def diff(self, n=1):
"""Calculate the n-th order differential of the function."""
# 2012-06-27 - 2012-07-11
x, y = self.diff(n=n-1).xy() if n > 1 else self.xy()
x = self._filter_double(x)
return type(self)(x=.5*(x[1:]+x[:-1]),
y=scipy.diff(y)/scipy.diff(x))
def gradient2(f): dM = g.grid_M[1] - g.grid_M[0] dD = g.grid_D[1] - g.grid_D[0] g1 = scipy.diff(f, 1, 0) / dM g2 = scipy.diff(f, 1, 1) / dD g3 = addNanRow(g1) g4 = addNanCol(g2) return [g3, g4]
def entropy2(values):
"""Calculate the entropy of vector values.
values will be flattened to a 1d ndarray."""
values = sp.asarray(values).flatten()
p = sp.diff(sp.c_[0,sp.diff(sp.sort(values)).nonzero(), values.size])/float(values.size)
H = (p*sp.log2(p)).sum()
return -H
def entropy2(values):
"""Calculate the entropy of vector values.
values will be flattened to a 1d ndarray."""
values = values.flatten()
M = len(sp.unique(values))
p = sp.diff(sp.c_[sp.diff(sp.sort(values)).nonzero(), len(values)])/float(len(values))
H = -((p*sp.log2(p)).sum())
return H
def test_respects_refractory_period(self):
refractory = 100 * pq.ms
st = self.invoke_gen_func(
self.highRate, max_spikes=1000, refractory=refractory)
self.assertGreater(
sp.amax(sp.absolute(sp.diff(st.rescale(pq.s).magnitude))),
refractory.rescale(pq.s).magnitude)
st = self.invoke_gen_func(
self.highRate, t_stop=10 * pq.s, refractory=refractory)
self.assertGreater(
sp.amax(sp.absolute(sp.diff(st.rescale(pq.s).magnitude))),
refractory.rescale(pq.s).magnitude)
def unique(a):
order = sp.lexsort(a.T)
a = a[order]
diff = sp.diff(a, axis=0)
ui = sp.ones(len(a), 'bool')
ui[1:] = (diff != 0).any(axis=1)
return a[ui]
def return_results(self, pores=None, throats=None, **kwargs):
r"""
Send results of simulation out the the appropriate locations.
This is a basic version of the update that simply sends out the main
result (quantity). More elaborate updates should be subclassed.
"""
if pores is None:
pores = self.Ps
if throats is None:
throats = self.Ts
phase_quantity = self._quantity.replace(self._phase.name + '_', '')
if phase_quantity not in self._phase.props():
self._phase[phase_quantity] = sp.nan
self._phase[phase_quantity][pores] = self[self._quantity][pores]
conn_arr = self._net.find_connected_pores(self.Ts)
dx = sp.squeeze(sp.diff(self[self._quantity][conn_arr], n=1, axis=1))
g = self['throat.conductance']
rate = sp.absolute(g * dx)
if 'throat.rate' not in self._phase.props():
self._phase['throat.rate'] = sp.nan
self._phase['throat.rate'][throats] = rate[throats]
logger.debug('Results of ' + self.name +
' algorithm have been added to ' + self._phase.name)
def decode(file_name):
border.rotate(file_name)
image = Image.open("temp.png")
q = border.find("temp.png")
ind = sp.argmin(sp.sum(q, 1), 0)
up_left = q[ind, 0] + 2
up_top = q[ind, 1] + 2
d_right = q[ind+1, 0] - 3
d_bottom = q[ind-1, 1] - 3
box = (up_left, up_top, d_right, d_bottom)
region = image.crop(box)
h_sum = sp.sum(region, 0)
m = argrelmax(sp.correlate(h_sum, h_sum, 'same'))
s = sp.average(sp.diff(m))
m = int(round(d_right - up_left)/s)
if m % 3 != 0:
m += 3 - m % 3
n = int(round(d_bottom - up_top)/s)
if n % 4 != 0:
n += 4 - n % 4
s = int(round(s))+1
region = region.resize((s*m, s*n), PIL.Image.ANTIALIAS)
region.save("0.png")
pix = region.load()
matrix = mix.off(rec.matrix(pix, s, m, n))
str2 = hamming.decode(array_to_str(matrix))
return hamming.bin_to_str(str2)
def qrsDetect(self, qrslead=0):
"""Detect QRS onsets using modified PT algorithm
"""
# If ecg is a vector, it will be used for qrs detection.
# If it is a matrix, use qrslead (default 0)
if len(self.data.shape) == 1:
self.raw_ecg = self.data
else:
self.raw_ecg = self.data[:,qrslead]
self.filtered_ecg = self.bpfilter(self.raw_ecg)
self.diff_ecg = scipy.diff(self.filtered_ecg)
self.sq_ecg = abs(self.diff_ecg)
self.int_ecg = self.mw_integrate(self.sq_ecg)
# Construct buffers with last 8 values
self._initializeBuffers(self.int_ecg)
peaks = self.peakDetect(self.int_ecg)
self.checkPeaks(peaks, self.int_ecg)
# compensate for delay during integration
self.QRSpeaks = self.QRSpeaks - 40 * (self.samplingrate / 1000)
#print ("length of qrs peaks and ecg", len(self.QRSpeaks), len(self.raw_ecg))
#print(self.QRSpeaks)
return self.QRSpeaks
def continuous_phase(phase, axis=0, center=False):
"""Add and subtract 2 pi such that the phase in the array is
as continuous as possible, along first or given axis. Optionally,
it also centers the phase data so that the average is smallest."""
phase = _n.array(phase, copy=0)
rowshape = list(phase.shape)
if len(rowshape) > 0:
rowshape[axis] = 1
slip = _n.concatenate([ _n.zeros(rowshape),
scipy.diff(phase, axis=axis) ],
axis=axis)
slip = _n.around(slip/(2*_n.pi))
cumslip = scipy.cumsum(slip, axis=axis)
phase = phase - 2*_n.pi*cumslip
else:
pass
if center:
offset = _n.around(scipy.average(phase, axis=axis)/(2*_n.pi))
offset = _n.reshape(offset, rowshape)
offset = _n.repeat(offset, cumslip.shape[axis], axis=axis)
phase = phase - 2*_n.pi*offset
return phase
def fitLength(t, v, startInd, startModel, vErr=0):
expInd = max(enumerate(diff(v)), key=lambda x:x[1])[0] + 1
startInd = max(expInd, startInd)
# only fit the exponential part of the traces
t, v = t[startInd:], v[startInd:]
# start with initial guess and fit parameters of model
startParams = [vErr] + [p for pair in startModel for p in pair]
try:
params, pCov = optimize.curve_fit(expSumParams, t, v, p0=startParams,
maxfev=500)
except RuntimeError as err:
if 'Number of calls to function has reached maxfev' in err.message:
print(err.message)
return [], float('Inf'), float('inf')
else:
raise
fitModel = [(tau, dV) for tau, dV in zip(params[1::2], params[2::2])]
vErr = params[0]
fitV = expSum(t, fitModel, vErr=vErr)
vResid = sqrt(sum((vn - fitVn)**2 for vn, fitVn in zip(v, fitV)) / len(fitV))
return fitModel, vErr, vResid
def getStepWindow(t, v):
# return time and voltage vectors during the stimulus period only
# find the point of maximum voltage, and cut off everything afterwards
maxInd, maxV = max(enumerate(v), key=lambda x: x[1])
minInd, minV = min(enumerate(v), key=lambda x: x[1])
if maxV - v[0] > v[0] - minV:
# this is a positive step
t = t[:maxInd]
v = scipy.array(v[:maxInd])
else:
# this is a negative step, flip it for now
t = t[:minInd]
v = v[0] - scipy.array(v[:minInd])
# re-center time to start at the point of maximum voltage change
diffV = diff(v)
dVInd, maxDV = max(enumerate(diffV), key=lambda x: x[1])
dVInd -= 1
while diffV[dVInd] > 0:
dVInd -= 1
dVInd += 1
t -= t[dVInd]
v -= v[dVInd]
return t, v, dVInd
def setUp(self) :
