def plot_freq(series,sampling_frequency=1):
"""
Purpose: Illustrate the power spectrum calculation for a given data series
Inputs: series-A data array to show the power spectrum for. Calls power_spectrum
sampling_frequency-(optional) IDK what for yet
Outputs: none
"""
t=sp.arange(0,len(series))/(1.0*sampling_frequency)
pylab.subplot(2,1,1)
pylab.plot(t,series)
pylab.xlabel('Time')
pylab.ylabel('Amplitude')
pylab.subplot(2,1,2)
n = len(series) # length of the signal
k = sp.arange(n)
T = n/sampling_frequency
frq = k/T # two sides frequency range
frq = frq[range(n/2)] # one side frequency range
Y = np.fft.fft(series)/n # fft computing and normalization
Y = Y[range(n/2)]
pylab.plot(frq,abs(Y),'r') # plotting the spectrum
pylab.xlabel('Freq (Hz)')
pylab.ylabel('|Y(freq)|')
pylab.show()
def setUp(self):
Reader = fitsGBT.Reader("./testdata/testfile_guppi_combined.fits",
feedback=0)
self.Blocks = Reader.read((), 1)
Data = self.Blocks[0]
Data.calc_freq()
params = {'dm_deweight_time_slope' : True}
Maker = dirty_map.DirtyMapMaker(params, feedback=0)
n_chan = Data.dims[-1]
Maker.n_chan = n_chan
Maker.pols = (1, 2, 3, 4)
Maker.pol_ind = 0
Maker.band_centres = (Data.freq[Data.dims[-1]//2],)
Maker.band_ind = 0
map = sp.zeros((Data.dims[-1], 32, 15))
map = al.make_vect(map, ('freq', 'ra', 'dec'))
map.set_axis_info('freq', Data.freq[Data.dims[-1]//2],
Data.field['CRVAL1'])
map.set_axis_info('ra', 218, 0.075)
map.set_axis_info('dec', 2, 0.075)
Maker.map = map
self.Maker = Maker
# The variances of each channel.
self.norms = (sp.arange(1., 2., 0.25)[:,None]
* (sp.arange(1., 2., 1./n_chan)[None,:]))
for Data in self.Blocks:
Data.data[...] = random.randn(*Data.data.shape)
Data.data *= sp.sqrt(self.norms[:,None,:])
Data.data += 50.
def makesumrule(ptype,plen,ts,lagtype='centered'):
""" This function will return the sum rule.
Inputs
ptype - The type of pulse.
plen - Length of the pulse in seconds.
ts - Sample time in seconds.
lagtype - Can be centered forward or backward.
Output
sumrule - A 2 x nlags numpy array that holds the summation rule.
"""
nlags = sp.round_(plen/ts)
if ptype.lower()=='long':
if lagtype=='forward':
arback=-sp.arange(nlags,dtype=int)
arforward = sp.zeros(nlags,dtype=int)
elif lagtype=='backward':
arback = sp.zeros(nlags,dtype=int)
arforward=sp.arange(nlags,dtype=int)
else:
arback = -sp.ceil(sp.arange(0,nlags/2.0,0.5)).astype(int)
arforward = sp.floor(sp.arange(0,nlags/2.0,0.5)).astype(int)
sumrule = sp.array([arback,arforward])
elif ptype.lower()=='barker':
sumrule = sp.array([[0],[0]])
return sumrule
def range_query_geno_local(self, idx_start=None, idx_end=None, chrom=None,pos_start=None, pos_end=None,windowsize=0):
"""
return an index for a range query on the genotypes
"""
if idx_start==None and idx_end==None and pos_start==None and pos_end==None and chrom==None:
return sp.arange(0,self.num_snps)
elif idx_start is not None or idx_end is not None:
if idx_start is None:
idx_start = 0
if idx_end is None:
idx_end = self.num_snps
res = sp.arange(idx_start,idx_end)
return res
elif chrom is not None:
res = self.geno_pos["chrom"]==chrom
elif pos_start is not None or pos_end is not None:
if pos_start is not None and pos_end is not None:
assert pos_start[0] == pos_end[0], "chromosomes have to match"
if pos_start is None:
idx_larger = sp.ones(self.num_snps,dtype=bool)
else:
idx_larger = (self.geno_pos["pos"]>=(pos_start[1]-windowsize)) & (self.geno_pos["chrom"]==pos_start[0])
if pos_end is None:
idx_smaller = sp.ones(self.num_snps,dtype=bool)
else:
idx_smaller = (self.geno_pos["pos"]<=(pos_end[1]+windowsize)) & (self.geno_pos["chrom"]==pos_end[0])
res = idx_smaller & idx_larger
else:
raise Exception("This should not be triggered")#res = sp.ones(self.geno_pos.shape,dtype=bool)
return sp.where(res)[0]
def test_covariate_shift(self):
n_sample = 100
# Biased training
var_bias = .5**2
mean_bias = .7
x_train = SP.random.randn(n_sample)*SP.sqrt(var_bias) + mean_bias
y_train = self.complete_sample(x_train)
# Unbiased test set
var = .3**2
mean = 0
x_test = SP.random.randn(n_sample)*SP.sqrt(var) + mean
x_complete = SP.hstack((x_train, x_test))
kernel = utils.getQuadraticKernel(x_complete, d=1) +\
10 * SP.dot(x_complete.reshape(-1, 1), x_complete.reshape(1, -1))
kernel = utils.scale_K(kernel)
kernel_train = kernel[SP.ix_(SP.arange(x_train.size),
SP.arange(x_train.size))]
kernel_test = kernel[SP.ix_(SP.arange(x_train.size, x_complete.size),
SP.arange(x_train.size))]
mf = MF(n_estimators=100, kernel=kernel_train, min_depth=0,
subsampling=False)
mf.fit(x_train.reshape(-1, 1), y_train.reshape(-1, 1))
response_gp = mf.predict(x_test.reshape(-1, 1), kernel_test, depth=0)
self.assertTrue(((response_gp - self.polynom(x_test))**2).sum() < 2.4)
def test_correlate(self) :
Data = self.blocks[0]
Data.calc_freq()
map = self.map
gain = 3.45
const = 2.14
# Set all data = gain*(cos(time_ind)).
Data.data[:,:,:,:] = gain*sp.cos(sp.arange(1,11)
[:,sp.newaxis,sp.newaxis,sp.newaxis])
# Explicitly set time mean to something known.
Data.data -= ma.mean(Data.data, 0)
Data.data += gain*const*Data.freq/800.0e6
# Now the Map.
map[:,:,:] = 0.0
# Set 10 pixels to match cos part of data.
map[:, range(10), range(10)] = (
sp.cos(sp.arange(1,11)[None, :]))
map[:, range(10), range(10)] -= ma.mean(
map[:, range(10), range(10)], 1)[:, None]
# Give Map a mean to test things out. Should really have no effect.
map[...] += 0.352*map.get_axis('freq')[:, None, None]/800.0e6
# Rig the pointing to point to those 10 pixels.
def rigged_pointing() :
Data.ra = map.get_axis('ra')[range(10)]
Data.dec = map.get_axis('dec')[range(10)]
Data.calc_pointing = rigged_pointing
solved_gains = smd.sub_map(Data, map, correlate=True)
# Now data should be just be gain*const*f, within machine precision.
Data.data /= gain*Data.freq/800.0e6
self.assertTrue(sp.allclose(Data.data[:,:,:,:], const))
self.assertTrue(sp.allclose(solved_gains, gain))
def audio_cb(self, data):
rospy.loginfo("Callback received!")
print "<Previous y_data len: " + str(len(self.y_data))
self.y_data.extend(data.data)
#self.y_data = data.data
print ">After y_data len: " + str(len(self.y_data))
print "--------------"
print "len of y_data: " + str(len(self.y_data))
excess_of_data = None
if len(self.y_data) > self.MAX_DATA:
print "excess of data: " + str(len(self.y_data) - self.MAX_DATA)
excess_of_data = len(self.y_data) - self.MAX_DATA
# self.x_data = arange(self.x_data[excess_of_data], (len(self.x_data) - 1) * 0.01, 0.01).tolist()
self.y_data = self.y_data[excess_of_data:]
print "<Previous x_data len: " + str(len(self.x_data))
if excess_of_data:
new_times = arange(self.x_data[-1], len(self.y_data) * 0.01 + self.x_data[-1], 0.01).tolist()
print "Initial time: " + str(self.x_data[-1])
self.x_data = new_times[:len(self.y_data)]
print "Final time: "+ str(self.x_data[-1])
else: # if we are just adding data to the array
new_times = arange(self.x_data[-1], len(data.data) * 0.01 + self.x_data[-1], 0.01).tolist()
self.x_data.extend(new_times[:len(self.y_data)])
print ">After x_data len: " + str(len(self.x_data))
if len(self.x_data) != len(self.y_data):
rospy.logerr("Error, not same size")
exit(0)
def plotSpectrum(y,Fs,image_name):
"""
Plots a Single-Sided Amplitude Spectrum of y(t)
"""
n = len(y) # length of the signal
subplot(2,1,1)
plot(arange(0,n),y)
xlabel('Time')
ylabel('Amplitude')
subplot(2,1,2)
k = arange(n)
T = n/Fs
frq = k/T # two sides frequency range
frq = frq[range(n/2)] # one side frequency range
Y = fft(y)/n # fft computing and normalization
Y = Y[range(n/2)]
plot(frq,abs(Y),'r') # plotting the spectrum
xlabel('Freq (Hz)')
ylabel('|Y(freq)|')
print "here"
#show()
savefig(image_name,dpi=110)
def test_rigged_pointing(self) :
Data = self.blocks[0]
Data.calc_freq()
map = self.map
# Set all data = (f + cal_ind)*time_ind
Data.data[:,:,:,:] = (sp.arange(-4.5, 5)
[:,sp.newaxis,sp.newaxis,sp.newaxis]
*(Data.freq/100e6))
Data.data[...] -= sp.mean(Data.data, 0)
Data.data[...] += (sp.arange(6,8).reshape((1,1,2,1)) * (Data.freq/100e6)
* sp.arange(-4.5, 5).reshape((10, 1, 1, 1)))
map[:,:,:] = 0.0
# Set 10 pixels to match data (except for cal_ind part).
map[:, range(10), range(10)] = (sp.arange(-4.5, 5)[None,:]
* map.get_axis('freq')[:,None]/100e6)
# We should be completely insensitive to the map mean. Th following
# should have no effect.
map[...] += 0.352*map.get_axis('freq')[:, None, None]/800.0e7
# Rig the pointing to point to those 10 pixels.
def rigged_pointing() :
Data.ra = map.get_axis('ra')[range(10)]
Data.dec = map.get_axis('dec')[range(10)]
Data.calc_pointing = rigged_pointing
smd.sub_map(Data, map)
