreen:
self.output.append( a )
plot( [x[0] for x in self.output], [x[1] for x in self.output], 'ro-' )
draw()
if not globdat.active:
self.outfile.close
def cmap_plot(cmdLine):
pylab.figure(figsize=[5,10])
a=outer(ones(10),arange(0,1,0.01))
subplots_adjust(top=0.99,bottom=0.00,left=0.01,right=0.8)
maps=[m for m in cm.datad if not m.endswith("_r")]
maps.sort()
l=len(maps)+1
for i, m in enumerate(maps):
print m
subplot(l,1,i+1)
pylab.setp(pylab.gca(),xticklabels=[],xticks=[],yticklabels=[],yticks=[])
imshow(a,aspect='auto',cmap=get_cmap(m),origin="lower")
pylab.text(100.85,0.5,m,fontsize=10)
# render plot
if cmdLine:
pylab.show(block=True)
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
status = 1
return status
def create_figure():
psd = test_correlog()
f = linspace(-0.5, 0.5, len(psd))
psd = cshift(psd, len(psd)/2)
plot(f, 10*log10(psd/max(psd)))
savefig('psd_corr.png')
def plot(self):
"""Plot the scores"""
from pylab import plot
plot(self.xdata, self.ydata)
xlabel("Number of computeScore calls")
ylabel("Score")
ylim([0, ylim()[1]])
def plot_cost(self):
if self.show_cost not in self.train_outputs[0][0]:
raise ShowNetError("Cost function with name '%s' not defined by given convnet." % self.show_cost)
train_errors = [o[0][self.show_cost][self.cost_idx] for o in self.train_outputs]
test_errors = [o[0][self.show_cost][self.cost_idx] for o in self.test_outputs]
numbatches = len(self.train_batch_range)
test_errors = numpy.row_stack(test_errors)
test_errors = numpy.tile(test_errors, (1, self.testing_freq))
test_errors = list(test_errors.flatten())
test_errors += [test_errors[-1]] * max(0,len(train_errors) - len(test_errors))
test_errors = test_errors[:len(train_errors)]
numepochs = len(train_errors) / float(numbatches)
pl.figure(1)
x = range(0, len(train_errors))
pl.plot(x, train_errors, 'k-', label='Training set')
pl.plot(x, test_errors, 'r-', label='Test set')
pl.legend()
ticklocs = range(numbatches, len(train_errors) - len(train_errors) % numbatches + 1, numbatches)
epoch_label_gran = int(ceil(numepochs / 20.)) # aim for about 20 labels
epoch_label_gran = int(ceil(float(epoch_label_gran) / 10) * 10) # but round to nearest 10
ticklabels = map(lambda x: str((x[1] / numbatches)) if x[0] % epoch_label_gran == epoch_label_gran-1 else '', enumerate(ticklocs))
pl.xticks(ticklocs, ticklabels)
pl.xlabel('Epoch')
# pl.ylabel(self.show_cost)
pl.title(self.show_cost)
def plot_matches(self, name, show_below = True, match_maximum = None):
""" 対応点を線で結んで画像を表示する
入力： im1,im2（配列形式の画像）、locs1,locs2（特徴点座標）
machescores（match()の出力）、
show_below（対応の下に画像を表示するならTrue）"""
im1 = self._image_1.get_array_image()
im2 = self._image_2.get_array_image()
self.appendimages()
im3 = self._append_image
if self._match_score is None:
self.match()
locs1 = self._image_1.get_shift_location()
locs2 = self._image_2.get_shift_location()
if show_below:
im3 = numpy.vstack((im3,im3))
pylab.figure(dpi=160)
pylab.gray()
pylab.imshow(im3, aspect = 'auto')
cols1 = im1.shape[1]
match_num = 0
for i,m in enumerate(self._match_score):
if m > 0 :
pylab.plot([locs1[i][0],locs2[m][0]+cols1], [locs1[i][1],locs2[m][1]], 'c')
match_num = match_num + 1
if match_maximum is not None and match_num >= match_maximum:
break
pylab.axis('off')
pylab.savefig(name, dpi=160)
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_heatingrate(data_dict, filename, do_show=True):
pl.figure(201)
color_list = ['b','r','g','k','y','r','g','b','k','y','r',]
fmtlist = ['s','d','o','s','d','o','s','d','o','s','d','o']
result_dict = {}
for key in data_dict.keys():
x = data_dict[key][0]
y = data_dict[key][1][:,0]
y_err = data_dict[key][1][:,1]
p0 = np.polyfit(x,y,1)
fit = LinFit(np.array([x,y,y_err]).transpose(), show_graph=False)
p1 = [0,0]
p1[0] = fit.param_dict[0]['Slope'][0]
p1[1] = fit.param_dict[0]['Offset'][0]
print fit
x0 = np.linspace(0,max(x))
cstr = color_list.pop(0)
fstr = fmtlist.pop(0)
lstr = key + " heating: {0:.2f} ph/ms".format((p1[0]*1e3))
pl.errorbar(x/1e3,y,y_err,fmt=fstr + cstr,label=lstr)
pl.plot(x0/1e3,np.polyval(p0,x0),cstr)
pl.plot(x0/1e3,np.polyval(p1,x0),cstr)
result_dict[key] = 1e3*np.array(fit.param_dict[0]['Slope'])
pl.xlabel('Heating time (ms)')
pl.ylabel('nbar')
if do_show:
pl.legend()
pl.show()
if filename != None:
pl.savefig(filename)
return result_dict
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 Doplots_monthly(mypathforResults,PlottingDF,variable_to_fill, Site_ID,units,item):
ANN_label=str(item+"_NN") #Do Monthly Plots
print "Doing MOnthly plot"
#t = arange(1, 54, 1)
NN_label='Fc'
Plottemp = PlottingDF[[NN_label,item]][PlottingDF['day_night']!=1]
#Plottemp = PlottingDF[[NN_label,item]].dropna(how='any')
figure(1)
pl.title('Nightime ANN v Tower by year-month for '+item+' at '+Site_ID)
try:
xdata1a=Plottemp[item].groupby([lambda x: x.year,lambda x: x.month]).mean()
plotxdata1a=True
except:
plotxdata1a=False
try:
xdata1b=Plottemp[NN_label].groupby([lambda x: x.year,lambda x: x.month]).mean()
plotxdata1b=True
except:
plotxdata1b=False
if plotxdata1a==True:
pl.plot(xdata1a,'r',label=item)
if plotxdata1b==True:
pl.plot(xdata1b,'b',label=NN_label)
pl.ylabel('Flux')
pl.xlabel('Year - Month')
pl.legend()
pl.savefig(mypathforResults+'/ANN and Tower plots by year and month for variable '+item+' at '+Site_ID)
#pl.show()
pl.close()
time.sleep(1)
----------------------------------------------'''
# ->> lower data resolution <<- #
#zoom_factor=0.5
zoom_factor=1 #0.5
#n_pts=500
n_pts=50
ncol=10
#_dmap_=d[:100,10]-np.mean(d[:100,10])
_dmap_=d[:n_pts,ncol]-np.mean(d[:n_pts,ncol])
dmap=sp.ndimage.interpolation.zoom(_dmap_, zoom_factor)
if False:
dk=np.fft.fft(dmap)
pk=np.abs(np.fft.fftshift(dk))**2.