# Read in just to fiugre out the band structure.
this_test_file = 'testdata/testfile_guppi_rotated.fits'
Reader = fitsGBT.Reader(this_test_file, feedback=0)
Blocks = Reader.read((0,),())
bands = ()
for Data in Blocks:
n_chan = Data.dims[3]
Data.calc_freq()
freq = Data.freq
delta = abs(sp.mean(sp.diff(freq)))
centre = freq[n_chan//2]
band = int(centre/1e6)
bands += (band,)
map = sp.zeros((n_chan, 15, 11))
map = algebra.make_vect(map, axis_names=('freq', 'ra', 'dec'))
map.set_axis_info('freq', centre, -delta)
map.set_axis_info('ra', 218, -0.2)
map.set_axis_info('dec', 2, 0.2)
algebra.save('./testout_clean_map_I_' + str(band) + '.npy', map)
self.params = {'sm_input_root' : 'testdata/',
'sm_file_middles' : ("testfile",),
'sm_input_end' : "_guppi_rotated.fits",
'sm_output_root' : "./testout_",
'sm_output_end' : "_sub.fits",
'sm_solve_for_gain' : True,
'sm_gain_output_end' : 'gain.pickle',
'sm_map_input_root' : './testout_',
'sm_map_type' : 'clean_map_',
'sm_map_polarizations' : ('I',),
'sm_map_bands' : bands
}
def whittaker(inY,inL=15,inD=2):
"""
cette fonction permet de lisser le signal d'entrée en utilisant le filtre de Whittaker.
ref: Eilers, P.H.C. (2003) "A perfect smoother", Analytical Chemistry, 75, 3631 – 3636.
Entrée:
inY: le signal à lisser
inL: correspond au parmètre de lissage. Plus il est grand plus le lissage est élevé. par défaut à 15
comme dans l'article :
Geng, L.; Ma, M.; Wang, X.; Yu, W.; Jia, S.; Wang, H. Comparison of Eight Techniques
for Reconstructing Multi-Satellite Sensor Time-Series NDVI Data Sets in the Heihe River Basin, China.
Remote Sens. 2014, 6, 2024-2049.
inD: ordre des differences de pénalités
"""
m=sp.size(inY)
E=sp.eye(m)
D=sp.diff(E,inD)
Z=E+ (inL*sp.dot(D,sp.transpose(D)))
ws=sp.linalg.solve(Z,inY)
return ws
def add_boundaries(self):
r'''
This method uses ``clone_pores`` to clone the surface pores (labeled
'left','right', etc), then shifts them to the periphery of the domain,
and gives them the label 'right_face', 'left_face', etc.
'''
x,y,z = self['pore.coords'].T
Lc = sp.amax(sp.diff(x)) #this currently works but is very fragile
offset = {}
offset['front'] = offset['left'] = offset['bottom'] = [0,0,0]
offset['back'] = [x.max()+Lc/2,0,0]
offset['right'] = [0,y.max()+Lc/2,0]
offset['top'] = [0,0,z.max()+Lc/2]
scale = {}
scale['front'] = scale['back'] = [0,1,1]
scale['left'] = scale['right'] = [1,0,1]
scale['bottom'] = scale['top'] = [1,1,0]
for label in ['front','back','left','right','bottom','top']:
ps = self.pores(label)
self.clone_pores(pores=ps,apply_label=[label+'_boundary','boundary'])
#Translate cloned pores
ind = self.pores(label+'_boundary')
coords = self['pore.coords'][ind]
coords = coords*scale[label] + offset[label]
self['pore.coords'][ind] = coords
def dw(self):
"""Calculates the Durbin-Waston statistic
"""
de = diff(self.e,1)
dw = dot(de,de) / dot(self.e,self.e)
return dw
def plot_disc_policy():
#First compute policy function...==========================================
N = 500
w = sp.linspace(0,100,N)
w = w.reshape(N,1)
u = lambda c: sp.sqrt(c)
util_vec = u(w)
alpha = 0.5
alpha_util = u(alpha*w)
alpha_util_grid = sp.repeat(alpha_util,N,1)
m = 20
v = 200
f = discretelognorm(w,m,v)
VEprime = sp.zeros((N,1))
VUprime = sp.zeros((N,N))
EVUprime = sp.zeros((N,1))
psiprime = sp.ones((N,1))
gamma = 0.1
beta = 0.9
m = 15
tol = 10**-9
delta = 1+tol
it = 0
while (delta >= tol):
it += 1
psi = psiprime.copy()
arg1 = sp.repeat(sp.transpose(VEprime),N,0)
arg2 = sp.repeat(EVUprime,N,1)
arg = sp.array([arg2,arg1])
psiprime = sp.argmax(arg,axis = 0)
for j in sp.arange(0,m):
VE = VEprime.copy()
VU = VUprime.copy()
EVU = EVUprime.copy()
VEprime = util_vec + beta*((1-gamma)*VE + gamma*EVU)
arg1 = sp.repeat(sp.transpose(VE),N,0)*psiprime
arg2 = sp.repeat(EVU,N,1)*(1-psiprime)
arg = arg1+arg2
VUprime = alpha_util_grid + beta*arg
EVUprime = sp.dot(VUprime,f)
delta = sp.linalg.norm(psiprime -psi)
wr_ind = sp.argmax(sp.diff(psiprime), axis = 1)
wr = w[wr_ind]
print w[250],wr[250]
#Then plot=================================================================
plt.plot(w,psiprime[250,:])
plt.ylim([-.5,1.5])
plt.xlabel(r'$w\prime$')
plt.yticks([0,1])
plt.savefig('disc_policy.pdf')
def qrs_detect(self, qrslead=0):
"""Detect QRS onsets using modified PT algorithm
"""
# If ecg is a vector, it will be used for qrs detection.
# If it is a matrix, use qrslead (default 0)
if len(self.data.shape) == 1:
self.raw_ecg = self.data
else:
self.raw_ecg = self.data[:,qrslead]
# butterworth bandpass filter 5 - 15 Hz
self.filtered_ecg = self._bpfilter(self.raw_ecg)
# differentiate
self.diff_ecg = scipy.diff(self.filtered_ecg)
# take absolute value (was square in original PT implementation)
self.abs_ecg = abs(self.diff_ecg)
# integrate
self.int_ecg = self._mw_integrate(self.abs_ecg)
# Construct buffers with last 8 values
self._initializeBuffers(self.int_ecg)
# collect all unique local peaks in the integrated ecg
peaks = self.peakDetect(self.int_ecg)
# classify each peak as QRS or noise
self.checkPeaks(peaks, self.int_ecg)
# compensate for delay during integration
self.QRSpeaks -= 40 * (self.samplingrate / 1000)
return self.QRSpeaks
def add_boundary_pores(self, labels=['top', 'bottom', 'front', 'back',
'left', 'right'], offset=None):
r"""
Add boundary pores to the specified faces of the network
Pores are offset from the faces of the domain.