# Now data should be just f*time_ind*(cal_ind+6), within 2.0 MHz/2.
Data.data /= sp.arange(-4.5, 5)[:,sp.newaxis,sp.newaxis,sp.newaxis]
Data.data /= Data.freq/100e6
# Relative tol of 1/700, is the frequency bin width.
self.assertTrue(sp.allclose(Data.data[:,:,0,:], 6.0, rtol=1.0/700))
self.assertTrue(sp.allclose(Data.data[:,:,1,:], 7.0, rtol=1.0/700))
def to_netcdf_file(self, dir=None, echo=False):
t1 = time.time()
if dir is None:
dir = self.data_dir
filename = "sweep_" + self.last_sweep_time + ".nc"
filename = os.path.join(dir, filename)
nc_file = netcdf.netcdf_file(filename, 'w')
n_range = self.trimmed_sweep.shape[1]
n_pulse = self.trimmed_sweep.shape[0]
pulse_dim = nc_file.createDimension("pulse_number", n_pulse)
pulse_var = nc_file.createVariable("pulse_number", int, ("pulse_number", ))
pulse_var.units = "pulse_number"
range_dim = nc_file.createDimension("range", n_range)
range_var = nc_file.createVariable("range", float, ("range", ))
range_var.units = "meters"
amplitude = nc_file.createVariable("amplitude", self.trimmed_sweep.dtype,
("pulse_number", "range"))
range_var[:] = sp.arange(0, self.range_resolution * n_range, self.range_resolution)
pulse_var[:] = sp.arange(n_pulse, dtype=int)
amplitude[:] = self.trimmed_sweep
amplitude.units = "ADC_counts"
amplitude.max_counts = self.ps.getMaxValue()
amplitude.min_counts = self.ps.getMinValue()
nc_file.max_range = self.max_range
nc_file.range_resolution = self.range_resolution
nc_file.sweep_time = self.last_sweep_time
nc_file.pulse_rate_nominal = self.pulse_rate
nc_file.rotation_period_nominal = self.rotation_period
nc_file.samples_per_segment = self.samples_per_segment
nc_file.close()
if echo:
print filename
print "Time to write data: ", str(time.time() - t1)
def save_plotSpectrum(y,Fs,image_name):
"""
Plots a Single-Sided Amplitude Spectrum of y(t)
"""
fig = Figure(linewidth=0.0)
fig.set_size_inches(fig_width,fig_length, forward=True)
Figure.subplots_adjust(fig, left = fig_left, right = fig_right, bottom = fig_bottom, top = fig_top, hspace = fig_hspace)
n = len(y) # length of the signal
_subplot = fig.add_subplot(2,1,1)
print "Fi"
_subplot.plot(arange(0,n),y)
xlabel('Time')
ylabel('Amplitude')
_subploti_2=fig.add_subplot(2,1,2)
k = arange(n)
T = n/Fs
frq = k/T # two sides frequency range
frq = frq[range(n/2)] # one side frequency range
Y = fft(y)/n # fft computing and normalization
Y = Y[range(n/2)]
_subplot_2.plot(frq,abs(Y),'r') # plotting the spectrum
xlabel('Freq (Hz)')
ylabel('|Y(freq)|')
print "here"
canvas = FigureCanvasAgg(fig)
if '.eps' in outfile_name:
canvas.print_eps(outfile_name, dpi = 110)
if '.png' in outfile_name:
canvas.print_figure(outfile_name, dpi = 110)
def Evolve_DE(self):
for i in scipy.arange(self.npop1):
# para cada individuo da populacao
# gera trial vector usado para perturbar individuo atual (indice i)
# a partir de 3 individuos escolhidos aleatoriamente na populacao e
# cujos indices sejam distintos e diferentes de i
invalido = True
while invalido:
j = random_integers(0,self.npop1-1,3)
invalido = (i in j)
invalido = invalido or (j[0] == j[1])
invalido = invalido or (j[1] == j[2])
invalido = invalido or (j[2] == j[0])
# trial vector a partir da mutacao de um alvo
u = self.pop1[j[0]] + self.beta*(self.pop1[j[1]] - self.pop1[j[2]])
# gera por crossover solucao candidata
c = self.pop1[i].copy()
# seleciona indices para crossover
# garantindo que ocorra crossover em
# pelo menos uma vez
j = random_integers(0,self.pop1.shape[1]-1)
for k in scipy.arange(self.pop1.shape[1]):
if (scipy.rand() < self.pr) or (k == j):
c[k] = u[k]
ans,c = self.resolve_desafio(c)
c_fit = self.avalia_aptidao1(ans)
# leva para proxima geracao quem tiver melhor fitness
if (c_fit > self.fit1[i]):
self.pop1[i] = c
self.fit1[i] = c_fit
self.ans1[i] = ans
def waveGen(): n = 4096 # samples freq0 = 0 # Hz samp_rate = 64 # Hz levels = 8 start_freq = 1 # Hz end_freq = 2 # Hz if (start_freq != end_freq): freq0 = arange(start_freq, end_freq, (end_freq - start_freq) / (n * 1.0)) else: freq0 = start_freq factor0 = samp_rate / freq0 time = arange(n)/float(samp_rate) wave0 = sin(2 * pi * freq0 * time) # errors = [random() - 0.5 for _ in range(n)] # wave0 += errors sampleList = list() for t in arange(len(time)): sample = [time[t], wave0[t]] sampleList.append(sample) return sampleList
def fit_gaussian_state(Q, P, W):
q = Q[0,:]
p = P[:,0]
m, n = W.shape
idx_to_q = interp1d(scipy.arange(n), q)
idx_to_p = interp1d(scipy.arange(m), p)
i_mean = find_mean(W)
try:
q0, p0 = idx_to_q(i_mean[0]), idx_to_p(i_mean[1])
s0 = 1./(W.max()*sqrt(2.*pi))
theta0 = 0.
def twoD_Gaussian(qp, a, b, c):
q, p = qp
det = a*c-b**2
if det<0:
raise RuntimeError
normalization = sqrt(det)/(2.*pi)
g = normalization*exp( -1./2.* (a*((q-q0)**2) + 2*b*(q-q0)*(p-p0) + c*((p-p0)**2)))
return g.ravel()
initial_guess = convert_params(s0, s0, theta0)
(a, b, c), pcov = curve_fit(twoD_Gaussian, (Q, P), W.ravel(), p0=initial_guess)
cov = scipy.array([[c, -b], [-b, a]])/(a*c-b**2)
dq = cov[0,0]
cqp = cov[0,1]
dp = cov[1,1]
except:
q0 = scipy.nan
p0 = scipy.nan
dq = scipy.nan
cqp = scipy.nan
dp = scipy.nan
return scipy.array([q0, p0, dq, cqp, dp])
def setUp(self):
# Make a positive definite noise matrix, clean map, and dirty_map.
self.nra = 10
self.ndec = 5
self.nf = 20
self.shape = (self.nf, self.nra, self.ndec)
self.size = self.nra * self.ndec * self.nf
# Clean map.
clean_map = sp.empty(self.shape, dtype=float)
clean_map = al.make_vect(clean_map, axis_names=('freq', 'ra', 'dec'))
clean_map[...] = sp.sin(sp.arange(self.nf))[:,None,None]
clean_map *= sp.cos(sp.arange(self.nra))[:,None]
clean_map *= sp.cos(sp.arange(self.ndec))
# Noise inverse matrix.
noise_inv = sp.empty(self.shape * 2, dtype=float)
noise_inv = al.make_mat(noise_inv, axis_names=('freq', 'ra', 'dec')*2,
row_axes=(0, 1, 2), col_axes=(3, 4, 5))
rand_mat = rand.randn(*((self.size,) * 2))
information_factor = 1.e6 # K**-2
rand_mat = sp.dot(rand_mat, rand_mat.transpose()) * information_factor
noise_inv.flat[...] = rand_mat.flat
# Dirty map.
dirty_map = al.partial_dot(noise_inv, clean_map)
# Store in self.
self.clean_map = clean_map
self.noise_inv = noise_inv
self.dirty_map = dirty_map
def optdelta(UY,UX,S,ldeltanull=None,numintervals=100,ldeltamin=-10.0,ldeltamax=10.0):
"""find the optimal delta"""
if ldeltanull==None:
nllgrid=SP.ones(numintervals+1)*SP.inf;
ldeltagrid=SP.arange(numintervals+1)/(numintervals*1.0)*(ldeltamax-ldeltamin)+ldeltamin;
nllmin=SP.inf;
for i in SP.arange(numintervals+1):
nllgrid[i]=nLLeval(ldeltagrid[i],UY,UX,S);
if nllgrid[i]<nllmin:
nllmin=nllgrid[i];
ldeltaopt_glob=ldeltagrid[i];
foundMin=False
for i in SP.arange(numintervals-1)+1:
continue
ee = 1E-8
#carry out brent optimization within the interval
if ((nllgrid[i-1]-nllgrid[i])>ee) and ((nllgrid[i+1]-nllgrid[i])>1E-8):
foundMin = True
ldeltaopt,nllopt,iter,funcalls = OPT.brent(nLLeval,(UY,UX,S),(ldeltagrid[i-1],ldeltagrid[i],ldeltagrid[i+1]),full_output=True);
if nllopt<nllmin:
nllmin=nllopt;
ldeltaopt_glob=ldeltaopt;
else:
ldeltaopt_glob=ldeltanull;
return ldeltaopt_glob;
def estimateBeta(X,Y,K,C=None,addBiasTerm=False,numintervals0=100,ldeltamin0=-5.0,ldeltamax0=5.0):
""" compute all pvalues
If numintervalsAlt==0 use EMMA-X trick (keep delta fixed over alternative models)
"""
n,s=X.shape;
n_pheno=Y.shape[1];
S,U=LA.eigh(K);
UY=SP.dot(U.T,Y);
UX=SP.dot(U.T,X);
if (C==None):
Ucovariate=SP.dot(U.T,SP.ones([n,1]));
else:
if (addBiasTerm):
C_=SP.concatenate((C,SP.ones([n,1])),axis=1)
Ucovariate=SP.dot(U.T,C_);
else:
Ucovariate=SP.dot(U.T,C);
n_covar=Ucovariate.shape[1];
beta = SP.empty((n_pheno,s,n_covar+1));
LL=SP.ones((n_pheno,s))*(-SP.inf);
ldelta=SP.empty((n_pheno,s));
sigg2=SP.empty((n_pheno,s));
pval=SP.ones((n_pheno,s))*(-SP.inf);
for phen in SP.arange(n_pheno):
UY_=UY[:,phen];
ldelta[phen]=optdelta(UY_,Ucovariate,S,ldeltanull=None,numintervals=numintervals0,ldeltamin=ldeltamin0,ldeltamax=ldeltamax0);
for snp in SP.arange(s):
UX_=SP.hstack((UX[:,snp:snp+1],Ucovariate));
nLL_, beta_, sigg2_=nLLeval(ldelta[phen,snp],UY_,UX_,S,MLparams=True);
beta[phen,snp,:]=beta_;
sigg2[phen,snp]=sigg2_;
LL[phen,snp]=-nLL_;
return beta, ldelta
def __init__(self,fitness_func,npop = 20,w = 0.5,c1 = 2.01,c2 = 2.02,debug = False):
seed()
self.debug = debug
self.c1 = c1
self.c2 = c2
self.w = w
self.ns = int(npop)
self.fitness_func = fitness_func
# gera pop inicial
if os.path.isfile("dump_pso.pkl"):
dump_fd = open("dump_pso.pkl",'r')
self.pop = cPickle.load(dump_fd)
self.fit = cPickle.load(dump_fd)
self.v = cPickle.load(dump_fd)
self.bfg = cPickle.load(dump_fd)
self.bfg_fitness = cPickle.load(dump_fd)
self.bfp = cPickle.load(dump_fd)
self.bfp_fitness = cPickle.load(dump_fd)
else:
self.pop = scipy.array([self.gera_individuo() for i in scipy.arange(self.ns)])
self.fit = scipy.zeros(self.ns)
# avalia fitness de toda populacao
for i in scipy.arange(self.ns):
self.fit[i],self.pop[i] = self.avalia_aptidao(self.pop[i])
# inicializa velocidades iniciais
self.v = scipy.zeros((self.ns,Dim))
# guarda a melhor posicao de cada particula
self.bfp = scipy.copy(self.pop)
self.bfp_fitness = scipy.copy(self.fit)
# guarda a melhor posicao global
self.bfg = self.pop[self.bfp_fitness.argmin()].copy()
self.bfg_fitness = self.bfp_fitness.min().copy()
def KramersKronigFFT(ImX_A): ''' Hilbert transform used to calculate real part of a function from its imaginary part uses piecewise cubic interpolated integral kernel of the Hilbert transform use only if len(ImX_A)=2**m-1, uses fft from scipy.fftpack ''' X_A = sp.copy(ImX_A) N = int(len(X_A)) ## be careful with the data type, orherwise it fails for large N if N > 3e6: A = sp.arange(3,N+1,dtype='float64') else: A = sp.arange(3,N+1) X1 = 4.0*sp.log(1.5) X2 = 10.0*sp.log(4.0/3.0)-6.0*sp.log(1.5) ## filling the kernel if N > 3e6: Kernel_A = sp.zeros(N-2,dtype='float64') else: Kernel_A = sp.zeros(N-2) Kernel_A = (1-A**2)*((A-2)*sp.arctanh(1.0/(1-2*A))+(A+2)*sp.arctanh(1.0/(1+2*A)))\ +((A**3-6*A**2+11*A-6)*sp.arctanh(1.0/(3-2*A))+(A+3)*(A**2+3*A+2)*sp.arctanh(1.0/(2*A+3)))/3.0 Kernel_A = sp.concatenate([-sp.flipud(Kernel_A),sp.array([-X2,-X1,0.0,X1,X2]),Kernel_A])/sp.pi ## zero-padding the functions for fft ImXExt_A = sp.concatenate([X_A[int((N-1)/2):],sp.zeros(N+2),X_A[:int((N-1)/2)]]) KernelExt_A = sp.concatenate([Kernel_A[N:],sp.zeros(1),Kernel_A[:N]]) ## performing the fft ftReXExt_A = -fft(ImXExt_A)*fft(KernelExt_A) ReXExt_A = sp.real(ifft(ftReXExt_A)) ReX_A = sp.concatenate([ReXExt_A[int((3*N+3)/2+1):],ReXExt_A[:int((N-1)/2+1)]]) return ReX_A
def plotmap(self,fig,ax):
""" This function will plot the map of Alaska. The data will be plotted
over it and will use the basemap class to position everything.