pl.plot(pk)
pl.show()
#->> data initialization <<- #
qe_dict={'calculate_dcov': True,
'fname_dcov': root+'result/r1d/dcov_r1d_fft_24.npz',
'map_zoom_factor': zoom_factor,
'get_bp_type': 'FFT',
}
''' #->> Initialzing quadratic estimator class <<- #
#->> parafname='same as parameter file'
#->> calculating dcov
'''
def process_surface_adjoint(config_filename,
filter_type='LAPLACE',
marker_name='airfoil',
chord_length=1.0):
print('')
print(
'-------------------------------------------------------------------------'
)
print(
'| SU2 Suite (Process Surface Adjoint) |'
)
print(
'-------------------------------------------------------------------------'
)
print('')
# some other defaults
c_clip = 0.01 # percent chord to truncate
fft_copy = 5 # number of times to copy the fft signal
smth_len = 0.05 # percent chord smoothing window length
lapl_len = 1e-4 # laplace smoothing parameter
# read config file
config_data = libSU2.Get_ConfigParams(config_filename)
surface_filename = config_data['SURFACE_ADJ_FILENAME'] + '.csv'
print surface_filename
mesh_filename = config_data['MESH_FILENAME']
gradient = config_data['OBJECTIVE_FUNCTION']
print('Config filename = %s' % config_filename)
print('Surface filename = %s' % surface_filename)
print('Filter Type = %s' % filter_type)
# read adjoint data
adj_data = np.genfromtxt(surface_filename,
dtype=float,
delimiter=',',
skip_header=1)
# read mesh data
mesh_data = libSU2_mesh.Read_Mesh(mesh_filename)
# proces adjoint data
P = map(int, adj_data[:, 0])
X = adj_data[:, 6].copy()
Y = adj_data[:, 7].copy()
Sens = adj_data[:, 1].copy()
PsiRho = adj_data[:, 2].copy()
I = range(0, len(P)) # important - for unsorting durring write
# store in dict by point index
adj_data_dict = dict(zip(P, zip(X, Y, Sens, PsiRho, I)))
# sort airfoil points
iP_sorted, _ = libSU2_mesh.sort_Airfoil(mesh_data, marker_name)
assert (len(iP_sorted) == len(P))
# rebuild airfoil loop
i = 0
for this_P in iP_sorted:
# the adjoint data entry
this_adj_data = adj_data_dict[this_P]
# re-sort
P[i] = this_P
X[i] = this_adj_data[0]
Y[i] = this_adj_data[1]
Sens[i] = this_adj_data[2]
PsiRho[i] = this_adj_data[3]
I[i] = this_adj_data[4]
# next
i = i + 1
#: for each point
# calculate arc length
S = np.sqrt(np.diff(X)**2 + np.diff(Y)**2) / chord_length
S = np.cumsum(np.hstack([0, S]))
# tail trucating, by arc length
I_clip_lo = S < S[0] + c_clip
I_clip_hi = S > S[-1] - c_clip
S_clip = S.copy()
Sens_clip = Sens.copy()
Sens_clip[I_clip_hi] = Sens_clip[I_clip_hi][0]
Sens_clip[I_clip_lo] = Sens_clip[I_clip_lo][-1]
# some edge length statistics
dS_clip = np.diff(S_clip)
min_dS = np.min(dS_clip)
mean_dS = np.mean(dS_clip)
max_dS = np.max(dS_clip)
#print 'min_dS = %.4e ; mean_dS = %.4e ; max_dS = %.4e' % ( min_dS , mean_dS , max_dS )
# --------------------------------------------
# APPLY FILTER
if filter_type == 'FOURIER':
Freq_notch = [1 / max_dS, np.inf] # the notch frequencies
Sens_filter, Frequency, Power = fft_filter(S_clip, Sens_clip,
Freq_notch, fft_copy)
#Sens_filter = smooth(S_clip,Sens_filter, 0.03,'blackman') # post smoothing
elif filter_type == 'WINDOW':
Sens_filter = window(S_clip, Sens_clip, smth_len, 'blackman')
elif filter_type == 'LAPLACE':
Sens_filter = laplace(S_clip, Sens_clip, lapl_len)
elif filter_type == 'SHARPEN':
Sens_smooth = smooth(S_clip, Sens_clip, smth_len / 5,
'blackman') # pre smoothing
Sens_smoother = smooth(S_clip, Sens_smooth, smth_len, 'blackman')
Sens_filter = Sens_smooth + (Sens_smooth - Sens_smoother) # sharpener
else:
raise Exception, 'unknown filter type'
# --------------------------------------------
# PLOTTING
if pylab_imported:
# start plot
fig = plt.figure(gradient)
plt.clf()
#if not fig.axes: # for comparing two filter calls
#plt.subplot(1,1,1)
#ax = fig.axes[0]
#if len(ax.lines) == 4:
#ax.lines.pop(0)
#ax.lines.pop(0)
# SENSITIVITY
plt.plot(S, Sens, color='b') # original
plt.plot(S_clip, Sens_filter, color='r') # filtered
plt.xlim(-0.1, 2.1)
plt.ylim(-5, 5)
plt.xlabel('Arc Length')
plt.ylabel('Surface Sensitivity')
#if len(ax.lines) == 4:
#seq = [2, 2, 7, 2]
#ax.lines[0].set_dashes(seq)
#ax.lines[1].set_dashes(seq)
plot_filename = os.path.splitext(surface_filename)[0] + '.png'
plt.savefig('Sens_' + plot_filename, dpi=300)
# zoom in
plt.ylim(-0.4, 0.4)
plt.savefig('Sens_zoom_' + plot_filename, dpi=300)
# SPECTRAL
if filter_type == 'FOURIER':
plt.figure('SPECTRAL')
plt.clf()
plt.plot(Frequency, Power)
#plt.xlim(0,Freq_notch[0]+10)
plt.xlim(0, 200)
plt.ylim(0, 0.15)
plt.xlabel('Frequency (1/C)')
plt.ylabel('Surface Sensitivity Spectal Power')
plt.savefig('Spectral_' + plot_filename, dpi=300)
#: if spectral plot
#: if plot