Parameters
----------
labels : string or list of strings
The labels indicating the pores defining each face where boundary
pores are to be added (e.g. 'left' or ['left', 'right'])
offset : scalar or array_like
The spacing of the network (e.g. [1, 1, 1]). This must be given
since it can be quite difficult to infer from the network,
for instance if boundary pores have already added to other faces.
"""
offset = sp.array(offset)
if offset.size == 1:
offset = sp.ones(3)*offset
for item in labels:
Ps = self.pores(item)
coords = sp.absolute(self['pore.coords'][Ps])
axis = sp.count_nonzero(sp.diff(coords, axis=0), axis=0) == 0
ax_off = sp.array(axis, dtype=int)*offset
if sp.amin(coords) == sp.amin(coords[:, sp.where(axis)[0]]):
ax_off = -1*ax_off
topotools.add_boundary_pores(network=self, pores=Ps, offset=ax_off,
apply_label=item + '_boundary')
def detect_signals():
vector, label = weeklydataset_sg_ndata(
"/media/4AC0AB31C0AB21E5/Documents and Settings/Claudio/Documenti/Thesis/Workloads/MSClaudio/ews/access_log-20110805.csv",
[],
)
x, target = aggregatebymins_sg_ndata(vector[1])
starttime = time.time()
y = array(target)
t = array(x)
thr = max(y) * 2 / 3
print thr
I = pylab.find(y > thr)
# print I
# pylab.plot(t,y, 'b',label='signal')
# pylab.plot(t[I], y[I],'ro',label='detections')
# pylab.plot([0, t[len(t)-1]], [thr,thr], 'g--')
J = pylab.find(diff(I) > 1)
argpeak = []
targetpeak = []
for K in split(I, J + 1):
ytag = y[K]
peak = pylab.find(ytag == max(ytag))
# pylab.plot(peak+K[0],ytag[peak],'sg',ms=7)
argpeak.append(peak + K[0])
targetpeak.append(ytag[peak])
eta = time.time() - starttime
print "time elapsed %f" % eta
return list(itertools.chain(*argpeak)), list(itertools.chain(*targetpeak))
def scanSound(self, source, minnotel):
binarized = source
scale = 60. / self.wavetempo * (binarized[0].size / self.duration)
noise_length = scale*minnotel
antinoised = sp.zeros_like(binarized)
for i in range(sp.shape(binarized)[0]):
new_line = binarized[i, :].copy()
diffed = sp.diff(new_line)
ones_keys = sp.where(diffed == 1)[0]
minus_keys = sp.where(diffed == -1)[0]
if(ones_keys.size != 0 and minus_keys.size != 0):
if(ones_keys[0] > minus_keys[0]):
new_line = self.cutNoise(
(0, minus_keys[0]), noise_length, new_line)
minus_keys = sp.delete(minus_keys, 0)
if(ones_keys[-1] > minus_keys[-1]):
new_line = self.cutNoise(
(ones_keys[-1], new_line.size-1), noise_length, new_line)
ones_keys = sp.delete(ones_keys, -1)
for j in range(sp.size(ones_keys)):
new_line = self.cutNoise(
(ones_keys[j], minus_keys[j]), noise_length, new_line)
antinoised[i, :] = new_line
return antinoised
def execute(self):
self.power_mat, self.thermal_expectation = self.full_calculation()
n_chan = self.power_mat.shape[1]
n_freq = self.power_mat.shape[0]
# Calculate the the mean channel correlations at low frequencies.
low_f_mat = sp.mean(self.power_mat[1:4 * n_chan + 1,:,:], 0).real
# Factorize it into preinciple components.
e, v = linalg.eigh(low_f_mat)
self.low_f_mode_values = e
# Make sure the eigenvalues are sorted.
if sp.any(sp.diff(e) < 0):
raise RuntimeError("Eigenvalues not sorted.")
self.low_f_modes = v
# Now subtract out the noisiest channel modes and see what is left.
n_modes_subtract = 10
mode_subtracted_power_mat = sp.copy(self.power_mat.real)
mode_subtracted_auto_power = sp.empty((n_modes_subtract, n_freq))
for ii in range(n_modes_subtract):
mode = v[:,-ii]
amp = sp.sum(mode[:,None] * mode_subtracted_power_mat, 1)
amp = sp.sum(amp * mode, 1)
to_subtract = amp[:,None,None] * mode[:,None] * mode
mode_subtracted_power_mat -= to_subtract
auto_power = mode_subtracted_power_mat.view()
auto_power.shape = (n_freq, n_chan**2)
auto_power = auto_power[:,::n_chan + 1]
mode_subtracted_auto_power[ii,:] = sp.mean(auto_power, -1)
self.subtracted_auto_power = mode_subtracted_auto_power
def get_fft(self, fs, taps, Npts):
Ts = 1.0/fs
fftpts = fftpack.fft(taps, Npts)
self.freq = scipy.arange(0, fs, 1.0/(Npts*Ts))
self.fftdB = 20.0*scipy.log10(abs(fftpts))
self.fftDeg = scipy.unwrap(scipy.angle(fftpts))
self.groupDelay = -scipy.diff(self.fftDeg)
def get_indices(arr, vals, disp=False):
"""
Get the indices of all the elements between vals[0] and vals[1].
Alternatively also between vals[2] and vals[3] if they are given.
Input:
arr : the array in which to look for the elements
vals : a list with either 2 or 4 values that corresponds
limits inbetween which the indices of the values
Optional argument(s):
disp : Bolean parameter, if True it displays start and end
index and the number of channels inbetween. Only works
for value lists of length 2.
Assumes the values in 'arr' is the mid values and that it is evenly
spaced for all values.
********************** Important! **********************************
The output indices are Python friendly, i.e. they are 0-based. Take
when using the indices in other software e.g. GILDAS, MIRIAD, which
are 1-based.
--------------------------------------------------------------------
oOO Changelog OOo
*2012/02
Added more documentation, "important" notice about indexing
*2011/07
Removed +1 in the output indices to be compatible with rest of
module, where Pythons 0-based indexing is used.
*2010/12
Doc written
*2010/06
Funciton created
"""
from scipy import concatenate, where, array, diff
dx = abs(0.5 * diff(arr)[0])
if len(vals) == 4:
v1, v2, v3, v4 = vals + array([-1, 1, -1, 1]) * dx
# if the user wants two velocity areas to calculate noise
low = where((arr >= v1) * (arr <= v2))[0]
high = where((arr >= v3) * (arr <= v4))[0]
channels = concatenate((low, high))
elif len(vals) == 2:
v1, v2 = vals + array([-1, 1]) * dx
# channels = where((arr>=v1)*(arr<v2))[0]+1
# this is because if +1 it is FITS/Fortran safe
# changed: removed +1 for consistency in program
channels = where((arr >= v1) * (arr <= v2))[0]
#
if disp and len(vals) == 2:
first, last = channels.min(), channels.max()
n = last - first + 1
print "\nFirst: %d,\n Last: %d\n Nchan: %d\n" % (first, last, n)
return channels
def spectral_gap( x, k = None ):
"""Minimum difference in eigenvalues"""
# Get the singular values
s = svdvals( x )
if k is not None:
s = s[:k]
return (sc.diff( s )).min() / s[0]
def getCanoHRF_tderivative(duration=25., dt=.5):
hcano = getCanoHRF()
hcano[-1] = 0.