Input
fig - The figure handle for the plots.
ax - The axes handle that the map will be plotted over.
Output
m - This is the handle for the basemap object.
"""
latlim2 = self.params['latbounds']
lonlim2 = self.params['lonbounds']
m = Basemap(projection='merc',lon_0=sp.mean(lonlim2),lat_0=sp.mean(latlim2),\
lat_ts=sp.mean(latlim2),llcrnrlat=latlim2[0],urcrnrlat=latlim2[1],\
llcrnrlon=lonlim2[0],urcrnrlon=lonlim2[1],\
rsphere=6371200.,resolution='i',ax=ax)
# draw coastlines, state and country boundaries, edge of map.
#m.drawcoastlines()
# m.drawstates()
# m.drawcountries()
m.readshapefile('st99_d00','states',drawbounds=True)
merstep = sp.round_((lonlim2[1]-lonlim2[0])/5.)
parstep = sp.round_((latlim2[1]-latlim2[0])/5.)
meridians=sp.arange(lonlim2[0],lonlim2[1],merstep)
parallels = sp.arange(latlim2[0],latlim2[1],parstep)
m.drawparallels(parallels,labels=[1,0,0,0],fontsize=10)
m.drawmeridians(meridians,labels=[0,0,0,1],fontsize=10)
plt.hold(True)
return m
def setData(self,x_c=None,x_r=None,x=None,gplvm_dimensions_r=None,gplvm_dimensions_c=None,y=None,**kw_args):
#previous interfaces used x,y; now e add x_r/x_c assuming x_r=x
self.y=y
self.n=y.shape[0]
self.d=y.shape[1]
if x_r is not None:
x = x_r
else:
x_r = SP.zeros([self.n,0])
if x is not None:
x_r = x
#GPLVM.GPLVM.setData(self,x = x_r,**kw_args)
#inputs for second covariance if applicable
if x_c is not None:
assert x_c.shape[0]==self.d, 'dimension missmatch'
else:
x_c = SP.zeros([self.d,0])
self.x_c = x_c
self.x_r = x_r
#useful input matrix which hold the size of the entire kronecker structure
self.xx = SP.zeros([self.x_r.shape[0]*self.x_c.shape[0],0])
#store rehsaped view of Y
self.nd = self.n*self.d
if gplvm_dimensions_r is None:
gplvm_dimensions_r = SP.arange(self.x_r.shape[1])
if gplvm_dimensions_c is None:
gplvm_dimensions_c = SP.arange(self.x_c.shape[1])
#store dimensions
self.gplvm_dimensions_r = gplvm_dimensions_r
self.gplvm_dimensions_c = gplvm_dimensions_c
self._invalidate_cache()
def _update_indicator(self,K,L):
""" update the indicator """
_update = {'term': self.n_terms*SP.ones((K,L)).T.ravel(),
'row': SP.kron(SP.arange(K)[:,SP.newaxis],SP.ones((1,L))).T.ravel(),
'col': SP.kron(SP.ones((K,1)),SP.arange(L)[SP.newaxis,:]).T.ravel()}
for key in _update.keys():
self.indicator[key] = SP.concatenate([self.indicator[key],_update[key]])
def numProj(self, ang=5, sym='d7', with_mirror=False): csym = abs(float(sym[1:])) ang = abs(float(ang)) if ang == 0.0: return 0 angrad = ang*math.pi/180.0 maxalt = math.pi/2.0 + angrad/1.99 maxaz = 2.0*math.pi/csym if sym[0].lower() == 'd': maxaz /= 2.0 numproj = 0 for alt in arange(0.0, maxalt, angrad): if alt < 1.0e-6: ### only one for top projection numproj+=1 continue ### calculate number of steps numsteps = math.floor(360.0/(ang*1.1547)); numsteps = math.floor(numsteps * math.sin(alt) + 0.5) if numsteps < 1.0e-3: ### only valid for c1, d1, c2 and d2 numsteps = 1.0 numsteps = csym * math.floor(numsteps/csym + 0.5) + 1.0e-6 ### calculate azimuthal step size azstep = 2.0*math.pi/numsteps if (maxaz/azstep) < 2.8: ### if less than 2.8 steps, use 2 steps azstep = maxaz/2.1 for az in arange(0.0, maxaz-azstep/4.0, azstep): if not with_mirror and az > math.pi-1.0e-3 and abs(alt-math.pi/2.0) < 1.0e-3: ### ignore half of the equator continue numproj+=1 return numproj
def triples2mat(triples,shape="csr"):
n = len(triples)
data = arange(n)
ij = arange(2*n).reshape(2,n)
for k,item in enumerate(triples):
ij[0][k],ij[1][k],data[k] = item
return scipy.sparse.coo_matrix((data, ij)).asformat(shape)
def getData(shot, tags=False,
probesort=True, internal=True, external=False):
if tags == False:
print 'tags must be specified in getMDSplus.getData(tags="typetagshere")'
return False
if type(tags)==str:
tags = [tags]
data = {}
data["Shot"] = shot
data["Tags"] = tags
if "RespModes" in tags or "AppModes"in tags:
data["gamma"] = getGamma(shot)
if "RespModes" in tags:
data["RespModes"] = getRespModes(shot)
data["Mtime"] = sp.arange(0, max(data["RespModes"].shape)/512, 1/512)
if "AppModes" in tags:
data["AppModes"] = getRespModes(shot)
data["Mtime"] = sp.arange(0, max(data["AppModes"].shape)/512, 1/512)
if "Bfield" in tags:
data["Bfield"] = getBfield(shot)
if "Bfield" in tags or "Appfield" in tags or "RespField" in tags:
data["Serials"] = getSerials(shot)
data["Position"] = getPosition(shot)
# a time field is created so that resampling can be kept track of within the dictionary
data["Btime"] = sp.arange(0, max(data["Bfield"].shape)/512, 1/512)
if probesort == True:
probeSort(shot, data, internal=internal, external=external)
if "RawData" in tags:
data["RawData"] = getRawData(shot)
return data
def getGenoID(self,i0=None,i1=None,pos0=None,pos1=None,chrom=None,pos_cum0=None,pos_cum1=None):
"""get genotype IDs.
Optionally the indices for loading subgroups the genotype IDs for all people
can be given in one out of three ways:
- 0-based indexing (i0-i1)
- position (pos0-pos1 on chrom)
- cumulative position (pos_cum0-pos_cum1)
If all these are None (default), then all genotypes are returned
Args:
i0: genotype index based selection (start index)
i1: genotype index based selection (stop index)
pos0: position based selection (start position)
pos1: position based selection (stop position)
chrom: position based selection (chromosome)
pos_cum0: cumulative position based selection (start position)
pos_cum1: cumulative position based selection (stop position)
Returns:
ID: scipy.array of genotype IDs (e.g. rs IDs)
"""
#position based matching?
if (i0 is None) and (i1 is None) and ((pos0 is not None) & (pos1 is not None) & (chrom is not None)) or ((pos_cum0 is not None) & (pos_cum1 is not None)):
i0,i1=self.getGenoIndex(pos0=pos0,pos1=pos1,chrom=chrom,pos_cum0=pos_cum0,pos_cum1=pose_cum1)
if "genotype_id" in list(self.geno.keys()):
if (i0 is not None) & (i1 is not None):
return self.geno["genotype_id"][i0:i1]
else:
return self.geno["genotype_id"][i0:i1]
else:
if (i0 is not None) & (i1 is not None):
return SP.arange(i0,i0)
else:
return SP.arange(self.genoM.shape[1])
pass
def eig(A, normal = False, iter = 100): '''Finds eigenvalues of an nxn array A. If A is normal, QRalg.eig may also return eigenvectors. Parameters ---------- A : nxn array May be real or complex normal : bool, optional Set to True if A is normal and you want to calculate the eigenvectors. iter : positive integer, optional Returns ------- v : 1xn array of eigenvectors, may be real or complex Q : (only returned if normal = True) nxn array whose columns are eigenvectors, s.t. A*Q = Q*diag(v) real if A is real, complex if A is complex For more on the QR algorithm, see Eigenvalue Solvers lab. ''' def getSchurEig(A): #Find the eigenvalues of a Schur form matrix. These are the #elements on the main diagonal, except where there's a 2x2 #block on the main diagonal. Then we have to find the #eigenvalues of that block. D = sp.diag(A).astype(complex) #Find all the 2x2 blocks: LD = sp.diag(A,-1) index = sp.nonzero(abs(LD)>.01)[0] #is this a good tolerance? #Find the eigenvalues of those blocks: a = 1 b = -D[index]-D[index+1] c = D[index]*D[index+1] - A[index,index+1]*LD[index] discr = sp.sqrt(b**2-4*a*c) #Fill in vector D with those eigenvalues D[index] = (-b + discr)/(2*a) D[index+1] = (-b - discr)/(2*a) return D n,n = A.shape I = sp.eye(n) A,Q = hessenberg(A,True) if normal == False: for i in sp.arange(iter): s = A[n-1,n-1].copy() Qi,R = la.qr(A-s*I) A = sp.dot(R,Qi) + s*I v = getSchurEig(A) return v elif normal == True: for i in sp.arange(iter): s = A[n-1,n-1].copy() Qi,R = la.qr(A-s*I) A = sp.dot(R,Qi) + s*I Q = sp.dot(Q,Qi) v = sp.diag(A) return v,Q
def gqr(A): """Finds the QR decomposition of A using Givens rotations. input: A, mxn array with m>=n output: Q, orthogonal mxm array R, upper triangular mxn array s.t QR = A """ def rotate(i,k,B): # create the Givens rotation matrix G to zero out the i,k entry of B c,s,r = solve(B[k,k],B[i,k]) r = sp.sqrt(B[k,k]**2 + B[i,k]**2) c = B[k,k]/r s = -B[i,k]/r G = sp.eye(m) G[i,i] = c G[k,k] = c G[k,i] = -s G[i,k] = s return G B = A.copy() m,n = B.shape G = sp.eye(m) #cycle through each nonzero subdiagonal element of B, and rotate it to zero for k in sp.arange(n-1): for i in sp.arange(k+1,m): if B[i,k] is not 0: H = rotate(i,k,B) B = sp.dot(H,B) G = sp.dot(H,G) return G.T, B
def PlotLc(id=None, dir=None, quarter=None, tset=None):
if id != None:
tset, status = GetLc(id=id, dir=dir, tr_out=True)
if tset is None:
return
elif tset == None:
print "no tset"
return
if quarter != None:
tset.tables[1] = tset.tables[1].where(tset.tables[1].Q == quarter)
if len(tset.tables[1].TIME) == 0:
print "No data for Q%d" % quarter
return
time = tset.tables[1].TIME
phase, inTr = TransitPhase(tset)
col = ["r", "g", "b", "y", "c", "m", "grey"]
npl, nobs = inTr.shape
pylab.figure(1)
pylab.clf()
pylab.plot(time, tset.tables[1].PDCSAP_FLUX, "k-")
for ipl in scipy.arange(npl):
list = inTr[ipl, :].astype(bool)
pylab.plot(time[list], tset.tables[1].PDCSAP_FLUX[list], ".", c=col[ipl])
l = scipy.isfinite(time)
pylab.xlim(time[l].min(), time[l].max())
ttl = "KIC %d, P=" % (tset.tables[0].KID[0])
for i in scipy.arange(npl):
ttl = "%s%.5f " % (ttl, tset.tables[0].Period[i])
if quarter != None:
ttl += "Q%d" % quarter
pylab.title(ttl)
return
def plotSpectrum(y,Fs):
"""
Plots a Single-Sided Amplitude Spectrum of y(t)
:param y: the signal
:param Fs: the sampling frequency
"""
n = len(y) # length of the signal
k = arange(n)
T = n/Fs
frq = k/T # Two sides frequency range
frq = np.squeeze(frq)
frq = frq[range(int(n/2))] # One side frequency range
Y = fft(y)/n # FFT computing and normalization
Y = Y[range(int(n/2))]
# Plot the signal in wall-clock time
subplot(2,1,1)
Ts = 1.0/Fs; # sampling interval
t = arange(0, 1.0*len(y)/Fs, Ts)
plot(t, y)
xlabel('Time')
ylabel('Amplitude')
# Plot the spectrum
subplot(2,1,2)
plot( frq, np.log(abs(Y)),'r') # Plotting the spectrum
xlabel('Freq (Hz)')
ylabel('log|Y(freq)|')
show()
def ldpred_gibbs(beta_hats,
genotypes=None,
start_betas=None,
h2=None,
n=None,
ns=None,
ld_radius=100,
num_iter=60,
burn_in=10,
p=None,
zero_jump_prob=0.01,
sampl_var_shrink_factor=0.9,
tight_sampling=False,
ld_dict=None,
reference_ld_mats=None,
ld_boundaries=None,
verbose=False,
print_progress=True):
"""
LDpred (Gibbs Sampler)
"""
# Set random seed to stabilize results
sp.random.seed(42)
t0 = time.time()
m = len(beta_hats)
ldpred_n, ldpred_inf_n = get_LDpred_sample_size(n, ns, verbose)
# If no starting values for effects were given, then use the infinitesimal model starting values.
if start_betas is None and verbose:
print(
'Initializing LDpred effects with posterior mean LDpred-inf effects.'
