def create_adjacency_matrix(self, data=None):
r"""
Returns a weighted adjacency matrix, in CSR format based on the
product of weight values sharing an interface.
"""
#
if data is None:
data = self.data_vector
#
weights = data[self._cell_interfaces[:, 0]]
weights = 2*weights * data[self._cell_interfaces[:, 1]]
#
# clearing any zero-weighted connections
indices = weights > 0
interfaces = self._cell_interfaces[indices]
weights = weights[indices]
#
# getting cell connectivity info
row = interfaces[:, 0]
col = interfaces[:, 1]
#
# append row & col to each other, and weights to itself
row = sp.append(row, interfaces[:, 1])
col = sp.append(col, interfaces[:, 0])
weights = sp.append(weights, weights)
#
# Generate sparse adjacency matrix in 'coo' format and convert to csr
num_blks = self.nx*self.nz
matrix = sprs.coo_matrix((weights, (row, col)), (num_blks, num_blks))
#
return matrix.tocsr()
def mix_prop_test():
energyfile = "energies_0_K"
vibfiles = ["0_thermo","1.54_thermo","1.3_thermo","2.3_thermo","1_thermo"]
efile = open(energyfile,'r')
efile.readline()
comp = sp.array([])
energy0 = sp.array([])
for line in efile:
comp = sp.append(comp,float(line.split()[0]))
energy0 = sp.append(energy0,float(line.split()[1]))
efile.close()
phase = []
for i in range(len(comp)):
phase.append(Phase(comp[i],energy0[i],vibfiles[i]))
vib_prop = []
for i in range(len(phase)):
vib_prop.append(phase[i].E_thermal)
vib_mix_prop = binary_mixing_property(vib_prop,comp,2)
# Text output of data
for i in range(len(phase[0].T)):
text = str(phase[0].T[i])
for j in range(len(phase)):
text += " "+str(vib_mix_prop[j,i])
print text
sys.exit()
# Graphical output of data
for i in range(len(phase)):
plt.plot(phase[i].T,vib_mix_prop[i])
plt.xlabel('T (K)')
plt.ylabel('Delta E_vib (meV/cation)')
plt.show()
def LatVsHeiArray(self):
""" """
self.altbins = arange(self.altlim[0], self.altlim[1] + self.altstp,
self.altstp)
for _alt in self.altbins:
if True:
hwm14Obj = HWM14(alt=_alt,
ap=self.ap,
glatlim=self.glatlim,
glatstp=self.glatstp,
glon=self.glon,
option=self.option,
verbose=self.verbose,
ut=self.ut)
else:
pass
Uwind = reshape(hwm14Obj.Uwind, (len(hwm14Obj.Uwind), 1))
Vwind = reshape(hwm14Obj.Vwind, (len(hwm14Obj.Vwind), 1))
self.Uwind = Uwind if _alt == self.altlim[0] else append(
self.Uwind, Uwind, axis=1)
self.Vwind = Vwind if _alt == self.altlim[0] else append(
self.Vwind, Vwind, axis=1)
self.glatbins = hwm14Obj.glatbins
self.Uwind = transpose(self.Uwind)
self.Vwind = transpose(self.Vwind)
def GP_train(x, y, cov_par, cov_func = None, cov_typ ='SE', \
cov_fixed = None, prior = None, \
MF = None, MF_par = None, MF_args = None, \
MF_fixed = None):
'''
Max likelihood optimization of GP hyper-parameters. Calls
GP_negloglik. Takes care of merging / splitting the fixed /
variable and cov / MF parameters
'''
if MF != None:
merged_par = scipy.append(cov_par, MF_par)
n_MF_par = len(MF_par)
fixed = scipy.append(scipy.zeros(len(cov_par), 'bool'), \
scipy.zeros(n_MF_par, 'bool'))
if (cov_fixed != None): fixed[0:-n_MF_par] = cov_fixed
if (MF_fixed != None): fixed[-n_MF_par:] = MF_fixed
if MF_args == None: MF_args = x[:]
else:
merged_par = cov_par[:]
n_MF_par = 0
fixed = scipy.zeros(len(cov_par), 'bool')
if cov_fixed != None: fixed[:] = cov_fixed
var_par_in = merged_par[fixed == False]
fixed_par = merged_par[fixed == True]
args = (x, y, cov_func, cov_typ, MF, n_MF_par, MF_args, fixed, \
fixed_par, prior)
var_par_out = \
sop.fmin(GP_negloglik, var_par_in, args, disp = 0)
par_out = scipy.copy(merged_par)
par_out[fixed == False] = var_par_out
par_out[fixed == True] = fixed_par
if MF != None:
return par_out[:-n_MF_par], par_out[-n_MF_par:]
else:
return par_out
def f(self,x,t):
N = len(x)/2
xdot = pl.array([])