tAxis = np.arange(0, duration+dt, dt)
hderiv = diff(hcano[1], n=1)/dt
hderiv = np.hstack(([0], hderiv))
return tAxis, hderiv
def zero_heading_indices(self, threshold=3000): ''' Returns the indices of the data blocks where the heading signal indicates that the antenna was at the zero point. ''' heading = self.heading_buffer[:, 0] i1, i2 = sp.where(sp.diff(heading) > threshold)[0][0:2] return i1, i2
def eigen_sep( X, k = None ):
"""Minimum difference in eigenvalues"""
# Get the eigenvalues
s = (eigvals( X )).real
if k is not None:
s = s[:k]
return min(abs(s).min(), abs(sc.diff( s )).min())
def envelopeFromArray(self, array):
envelope=[]
diffs=scipy.diff(array)
#identifies envelope peaks via first derivative
for index in range( 1,len(diffs) ):
if diffs[index] <= 0 and diffs[index-1] >= 0:
envelope.append(array[index])
return envelope
def updateStates(self):
peak_deltas = scipy.diff(self.peaks)
trough_deltas = scipy.diff(self.troughs)
peak_envelope = self.envelopeFromArray(self.peaks)
trough_envelope = self.envelopeFromArray([-trough for trough in self.troughs])
peak_envelope_deltas = scipy.diff(peak_envelope)
trough_envelope_deltas = scipy.diff(trough_envelope)
envelope_detected = (len(peak_envelope_deltas) > 0 and
len(trough_envelope_deltas) > 0)
[unstable, limit_cycle, converging, converged] = [True, True, True, True]
if len(self.peaks) > 1 and len(self.troughs) > 1:
#only unstable if error always rises
unstable = ((peak_deltas > 0.0).all() or
(trough_deltas < 0.0).all() or
(envelope_detected and
(peak_envelope_deltas > 0.0).all() and
(trough_envelope_deltas > 0.0).all()))
#only converging if error is always decreasing
converging = (((peak_deltas < 0.0).all() and (trough_deltas > 0.0).all()) or
(envelope_detected and
(peak_envelope_deltas < 0.0).all() and
(trough_envelope_deltas < 0.0).all()))
#in a limit cycle if error ever rises
limit_cycle = not converging and not unstable
else:
[unstable, limit_cycle, converging] = [False, False, False]
#only converged if both final peak and trough are below
#converged threshold
if len(self.peaks) > 0 and len(self.troughs) > 0:
converged = ((self.peaks[-1] < self.convergence_level) and
(self.troughs[-1] > -self.convergence_level))
else:
converged = False
self.flags["unstable"] = unstable
self.flags["limit_cycle"] = limit_cycle
self.flags["converging"] = converging
self.flags["converged"] = converged
def compute_FFFS(x, y, xt, yt, param_grid_fffs):
maxVar = param_grid_fffs['maxvar']
clf = npfs.GMMFeaturesSelection()
clf.learn_gmm(x, y)
idx, crit, [] = clf.selection('forward',
x,
y,
criterion='F1Mean',
varNb=maxVar,
nfold=5)
d_crit = sp.diff(crit) / crit[:-1]
nv = sp.where(d_crit < param_grid_fffs['threshold'])[0][0]
print("Number of variables {}".format(nv))
yp = clf.predict_gmm(xt, featIdx=idx[:nv])[0]
return f1_score(yt, yp, average='weighted')
def pyglowinput(
latlonalt=[65.1367, -147.4472, 250.00],
dn_list=[datetime(2015, 3, 21, 8, 00),
datetime(2015, 3, 21, 20, 00)],
z=None):
if z is None:
z = sp.linspace(50., 1000., 200)
dn_diff = sp.diff(dn_list)
dn_diff_sec = dn_diff[-1].seconds
timelist = sp.array([calendar.timegm(i.timetuple()) for i in dn_list])
time_arr = sp.column_stack((timelist, sp.roll(timelist, -1)))
time_arr[-1, -1] = time_arr[-1, 0] + dn_diff_sec
v = []
coords = sp.column_stack((sp.zeros((len(z), 2), dtype=z.dtype), z))
all_spec = ['O+', 'NO+', 'O2+', 'H+', 'HE+']
Param_List = sp.zeros((len(z), len(dn_list), len(all_spec), 2))
for idn, dn in enumerate(dn_list):
for iz, zcur in enumerate(z):
latlonalt[2] = zcur
pt = Point(dn, *latlonalt)
pt.run_igrf()
pt.run_msis()
pt.run_iri()
# so the zonal pt.u and meriodinal winds pt.v will coorispond to x and y even though they are
# supposed to be east west and north south. Pyglow does not seem to have
# vertical winds.
v.append([pt.u, pt.v, 0])
for is1, ispec in enumerate(all_spec):
Param_List[iz, idn, is1, 0] = pt.ni[ispec] * 1e6
Param_List[iz, idn, :, 1] = pt.Ti
Param_List[iz, idn, -1, 0] = pt.ne * 1e6
Param_List[iz, idn, -1, 1] = pt.Te
Param_sum = Param_List[:, :, :, 0].sum(0).sum(0)
spec_keep = Param_sum > 0.
species = sp.array(all_spec)[spec_keep[:-1]].tolist()
species.append('e-')
Param_List[:, :] = Param_List[:, :, spec_keep]
Iono_out = IonoContainer(coords,
Param_List,
times=time_arr,
species=species)
return Iono_out
def trainBursts(train, aBinSize=0.05, maxTime=1.0, alpha=0.95):
"""
Find bursts of high activity (high instantaneous firing rate) in a train of pulses with respect to a statistical threshold upQuant. Example:
bursts= trainBursts(train, aBinSize=0.05, maxTime=1.0, alpha=0.95)
"""
nSpikes=len(train)
isi= sc.zeros(nSpikes);
dIFR= sc.zeros(nSpikes)
isi[1:]= train[1:]-train[:-1]
ifr=1/isi
dIFR[1:]= (((ifr[1:]-ifr[:-1])/isi[1:]) + ((ifr[1:]-ifr[:-1])/isi[:-1]))/2.0
ifrCDF,ifrCDFInverse= calcCDF(ifr,graph=0)
#isiCDF,isiCDFInverse= calcCDF(isi,graph=0)
# Find spikes during high activity
ifrUpThresh= calcThresholdsFromCDF(ifrCDFInverse, (alpha,))
ifrDnThresh= calcThresholdsFromCDF(ifrCDFInverse, (1-alpha,))
#isiThresh= calcThresholdsFromCDF(isiCDFInverse, (alpha,))
#rHighInds= sc.where( ifr>ifrThresh)[0]
rHighInds= sc.where( ifr>ifrUpThresh)[0]