)
print('Calculating LDpred-inf effects.')
start_betas = LDpred_inf.ldpred_inf(
beta_hats,
genotypes=genotypes,
reference_ld_mats=reference_ld_mats,
h2=h2,
n=ldpred_inf_n,
ld_window_size=2 * ld_radius,
verbose=False)
curr_betas = sp.copy(start_betas)
assert len(
curr_betas
) == m, 'Betas returned by LDpred_inf do not have the same length as expected.'
curr_post_means = sp.zeros(m)
avg_betas = sp.zeros(m)
# Iterating over effect estimates in sequential order
iter_order = sp.arange(m)
# Setting up the marginal Bayes shrink
const_dict = prepare_constants(ldpred_n, ns, m, p, h2,
sampl_var_shrink_factor)
for k in range(num_iter): # Big iteration
h2_est = max(0.00001, sp.sum(curr_betas**2))
if tight_sampling:
# Force an alpha shrink if estimates are way off compared to heritability estimates.
#(May improve MCMC convergence.)
alpha = min(1.0 - zero_jump_prob, 1.0 / h2_est,
(h2 + 1.0 / sp.sqrt(ldpred_n)) / h2_est)
else:
alpha = 1.0 - zero_jump_prob
rand_ps = sp.random.random(m)
rand_norms = stats.norm.rvs(0.0, 1, size=m) * const_dict['rv_scalars']
for i, snp_i in enumerate(iter_order):
if ld_boundaries is None:
start_i = max(0, snp_i - ld_radius)
focal_i = min(ld_radius, snp_i)
stop_i = min(m, snp_i + ld_radius + 1)
else:
start_i = ld_boundaries[snp_i][0]
stop_i = ld_boundaries[snp_i][1]
focal_i = snp_i - start_i
#Figure out what sample size and constants to use
cd = get_constants(snp_i, const_dict)
# Local LD matrix
D_i = ld_dict[snp_i]
# Local (most recently updated) effect estimates
local_betas = curr_betas[start_i:stop_i]
# Calculate the local posterior mean, used when sampling.
local_betas[focal_i] = 0.0
res_beta_hat_i = beta_hats[snp_i] - sp.dot(D_i, local_betas)
b2 = res_beta_hat_i**2
d_const_b2_exp = cd['d_const'] * sp.exp(-b2 * cd['n'] / 2.0)
if sp.isreal(d_const_b2_exp):
numerator = cd['c_const'] * sp.exp(-b2 / (2.0 * cd['hdmpn']))
if sp.isreal(numerator):
if numerator == 0.0:
postp = 0.0
else:
postp = numerator / (numerator + d_const_b2_exp)
assert sp.isreal(
postp
), 'The posterior mean is not a real number? Possibly due to problems with summary stats, LD estimates, or parameter settings.'
else:
postp = 0.0
else:
postp = 1.0
curr_post_means[snp_i] = cd['hdmp_hdmpn'] * postp * res_beta_hat_i
if rand_ps[i] < postp * alpha:
# Sample from the posterior Gaussian dist.
proposed_beta = rand_norms[
snp_i] + cd['hdmp_hdmpn'] * res_beta_hat_i
else:
# Sample 0
proposed_beta = 0.0
curr_betas[snp_i] = proposed_beta # UPDATE BETA
if verbose and print_progress:
sys.stdout.write('\r%0.2f%%' % (100.0 *
(min(1,
float(k + 1) / num_iter))))
sys.stdout.flush()
if k >= burn_in:
avg_betas += curr_post_means # Averaging over the posterior means instead of samples.
if verbose and print_progress:
sys.stdout.write('\r%0.2f%%\n' % (100.0))
sys.stdout.flush()
avg_betas = avg_betas / float(num_iter - burn_in)
t1 = time.time()
t = (t1 - t0)
if verbose:
print('Took %d minutes and %0.2f seconds' % (t / 60, t % 60))
return {'betas': avg_betas, 'inf_betas': start_betas}
freerun_steps = 1000
training_sample_length = 5000
n_training_samples = 3
test_sample_length = 5000
train_signals = Oger.datasets.mackey_glass(sample_len=training_sample_length, n_samples=n_training_samples)
test_signals = Oger.datasets.mackey_glass(sample_len=test_sample_length, n_samples=1)
reservoir = Oger.nodes.LeakyReservoirNode(output_dim=400, leak_rate=0.4, input_scaling=.05, bias_scaling=.2, reset_states=False)
readout = Oger.nodes.RidgeRegressionNode()
Oger.utils.enable_washout(Oger.nodes.RidgeRegressionNode, 500)
flow = Oger.nodes.FreerunFlow([reservoir, readout], freerun_steps=freerun_steps)
gridsearch_parameters = {readout:{'ridge_param': 10 ** scipy.arange(-4, 0, .3)}}
# Instantiate an optimizer
loss_function = Oger.utils.timeslice(range(training_sample_length - freerun_steps, training_sample_length), Oger.utils.nrmse)
opt = Oger.evaluation.Optimizer(gridsearch_parameters, loss_function)
# Do the grid search
opt.grid_search([[], train_signals], flow, cross_validate_function=Oger.evaluation.leave_one_out)
# Get the optimal flow and run cross-validation with it
opt_flow = opt.get_optimal_flow(verbose=True)
print 'Freerun on test_signals signal with the optimal flow...'
opt_flow.train([[], train_signals])
freerun_output = opt_flow.execute(test_signals[0][0])
#!/usr/bin/env python
from sys import argv
from scipy import array, arange
from scipy.misc import toimage
from itertools import product
from pprint import pprint
edge = 60
half = edge / 2
check = 10
argc = len(argv)
if argc >= 2:
temp = int(argv[1])
if 1024 >= temp >= 60:
edge = temp
half = edge / 2
if argc >= 3:
temp = int(argv[2])
if half >= temp >= 1:
check = temp
shape = (edge, edge)
XY = list(product(arange(edge), repeat=2))
value = [255 * int((x / check) & 1 == (y / check) & 1) for (x, y) in XY]
board = array(value).reshape(shape)
image = toimage(board)
image.save('img/checkers_%04d_%02d.png' % (edge, check))
print 'setting up interface'
comm = Motor_Comm()
comm.enable()
comm.standby('off')
comm.loop_mode('off')
dt = comm.dt()
num_motor = comm.num_motor()
if 1:
print 'creating kinematics'
T = 2.5
num_period = 5.0
n = int(num_period * T / dt)
t = scipy.arange(0.0, n) * dt
x = scipy.zeros((n, num_motor))
for i in range(0, num_motor):
x[:, i] = kine(t, T)
print 'loading outscan buffer'
comm.load_os_buffer(x)
#comm.print_status()
print 'moving to start'
comm.move2start()
print 'outscanning buffer'
comm.start()
comm.wait()
def tdo_fft(inputfile, outputfile):
''' Perform Fourier transform and return frequency evolution '''
# Input parameters
fourier_le = 1024 # Fourier length
time_le = 1024 # timewindow
dfmin = 0.01 # Frequency resolution
dt = 2e-8 # timestep of acquisition
load_balancing = 1
# Lecture du fichier
fid = open(inputfile, 'rb')
fid.seek(512) # Skip useless header
V = fromfile(fid, int16, -1, '')
fid.close()
pstart = 1 # First timewindow
pend = int(floor(
(len(V) - 4 * fourier_le) / time_le)) + 1 # Last timewindow
t = arange(0, fourier_le) * dt
# Approximation of main frequency
Vf = abs(real(fft(V[0:fourier_le])))
tf = fftfreq(fourier_le, dt)
fmax = zeros((pend + 2 - pstart, 2))
fmax[0, 1] = tf[argmax(Vf[0:int(fourier_le / 2)])]
fmax[0, 0] = time_le * dt / 2
# Calculation of constants
expon = -2j * pi * t
deltaf0 = tf[1] / 1000
if deltaf0 < dfmin:
deltaf0 = 10 * dfmin
# Start jobs
job_server = pp.Server()
ncpus = int(job_server.get_ncpus())
serv_jobs = []
# Load-balancing
# Last processes are faster
# If nprocess = ncpus, half of the core remains mostly idle
if load_balancing == 1:
nprocess = ncpus * 4
else:
nprocess = ncpus
pstart_b = pstart
for i in range(0, nprocess):
if nprocess == 1:
pend_b = pend
else:
pend_b = int(pstart_b + floor(pend / nprocess))
print(pstart_b, pend_b)
args_tuple = (pstart_b, pend_b+1, \
V[pstart_b*time_le:(pend_b+1)*time_le+fourier_le], \
dt, dfmin, deltaf0, expon, fourier_le, time_le,)
serv_jobs.append(job_server.submit(find_freq, args_tuple, \
(local_trapz,)))
pstart_b = pend_b
pstart_b = pstart
for i in range(0, nprocess):
if nprocess == 1:
pend_b = pend
else:
pend_b = int(pstart_b + floor(pend / nprocess))
fmax[pstart_b:pend_b, :] = serv_jobs[i]()
pstart_b = pend_b
# Save calculation in file
savetxt(outputfile, fmax)
job_server.print_stats()
def find_freq(ps, pe, V, dt, dfmin, deltaf0, expon, fourier_le, time_le):
'''Perform DFT of signal and return main frequency'''
from scipy import zeros, real, fft, argmax, exp, arange, cos, pi, mean
from scipy.fftpack import fftfreq
Vf = abs(real(fft(V[0:fourier_le] - mean(V[0:fourier_le]))))
tf = fftfreq(fourier_le, dt)
fmax = zeros((pe - ps, 2))
fmax[0, 1] = tf[argmax(Vf[0:int(fourier_le / 2)])]
fmax[0, 0] = (ps * time_le + fourier_le / 2) * dt
# Rectangular
#window = ones(fourier_le)
# Cosinus
window = arange(0, fourier_le)
window = 1 - cos(window * 2 * pi / (fourier_le - 1))
for i in xrange(1, pe - ps):
# Utilisation de la dernière valeur comme point de depart
a = fmax[i - 1, 1]
V_temp = window * V[i * time_le:i * time_le + fourier_le]
# Previous frequency spectral weight
# Complex exponential time consuming
# Need a smarter way to perform this calculations
deltaf = deltaf0
essaimax = abs(local_trapz(V_temp * exp(expon * a)))
# Calculation of local derivative of Fourier transform
# If derivative positive, then search for frequency in growing direction
if abs(local_trapz(V_temp * exp(expon * (a + deltaf)))) > essaimax:
while abs(deltaf) > dfmin:
F = abs(local_trapz(V_temp * exp(expon * (a + deltaf))))
if F > essaimax:
essaimax = F
a += deltaf
else:
deltaf = -deltaf / 5
if (abs(deltaf) < dfmin) and (abs(deltaf) > dfmin * 4.9):
deltaf = deltaf / abs(deltaf) * 1.01 * dfmin
# Store frequency
fmax[i, 0:2] = [((i + ps) * time_le + fourier_le / 2) * dt,
a - 2.5 * deltaf]
# Lower frequency otherwise
else:
while abs(deltaf) > dfmin:
F = abs(local_trapz(V_temp * exp(expon * (a - deltaf))))
if F > essaimax:
essaimax = F
a -= deltaf
else:
deltaf = -deltaf / 5
if (abs(deltaf) < dfmin) and (abs(deltaf) > dfmin * 4.9):
deltaf = deltaf / abs(deltaf) * 1.01 * dfmin
# Store frequency
fmax[i, 0:2] = [((i + ps) * time_le + fourier_le / 2) * dt,
a + 2.5 * deltaf]
return fmax[1:, :]
color='g',
linestyle='dashed')
grid()
subplot(212)
ylabel(r'$\bar{u}^s$')
xlabel(r't')
plt.ylim(-2.1, 2.1)
plt.xlim(xmin=.49)
p1 = plot(dataPlot[4900:, 0], dataPlot[4900:, 3])
#p2 = plot(dataPlot[4900:, 0], np.sin(50*dataPlot[4900:, 0]))
#plt.legend((p1[0], p2[0]), (r'$\bar{u}^s(t)$', r'$-\rho(t)$'), ncol=2)
savefig('esmc_sigma_u_z')
u_z = dataPlot[4900:, 3]
n = len(u_z)
Y = scipy.fft(dataPlot[4900:, 3]) / n
k = arange(n)
T = n * h
frq = k / T
frq = frq[list(range(n / 2))]
Y = Y[list(range(n / 2))]
plot(frq, abs(Y), 'r')
xlabel(r'freq (Hz)')
title(r'Frequency spectrum of $\bar{u}^s$')
savefig('esmc_u_freq.png')
# TODO
# compare with the reference
#ref = getMatrix(SimpleMatrix("result.ref"))
#if (norm(dataPlot - ref[1:,:]) > 1e-12):