# --------------------------------------------
# SAVE SURFACE FILE
# reorder back to input surface points
Sens_out = np.zeros(len(S))
Sens_out[I] = Sens_filter # left over from sort
adj_data[:, 1] = Sens_out
# get surface header
surface_orig = open(surface_filename, 'r')
header = surface_orig.readline()
surface_orig.close()
# get list of prefix names
prefix_names = libSU2.get_AdjointPrefix(None)
prefix_names = prefix_names.values()
# add filter prefix, before adjoint prefix
surface_filename_split = surface_filename.rstrip('.csv').split('_')
if surface_filename_split[-1] in prefix_names:
surface_filename_split = surface_filename_split[0:-1] + [
'filtered'
] + [surface_filename_split[-1]]
else:
surface_filename_split = surface_filename_split + ['filtered']
surface_filename_new = '_'.join(surface_filename_split) + '.csv'
# write filtered surface file (only updates Sensitivity)
surface_new = open(surface_filename_new, 'w')
surface_new.write(header)
for row in adj_data:
for i, value in enumerate(row):
if i > 0:
surface_new.write(', ')
if i == 0:
surface_new.write('%i' % value)
else:
surface_new.write('%.16e' % value)
surface_new.write('\n')
surface_new.close()
print('')
print(
'----------------- Exit Success (Process Surface Adjoint) ----------------'
)
print('')
return
INPUT = (S0, I0, R0)
def diff_eqs(INP, t):
'''The main set of equations'''
Y = np.zeros((3))
V = INP
Y[0] = -a* V[0]*V[1]+e*V[1]*V[2]-d*V[0]
Y[1] = a* V[0]*V[1]-b*V[1]+c*V[1]*V[2]
Y[2] = b*V[1]+d*V[0]-c*V[1]*V[2]
return Y # For odeint
t_start = 0.0;t_end = ND;t_inc = TS
t_range = np.arange(t_start, t_end + t_inc, t_inc)
RES = spi.odeint(diff_eqs, INPUT, t_range)
print
RES
# Ploting
pl.subplot(111)
pl.plot(RES[:, 1], '-r', label='Infectious')
pl.plot(RES[:, 0], '-g', label='Susceptibles')
pl.plot(RES[:, 2], '-k', label='Recovereds')
pl.legend(loc=0)
pl.title('dy_SIR.py')
pl.xlabel('Time')
pl.ylabel('Infectious Susceptibles and Recovereds')
pl.xlabel('Time')
pl.show()
print "Deldatashape", Deldata.shape
#import IPython; IPython.embed()
#print "shapes of arrays:", data1.shape, data2.shape
#Bootstrap resampling
B = 100
bootmean, booterr = boot_simple.bootstrap(B, Deldata)
#print bootmean
#plotting
fig = p.figure()
ax = fig.add_subplot(411)
#plotp.P_v_Eta(ax,kz,P)
ax.set_xlabel('kz')
ax.set_ylabel(r'$P(k) K^{2} (h^{-1} Mpc)^{3}$')
p.plot(kz, P, 'bo')
p.plot(kz, Q, 'go')
p.plot(kz, (10 * 2 * n.pi**2) / n.abs(kz)**3, 'ro') #input
ax.set_yscale('log')
ax = fig.add_subplot(412)
#ax.errorbar(kz, n.abs(bootmean), yerr=booterr, fmt='ok', ecolor='gray', alpha=0.5)
ax.errorbar(k,
n.abs(bootmean),
yerr=booterr,
fmt='ok',
ecolor='gray',
alpha=0.5)
#ax.set_ylim([0,0.5])
#ax.set_yscale('log')
ax.set_xlabel('kz')
ax.set_ylabel(r'$P(k) K^{2} (h^{-1} Mpc)^{3}$')
# define a font properties using dict
font = {'family' : 'serif',
'color' : 'red',
'weight' : 'normal',
'size' : 11
}
# importing data from a file
data = genfromtxt('data_plot.txt')
# separating data [raw : column]
mass = data[:, 0]
radius = data[:, 1]
print(mass)
# plot data
plot(mass, radius, 'r', label=r'data plot')
# add title and axis's label
plt.title(r'Contoh Relasi Masa dan Radius Bintang', fontdict=font)
plt.xlabel(r'$M {\odot}$', fontdict=font)
plt.ylabel(r'$M {\odot}$', fontdict=font)
plt.legend(loc='upper right') # add a legend
plt.grid(True) # start to grid a plot
# Tweak spacing to prevent clipping of ylabel
plt.subplots_adjust(left=0.10)
plt.show()
if __name__ == "__main__":
import pylab as pl
a = np.random.power(0.01, size=1000)
N_bin = 9
bins = to_constant_bin_number(a, N_bin)
weight_sums = [np.sum(b) for b in bins]
#show max values of a and weight sums of the bins
print(np.sort(a)[-1:-11:-1], weight_sums)
#plot distribution
pl.plot(np.arange(N_bin), [np.sum(b) for b in bins])
pl.ylim([0, max([np.sum(b) for b in bins]) + 0.1])
b = {'a': 10, 'b': 10, 'c': 11, 'd': 1, 'e': 2, 'f': 7}
bins = to_constant_bin_number(b, 4)
print("===== dict\n", b, "\n", bins)
lower_bound = None
upper_bound = None
b = (('a', 10), ('b', 10), ('c', 11), ('d', 1), ('e', 2), ('f', 7))
bins = to_constant_bin_number(b,
4,
weight_pos=1,
lower_bound=lower_bound,
upper_bound=upper_bound)
c = connection(pre, post, [1, 1])
sim = simulation(2, dt=0.0001)
sim.monitor(post, [
'u',
], 0.001)
run_sim(sim, [pre, post], [c])
figure(figsize=(15, 5))
m = sim.monitors['u']
m.plot()
for t, n in pre.saved_spikes:
plot([t, t], [0, 0.1], 'g', linewidth=3)
# In[7]:
pre.saved_spikes
# In[8]:
pre = neurons.poisson_pattern([10])
post = neurons.srm0(1)
post.smoothed = True
post.tau = 0.1
post.a = 10
post2 = neurons.srm0(1)
print("Delta: ", deltaMax, " isConverged: ", isConverged,
" isPolicyStable: ", isPolicyStable)
if (isPolicyStable):
print("Stable policy achieved!")