lHighInds= rHighInds-1
highInds= sc.union1d(rHighInds,lHighInds)
highSpikeTimes= train[highInds]
#lowSpikeTimes= train[lowInds]
aa= sc.zeros(len(highInds))
aa[1:]= sc.diff(highInds)
#bb= sc.zeros(len(lowInds))
#bb[1:]= sc.diff(lowInds)
startInds=sc.where(aa!=1)[0]
burstStarts= highSpikeTimes[startInds]
burstEnds= highSpikeTimes[startInds-1]
nBursts= len(burstStarts)
burstStarts=burstStarts[:-1]
burstEnds=burstEnds[1:]
pBurst = sc.float32(nBursts)/nSpikes
burstDurs = burstEnds-burstStarts
c,b= xcorr(train,train, aBinSize, maxTime, minTime=0)
cHz = c/aBinSize
c[0]=0.0
bursts={"train": train,
"highInds":highInds, "highSpikeTimes":highSpikeTimes,
"burstStarts":burstStarts, "burstEnds":burstEnds,
"nBursts":nBursts, "nSpikes": nSpikes, "pBurst": pBurst, "burstDurs": burstDurs,
"alpha":alpha,
"ifr":ifr, "ifrCDF":ifrCDF, "ifrCDFInverse":ifrCDFInverse,"ifrThresh":ifrUpThresh,
"isi":isi, #"isiCDF":isiCDF, "isiCDFInverse":isiCDFInverse,"isiThresh":isiThresh,
"dIFR":dIFR,
"aCorrHz":cHz, "aCorrBins":b}
return bursts
def test_optdiv3(beta=0.9, grid=scipy.arange(21.0), zDraws=scipy.array([-1.0]*25 + [1.0]*75), useValueIter=True):
time1 = time.time()
localvars = {}
def postVIterCallbackFn(nIter, currentVArray, newVArray, optControls, stoppingResult):
global g_iterList
(stoppingDecision, diff) = stoppingResult
print("iter %d, diff %f" % (nIter, diff))
localvars[0] = nIter
def postPIterCallbackFn(nIter, newVArray, currentPolicyArrayList, greedyPolicyList, stoppingResult):
(stoppingDecision, diff) = stoppingResult
print("iter %d, diff %f" % (nIter, diff))
localvars[0] = nIter
initialVArray = grid; # initial guess for V: a linear fn
initialPolicyArray = grid; # initial guess for d: pay out everything
params = OptDivParams3(grid, beta, zDraws);
if (useValueIter == True):
result = bellman.grid_valueIteration([grid], initialVArray, params, postIterCallbackFn=postVIterCallbackFn, parallel=True)
(nIter, currentVArray, newVArray, optControls) = result
else:
result = bellman.grid_policyIteration([grid], [initialPolicyArray], initialVArray, params, postIterCallbackFn=postPIterCallbackFn, parallel=False)
(nIter, currentVArray, currentPolicyArrayList, greedyPolicyList) = result
newVArray = currentVArray
optControls = currentPolicyArrayList
time2 = time.time()
nIters = localvars[0]
print("total time: %f, avg time: %f" % (time2-time1, (time2-time1)/nIters))
optd_fn = linterp.LinInterp1D(grid, optControls[0])
# plot V
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(grid, newVArray)
dx = grid[1] - grid[0]
deriv = scipy.diff(newVArray) / dx
ax.plot(grid[:-1], deriv)
ax.set_xlabel("M")
ax.set_ylabel("V")
# plot optimal d
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(grid, optControls[0])
ax.set_xlabel("M")
ax.set_ylabel("optimal d")
plt.show()
return result
def get_CR(List, Repeat):
if len(set(List)) == 1: # NO CR if list has only identical elements
return [0, 0]
else:
AllMeans = [
] # List of model(!) sample means for every bootstrap iteration
AllProbs = [
] # List of model(!) sample posterior prob. for every iteration
ProbOfMean = {}
N = len(List) # Number of data points
for i in range(Repeat): # Repeated bootstrap iterations
Rands = [
0
] # Following Rubin et al. to get data probabilities from Dirichlet distrib.
CurrAvg = 0
for j in range(N - 1):
Rands.append(random.random())
Rands.append(1)
Rands.sort()
P = scipy.diff(
Rands
) # List of random numbers that add to 1 and are used as data probabilities
for j in range(N):
CurrAvg += P[j] * List[j] # Sample mean
AllMeans.append(CurrAvg)
AllProbs.append(1) # Posterior weights are 1 (i.e. no weighting)
for k in range(len(AllMeans)):
ProbOfMean[AllMeans[k]] = AllProbs[k]
AllMeans.sort()
TotalProb = sum(AllProbs)
CumulProb = 0
perc_min = 0
perc_max = 0
for m in AllMeans: # Iterating through sorted means, identifying that mean at which a certain percentile of probs is reached
CumulProb += ProbOfMean[m]
if (CumulProb > 0.025 * TotalProb) and (perc_min == 0):
perc_min = m
if (CumulProb > 0.975 * TotalProb) and (perc_max == 0):
perc_max = m
return [
perc_min, perc_max
] # Credibility Region is defined by min/max percentiles of sampling means
def weight_radial(catalogue, rwidth=rwidth, redges=redges):
self.logger.info('Radial integral constraint.')
distance = catalogue.distance()
dmin, dmax = distance.min(), distance.max()
self.logger.info('Comoving distances: {:.1f} - {:.1f}.'.format(
dmin, dmax))
if redges is not None:
radialedges = scipy.array(redges)
rwidth = scipy.mean(scipy.diff(radialedges))
rmin, rmax = radialedges.min(), radialedges.max()
if (rmin > dmin) or (rmax < dmax):
raise ValueError(
'Provided radial-edges ({:.1f} - {:.1f}) do not encompass the full survey ({:.1f} - {:.1f}).'
.format(rmin, rmax, dmin, dmax))
self.logger.info(
'Provided radial-edges of width: {:.1f} and range: {:.1f} - {:.1f}.'
.format(rwidth, rmin, rmax))
nbins = len(radialedges) - 1
else:
self.logger.info(
'Provided radial-width: {:.1f}.'.format(rwidth))
nbins = scipy.rint((dmax - dmin) / rwidth).astype(int)
radialedges = scipy.linspace(dmin, dmax + 1e-9, nbins + 1)
self.logger.info(
'There are {:d} radial-bins with an average of {:.1f} objects.'