# print("Warning. The result is rather different from the reference file.")
def run_demo():
LG.basicConfig(level=LG.INFO)
#1. simulate data from a linear PCA model
N = 25
K = 5
D = 200
SP.random.seed(1)
S = SP.random.randn(N,K)
W = SP.random.randn(D,K)
Y = SP.dot(W,S.T).T
Y+= 0.5*SP.random.randn(N,D)
#use "standard PCA"
[Spca,Wpca] = gplvm.PCA(Y,K)
#reconstruction
Y_ = SP.dot(Spca,Wpca.T)
if 1:
#use linear kernel
covariance = linear.LinearCFISO(n_dimensions=K)
hyperparams = {'covar': SP.log([1.2])}
if 0:
#use ARD kernel
covariance = se.SqexpCFARD(n_dimensions=K)
hyperparams = {'covar': SP.log([1]*(K+1))}
#initialization of X at arandom
X0 = SP.random.randn(N,K)
X0 = Spca
hyperparams['x'] = X0
#standard Gaussian noise
likelihood = lik.GaussLikISO()
hyperparams['lik'] = SP.log([0.1])
g = gplvm.GPLVM(covar_func=covariance,likelihood=likelihood,x=X0,y=Y,gplvm_dimensions=SP.arange(X0.shape[1]))
#specify optimization bounds:
bounds = {}
bounds['lik'] = SP.array([[-5.,5.]]*D)
hyperparams['x'] = X0
print "running standard gplvm"
[opt_hyperparams,opt_lml2] = opt.opt_hyper(g,hyperparams,gradcheck=False)
print "optimized latent X:"
print opt_hyperparams['x']
def preTrain(Y,
terms,
P_I,
noise='gauss',
nFix=None,
priors=None,
covariates=None):
"""Pre-train the slalom factor analysis model.
Helper function to pre-train the slalom factor analysis model to achieve
faster convergence and obtain an initial update order. Called by `initFA`.
Args:
Y (array_like): Matrix of normalised count values of `N` cells
and `G` variable genes in log-space.
Dimension (:math:`N\\times G`).
terms (vector_like): Names of `K` annotated gene sets. Dimension
(:math:`K\\times 0`).
P_I (array_like): Matrix specifying the likelihood of
whether a gene is annotated to a specific factor.
Dimension (:math:`G\\times K`).
noise (str): Specifies the observation noise model. Should be either `'gauss'`,`'hurdle'` or `'poisson'`.
Defaults to `gauss`.
nFix (int): Number of terms which should be fixed and updated first. Defaults to `None`,
resulting in the number of unannotated factors being updated first.
Returns:
A vector containing the initial update order of the terms
"""
init_params = {}
init_params['noise'] = noise
init_params['iLatent'] = SP.where(terms == 'hidden')[0]
init_params['iLatentSparse'] = SP.array(
[]) #SP.where(terms=='hiddenSparse')[0]
if not (covariates is None):
init_params['Known'] = covariates
learnPi = False
pi = P_I.copy()
K = pi.shape[1]
#data for sparseFA instance
pi[pi > .8] = 1 - 1e-100 # 0.99#1-1e-100#0.9999
pi[pi < .2] = 1e-100 #1e-8
init = {
'init_data': CGauss(Y),
'Pi': pi,
'terms': terms,
'noise': noise,
'covariates': covariates
}
sigmaOff = 1E-3
sparsity = 'VB'
#prior on noise level
if priors is None:
priors = {'Eps': {'priors': [1E-3, 1E-3]}}
#how to initialize network?
#initType = 'pcaRand'
terms0 = terms
pi0 = pi.copy()
FA0 = slalom.CSparseFA(components=K,
sigmaOff=sigmaOff,
sigmaOn=SP.ones(pi.shape[1]) * 1.0,
sparsity=sparsity,
nIterations=50,
permutation_move=False,
priors=priors,
initType='pcaRand',
learnPi=learnPi)
FA0.init(**init)
if nFix == None:
nFix = FA0.nKnown + FA0.nLatent
#Fit PCA
pca = PCA(n_components=1) #,svd_solver='full')
pca.fit(FA0.Z.E1)
X = pca.transform(FA0.Z.E1)
#Sort by correlation to PC1
MPC = abs(vcorrcoef(FA0.S.E1[:, SP.argsort(FA0.W.Ilabel)].T, X.T))[nFix:]
Ipi = SP.argsort(-MPC.ravel())
IpiRev = SP.argsort(MPC.ravel())
mRange = list(range(FA0.components))
mRange[nFix:] = Ipi + nFix
mRangeRev = list(range(FA0.components))
mRangeRev[nFix:] = IpiRev + nFix
#Run model for 50 iterations
pi = pi0[:, mRange]
terms = terms0[mRange]
init = {'init_data': CGauss(Y), 'Pi': pi, 'terms': terms, 'noise': noise}
FA = slalom.CSparseFA(components=K,
sigmaOff=sigmaOff,
sigmaOn=SP.ones(pi.shape[1]) * 1.0,
sparsity=sparsity,
nIterations=50,
permutation_move=False,
priors=priors,
initType='pcaRand',
learnPi=learnPi)
FA.shuffle = True
FA.nScale = 30
FA.init(**init)
for j in range(50):
FA.update()
#Run reverse model for 50 iterations
pi = pi0[:, mRangeRev]
terms = terms0[mRangeRev]
init = {'init_data': CGauss(Y), 'Pi': pi, 'terms': terms, 'noise': noise}
FArev = slalom.CSparseFA(components=K,
sigmaOff=sigmaOff,
sigmaOn=SP.ones(pi.shape[1]) * 1.0,
sparsity=sparsity,
nIterations=50,
permutation_move=False,
priors=priors,
initType='pcaRand',
learnPi=learnPi)
FArev.shuffle = True
FArev.nScale = 30
FArev.init(**init)
#FArev.iterate(forceIterations=True, nIterations=nIterations)
for j in range(50):
FArev.update()
#import pdb
IpiM = (-(0.5 * (1. / FArev.Alpha.E1[SP.argsort(mRangeRev)][nFix:]) + .5 *
(1. / FA.Alpha.E1[SP.argsort(mRange)][nFix:]))).argsort()
# IpiM = (-(0.5*(1./FArev.Alpha.E1[SP.argsort(mRangeRev)][nFix:]*FArev.S.E1[:,SP.argsort(mRangeRev)][:,nFix:].std(0))+.5*(1./FA.Alpha.E1[SP.argsort(mRange)][nFix:]*FA.S.E1[:,SP.argsort(mRange)][:,nFix:].std(0)))).argsort()
Ilabel = SP.hstack([SP.arange(nFix), IpiM + nFix])
return Ilabel
# Create input import scipy import loudia fundamental = 440.0 harmonics = 5 frameSize = 128 fftSize = 512 sampleRate = 8000 a_zeros = scipy.zeros( frameSize ) a_ones = scipy.ones( frameSize ) a_random = scipy.random.random( frameSize ) a_sine = scipy.cos(2 * scipy.pi * 440 * scipy.arange( frameSize ) / sampleRate + scipy.pi/4.0) a_sine += (a_random - 0.5) * 1.0 # Loudia's solution # --------------------------------- # window = loudia.Window(frameSize, loudia.Window.HAMMING) fft = loudia.FFT(fftSize) peaks = loudia.PeakDetectionComplex(5, 4) peaksinterp = loudia.PeakInterpolationComplex() trajs = loudia.PeakTracking(5, 4, 3) r_sine_windowed = window.process(a_sine) r_sine_mag = fft.process(r_sine_windowed) r_sine_peakpos, r_sine_peakmag, r_sine_peakphase = peaks.process(r_sine_mag) r_sine_peakipos, r_sine_peakimag, r_sine_peakphasei = peaksinterp.process(r_sine_mag, r_sine_peakpos, r_sine_peakmag, r_sine_peakphase)
def run(P):
import pyfits, os, scipy, pylab
web = '/afs/slac.stanford.edu/u/ki/pkelly/' # os.environ['sne'] + '/photoz/COSMOS_' + set + '_' + ext + '/'
os.system('mkdir -p ' + web)
print 'web', web
comp = open(web + '/comp.html', 'w')
print 'loading cosmos'
C = pyfits.open(
'/nfs/slac/g/ki/ki05/anja/SUBARU/COSMOS_PHOTOZ/PHOTOMETRY_W-C-IC_' +
ext + '/cosmos_lephare.cat')['OBJECTS'].data
print 'loading BPZ'
U = pyfits.open(
'/nfs/slac/g/ki/ki05/anja/SUBARU/COSMOS_PHOTOZ/PHOTOMETRY_W-C-IC_' +
ext + '/COSMOS_PHOTOZ.APER.1.' + set +
'.list.all.bpz.tab')['STDTAB'].data
print 'loading PDZ'
print 'done'
params = {
'backend': 'ps',
'text.usetex': True,
'ps.usedistiller': 'xpdf',
'ps.distiller.res': 6000
}
pylab.rcParams.update(params)
fig_width = 6
fig_height = 6
fig_size = [fig_width, fig_height]
params = {
'axes.labelsize': 16,
'text.fontsize': 16,
'legend.fontsize': 15,
'xtick.labelsize': 16,
'ytick.labelsize': 16,
'figure.figsize': fig_size
}
pylab.rcParams.update(params)
for low, high in [[0, 0.1], [0.1, 0.2], [0.2, 0.3], [0.3, 0.4], [0.4, 0.5],
[0.5, 0.6], [0.6, 0.7], [0.7, 0.8], [0.8, 0.9],
[0.9, 1.0], [1.0, 1.2], [3, 4]]:
file = ext + '_' + str(low) + '_' + str(high) + 'interval.png'
comp.write('<img src=' + file + '></img>\n')
if True:
pylab.clf()
out_zs = (U.field('BPZ_Z_B') < high) * (
U.field('BPZ_Z_B') > low) * (U.field('BPZ_ODDS') >
0) * (C.field('zp_best') > 0)
cosmos_zs = C.field('zp_best')[out_zs]
multiple = 7
bins = scipy.arange(0, 4., 0.01 * multiple)
n, bins, patches = pylab.hist(cosmos_zs, bins=bins, histtype='bar')
pylab.clf()
mask = out_zs[:]
pdz_zs_raw = P[mask].sum(axis=0) / mask.sum()
pdz_zs = []
sum = 0
for i in range(len(pdz_zs_raw)):
if (i + 1) % multiple == 0:
pdz_zs.append(sum)
sum = 0
sum += pdz_zs_raw[i]
print pdz_zs
x = bins[:-1]
y = pdz_zs[:len(bins[:-1])]
y[0] = 0
print x, y
y_cosmos = n / float(len(cosmos_zs))
print(y_cosmos)
pylab.bar(x,
y_cosmos,
width=x[1] - x[0],
facecolor='red',
linewidth=0,
label='COSMOS')
pylab.bar(x,
y,
width=x[1] - x[0],
facecolor='none',
edgecolor='black',
label='BPZ')
import scipy, pylab
zs = scipy.arange(0.01000, 4.0100, 0.0100)
#pylab.plot([0,1],[0,1],c='red')
#pylab.xlim([0,1])
#pylab.ylim([0,1])
#pylab.title('ALL')
pylab.legend(frameon=False)
pylab.figtext(0.62,
0.73,
'$' + str(low) + '< z_B < ' + str(high) + '$',
size=15)
pylab.figtext(0.62,
0.68,
str(len(cosmos_zs)) + ' Galaxies',
size=15)
pylab.figtext(0.62, 0.63, 'BVRIZ', size=15)
pylab.ylabel('Probability Density')
pylab.xlabel('Redshift')
print web + file
pylab.savefig(web + file)
pylab.savefig(web + file.replace('.png', '.pdf'))
pylab.savefig(web + file.replace('.png', '.ps'))
#pdz.write('<img width=600px src=all.png></img><br>\n')
comp.close()
def initFA(Y, terms, I, gene_ids=None, nHidden=3, nHiddenSparse = 0,pruneGenes=True, FPR=0.99, FNR=0.001, \
noise='gauss', minGenes=20, do_preTrain=True, nFix=None, priors=None, covariates=None, dropFactors=True, learnPi=False):
"""Initialise the slalom factor analysis model.