pl.figure()
for e in visualizationSweeps:
if e < len(agent.valueTables):
printMatrix_pol = np.zeros(env.nStates - 2, dtype=np.int)
printMatrix_val = np.zeros(env.nStates - 2, dtype=np.float)
for i in range(env.nStates - 2):
action = agent.selectAction(i + 1, env.getAvailableActions())
printMatrix_val[i] = agent.valueTables[e - 1][i]
printMatrix_pol[i] = action
pl.plot(printMatrix_val, label="Sweep " + str(e))
pl.xlabel("Capital")
pl.ylabel("Value estimates")
pl.title("p=" + str(prob_heads))
pl.legend()
printMatrix_pol = np.zeros(env.nStates - 2, dtype=np.int)
printMatrix_val = np.zeros(env.nStates - 2, dtype=np.float)
for i in range(env.nStates - 2):
action = agent.selectAction(i + 1, env.getAvailableActions())
printMatrix_val[i] = agent.valueTable[i]
printMatrix_pol[i] = action
print("Final value estimates and policy")
print(printMatrix_val)
print()
print(printMatrix_pol)
zbeg = int(zoomints[l][0] / dx)
zend = int(zoomints[l][1] / dx)
xt = x[xbeg:zbeg:igap] + x[zbeg:zend:zoomgap[l]] + x[
zend:xend:igap]
ht = h[xbeg:zbeg:igap] + h[zbeg:zend:zoomgap[l]] + h[
zend:xend:igap]
else:
xbeg = int(cxlim[0] / dx)
xend = int(cxlim[1] / dx)
xt = x[xbeg:xend:igap]
ht = h[xbeg:xend:igap]
x = array(xt)
h = array(ht)
s = str(wdirords[k])
plot(x, h, label=s)
ylim(cylim)
xlim(cxlim)
xlabel("$x$ ($m$)")
ylabel("$h$ ($m$)")
#legend()
gap = gap * gapf[l]
"""
plot(x,u ,'-b')
ylim([-0.1,2])
xlim([0,1000])
s = "Dam Break: " + wdirord + " dx = " + str(dx)
title(s)
xlabel("x (m)")
ylabel("u (m/s)")
"""
u0 = [0, 0]
print 'f(x0) = ', f(0., x0, u0)
# part 1:
t_, x_, x1_, x2_ = sim(f, total_t, x0, u0, dt=4e-2)
for i in range(1, 6):
xinit = x0 + np.array([0, 0, 0, 0, 10 * i * math.pi / 180.0])
t_, x_, x1_, x2_ = sim(f, total_t, xinit, u0, dt=4e-2)
print "a=" + str(i) + " : x(t)=", x_[60 / (4e-2) - 1, :]
# Here is the result for part 1 #
xta1 = np.array([1.82100427, 5.65061528, -0.87326504, 0.46588623, 2.79551686])
xta2 = np.array([0.81212008, 5.88098381, -0.94089848, 0.30716749, 2.97004978])
xta3 = np.array([-0.22143997, 5.93266163, -0.97994319, 0.13911562, -3.1386026])
xta4 = np.array(
[-1.24827168, 5.80407852, -0.98921283, -0.0331632, -2.96406967])
xta5 = np.array(
[-2.23717529, 5.49914142, -0.96842573, -0.20443439, -2.78953675])
# part 2:
a_ = np.array([1, 2, 3, 4])
for i in range(5):
plt.figure()
lineObjects = plt.plot(
a_,
np.array([(xta2[i] - xta1[i]) / 1.0, (xta3[i] - xta2[i]) / 2.0,
(xta4[i] - xta3[i]) / 3.0, (xta5[i] - xta4[i]) / 4.0]), '.-')
plt.title('x' + str(i + 1))
plt.show()
def validate(label,
target,
predictions,
baseline=0.5,
compute_auc=False,
quiet=True):
""" Validates binary predictions, computes confusion matrix and AUC.
Given a vector of predictions and actual values, scores how well we
did on a prediction.
Args:
label: label of what we're validating
target: vector of actual results
predictions: predicted results. May be a probability vector,
in which case we'll sort it and take the most confident values
where baseline is the proportion that we want to take as True
predictions. If a prediction is 1.0 or 0.0, however, we'll take
it to be a true or false prediction, respectively.
compute_auc: If true, will compute the AUC for the predictions.
If this is true, predictions must be a probability vector.
"""
if len(target) != len(predictions):
raise Exception('Length mismatch %d vs %d' %
(len(target), len(predictions)))
if baseline > 1.0:
# Baseline number is expected count, not proportion. Get the proportion.
baseline = baseline * 1.0 / len(target)
#Make an iterator that aggregates elements from each of the iterables.