.format(nbins,
len(catalogue) * 1. / nbins))
ibin = scipy.digitize(distance, radialedges, right=False) - 1
for iaddbin in range(catalogue.attrs['naddbins']):
mask = catalogue['iaddbin'] == iaddbin
wcounts = scipy.bincount(ibin[mask],
weights=catalogue['Weight'][mask],
minlength=nbins)
catalogue['Weight'][mask] /= wcounts[ibin[mask]]
attrs = {'radialedges': radialedges, 'nbins': nbins}
def bin(catalogue):
return scipy.digitize(
catalogue.distance(), radialedges, right=False) - 1
return attrs, bin
def combine(cls,ensembles,errors={},params=[]):
assert (scipy.diff(map(len,ensembles)) == 0).all()
self = ensembles[0].deepcopy()
self.weights = {}
for par in params:
if errors.get(par,None) is None:
errors[par] = [e.std(par) for e in ensembles]
err = scipy.array(errors[par])
corr = scipy.corrcoef([e[par] for e in ensembles])
cov = corr * err[:,None].dot(err[None,:])
invcov = scipy.linalg.inv(cov)
self.weights[par] = scipy.sum(invcov,axis=-1)/scipy.sum(invcov)
self.logger.info('Using for {} weights: {}.'.format(par,self.weights[par]))
for key in self._ARGS:
tmp = getattr(self,key)
tmp[par] = scipy.average([getattr(e,key)[par] for e in ensembles],weights=self.weights[par])
return self
def compute(
self,
anaSigList,
sign='-',
left_sweep=0.001,
right_sweep=0.002,
baseline_time=.05,
rise_time=.001,
peak_time=.001,
threshold=20.,
window=.0001,
):
anaSig = anaSigList[0]
sr = anaSig.sampling_rate
nb = int(baseline_time * sr)
nb = int(nb / 2.) * 2 + 1
nr = int(rise_time * sr)
np = int(peak_time * sr)
print peak_time, np, sr
nw = int(window * sr)
sigBase = convolve(anaSig.signal, ones(nb, dtype='f') / nb, 'same')
#~ sigBase = signal.medfilt(anaSig.signal , kernel_size = nb)
sigPeak = convolve(anaSig.signal, ones(np, dtype='f') / np, 'same')
if sign == '-':
aboves = sigBase[:-(nr + nb / 2 + np / 2
)] - sigPeak[nr + nb / 2 + np / 2:] > threshold
elif sign == '+':
aboves = sigPeak[nr + nb / 2 + np / 2:] - sigBase[:-(
nr + nb / 2 + np / 2)] > threshold
print aboves
# detection when n point consecutive more than window
aboves = aboves.astype('f')
aboves[0] = 0
aboves[-1] = 0
indup, = where(diff(aboves) > .5)
return indup + nr + nb / 2 + np / 2
#~ inddown, = where( diff(aboves)<-.5)
#~ print indup
print inddown
def frequency(p, m, theta_begin, alpha, dthe=3):
Nu = np.zeros(len(alpha))
if p == 1:
flag_p = 1
fName = '单角度数据//m={:.2f},p={:d},theta={:.2f}'.format(m, p, theta_begin)
theta_max = def2sca(theta_def(90, p, m), p)
# ************************************************************************************
# print('p={},m={:.2f},theta={},theta_max={:.2f}'.format(p,m,theta_begin,theta_max))
# ************************************************************************************
if theta_begin > theta_max:
flag_p = 0
# *********************************************************
# print('该角度范围无对应{}阶光线'.format(p))
# *********************************************************
if p == 2:
flag_p = 2
fName = '单角度数据//m={:.2f},p={:d},theta={:.2f}'.format(m, p, theta_begin)
theta_e = arccos(np.sqrt((m**2 - 1) / (p**2 - 1))) * 180 / pi
theta_min = min(def2sca(theta_def(90, p, m), p),
def2sca(theta_def(theta_e, p, m), p))
print('p={},m={:.2f},theta={},theta_min={:.2f}'.format(
p, m, theta_begin, theta_min))
if theta_begin < theta_min:
flag_p = 0
# *********************************************************
# print('该角度范围无对应{}阶光线'.format(p))
# *********************************************************
if flag_p:
for i_alpha in range(len(alpha)):
pdiff = []
# 注意！！！！这里如果直接求导得到频率必须是将散射角间隔分为恰好一度！
M = 2
ths = np.linspace(theta_begin, theta_begin + dthe, M)
for _ in ths:
pdiff.append(phase_diff(_, alpha[i_alpha], 0, p, m))
pdiff = np.array(pdiff).reshape(1, M) # 将列表转为数组
pdd = abs(diff(pdiff)) # 求导，斜率取正
Nu[i_alpha] = pdd[0][0] / (2 * pi * dthe / (M - 1))
return Nu, fName
def Problem5Real():
N = 500
w = sp.linspace(0,100,N)
w = w.reshape(N,1)
u = lambda c: sp.sqrt(c)
util_vec = u(w)
alpha = 0.5
alpha_util = u(alpha*w)
alpha_util_grid = sp.repeat(alpha_util,N,1)
m = 20
v = 200
f = discretelognorm(w,m,v)
VEprime = sp.zeros((N,1))
VUprime = sp.zeros((N,N))
EVUprime = sp.zeros((N,1))
gamma = 0.1
beta = 0.9
tol = 10**-9
delta1 = 1+tol
delta2 = 1+tol
it = 0
while ((delta1 >= tol) or (delta2 >= tol)):
it += 1
VE = VEprime.copy()
VU = VUprime.copy()
EVU = EVUprime.copy()
VEprime = util_vec + beta*((1-gamma)*VE + gamma*EVU)
arg1 = sp.repeat(sp.transpose(VE),N,0)
arg2 = sp.repeat(EVU,N,1)
arg = sp.array([arg2,arg1])
VUprime = alpha_util_grid + beta*sp.amax(arg,axis = 0)
psi = sp.argmax(arg,axis = 0)
EVUprime = sp.dot(VUprime,f)
delta1 = sp.linalg.norm(VEprime - VE)
delta2 = sp.linalg.norm(VUprime - VU)
#print(delta1)
wr_ind = sp.argmax(sp.diff(psi), axis = 1)
wr = w[wr_ind]
return wr
def load_frame_ROI(self, in_dir, lane):
"""
Load the frame and ROI data.
Parameters
----------
lane: int
lane number of walking arena; prob from 0 to 4.
dir: str
directory of exp data csv from DLC
"""
filename = os.path.join(in_dir, 'lane_%s_topbyroi.txt' % lane)
with open(filename, 'r') as fp:
self.frm_ROI = sp.loadtxt(fp)
self.ROI_switch_idxs = sp.where(sp.diff(self.frm_ROI[:, 1]) != 0)[0]
def update_results(self):
r'''
Send results of simulation out the the appropriate locations.
This is a basic version of the update that simply sends out the main
result (quantity). More elaborate updates should be subclassed.
'''
phase_quantity = self._quantity.replace(self._phase.name + '_', "")
self._phase[phase_quantity] = self[self._quantity]
dx = sp.squeeze(
sp.diff(self[self._quantity][self._net.find_connected_pores(
self.throats())],
n=1,
axis=1))
g = self['throat.conductance']
self._phase['throat.rate'] = sp.absolute(g * dx)
self._logger.debug('Results of ' + self.name +
' algorithm have been added to ' + self._phase.name)
def get_edges(routes):
results = []
for timetable in walk_timetables(routes):
origin = timetable['timetable']['departureStopId']
for route in timetable['timetable']['routes']:
for intervals in route['stationIntervals']:
stops = [origin] + [x['stopId'] for x in intervals['intervals']]
edges = [[s, t] for s, t in zip(stops, stops[1:])]
times = [0] + [x['timeToArrival'] for x in intervals['intervals']]
weights = list(sp.diff(sp.array(times)))
results.extend([[s, t, w] for (s, t), w in zip(edges, weights)])
results = pd.DataFrame(results, columns=['origin', 'destination', 'time'])
results = results.groupby(['origin', 'destination']).mean()
return results
def build_block_toeplitz_from_xcorrs(tf, chan_set, xcorrs, dtype=None):
"""builds a block toeplitz matrix from a set of channel xcorrs
:type tf: int
:param tf: desired lag in samples
:type chan_set: list
:param chan_set: list of channel ids to build the channel set from. the
block covariance matrix will be build so that blocks are ordered from
lower to higher channel id.
:type xcorrs: XcorrStore
:param xcorrs: XcorrStore object holding the xcorrs for various channel
combinations
:type dtype: dtype derivable
:param dtype: will be passed to the constructor for the matrix returned.
Default=None
"""
# init and checks
assert tf <= xcorrs._tf
chan_set = sorted(chan_set)
nc = len(chan_set)
assert all(sp.diff(chan_set) >= 1)
assert max(chan_set) < xcorrs._nc
assert all([key in xcorrs for key in build_idx_set(chan_set)
]), 'no data for requested channels'
rval = sp.empty((tf * nc, tf * nc), dtype=dtype)
# build blocks and insert into fout
for i in xrange(nc):
m = chan_set[i]
for j in xrange(i, nc):
n = chan_set[j]
xc = xcorrs[m, n]
sample0 = xc.size / 2
r = xc[sample0:sample0 + tf]
c = xc[sample0 + 1 - tf:sample0 + 1][::-1]
#c = xc[sample0:sample0 - tf:-1]
block_ij = sp_la.toeplitz(c, r)
rval[i * tf:(i + 1) * tf, j * tf:(j + 1) * tf] = block_ij
if i != j:
rval[j * tf:(j + 1) * tf, i * tf:(i + 1) * tf] = block_ij.T
# return
return rval
def isi(t, V, spike_thresh=0):
"""isi_mean, isi_dev = isi(t, V, spike_thresh=0)
Given voltage (V) and time (t) vectors, isi calculates the mean interspike
interval (isi_mean) and the standard deviation of the interspike interval
(isi_dev).