Required 3 inputs are first, a gene expression matrix `Y` containing normalised count values of `N` cells and `G`
variable genes in log-space, second a vector `terms` contaning the names of all annotated gene set (correspondig to annotated factors)
and third, a binary indicator matrix `I` linking `G` genes to `K` terms by indicating which genes are annotated to each factor.
A variety of options can be specified as described below.
Args:
Y (array_like): Matrix of normalised count values of `N` cells
and `G` variable genes in log-space.
Dimension (:math:`N\\times G`).
terms (vector_like): Names of `K` annotated gene sets. Dimension
(:math:`K\\times 0`).
I (array_like): Indicator matrix specifying
whether a gene is annotated to a specific factor.
Dimension (:math:`G\\times K`).
gene_ids (array_like): Gene identifiers (opitonal, defaults to None)
FNR (float): False negative rate of annotations.
Defaults to 0.001
FPR (float): False positive rate of annotations.
Defaults to 0.99
nHidden (int): Number of unannotated dense factors. Defaults to 3.
nHiddenSparse (int): Number of unannotated sparse factors. Defaults to 0.
This value should be changed to e.g. 5 if the diagnositcs fail.
pruneGenes (bool): prune genes that are not annotated to a least one factor. This option allows fast inference and
should be set to `True` either if the
key objective is to rank factors or if the annotations cover all genes of interest.
Defaults to `True`.
dropFactors (bool): drop factors from update schedule once they are shut off. In practice, factors that are switched off
at some point during inference are usuallly not switched off. Allows faster inference. Defaults to `True`.
Currently only supported for the Gaussian noise model.
noise (str): Specifies the observation noise model. Should be either `'gauss'`,`'hurdle'` or `'poisson'`.
Defaults to `gauss`.
minGenes (int): minimum number of genes required per term to retain it
Defaults to `20`.
do_preTrain (bool): Boolean switch indicating whether pre-training should be used to establish the initial
update order. Can be set to `False` for very large datasets.
Defaults to `True`
priors (dict): Dictionary containing the hyperparameters of the priors for `Alpha`, `Eps` and Pi (`PiDense` and `PiSparse`).
Defaults to None; in this case default values are used.
covariates (array_like): Matrix with known covariates that are controlled for when fitting the model. Defaults to `None`.
learnPi (bool): Learn sparsity of spearse hidden factors (default False)
Returns:
A :class:`slalom.CSparseFA` instance.
"""
#check for consistency of input parameters
[num_cells, num_genes] = Y.shape
num_terms = I.shape[1]
assert I.shape[
0] == num_genes, 'annotation needs to be matched to gene input dimension'
assert noise in ['gauss', 'hurdle', 'poisson'], 'invalid noise model'
assert 0 < FNR < 1, 'FNR is required to be between 0 and 1'
assert 0 < FNR < 1, 'FPR is required to be between 0 and 1'
if noise == "hurdle" and dropFactors == True:
dropFactors = False
print(
"dropFactors only supported for gauss noise model. Set to False.")
#make sure the annotation is boolean
I = (I > .5)
#. filter annotation by min number of required genes
Iok = I.sum(axis=0) > minGenes
terms = terms[Iok]
I = I[:, Iok]
num_terms = I.shape[1]
#create initial pi matrix, which corresponds to the effective prior probability of an annotated link
pi = SP.zeros([num_genes, num_terms], dtype='float')
#default FNR
pi[:] = FNR
#active links
pi[I] = FPR
#prune genes?
if pruneGenes == True:
idx_genes = SP.sum(I, 1) > 0
Y = Y[:, idx_genes]
pi = pi[idx_genes, :]
if not (gene_ids is None):
gene_ids = SP.array(gene_ids)[idx_genes]
else:
idx_genes = SP.arange(Y.shape[1])
if Y.shape[1] > 10000:
print(
"For large datasets we recommend setting the pruneGenes option to True."
)
#center data for Gaussian observation noise
if noise == 'gauss':
Y -= SP.mean(Y, 0)
#include hidden variables
if nHiddenSparse > 0:
piSparse = SP.ones((Y.shape[1], nHiddenSparse)) * .01
idxVar = SP.argsort(-Y.var(0))
for iH in range(piSparse.shape[1]):
idxOnH = SP.random.choice(idxVar[:100], 20, replace=False)
piSparse[idxOnH, iH] = 0.99
pi = SP.hstack([piSparse, pi])
thiddenSparse = SP.repeat('hiddenSparse', nHiddenSparse)
termsHiddnSparse = [
'%s%s' % t for t in zip(thiddenSparse, SP.arange(nHiddenSparse))
]
terms = SP.hstack([termsHiddnSparse, terms])
num_terms += nHiddenSparse
thidden = SP.repeat('hidden', nHidden)
termsHidden = ['%s%s' % t for t in zip(thidden, SP.arange(nHidden))]
terms = SP.hstack([termsHidden, terms])
pi = SP.hstack([SP.ones((Y.shape[1], nHidden)) * .99, pi])
num_terms += nHidden
if not (covariates is None):
if len(covariates.shape) == 1:
covariates = covariates[:, SP.newaxis]
nKnown = covariates.shape[1]
pi = SP.hstack([SP.ones((Y.shape[1], nKnown)) * .99, pi])
num_terms += nKnown
tcovariates = SP.repeat('covariate', nKnown)
termsCovariates = [
'%s%s' % t for t in zip(tcovariates, SP.arange(nKnown))
]
terms = SP.hstack([termsCovariates, terms])
#mean term for non-Gaussian noise models
if noise != 'gauss':
terms = SP.hstack(['bias', terms])
pi = SP.hstack([SP.ones((Y.shape[1], 1)) * (1. - 1e-10), pi])
num_terms += 1
if do_preTrain == True:
Ilabel = preTrain(Y,
terms,
pi,
noise=noise,
nFix=nFix,
priors=priors,
covariates=covariates)
pi = pi[:, Ilabel]
terms = terms[Ilabel]
init = {
'init_data': CGauss(Y),
'Pi': pi,
'terms': terms,
'noise': noise,
'covariates': covariates,
"dropFactors": dropFactors
}
if not gene_ids is None:
gene_ids = SP.array(gene_ids)
FA = slalom.CSparseFA(components=num_terms,
idx_genes=idx_genes,
gene_ids=gene_ids,
priors=priors,
learnPi=learnPi)
FA.saveInit = False
FA.init(**init)
return FA
import scipy
import matplotlib.pyplot as plt
p = 0.5
n = 300
k = 200
victory = 10
ruin = 0
interval = victory - ruin + 1
winLose = 2 * (scipy.random.random((n, k, interval)) <= p) - 1
totals = scipy.cumsum(winLose, axis=0)
start = scipy.multiply.outer(scipy.ones((n + 1, k), dtype=int),
scipy.arange(ruin, victory + 1, dtype=int))
paths = scipy.zeros((n + 1, k, interval), dtype=int)
paths[1:n + 1, :, :] = totals
paths = paths + start
def match(a, b, nomatch=None):
return b.index(a) if a in b else nomatch
# arguments: a is a scalar, b is a python list, value of nomatch is scalar
# returns the position of first match of its first argument in its second argument
# but if a is not there, returns the value nomatch
# modeled on the R function "match", but with less generality
hitVictory = scipy.apply_along_axis(
def plotRelevance(FA,
Nactive=20,
stacked=True,
madFilter=0.4,
annotated=True,
unannotated=False,
unannotated_sparse=False):
"""Plot results of slalom
Identified factors and corresponding gene set size ordered by relevance (white = low relevance; black = high relevance).
Top panel: Gene set augmentation, showing the number of genes added (red) and removed (blue) by the model for each factor.
Args:
FA (:class:`slalom.CSparseFA`): Factor analysis object, usually generated using `initFA` function
Nactive (int): Numer of terms to be plotted
stacked (bool): Boolean variable indicating whether bars should be stacked
db (str): Name of database used, either 'MSigDB' or 'REACTOME'
madFilter (float): Filter factors by this mean absolute deviation to exclude outliers.
For large datasets this can be set to 0.
annotated (bool): Indicates whether annotated factors should be plotted. Defaults to True.
unannotated (bool): Indicates whether unannotated factors should be plotted. Defaults to False.
unannotated (bool): Indicates whether unannotated sparse factors should be plotted. Defaults to False.
"""
pltparams = {
'backend': 'pdf',
'axes.labelsize': 12,
'font.size': 12,
'legend.fontsize': 13,
'xtick.labelsize': 14,
'ytick.labelsize': 12,
'text.usetex': False
}
plt.rcParams.update(pltparams)
pattern_hidden = re.compile('hidden*')
pattern_bias = re.compile('bias')
terms = FA.getTerms(annotated=annotated,
unannotated=unannotated,
unannotated_sparse=unannotated_sparse)
i_use = list()
if unannotated_sparse == True:
i_use.extend(FA.iLatentSparse)
if unannotated == True:
i_use.extend(FA.iLatent)
if annotated == True:
i_use.extend(
SP.setxor1d(
SP.hstack([
SP.where(FA.terms == 'bias')[0], FA.iLatentSparse,
FA.iLatent
]), SP.arange(len(FA.terms))))
i_use = SP.array(i_use)
X = FA.getX()[:, i_use]
Iprior = FA.getAnnotations()[:, i_use]
Iposterior = FA.getZ()[:, i_use] > .5
rel = FA.getRelevance()[i_use]
MAD = mad(X)
R = (MAD > madFilter) * (rel)
terms = SP.array(terms)
Nactive = min(SP.sum(R > 0), Nactive)
#terms change,s etc.
Nprior = Iprior.sum(axis=0)
#gains
Ngain = (Iposterior & (~Iprior)).sum(axis=0)
#loss
Nloss = ((~Iposterior & (Iprior))).sum(axis=0)
#sort terms by relevance
Iactive = R.argsort()[::-1][0:Nactive]
RM = R[Iactive, SP.newaxis]
xticks_range = SP.arange(Nactive)
terms[terms == 'hidden'] = 'Unannotated'
terms[terms == 'hiddenSparse'] = 'Unannotated-sparse'
xticks_text = list(terms[Iactive])
n_gain = []
n_loss = []
n_prior = []
for i in range(Nactive):
n_gain += [Ngain[Iactive[i]]]
n_loss += [-1.0 * Nloss[Iactive[i]]]
n_prior += [Nprior[Iactive[i]]]
width = 0.6
left = SP.arange(Nactive) - 0.5 + (1. - width) / 2.
fig = plt.figure(2, figsize=(10, 6))
fig.subplots_adjust(bottom=0.3)
gs = mpl.gridspec.GridSpec(2,
2,
height_ratios=[2., 1.],
width_ratios=[1., 0.05])
gs.update(hspace=0.1)
#fig.text(0.06, 0.6, 'Number of annotated genes', ha='center', va='center', rotation='vertical', fontsize=17)
#################################################################################
ax1 = plt.subplot(gs[1, 0])
simpleaxis(ax1)
ax1.set_xlabel('Active pathways', fontsize=15)
ax1.set_ylabel('Gene set size', fontsize=13.5)
#im = ax1.imshow(SP.append(RM.T,[[0]],axis=1),origin=[0,0],interpolation='nearest',cmap='Greys',aspect='auto')
minima = 0
maxima = max(RM)
norm = mpl.colors.Normalize(vmin=minima, vmax=maxima, clip=True)
mapper = mpl.cm.ScalarMappable(norm=norm, cmap='Greys')
colors = []
for v in RM.flatten():
colors += [mapper.to_rgba(v)]
#colors = []
#for i in xrange(RM.shape[0]):
# colors += [im.cmap(im.norm(RM[i]))[0,:-1]]
y_max = Nprior[Iactive].max() + 100.