zipped = sorted(zip(target, predictions), key=lambda tup: -tup[1])
expect = len(target) * baseline
(true_pos, true_neg, false_pos, false_neg) = (0, 0, 0, 0)
for index in xrange(len(target)):
(yval, prob) = zipped[index]
if float(prob) == 0.0:
predicted = False
elif float(prob) == 1.0:
predicted = True
else:
predicted = index < expect
if predicted:
if yval:
true_pos += 1
else:
false_pos += 1
else:
if yval:
false_neg += 1
else:
true_neg += 1
pos = true_pos + false_neg
neg = true_neg + false_pos
# P(1 | predicted(1)) and P(0 | predicted(f))
pred_t = true_pos + false_pos
pred_f = true_neg + false_neg
prob1_t = true_pos * 1.0 / pred_t if pred_t > 0.0 else -1.0
prob0_f = true_neg * 1.0 / pred_f if pred_f > 0.0 else -1.0
# Lift = P(1 | t) / P(1)
prob_1 = pos * 1.0 / (pos + neg)
lift = prob1_t / prob_1 if prob_1 > 0 else 0.0
accuracy = (true_pos + true_neg) * 1.0 / len(target)
if compute_auc:
y_bool = [True if yval else False for (yval, _) in zipped]
x_vec = [xval for (_, xval) in zipped]
auc_value = roc_auc_score(y_bool, x_vec)
fpr, tpr, _ = roc_curve(y_bool, x_vec)
pl.plot(fpr,
tpr,
lw=1.5,
label='ROC %s (area = %0.2f)' % (label, auc_value))
pl.xlabel('False Positive Rate', fontsize=18)
pl.ylabel('True Positive Rate', fontsize=18)
pl.title('ROC curve', fontsize=18)
auc_value = '%0.03g' % auc_value
else:
auc_value = 'NA'
print '(%s) Lift: %0.03g Auc: %s' % (label, lift, auc_value)
if not quiet:
print ' Base: %0.03g Acc: %0.03g P(1|t): %0.03g P(0|f): %0.03g' % (
baseline, accuracy, prob1_t, prob0_f)
print ' Fp/Fn/Tp/Tn p/n/c: %d/%d/%d/%d %d/%d/%d' % (
false_pos, false_neg, true_pos, true_neg, pos, neg, len(target))
for line in mse:
xy = line.split()
X.append(float(xy[0]))
Y.append(float(xy[1]))
for line in res:
RES.append(float(line.split()[1]))
for line in des:
DES.append(float(line))
for line in mse_test:
MSE_TEST.append(float(line.split()[1]))
pl.figure()
pl.xlabel('epochs')
pl.ylabel('MSE')
pl.title('MSE for training data (60% of total data)')
pl.plot(X,Y, label='Training MSE')
pl.plot(X,MSE_TEST, label='Test MSE')
pl.grid()
pl.figure()
pl.xlabel('Years')
pl.ylabel('Scaled Output')
pl.title('Desired and Forward Pass Output on test data (40% of total data)')
pl.plot(RES[187:], label='result')
pl.plot(DES[187:], label='desired')
pl.legend()
pl.grid()
pl.figure()
pl.xlabel('Years')
pl.ylabel('Scaled Output')
pl.title('Desired and Forward Pass Output on training data (to check overfitting)')
pl.plot(RES[0:186], label='result')
# -*- coding: utf-8 -*- """ Created on Thu Sep 10 11:27:28 2015 @author: NigmatullinR """ import scipy.io.wavfile as sw import numpy as np import pylab as plb name = 'voice.wav' f = open(name, 'rb') [fr, dti] = sw.read(f) f.close() outN = dti[5:300] print 'length', len(dti) print 'sampling frequency', fr print 'signal example', np.float32(dti[5:300]) plb.figure() plb.plot(outN)
transOffset = offset_copy(ax.transData,
fig=fig,
x=0.05,
y=0.10,
units='inches')
# for i in xrange(len(data['code'])):
# if data['price'][i] <= 0 or data['gdp'][i] <= 0:
# continue
# if data['oilout'][i] > data['oilin'][i]:
# fuel = False
# else:
# fuel = True
# symbol = "kx" if fuel else 'ko'
# pl.plot(np.log(data['gdp'][i]), data['price'][i], symbol)
# # pl.text(data[i,0], data[i,4], '%.1f' % (fuel), transform=transOffset)
# pl.text(np.log(data['gdp'][i]), data['price'][i], data['name'][i], transform=transOffset)
total = []
for i in xrange(len(data['code'])):
if data['price'][i] > 0:
total += [(data['code'][i], data['price'][i])]
total2 = sorted(total, key=lambda x: x[1])
for j, v in enumerate(total2):
pl.plot(j, v[1])
pl.text(j, v[1], v[0], transform=transOffset)
pl.show()
if ar1 == ar2:
nlth = interpolate_dict(lb, nbs_ar1xar1, lth, spectra)
else:
Rlth = interpolate_dict(lb, Rb, lth, spectra)
nlth_ar1xar1 = interpolate_dict(lb, nbs_ar1xar1, lth, spectra)
nlth_ar2xar2 = interpolate_dict(lb, nbs_ar2xar2, lth, spectra)
nlth = {}
for spec in spectra:
nlth[spec] = Rlth[spec] * np.sqrt(
nlth_ar1xar1[spec] * nlth_ar2xar2[spec])
for spec in spectra:
plt.figure(figsize=(12, 12))
plt.plot(lth,
nlth[spec],
label="interpolate",
color="lightblue")
if ar1 == ar2:
nbs = nbs_ar1xar1[spec]
else:
nbs = nbs_ar1xar2[spec]
plt.plot(lb,
nbs,
".",
label="%s %sx%s" % (sv, ar1, ar2),
color="red")
plt.legend(fontsize=20)
plt.savefig("%s/noise_interpolate_%sx%s_%s_%s.png" %
(plot_dir, ar1, ar2, sv, spec),
bbox_inches="tight")
model_path = os.path.join(save_dir, model_name)
model.save(model_path)
print('Saved trained model at %s ' % model_path)