You can optionally specify the spike threshold (defaults to 0).
This uses an assumption that every time it spikes, the voltage increases
above the given spike threshold.
The method used here is not robust. If the data is noisy then there will
likely be false positives. With a model however, it should work very
well.
"""
time = t[sp.logical_and(V[:-1] < spike_thresh, V[1:] >= spike_thresh)]
dt = sp.diff(time)
return sp.mean(dt), sp.std(dt)
def time_diff(ts,order=1):
""" Generate left side derative of a ts of input orders.
Parameters
-----------
ts : :class:`~vtools.data.timeseries.TimeSeries`
Series to interpolate. Must has data of one dimension, and regular.
order : int
Order of derative.
Returns
-------
result : vtools.data.time_series.TimeSeries
A regular series with derative.
Raise
--------
ValueError
If input time series is shorter than order+1 or is not regular.
"""
if len(ts)<order+1:
raise ValueError("input timeseries is not"
"long enough.")
if not ts.is_regular():
raise ValueError("time_diff only support regular"
"time series for the time being.")
delta_data=diff(ts.data,order)
rt_start=ts.times[order]
interval=ts.interval
prop=deepcopy(ts.props)
prop[AGGREGATION]=INDIVIDUAL
prop[TIMESTAMP]=INST
rt=rts(delta_data,rt_start,interval,prop)
return rt
def test_statistical_physical_units(self):
n_trials = 1000
n_points = 200
dt = 0.001
window = sp.ones(n_points, dtype=float)
power = sp.zeros(n_points // 2)
for ii in range(n_trials):
wave = self.amp1 * random.randn(n_points)
power += npow.prune_power(npow.calculate_power(wave)).real
power /= n_trials
power = npow.make_power_physical_units(power, dt)
freqs = npow.ps_freq_axis(dt, n_points)
df = abs(sp.mean(sp.diff(freqs)))
# The integral of the power spectrum should be the variance. Factor of
# 2 get the negitive frequencies.
integrated_power = sp.sum(power) * df * 2
self.assertTrue(
sp.allclose(integrated_power / self.amp1**2,
1.0,
atol=4.0 * (2.0 / sp.sqrt(n_trials * n_points))))
def rebin(self, xnew):
"""
Rebin the spectrum on a new grid named xnew
"""
#Does not need equal spaced bins, but why would you not?
xnew.sort()
fbin = sp.zeros(xnew.size)
efbin = sp.zeros(xnew.size)
#up sampling is just interpolation
m = (self.wv >= xnew[0]) * (self.wv <= xnew[-1])
if self.wv[m].size <= xnew.size - 1:
fbin, efbin = self.interp(xnew)
else:
#down sampling--
#1) define bins so that xnew is at the center.
#2) interpolate to account for fractional pixel weights
#3) take the mean within each bin
db = 0.5 * sp.diff(xnew)
b2 = xnew[1::] - db
b2 = sp.insert(b2, 0, xnew[0])
insert = sp.searchsorted(self.wv, b2)
xinsert = sp.insert(self.wv, insert, xnew)
xinsert = sp.unique(xinsert)
yinsert, zinsert = self.interp(xinsert)
i = sp.digitize(xinsert, b2)
for j in range(b2.size):
iuse = sp.where(i == j + 1)[0]
fbin[j] = sp.mean(yinsert[iuse])
efbin[j] = sp.mean(zinsert[iuse])
self._wv = xnew
if self.ef is not None:
self._ef = efbin
self.f = fbin
assert self.wv.size == self.f.size
def auc(y, prob, w):
if len(w) == 0:
mindiff = scipy.amin(scipy.diff(scipy.unique(prob)))
pert = scipy.random.uniform(0, mindiff / 3, prob.size)
t, rprob = scipy.unique(prob + pert, return_inverse=True)
n1 = scipy.sum(y, keepdims=True)
n0 = y.shape[0] - n1
u = scipy.sum(rprob[y == 1]) - n1 * (n1 + 1) / 2
result = u / (n1 * n0)
else:
op = scipy.argsort(prob)
y = y[op]
w = w[op]
cw = scipy.cumsum(w)
w1 = w[y == 1]
cw1 = scipy.cumsum(w1)
wauc = scipy.sum(w1 * (cw[y == 1] - cw1))
sumw = cw1[-1]
sumw = sumw * (c1[-1] - sumw)
result = wauc / sumw
return (result)
def setgrid(extent):
dn = 1000
width = extent[1] - extent[0]
height = extent[3] - extent[2]
Y = np.linspace(extent[2], extent[3], dn + 1)
rsize = scipy.diff(Y)[0]
Y = setXY(Y)
Y = np.expand_dims(Y, axis=1)
N_x = int(np.ceil(width / rsize))
Y = np.repeat(Y, N_x, axis=1)
X = np.zeros((N_x + 1, ))
X[0] = extent[0]
for i in range(N_x):
X[i + 1] = X[i] + rsize
X = setXY(X)
X = np.expand_dims(X, axis=0)
X = np.repeat(X, dn, axis=0)
return X, Y, dn, N_x, rsize
def rgb_hist(I, ax, bins=256):
# run over red, green, and blue channels
channels = ('r', 'g', 'b')
for i, color in enumerate(channels):
# get count pixel intensities for this channel
counts, bins, patches = plt.hist(I[:, :, i].flatten(),
bins=bins,
normed=True,
visible=False)
# hack: choose mid-point of bins as centers
centers = bins[:-1] + sp.diff(bins) / 2
# line plot with fill
plt.plot(centers, counts, color=color)
ax.fill_between(centers, 0, counts, color=color, alpha=0.25)
# hack for matlab's axes('square') function
# http://www.mail-archive.com/[email protected]/msg08388.html
plt.axis('tight')
ax.set_aspect(1. / ax.get_data_ratio())
def get_refperiod_violations(spike_trains, refperiod, progress=None):
""" Return the refractory period violations in the given spike trains
for the specified refractory period.
:param dict spike_trains: Dictionary of lists of
:class:`neo.core.SpikeTrain` objects.
:param refperiod: The refractory period (time).
:type refperiod: Quantity scalar
:param progress: Set this parameter to report progress.
:type progress: :class:`.progress_indicator.ProgressIndicator`
:returns: Two values:
* The total number of violations.
* A dictionary (with the same indices as ``spike_trains``) of
arrays with violation times (Quantity 1D with the same unit as
``refperiod``) for each spike train.