bar_rel_importance = ax1.bar(left=SP.arange(Nactive) - 0.5,
width=1.05,
height=[y_max] * len(n_prior),
bottom=0,
color=colors,
log=True,
edgecolor='none')
bar_annotated = ax1.bar(left=left,
width=width,
height=n_prior,
bottom=0,
color='w',
log=True,
alpha=0.6,
edgecolor='k')
ax1.set_ylim([10, y_max])
ax1.set_xlim([0, Nactive])
#ax1.set_yticks([])
#ax1.set_yscale('log')
plt.xticks(xticks_range, xticks_text, rotation=45, fontsize=14, ha='right')
color_bar_ax = plt.subplot(gs[1, 1])
mpl.colorbar.ColorbarBase(color_bar_ax,
cmap='Greys',
norm=norm,
orientation='vertical',
ticks=[minima, maxima])
#color_bar = fig.colorbar(im, cax=color_bar_ax,ticks=[0., RM.max()])
color_bar_ax.set_yticklabels([0, 1])
#color_bar_ax.set_yticklabels([0,round(RM.max(),3)])
#color_bar_ax.set_ylabel('Rel. importance')
#color_bar.outline.set_visible(False)
#################################################################################
ax0 = plt.subplot(gs[0, 0], sharex=ax1)
simpleaxis(ax0)
if stacked:
bar_gain = ax0.bar(left=left,
width=width,
height=n_gain,
bottom=0,
color='#861608')
bar_loss = ax0.bar(left=left,
width=width,
height=n_loss,
bottom=0,
color='#0c09a0')
else:
bar_gain = ax0.bar(left=SP.arange(Nactive) - 0.5,
width=0.5,
height=n_gain,
bottom=0,
color='#861608')
bar_loss = ax0.bar(left=SP.arange(Nactive),
width=0.5,
height=n_loss,
bottom=0,
color='#0c09a0')
#figure out range to make ylim symmatrix
ax0.axhline(y=0, linestyle='-', color='gray')
#ax0.set_yscale('symlog')
gap = SP.ceil(max(max(n_gain), abs(min(n_loss))) / 4.)
y_max = SP.ceil(max(n_gain) / gap)
y_min = SP.floor(min(n_loss) / gap)
yticks = SP.arange(y_min * gap, y_max * gap, gap)
ax0.set_yticks(yticks)
ax0.set_ylabel('Gene set augemntation', fontsize=13.5)
ax0.legend((bar_gain[0], bar_loss[0]), ('Gain', 'Loss'),
ncol=1,
loc='center left',
bbox_to_anchor=(1, 0.5),
frameon=False,
fontsize=15)
plt.setp(ax0.get_xticklabels(), visible=False)
plt.show()
return fig
def __init__(self, grid, data):
self.n = data.shape[-1]
grid_aug = grid + [s.arange(data.shape[-1])]
self.itp = RegularGridInterpolator(grid_aug, data)
def __init__(self, columns, tag, default=None):
"""Create a Trace object and fill it with data
Parameters:
:param columns: dict of 1D data arrays. column names either:
"time" (or any other value in known_time_labels) to be automatically recognized as time vector
mass (int) to be automatically recognized as data corresponding to given mass
arbitrary string to be manually assigned to timetrace via self.set_timecol
:param tag: dict of metadata
time_unit unit of time vector
title set data title
:param default: dict of default values (see set_default_values for understood options)
:return None
"""
self.type = "Trace"
self.columns = {}
self.filled = False # Trace contains data (Boolean)
self.deconvoluted = False # deconvolute function has been used on the data
self.calibrated = False # calibrate function has been used on the data
bloc_len = 0 # length of shortest data column
self.echo = True
# Load the default values for the object
if default == None:
self.def_val = load_default_values({})
else:
self.def_val = load_default_values(default)
if type(tag) != dict: # if tag is not provided in the correct format
self.tag = {"raw_tag": tag} # store it anyway
else:
self.tag = tag
self.tag["init_errors"] = [] # Errors encountered in Trace.__init__
header_int = [] # List of recorded masses, represented by integers
lengths = {} # Lengths of all of the columns
for key in columns:
# Check if all columns have the same length
lengths[key] = len(columns[key])
try:
value = int(key)
header_int.append(value)
self.columns[value] = sp.array(columns[key])
except ValueError:
self.columns[key] = sp.array(columns[key])
if len(header_int) == 0:
self.tag["init_errors"].append(103)
try:
bloc_len = min(lengths.values()) # shortest column length
for key in self.columns:
# If a column is longer than the shortest column (bloc_len)
# drop any datapoints beyond bloc_len
self.columns[key] = self.columns[key][:bloc_len]
if (bloc_len == 0
): # at least one zero-lenght column was included in the data
self.tag["init_errors"].append(102)
except ValueError:
self.tag["init_errors"].append(101)
# Create the column of indices of datapoints
self.columns["index"] = sp.arange(bloc_len)
if len(header_int) > 0 and bloc_len > 0:
self.filled = True # Trace contains technically OK data
# set the time column
time_col_candidates = list(
set(self.columns.keys()) & set(known_time_labels))
try:
self.set_timecol(time_col_candidates[0])
except:
# if no label is recognized, set the index column as the time column
self.set_timecol("index")
self.header_int = sp.array(sorted(header_int))
# Title of the Trace object
# If 'title' is not provided in the tag, use default value
if "title" not in self.tag:
self.tag["title"] = self.def_val["trace_name"]
# Initialize mass-space and cracking patterns
# This has now been moved to RGA_base_container
RGA_base_container.__init__(self)
import numpy as np
from scipy import sqrt, exp, log, pi
from scipy import zeros, sqrt, shape
import random
import pandas as pd
import os
from datetime import datetime as dt
from scipy.optimize import minimize
from scipy.stats import norm
## 1. 정규분포 ##
#표준 정규분포로부터 난수 생성
x = sp.random.standard_normal(size=10)
print(x)
x = sp.arange(-3, 3, 0.01)
y = stats.norm.pdf(x)
plt.plot(x, y)
plt.title("standard normal disstribution")
plt.xlabel('x')
plt.ylabel('y')
plt.show()
#시드 난수
sp.random.seed(12345)
x = sp.random.normal(0, 1, 20)
print(x[:5])
#정규분포 난수 생성
mean = 0.1
std = 0.2
def __call__(self, points):
res = []
for v in s.arange(self.n):
p_aug = s.concatenate((points, s.array([v])), axis=0)
res.append(self.itp(p_aug))
return res
def plot_cov(self):
cov = self._co
if False:
###
plt.plot(sp.diag(cov))
plt.grid()
plt.show()
###
plt.plot(sp.diag(cov) * self._nb)
plt.grid()
plt.show()
###
plt.plot(sp.diag(cov) * self._rt)
plt.grid()
plt.show()
if True:
cor = utils.getCorrelationMatrix(cov)
###
#tcor = cor.copy()
#tcor[tcor==1.] = sp.nan
#plt.imshow(tcor, interpolation='nearest')
#plt.show()
###
yMin = None
yMax = None
for i in range(3):
mcor = sp.asarray([
sp.mean(sp.diag(cor, k=i + self._nt * k))
for k in sp.arange(self._np)
])
plt.plot(sp.arange(mcor.size) * self._binSize,
mcor,
linewidth=2,
label=r"$\Delta r_{\perp} = " +
str(int(i * self._binSize)) + "$")
if yMin is None:
yMin = mcor.min()
else:
yMin = min(yMin, mcor.min())
if yMax is None:
if i == 0:
yMax = mcor[1:].max()
else:
yMax = mcor.max()
else:
if i == 0:
yMax = max(yMax, mcor[1:].max())
else:
yMax = max(yMax, mcor.max())
plt.ylim([yMin, yMax])
plt.xlabel(r"$\Delta r_{\parallel} \, [h^{-1} \, \mathrm{Mpc}]$",
fontsize=20)
plt.ylabel(
r"$\overline{Corr}(\Delta r_{\parallel},\Delta r_{\perp})$",
fontsize=20)
plt.legend(fontsize=20, numpoints=1, ncol=2, loc=1)
plt.grid()
plt.tight_layout()
#plt.savefig(self._title)
#plt.clf()
plt.show()
return
print(last + ' Arnorm = %12.4e' % (Arnorm,))
print(last + msg[istop+1])
if istop == 6:
info = maxiter
else:
info = 0
return (postprocess(x),info)
if __name__ == '__main__':
from scipy import ones, arange
from scipy.linalg import norm
from scipy.sparse import spdiags
n = 10
residuals = []
def cb(x):
residuals.append(norm(b - A*x))
# A = poisson((10,),format='csr')
A = spdiags([arange(1,n+1,dtype=float)], [0], n, n, format='csr')
M = spdiags([1.0/arange(1,n+1,dtype=float)], [0], n, n, format='csr')
A.psolve = M.matvec
b = 0*ones(A.shape[0])
x = minres(A,b,tol=1e-12,maxiter=None,callback=cb)
# x = cg(A,b,x0=b,tol=1e-12,maxiter=None,callback=cb)[0]
enddate = (2016, 12, 31)
#
y0 = pd.Series(ret_f('IBM', begdate, enddate))
x0 = pd.Series(ret_f('^GSPC', begdate, enddate))
#
d = quotes_historical_yahoo_ochl('^GSPC',
begdate,
enddate,
asobject=True,
adjusted=True).date[0:-1]
lag_year = d[0].strftime("%Y")
y1 = []
x1 = []
beta = []
index0 = []
for i in sp.arange(1, len(d)):
year = d[i].strftime("%Y")
if (year == lag_year):
x1.append(x0[i])
y1.append(y0[i])
else:
(beta, alpha, r_value, p_value, std_err) = stats.linregress(y1, x1)
alpha = round(alpha, 8)
beta = round(beta, 3)
r_value = round(r_value, 3)
p_vaue = round(p_value, 3)
print(year, alpha, beta, r_value, p_value)
x1 = []
y1 = []
lag_year = year
""" Name : c11_03_standard_normal_dist.py Book : Python for Finance (2nd ed.) Publisher: Packt Publishing Ltd. Author : Yuxing Yan Date : 6/6/2017 email : [email protected] [email protected] """ import scipy as sp import scipy.stats as stats x = sp.arange(-3, 3, 0.01) ret = stats.norm.pdf(x) confidence = 0.99 position = 10000 z = stats.norm.ppf(1 - confidence) print("z=", z) zES = -stats.norm.pdf(z) / (1 - confidence) print("zES=", zES) std = sp.std(ret) VaR = position * z * std print("VaR=", VaR) ES = position * zES * std print("ES=", ES)
def func_nAg(WLs):
ep = 3.691 - 9.1522**2 / ((1240 / WLs)**2 + 1j * 0.021 * (1240 / WLs))
index = sqrt(ep)
return index # 銀の誘電関数
def func_nTiO2(WLs):
ep = 5.193 + 0.244 / ((WLs / 1000)**2 - 0.0803)
index = sqrt(ep)
return index # TiO2の誘電関数
WLmin = 300 # 波長(短波長側) 〔nm〕
WLmax = 1000 # 波長(長波長側) 〔nm〕
WLperiod = 1 # 波長間隔 〔nm〕
WLx = arange(WLmin, WLmax + 1, WLperiod) # 波長の配列
NumWLx = int((WLmax - WLmin) / WLperiod) + 1 # 波長の数
k0 = 2 * pi / WLx # 各波長の波数
nTiO2 = zeros((NumWLx), dtype=complex) # Ti02 屈折率の配列の初期化
nAg = zeros((NumWLx), dtype=complex) # Ag 屈折率の配列の初期化
for i in range(NumWLx):
nTiO2[i] = func_nTiO2(WLx[i]) # Ti02 屈折率の生成
nAg[i] = func_nAg(WLx[i]) # Ag 屈折率の生成
epx = 0.5 * (nTiO2**2 + nAg**2) # EMA による誘電率の計算 x 方向
epz = 2 * (nTiO2**2) * (nAg**2) / ((nTiO2**2) + (nAg**2)) # EMA による誘電率の計算 z 方向
plt.figure(figsize=(8, 6))
# x 方向有効媒質の誘電率(実部)のプロット
if __name__ == '__main__':
# Load data set
X, y = rt.get_samples_from_roi('../Data/university.tif',
'../Data/university_gt.tif')
sc = StandardScaler()
X = sc.fit_transform(X)
# Split the data
X_train, X_test, y_train, y_test = train_test_split(X,
y,
train_size=0.1,
random_state=0,
stratify=y)
# Parameters
param_grid_svm = dict(gamma=2.0**sp.arange(-4, 4),
C=10.0**sp.arange(0, 3)) # SVM
param_grid_linear_svm = dict(C=10.0**sp.arange(-2, 3)) # LinearSVM
param_grid_rf = dict(n_estimators=sp.arange(10, 150, 10)) # RF
param_grid_fffs = dict(maxvar=20, threshold=0.001) # FFFS
param_grid_knn = dict(n_neighbors=sp.arange(1, 50, 5))
F1, CT = [], []
# Start the classification: SVM
ts = time.time()
F1.append(compute_SVM(X_train, y_train, X_test, y_test, param_grid_svm))
CT.append(time.time() - ts)
# Start the classification: RF
ts = time.time()
F1.append(compute_RF(X_train, y_train, X_test, y_test, param_grid_rf))
def f1(x): aux = 0 for i in scipy.arange(x.shape[0]-1): aux = aux + 100*(x[i+1] - x[i]**2)**2+(x[i]-1)**2 return aux
def compute_ext(filt, N=0.78):
print '''COMPUTING EXTINCTION COEFFICIENT USING FITZPATRICK99 EXTINCTION LAW'''
odonnell_ext_1_um = 1.32 # A(1 um) / E(B-V) where R_v = 3.1
import scipy, math
sed = scipy.loadtxt(os.environ['BIGMACS'] + '/munari.sed')
''' now stitch together with blackbody spectrum '''
longwave = sed[-1,0]
flux = sed[-1,1]
wavelength = sed[:,0].tolist()
source = sed[:,1].tolist()
a = flux / longwave**-3.