# Score trained model.
scores = model.evaluate(test_tensors, test_targets, verbose=1)
print('Test loss:', scores[0])
print('Test accuracy:', scores[1])
model.load_weights(file_path)
mushroom_predictions = [np.argmax(model.predict(np.expand_dims(tensor, axis=0))) for tensor in test_tensors]
test_accuracy = 100*np.sum(np.array(mushroom_predictions)==np.argmax(test_targets, axis=1))/len(mushroom_predictions)
print('Test accuracy: %.4f%%' % test_accuracy)
print(history.history.keys())
# summarize history for accuracy
plt.plot(history.history['acc'])
plt.plot(history.history['val_acc'])
plt.title('model accuracy')
plt.ylabel('accuracy')
plt.xlabel('epoch')
plt.legend(['train', 'test'], loc='upper left')
plt.show()
# summarize history for loss
plt.plot(history.history['loss'])
plt.plot(history.history['val_loss'])
plt.title('model loss')
plt.ylabel('loss')
plt.xlabel('epoch')
plt.legend(['train', 'test'], loc='upper left')
plt.show()
print 'stopped early'
break
win.logOnFlip(msg='frame=%i' %frameN, level=logging.EXP)
win.flip()
win.close()
#calculate some values
intervalsMS = pylab.array(win.frameIntervals[1:])*1000
m=pylab.mean(intervalsMS)
sd=pylab.std(intervalsMS)
# se=sd/pylab.sqrt(len(intervalsMS)) # for CI of the mean
distString= "Mean=%.1fms, s.d.=%.1f, 99%%CI(frame)=%.2f-%.2f" %(m,sd,m-2.58*sd,m+2.58*sd)
nTotal=len(intervalsMS)
nDropped=sum(intervalsMS>(1.5*m))
droppedString = "Dropped/Frames = %i/%i = %.3f%%" %(nDropped,nTotal, 100*nDropped/float(nTotal))
#plot the frameintervals
pylab.figure(figsize=[20,10])
pylab.subplot(1,2,1)
pylab.plot(intervalsMS, '-')
pylab.ylabel('t (ms)')
pylab.xlabel('frame N')
pylab.title(droppedString)
#
pylab.subplot(1,2,2)
pylab.hist(intervalsMS, 50, normed=0, histtype='stepfilled')
pylab.xlabel('t (ms)')
pylab.ylabel('n frames')
pylab.title(distString)
pylab.show()
def displayFibs(n):
(xvals, yvals) = gatherFacts(n)
plt.figure('fibs')
plt.plot(xvals, yvals, label='fibonacci')
plt.show()
p=p,
dview=dview,
Ain=None,
method_deconvolution='oasis',
skip_refinement=False)
cnm = cnm.fit(images)
crd = plot_contours(cnm.A, Cn, thr=0.9)
C_dff = extract_DF_F(Yr,
cnm.A,
cnm.C,
cnm.bl,
quantileMin=8,
frames_window=200,
dview=dview)
pl.figure()
pl.plot(C_dff.T)
else:
rf = 14 # half-size of the patches in pixels. rf=25, patches are 50x50
stride = 6 # amounpl.it of overlap between the patches in pixels
K = 6 # number of neurons expected per patch
gSig = [6, 6] # expected half size of neurons
merge_thresh = 0.8 # merging threshold, max correlation allowed
p = 1 # order of the autoregressive system
save_results = False
cnm = cnmf.CNMF(n_processes,
k=K,
gSig=gSig,
merge_thresh=0.8,
p=0,
dview=dview,
som.random_weights_init(X)
som.train_random(data = X, num_iteration = 100)
# Visualizing the results
from pylab import bone, pcolor, colorbar, plot, show
bone()
pcolor(som.distance_map().T)
colorbar()
markers = ['o', 'x']
colors = ['r', 'g']
for i, x in enumerate(X):
w = som.winner(x)
plot(w[0] + 0.5,
w[1] + 0.5,
markers[1],
markeredgecolor = colors[1],
markerfacecolor = 'None',
markersize = 10,
markeredgewidth = 2)
show()
# Finding the frauds
mappings = som.win_map(X)
grp1 = np.concatenate((mappings[(6,2)], mappings[(3,5)], mappings[(1,6)], mappings[(2,7)]), axis = 0)
grp1 = sc.inverse_transform(grp1)
grp2 = np.concatenate((mappings[(0,0)], mappings[(0,9)], mappings[(9,0)], mappings[(8,9)], mappings[(9,8)], mappings[(9,4)]), axis = 0)
grp2 = sc.inverse_transform(grp2)
grp3 = np.concatenate((mappings[(1,0)], mappings[(5,5)], mappings[(8,3)], mappings[(5,9)]), axis = 0)
grp3 = sc.inverse_transform(grp3)
grp4 = np.concatenate((mappings[(0,4)], mappings[(0,2)], mappings[(8,2)], mappings[(3,9)], mappings[(0,7)]), axis = 0)
grp4 = sc.inverse_transform(grp4)
def main(xyz):
#########################
#some err
##############
xyz_acc = xyz
mod_acc_mean = np.mean(np.sqrt((xyz_acc * xyz_acc).sum(axis=1)))
assert isinstance(xyz_acc, np.ndarray)
assert xyz_acc.shape[0] >= 10
assert xyz_acc.shape[1] == 3
assert mod_acc_mean >= 5 and mod_acc_mean <= 50
##########################################
#fea visual filter ->valid data
#################################################
#########load pickle
#xyz=load_pickle(dataPath+'xyz-watchphone-nov-'+class_type)
######clean data
#xyz=xyz[:4087,:]
xyz_abs = np.abs(xyz)
#########visual
x_axis = xyz.shape[0] #500 200 1000
y_axis = 30
ind = np.arange(xyz.shape[0])
plt.figure()
plt.subplot(211)
plt.title('xyz')
plt.plot(ind, xyz[:, 0], 'r-', ind, xyz[:, 1], 'y.', ind, xyz[:, 2], 'b--')
#plt.xlim(0,9000);#plt.ylim(0,y_axis)
#plt.show()
###########################
#generate obs x y [n,3]->[n_obs,10,3] ->[n_obs,4x3]
############################
fea = xyz
kernel_sz = 10.
stride = kernel_sz
obs_list = []
num = int((xyz.shape[0] - kernel_sz) / stride) + 1
for i in range(num)[:]: #[0,...100] total 101
obs = fea[i * stride:i * stride + kernel_sz, :] #[10,3]
if obs.shape[0] == kernel_sz:
v = np.array([fea4(obs[:, i])
for i in range(obs.shape[1])]).flatten()
obs_list.append(v) #[10,3]->[3x4,]
x_arr = np.array(obs_list)
print 'x', x_arr.shape #[n-obs,12]
#####
#save2pickle([x_arr,y_arr],'xy-'+class_type) #[n,12][n,]
xy = np.concatenate((x_arr, np.zeros((x_arr.shape[0], 1))), axis=1)
print xy.shape #[n,13]
#
#dataSet=[list(xy[i,:]) for i in range(xy.shape[0]) ] #nx13 list
#dataSet=np.array([xy[i,:] for i in range(xy.shape[0]) ] ) #nx13 array
#
dataSet = xy
#load model trees
many_stumps = load_pickle(dataPath + 'rf-para-watchphone')
#test
X_test = dataSet #[n,13]
#####ensemble test [ [],[]...] []=[tree,dim_list,accuracy]
n_val = X_test.shape[0]
dim_val = X_test.shape[1] - 1 #[n,13] 12+1
f_label_mat = np.zeros((n_val, many_stumps.__len__())) #[n,10stump]
for ind in range(many_stumps.__len__()): #[3,5,8,11..]