:rtype: int, dict """
if type(refperiod) != pq.Quantity or \
refperiod.simplified.dimensionality != pq.s.dimensionality:
raise ValueError('refperiod must be a time quantity!')
if not progress:
progress = ProgressIndicator()
total_violations = 0
violations = {}
for u, tL in spike_trains.iteritems():
violations[u] = []
for i, t in enumerate(tL):
st = t.copy()
st.sort()
isi = sp.diff(st)
violations[u].append(st[isi < refperiod].rescale(refperiod.units))
total_violations += len(violations[u][i])
progress.step()
return total_violations, violations
def get_ROI_splits(self): """ Get the frames corresponding to a beginning and end of an ROI. """ # The columns of ROI_splits are: ROI, beg idx, end idx, slot number self.ROI_splits = sp.zeros(4) for iS in range(self.num_slots): split_idxs = sp.nonzero(sp.diff(self.corr_ROI[:, iS]))[0] split_idxs = sp.hstack(([-1], split_idxs)) if (self.num_frames - 1) not in split_idxs: split_idxs = sp.hstack((split_idxs, self.num_frames - 1)) for iI in range(len(split_idxs) - 1): idx_beg = split_idxs[iI] + 1 idx_end = split_idxs[iI + 1] + 1 if idx_beg+1 >= self.num_frames: continue arr = [self.corr_ROI[idx_beg + 1, iS], idx_beg, idx_end, iS] self.ROI_splits = sp.vstack((self.ROI_splits.T, arr)).T self.ROI_splits = self.ROI_splits.astype(int)
def loadaerdat(datafile='/tmp/aerout.dat', stas=None, nEvents=None, datatype="II"):
aerdatafh = open(datafile, 'rb')
k = 0
while aerdatafh.readline()[0] == "#":
k += 1
continue
tmp = aerdatafh.read()
n = len(tmp) / struct.calcsize('>' + datatype)
tmad = struct.unpack_from('>' + datatype * n, tmp)
dat = np.array(tmad)
dat = dat.reshape(dat.shape[0] / 2, 2)
if nEvents == None:
nEvents = n
if stas == None:
return dat
else:
tm = np.concatenate([[0], sp.diff(dat[:nEvents, 1])])
ad = stas.STAddrPhysicalExtract(dat[:nEvents, 0]).transpose()
return [tm, ad]
def __init__(self, ta_object: MDTrajectory,
box_size: tuple, grid_size: np.ndarray,
frag_id: int = 0, average_solute: bool = False):
""" Create a pcf ta_object.
Parameters
----------
ta_object : MDTrajectory
Object with all information about the MD trajectory
box_size : tuple(3)
Size of cubic grid where to evaluate the PCF
grid_size : np.ndarray((Npoints,3), dtype=float)
Number of points in each direction.
frag_id : int
Index indicating which molecule(s) to take as solute.
By default solute = 0.
average_solute : bool
Whether the solute molecules also need to be averaged.
"""
self.ta_object = ta_object
histogram_range = np.asarray([-box_size/2., box_size/2.]).T
self.ta_object.align_along_trajectory(frag_id, self.ta_object.topology, to_file=True)
if average_solute:
self.ta_object.get_average_structure(frag_id)
# Align solvent and find the averaged structure
edges, self.pcf = self.ta_object.compute_pair_correlation_function(histogram_range,
grid_size, frag_id)
self.grid_size = grid_size
self.npoints = np.cumprod(grid_size)[-1]
self.delta = sp.diff(edges)
edges = np.array(edges)
# NOTE: only works for cubic grids
self.points = edges[:, :-1] + self.delta/2.0
self.total_frames = self.ta_object.nframes
# Initialize Pybind Class
self.pbox = BoxGrid(grid_size, self.points)
self.bohr = 0.529177249
def _(ops, locs, n):
'''
Put operators in a circuit and compile them.
notice the big end are high loc bits!
Args:
ops (list): list of single bit operators.
locs (list): list of positions.
n (int): total number of bits.
Returns:
array: resulting matrix.
'''
if np.ndim(locs) == 0:
locs = [locs]
if not isinstance(ops, (list, tuple)):
ops = [ops]
locs = np.asarray(locs)
locs = n - locs
order = np.argsort(locs)
locs = np.concatenate([[0], locs[order], [n + 1]])
return _wrap_identity([ops[i] for i in order], np.diff(locs) - 1)
def to_window(self, **params):
window = MuFunction(**params)
window.k = self.k
window.window = scipy.asarray([res.counts for res in self.result])
with warnings.catch_warnings():
warnings.simplefilter('ignore', category=RuntimeWarning)
window.mu = scipy.ma.average([res.mu for res in self.result],
weights=window.window,
axis=0).data
muedges = self.result[0].muedges
mupositive = len(muedges) // 2
muedges = muedges[mupositive:]
assert muedges[0] == 0 and (muedges >= 0).all()
window.mu = scipy.mean(
[window.mu, -window.mu[::-1]],
axis=0)[mupositive:] #-1 because we took half of the shell
window.window = scipy.sum([window.window, window.window[:, ::-1]],
axis=0)[:, mupositive:]
empty = scipy.isnan(window.mu)
window.mu[empty] = edges_to_mid(muedges)[empty]
window.error = scipy.sqrt(window.window)
#print window.window.shape
norm = scipy.sum(window.window * scipy.diff(muedges),
axis=-1) / (muedges[-1] - muedges[0])
window.window /= norm[:, None]
window.error /= norm[:, None]
window.pad_zero()
return window
def ROI_corrected(self): """ Correct ROI by incorporating minimum transition time """ for iS in range(self.num_slots): # Indices at which ROI changes splits = sp.nonzero(sp.diff(self.raw_ROI[:, iS]))[0] # For each of these transitions, check length for false transitions for iSplit in sp.arange(len(splits))[::-1]: # Frame-length of the current ROI split_beg = splits[iSplit - 1] split_end = splits[iSplit] split_len = split_end - split_beg # If ROI is too short, keep moving backward until you find an # ROI of sufficient length (i.g. ROI > min_ROI_frames) split_shift = 0 while split_len < self.min_ROI_frames: split_shift += 1 # If at beginning of array; break the loop if iSplit - split_shift < 0: break split_shift_beg = splits[iSplit - split_shift - 1] split_shift_end = splits[iSplit - split_shift] split_len = split_shift_end - split_shift_beg # Change all false regions back to ROI of sufficient length if split_shift > 0: frames_to_change = range(split_shift_end, split_end + 1) self.corr_ROI[frames_to_change, iS] = \ self.raw_ROI[split_shift_end, iS]
def add_boundary_pores(
self,
labels=['top', 'bottom', 'front', 'back', 'left', 'right'],
spacing=None):
r"""
Add boundary pores to the specified faces of the network
Pores are offset from the faces by 1/2 of the given ``spacing``, such
that they lie directly on the boundaries.
Parameters
----------
labels : string or list of strings
The labels indicating the pores defining each face where boundary
pores are to be added (e.g. 'left' or ['left', 'right'])
spacing : scalar or array_like
The spacing of the network (e.g. [1, 1, 1]). This must be given
since it can be quite difficult to infer from the network,
for instance if boundary pores have already added to other faces.
"""
spacing = sp.array(spacing)
if spacing.size == 1:
spacing = sp.ones(3) * spacing
for item in labels:
Ps = self.pores(item)
coords = sp.absolute(self['pore.coords'][Ps])
axis = sp.count_nonzero(sp.diff(coords, axis=0), axis=0) == 0
offset = sp.array(axis, dtype=int) * spacing / 2
if sp.amin(coords) == sp.amin(coords[:, sp.where(axis)[0]]):
offset = -1 * offset
topotools.add_boundary_pores(network=self,
pores=Ps,
offset=offset,
apply_label=item + '_boundary')
def to_window(self, **params):
window = WindowFunction1D(**params)
sedges = self.result.sedges
window.poles = self.result.ells
window.los = self.result.los
if hasattr(self.result, 's'):
window.s = self.result.s
empty = scipy.isnan(window.s)
window.s[empty] = edges_to_mid(sedges)[empty]
else:
window.s = edges_to_mid(sedges)
window.window = self.result.counts
volume = -scipy.diff(s_to_cos(sedges))
window.window /= volume[None, ...]
window.pad_zero()
window.s = s_to_cos(window.s)[::-1]
window.window[0] = window.window[0][::-1]
return window