for wave in scipy.arange(11500,20000,25):
wavelength.append(wave)
source.append(a*wave**-3.)
import scipy
from scipy import interpolate
sedSpline = interpolate.interp1d(wavelength, source,
bounds_error = True,
)
#s_od = N*odonnell_ext_1_um*odonnell(scipy.arange(3000,20000))
#s_od = fitzpatrick(scipy.arange(3000,20000))
#import pylab
#pylab.clf()
#pylab.plot(scipy.arange(3000,20000),s_od)
#pylab.xlim([3000,20000])
#pylab.show()
''' source flux is ergs / s / Ang '''
filt_wavelength = filt['wavelength']
filt_response = filt['response']
throw_out = scipy.zeros(len(filt_wavelength))
''' trim off zero-valued tails of response function'''
for i in range(len(filt_wavelength)):
if filt_response[i] == 0:
throw_out[i]= 1.
else: break
for i in range(len(filt_wavelength)):
if filt_response[len(filt_response)-1-i] == 0:
throw_out[len(filt_response)-1-i]= 1.
else: break
filt_wavelength = filt_wavelength[throw_out==0.]
filt_response = filt_response[throw_out==0.]
#print scipy.array([(filt_wavelength[i]) for i in range(len(filt_wavelength[:-1]))])
#print scipy.array([fitzpatrick(filt_wavelength[i]) for i in range(len(filt_wavelength[:-1]))])
numerator = scipy.array([10.**(fitzpatrick(filt_wavelength[i])/-2.5)*sedSpline(filt_wavelength[i])*filt_wavelength[i]*(filt_response[i])*(filt_wavelength[i+1]-filt_wavelength[i]) for i in range(len(filt_wavelength[:-1]))])
denom = scipy.array([source[i]*filt_wavelength[i]*(filt_response[i])*(filt_wavelength[i+1]-filt_wavelength[i]) for i in range(len(filt_wavelength[:-1]))])
coeff = -2.5*math.log10(numerator.sum()/denom.sum())
print filt['name'], coeff, 'coeff'
return coeff
def region_interface_areas(regions, areas, voxel_size=1, strel=None):
r"""
Calculates the interfacial area between all pairs of adjecent regions
Parameters
----------
regions : ND-array
An image of the pore space partitioned into individual pore regions.
Note that zeros in the image will not be considered for area
calculation.
areas : array_like
A list containing the areas of each regions, as determined by
``region_surface_area``. Note that the region number and list index
are offset by 1, such that the area for region 1 is stored in
``areas[0]``.
voxel_size : scalar
The resolution of the image, expressed as the length of one side of a
voxel, so the volume of a voxel would be **voxel_size**-cubed. The
default is 1.
strel : array_like
The structuring element used to blur the region. If not provided,
then a spherical element (or disk) with radius 1 is used. See the
docstring for ``mesh_region`` for more details, as this argument is
passed to there.
Returns
-------
A named-tuple containing 2 arrays. ``conns`` holds the connectivity
information and ``area`` holds the result for each pair. ``conns`` is a
N-regions by 2 array with each row containing the region number of an
adjacent pair of regions. For instance, if ``conns[0, 0]`` is 0 and
``conns[0, 1]`` is 5, then row 0 of ``area`` contains the interfacial
area shared by regions 0 and 5.
"""
print('_' * 60)
print('Finding interfacial areas between each region')
from skimage.morphology import disk, square, ball, cube
im = regions.copy()
if im.ndim == 2:
cube = square
ball = disk
# Get 'slices' into im for each region
slices = spim.find_objects(im)
# Initialize arrays
Ps = sp.arange(1, sp.amax(im) + 1)
sa = sp.zeros_like(Ps, dtype=float)
sa_combined = [] # Difficult to preallocate since number of conns unknown
cn = []
# Start extracting area from im
for i in tqdm(Ps):
reg = i - 1
s = extend_slice(slices[reg], im.shape)
sub_im = im[s]
mask_im = sub_im == i
sa[reg] = areas[reg]
im_w_throats = spim.binary_dilation(input=mask_im, structure=ball(1))
im_w_throats = im_w_throats * sub_im
Pn = sp.unique(im_w_throats)[1:] - 1
for j in Pn:
if j > reg:
cn.append([reg, j])
merged_region = im[(
min(slices[reg][0].start, slices[j][0].start)
):max(slices[reg][0].stop, slices[j][0].stop), (
min(slices[reg][1].start, slices[j][1].start)
):max(slices[reg][1].stop, slices[j][1].stop)]
merged_region = ((merged_region == reg + 1) +
(merged_region == j + 1))
mesh = mesh_region(region=merged_region, strel=strel)
sa_combined.append(mesh_surface_area(mesh))
# Interfacial area calculation
cn = sp.array(cn)
ia = 0.5 * (sa[cn[:, 0]] + sa[cn[:, 1]] - sa_combined)
ia[ia < 0] = 1
result = namedtuple('interfacial_areas', ('conns', 'area'))
result.conns = cn
result.area = ia * voxel_size**2
return result
def main():
gr_estimators = {
"simple": digital.SNR_EST_SIMPLE,
"skew": digital.SNR_EST_SKEW,
"m2m4": digital.SNR_EST_M2M4,
"svr": digital.SNR_EST_SVR
}
py_estimators = {
"simple": snr_est_simple,
"skew": snr_est_skew,
"m2m4": snr_est_m2m4,
"svr": snr_est_svr
}
parser = OptionParser(option_class=eng_option, conflict_handler="resolve")
parser.add_option(
"-N",
"--nsamples",
type="int",
default=10000,
help="Set the number of samples to process [default=%default]")
parser.add_option("",
"--snr-min",
type="float",
default=-5,
help="Minimum SNR [default=%default]")
parser.add_option("",
"--snr-max",
type="float",
default=20,
help="Maximum SNR [default=%default]")
parser.add_option("",
"--snr-step",
type="float",
default=0.5,
help="SNR step amount [default=%default]")
parser.add_option("-t",
"--type",
type="choice",
choices=gr_estimators.keys(),
default="simple",
help="Estimator type {0} [default=%default]".format(
gr_estimators.keys()))
(options, args) = parser.parse_args()
N = options.nsamples
xx = scipy.random.randn(N)
xy = scipy.random.randn(N)
bits = 2 * scipy.complex64(scipy.random.randint(0, 2, N)) - 1
#bits =(2*scipy.complex64(scipy.random.randint(0, 2, N)) - 1) + \
# 1j*(2*scipy.complex64(scipy.random.randint(0, 2, N)) - 1)
snr_known = list()
snr_python = list()
snr_gr = list()
# when to issue an SNR tag; can be ignored in this example.
ntag = 10000
n_cpx = xx + 1j * xy
py_est = py_estimators[options.type]
gr_est = gr_estimators[options.type]
SNR_min = options.snr_min
SNR_max = options.snr_max
SNR_step = options.snr_step
SNR_dB = scipy.arange(SNR_min, SNR_max + SNR_step, SNR_step)
for snr in SNR_dB:
SNR = 10.0**(snr / 10.0)
scale = scipy.sqrt(2 * SNR)
yy = bits + n_cpx / scale
print "SNR: ", snr
Sknown = scipy.mean(yy**2)
Nknown = scipy.var(n_cpx / scale)
snr0 = Sknown / Nknown
snr0dB = 10.0 * scipy.log10(snr0)
snr_known.append(float(snr0dB))
snrdB, snr = py_est(yy)
snr_python.append(snrdB)
gr_src = blocks.vector_source_c(bits.tolist(), False)
gr_snr = digital.mpsk_snr_est_cc(gr_est, ntag, 0.001)
gr_chn = channels.channel_model(1.0 / scale)
gr_snk = blocks.null_sink(gr.sizeof_gr_complex)
tb = gr.top_block()
tb.connect(gr_src, gr_chn, gr_snr, gr_snk)
tb.run()
snr_gr.append(gr_snr.snr())
f1 = pylab.figure(1)
s1 = f1.add_subplot(1, 1, 1)
s1.plot(SNR_dB, snr_known, "k-o", linewidth=2, label="Known")
s1.plot(SNR_dB, snr_python, "b-o", linewidth=2, label="Python")
s1.plot(SNR_dB, snr_gr, "g-o", linewidth=2, label="GNU Radio")
s1.grid(True)
s1.set_title('SNR Estimators')
s1.set_xlabel('SNR (dB)')
s1.set_ylabel('Estimated SNR')
s1.legend()
f2 = pylab.figure(2)
s2 = f2.add_subplot(1, 1, 1)
s2.plot(yy.real, yy.imag, 'o')
pylab.show()
# Potassium
def I_K(V, n): return g_K * n ** 4 * (V - E_K)
# Leak
def I_L(V): return g_L * (V - E_L)
# External current
start=5
finish=105
def I_inj(t, voltage):
return voltage * (t > start) - voltage * (t > finish)
# return 10*t
# The time to integrate over
dt=0.05
t = sp.arange(0.0, 110.0, dt)
I = np.linspace(1,2.5,10)
plt.figure()
for i in range(len(I)):
plt.plot(t, I_inj(t, I[i]))
plt.xlabel('t (ms)')
plt.ylabel('$I_{inj}$ ($\\mu{A}/cm^2$)')
plt.legend(I)
plt.show()
plt.figure()
for i in range(len(I)):
def dALLdt(X, t):
V, m, h, n = X
def objFunction(W, R, target_ret):
stock_mean = np.mean(R, axis=0)
port_mean = np.dot(W, stock_mean) # portfolio mean
#cov=np.cov(R.T) # var-cov matrix
cov = cov0
port_var = np.dot(np.dot(W, cov), W.T) # portfolio variance
penalty = 2000 * abs(port_mean - target_ret) # penalty 4 deviation
return np.sqrt(port_var) + penalty # objective function
R0 = ret_monthly(stocks[0]) # starting from 1st stock
n_stock = len(stocks) # number of stocks
std1 = std_f(stocks[0])
std2 = std_f(stocks[1])
for jj in sp.arange(1):
k = 0.1 * std1 * std2
#cov0=sp.array([[0.00266285,0.00037303],[0.00037303,0.0021296]])
#cov0=sp.array([[std1**2,k],[k,std2**2]])
cov0 = sp.array([[std1**2, 0.00037303], [0.00037303, std2**2]])
for i in xrange(1, n_stock): # merge with other stocks
x = ret_monthly(stocks[i])
R0 = pd.merge(R0, x, left_index=True, right_index=True)
R = np.array(R0)
out_mean, out_std, out_weight = [], [], []
stockMean = np.mean(R, axis=0)
for r in np.linspace(np.min(stockMean), np.max(stockMean), num=100):
W = np.ones([n_stock]) / n_stock # starting from equal weights
b_ = [(0, 1) for i in range(n_stock)] # bounds, here no short
c_ = ({'type': 'eq', 'fun': lambda W: sum(W) - 1.}) #constraint