dim_sample = many_stumps[ind][1]
tree = many_stumps[ind][0]
for obs in range(n_val):
pred = classify(tree, X_test[obs, :]) #13=12+1
f_label_mat[obs, ind] = pred
##
#f_label majority vote
maj_vote = np.zeros((n_val, )) #[n,]
for i in range(f_label_mat.shape[0]): #[n,10stump]
vote1 = f_label_mat[i, :].sum()
vote0 = (1 - f_label_mat[i, :]).sum()
maj_vote[i] = [1 if vote1 > vote0 else 0][0]
##calculate accuracy
#y_true=X_test[:,-1]
#accuracy=T.mean(T.eq(maj_vote,y_true)).eval();print 'accur dt ensemble',accuracy
plt.subplot(2, 1, 2)
plt.title('predict watch or not watch over time')
plt.plot(np.where(maj_vote == 0)[0],
np.zeros((np.where(maj_vote == 0)[0].shape[0], )),
'bo',
label='watch')
plt.plot(np.where(maj_vote == 1)[0],
np.ones((np.where(maj_vote == 1)[0].shape[0], )),
'y^',
label='notwatch')
plt.legend()
plt.xlabel('time')
plt.ylabel('predicted class')
#plt.show()
#class_dic={'watch':0,'notwatch':1}
class_dic = {0: 'watch', 1: 'notwatch'}
label_list = [class_dic[i] for i in maj_vote]
print 'predict', label_list
return label_list # [string,...]predict label
normalize_dataset(dataset, minmax)
inputs = []
outputs = []
for row in dataset:
inputs.append(row[0:-1])
outputs.append(row[2:])
#X = np.array([[0,0,1],
# [0,1,1],
# [1,0,1],
# [1,1,1]])
X = np.array(inputs)
#y = np.array([[0],
# [1],
# [1],
# [0]])
y = np.array(outputs)
cols = X.T
xlabel("Instances")
ylabel("Inputs and Outputs")
title("Data Visualization")
plot(cols[0], label='Show')
plot(cols[1], label='Network') #, 'b')
plot(outputs, label='Fall-off') #, 'r')
legend(bbox_to_anchor=(1.05, 1), loc=2, borderaxespad=0.)
show()
from vendor.nfb.pynfb.signal_processing.helpers import get_outliers_mask
import numpy as np
from PyQt5 import QtGui, QtWidgets
from vendor.nfb.pynfb.protocols.ssd.topomap_selector_ica import ICADialog
fs = 1000
band = (8, 14)
channels = ['Fp1', 'Fp2', 'F7', 'F3', 'Fz', 'F4', 'F8', 'Ft9', 'Fc5', 'Fc1', 'Fc2', 'Fc6', 'Ft10', 'T3', 'C3', 'Cz',
'C4', 'T4', 'Tp9', 'Cp5', 'Cp1', 'Cp2', 'Cp6', 'Tp10', 'T5', 'P3', 'Pz', 'P4', 'T6', 'O1', 'Oz', 'O2']
data = [loadmat(r'C:\Users\Nikolai\Desktop\Liza_diplom_data\Liza_diplom_data\treatment\p25\day2\proba{}.mat'.format(k))['X1Topo'].T for k in range(1, 16)]
df = pd.DataFrame(data=np.concatenate(data), columns=channels)
for ch in['Pz', 'Cz']:
channels.remove(ch)
del df[ch]
df = df.loc[~get_outliers_mask(df[channels])]
#plt.plot(*welch(df['C3'], fs, nperseg=4*fs))
plt.plot(df[channels])
plt.show()
#plt.show()
#df['C3env'] = np.abs(hilbert(fft_filter(df['C3'], fs, band)))
#df['C4env'] = np.abs(hilbert(fft_filter(df['C4'], fs, band)))
#plt.plot(df['C3env']+df['C4env'])
a = QtWidgets.QApplication([])
(rej, filt, topo, _unmix, _bandpass, _) = ICADialog.get_rejection(df.iloc[:fs*60*3], channels, fs)
df['SMR'] = np.dot(df.as_matrix(), filt)
df.to_pickle('p4')
plt.plot(df['SMR'])
plt.show()
ydata = np.array([0.1, 0.81, 4.03, 9.1, 15.99, 24.2, 37.2])
#fit a third order polynomial
from pylab import polyfit, plot, xlabel, ylabel, show, legend, savefig
pars = polyfit(xdata, ydata, 3)
print 'pars from polyfit: {0}'.format(pars)
## numpy method returns more data
A = np.column_stack([xdata**3, xdata**2, xdata, np.ones(len(xdata), np.float)])
pars_np, resids, rank, s = np.linalg.lstsq(A, ydata)
print 'pars from np.linalg.lstsq: {0}'.format(pars_np)
'''
we are trying to solve Ax = b for x in the least squares sense. There
are more rows in A than elements in x so, we can left multiply each
side by A^T, and then solve for x with an inverse.
A^TAx = A^Tb
x = (A^TA)^-1 A^T b
'''
# not as pretty but equivalent!
pars_man = np.dot(np.linalg.inv(np.dot(A.T, A)), np.dot(A.T, ydata))
print 'pars from linear algebra: {0}'.format(pars_man)
#but, it is easy to fit an exponential function to it!
# y = a*exp(x)+b
Aexp = np.column_stack([np.exp(xdata), np.ones(len(xdata), np.float)])
pars_exp = np.dot(np.linalg.inv(np.dot(Aexp.T, Aexp)), np.dot(Aexp.T, ydata))
plot(xdata, ydata, 'ro')
fity = np.dot(A, pars)
plot(xdata, fity, 'k-', label='poly fit')
plot(xdata, np.dot(Aexp, pars_exp), 'b-', label='exp fit')
xlabel('x')
ylabel('y')
legend()
savefig('images/curve-fit-1.png')
hexNeighbours[1] = oldUniverseList[currentRow - 1][currentColumn - 1]
if (currentColumn + 1) < cellCountX: # CELL 4 ODD
hexNeighbours[4] = oldUniverseList[currentRow][currentColumn + 1]
if (currentRow + 1) < cellCountY: # CELL 5 ODD
hexNeighbours[5] = oldUniverseList[currentRow + 1][currentColumn + 1]
# Get the new state by sending the currentCell value + string of all neighbours
hexNeighbours = "".join(hexNeighbours) # join the characters into 1 string
newUniverseRow += getNewState2DHex(oldUniverseList[currentRow][currentColumn], hexNeighbours)
universeList[currentRow] = newUniverseRow
#print RES
#Ploting
pl.subplot(3, 1, 1)
pl.plot(map(itemgetter(3), RES), map(itemgetter(2), RES), '-r', label='Infected')
pl.plot(map(itemgetter(3), RES), map(itemgetter(0), RES), '-b', label='Normal')
pl.legend(loc=0)
pl.title('Infected and Normal')
pl.xlabel('Time')
pl.ylabel('Count')
pl.subplot(3, 1, 2)
pl.plot(map(itemgetter(3), RES), map(itemgetter(1), RES), '-r', label='Susceptibles')
pl.plot(map(itemgetter(3), RES), map(itemgetter(0), RES), '-b', label='Normal')
pl.legend(loc=0)
pl.title('Susceptibles and Normal')
pl.xlabel('Time')
pl.ylabel('Count')
pl.subplot(3, 1, 3)
for i in xrange(X.size):
griddata.addSample([X.ravel()[i], Y.ravel()[i]], [0])
griddata._convertToOneOfMany(
) # this is still needed to make the fnn feel comfy
for i in range(20):
trainer.trainEpochs(1)
trnresult = percentError(trainer.testOnClassData(), trndata['class'])
tstresult = percentError(trainer.testOnClassData(dataset=tstdata),
tstdata['class'])
print "epoch: %4d" % trainer.totalepochs, \
" train error: %5.2f%%" % trnresult, \
" test error: %5.2f%%" % tstresult
out = fnn.activateOnDataset(griddata)
out = out.argmax(axis=1) # the highest output activation gives the class
out = out.reshape(X.shape)
figure(1)
ioff() # interactive graphics off
clf() # clear the plot
hold(True) # overplot on
for c in [0, 1, 2]:
here, _ = where(tstdata['class'] == c)
plot(tstdata['input'][here, 0], tstdata['input'][here, 1], 'o')
if out.max() != out.min(): # safety check against flat field
contourf(X, Y, out) # plot the contour
ion() # interactive graphics on
draw() # update the plot
ioff()
show()
from pylab import plot,show,xlabel
from numpy import linspace,sin,loadtxt,cos
x=linspace(0,10,100)
print(x)
y=sin(x)
#plot(x,y)
#show()
a=open("test.dat","w")
for i in range(len(x)):
a.write("%.2f %.2f\n" % (x[i],y[i]))
a.close()
b=loadtxt("test.dat",float)
plot(b[:,0],b[:,1],"r--")
t=cos(x)
xlabel("Radians")
plot(x,t,"b--")
show()
# -*- coding: utf-8 -*- import scipy.signal as signal import numpy as np import pylab as pl h1 = signal.remez(201, (0, 0.18, 0.2, 0.50), (0.01, 1)) h2 = signal.remez(201, (0, 0.38, 0.4, 0.50), (1, 0.01)) h3 = np.convolve(h1, h2) w, h = signal.freqz(h3, 1) pl.plot(w/2/np.pi, 20*np.log10(np.abs(h))) pl.legend() pl.xlabel(u"正规化频率 周期/取样") pl.ylabel(u"幅值(dB)") pl.title(u"低通和高通级联为带通滤波器") pl.show()
# plt.ylabel('loss')
# plt.legend(['greedy'])
# #plt.title(fn)
# plt.tight_layout()
for res in results[1:]:
im = cc.wire_network(res['network'],give_dense=True).detach().numpy().reshape(im_size,order='F')
params=res['num_params']
error=np.linalg.norm((image-im).ravel())/np.linalg.norm(image.ravel())*100
if xp == 'einstein':
plt.subplot(nploty,nplotx,subplot_index)
subplot_index += 1
plt.imshow(im/255)
plt.axis('off')
plt.title(f"#param.:{params},\ntest error:{error:.2f}%",fontsize=4)
plt.tight_layout()
plt.style.use('ggplot')
plt.figure()
plt.plot(greedy_params,greedy_errors,'-')
plt.plot(tr_als_params,tr_als_errors,'-')
plt.plot(tt_als_params,tt_als_errors,'-')
plt.legend("Greedy TR-ALS TT-ALS".split())
plt.xlabel("parameters")
plt.ylabel("relative error")
plt.tight_layout()
plt.show()
woman = woman[:shortest]
man = man[:shortest]
np.random.seed(101)
noise = np.random.uniform(-1, 1, len(man))
sources = np.stack((woman, man, noise))
A = np.random.uniform(-1, 1, (3, 3))
linear_mix = np.dot(A, sources)
pnl_mix = linear_mix.copy()
pnl_mix[0] = np.tanh(pnl_mix[0])
pnl_mix[1] = (pnl_mix[1] + pnl_mix[1]**3) / 2
pnl_mix[2] = np.exp(pnl_mix[2])
return linear_mix, pnl_mix, A, sources
if __name__ == '__main__':
linear_mix, pnl_mix, A, sources = get_data()
wavfile.write('./mixtape1.wav', rate=rate, data=linear_mix[0])
wavfile.write('./mixtape2.wav', rate=rate, data=linear_mix[1])
wavfile.write('./mixtape3.wav', rate=rate, data=linear_mix[2])
wavfile.write('./pnlmixtape1.wav', rate=rate, data=pnl_mix[0])
wavfile.write('./pnlmixtape2.wav', rate=rate, data=pnl_mix[1])
wavfile.write('./pnlmixtape3.wav', rate=rate, data=pnl_mix[2])
pl.subplot(311)
pl.plot(man)
pl.subplot(312)
pl.plot(woman)
pl.subplot(313)
pl.plot(noise)
pl.show()