# modulus the x for periodicity.
x[N:2*N]= x[N:2*N]%self.d
# HERE ---->> 1Dify
for i in range(N):
temp = 0.0
for j in range(N):
if i == j:
continue
#repulsive x interparticle force of j on i
temp += self.qq*(x[N+i]-x[N+j])/(pl.sqrt((x[N+i]-x[N+j])**2)**3)
# All of the forces coming from the 'same' paricle but from other 'cells' due to the
# periodic contrains can be wraped up in a sum that converges to an aswer that can
# be expressed in terms of polygamma functions (se pg 92 of notebook).
temp += self.qq*(polygamma(1,(self.d+x[N+i]-x[N+j])/self.d)-polygamma(1,1.0-((x[N+i]-x[N+j])/self.d)))/(self.d**2)
# EC x force on particle i
for a in range(2):
temp+=self.As[i]*pl.sin(x[N+i]-a*pl.pi)*pl.cos(t-a*pl.pi)/(pl.cosh(1.0)-pl.cos(x[N+i]-a*pl.pi))
temp -= self.beta*x[i]
xdot = pl.append(xdot,temp)
for i in range(N):
xdot = pl.append(xdot,x[i])
return xdot
def calculate_difference(frames_energy):
"""calculate difference of energies
Implementation following paper "A Highly Robust Audio Fingerprinting System"
:math:`F(n,m)=1` if :math:`E(n,m)-E(n,m+1)-(E(n-1,m)-E(n-1,m+1))>0`
:math:`F(n,m)=0` if :math:`E(n,m)-E(n,m+1)-(E(n-1,m)-E(n-1,m+1))\leq 0`
:param frames_energy: frames of energys
:type frames_energy: scipy.array
:return: fingerint
"""
log.debug('Fingerprinting: calculate_difference')
# fingerprint vector
fingerprint = scipy.array([], dtype=int)
# first frame is defined as previous frame
prev_frame = frames_energy[0]
print str(len(frames_energy))
del frames_energy[0]
for n, frame in enumerate(frames_energy):
# every energy of frequency bands until length-1
for m in range(len(frame)-1):
# calculate difference with formula from paper
if (frame[m]-frame[m+1]-(prev_frame[m]-prev_frame[m+1]) > 0):
fingerprint = scipy.append(fingerprint, 1)
else:
fingerprint = scipy.append(fingerprint, 0)
prev_frame = frame
return fingerprint
def load_shapes(self, narrow_shape, wide_shape):
self.signal_group = []
for i in range(10):
for j in range(10):
signal = scipy.array([])
for k in range(5):
if codes[i][k] == "n":
signal = scipy.append(signal, narrow_shape)
else:
signal = scipy.append(signal, wide_shape)
if codes[j][k] == "n":
signal = scipy.append(signal, scipy.zeros(len(narrow_shape)))
else:
signal = scipy.append(signal, scipy.zeros(len(wide_shape)))
signal /= pnorm(signal)
self.signal_group.append(signal)
self.value_group.append(value_map(i, j))
def load_shapes( self, narrow_shape, wide_shape ):
self.ref_signals = []
for i in range(10):
for j in range(10):
signal = scipy.array([])
for k in range(5):
if ( codes[i][k] == 'n' ):
signal = scipy.append( signal, narrow_shape )
else:
signal = scipy.append( signal, wide_shape )
if ( codes[j][k] == 'n' ):
signal = scipy.append( signal, scipy.zeros(len(narrow_shape)) )
else:
signal = scipy.append( signal, scipy.zeros(len(wide_shape)) )
signal /= norm(signal);
self.ref_signals.append( signal )
self.ref_values.append( value_map(i,j) )
def f(self,x,t):
# x[N+i] is the position of i^th particle
# x[i] is the velocity of i^th particle
# This initilazation should be slightly faster than re-doing "len(x)"
xdot = pl.array([])
for i in range(self.N):
# temp is to have a variable to keep adding terms of the "field" and the interactions to
# so we can do things peicewise. start with the field contribution
temp = 0.0
#print('1st temp:' + str(temp))
for j in range(self.N):
if i == j:
continue
# interaction force of j on i
temp += (self.I/(2.0*self.N))*pl.sin(x[self.N+i]-x[self.N+j])
#print('2nd temp:' + str(temp))
# What we have as temp is the second derivative of the position i.e v_dot -> so these
# are the first in the array
xdot = pl.append(xdot,temp)
#print('xdot: ' + str(xdot))
# The second in the array are just the first deriviative of the positions i.e v wich is what
# were the first values in the input array.
xdot = pl.append(xdot,x[:self.N])
return xdot
def f(self,x,t):
N = len(x)/2
xdot = pl.array([])
# modulus the x for periodicity.
x[N:2*N]= x[N:2*N]%self.d
# HERE ---->> 1Dify
for i in range(N):
temp = 0.0
for j in range(N):
if i == j:
continue
#repulsive x interparticle force of j on i
temp += self.qq*(x[N+i]-x[N+j])/(pl.sqrt((x[N+i]-x[N+j])**2)**3)
# All of the forces coming from the 'same' paricle but from other 'cells' due to the
# periodic contrains can be wraped up in a sum that converges to an aswer that can
# be expressed in terms of polygamma functions (se pg 92 of notebook).
# Note on the sign (xi-xj or xj-xi). Changing the sign of the xi-xj term (i.e. which
# particle are we considering forces on) changes the direction of the force
# apropriately.
temp += self.qq*(polygamma(1,(self.d+x[N+i]-x[N+j])/self.d)-polygamma(1,1.0-((x[N+i]-x[N+j])/self.d)))/(self.d**2)
# periodic force on particle i
temp += self.As[i]*pl.sin(x[N+i])*pl.cos(t)
temp -= self.beta*x[i]
xdot = pl.append(xdot,temp)
for i in range(N):
xdot = pl.append(xdot,x[i])
return xdot
def onclick(self, event):
print 'button=%d, x=%d, y=%d, xdata=%f, ydata=%f'%(event.button, event.x, event.y, event.xdata, event.ydata)
x=SP.append(self.x, event.xdata)
self.y=SP.append(self.y, event.ydata)
self.x= x[:,SP.newaxis]
self.on_show()
self.status_text.setText("New data point: x=%f, y=%f"%(event.xdata, event.ydata))
def f(self,x,t):
# for now masses just = 1.0
# the 4.0 only works for 2D
N = len(x)/4
xdot = pl.array([])
# modulus the y component to keep periodicity right.
x[3*N:4*N]= x[3*N:4*N]%self.yd
# x too
x[2*N:3*N]= x[2*N:3*N]%self.xd
for i in range(N):
temp = 0.0
for j in range(N):
if i == j:
continue
#repulsive x interparticle force of j on i
r_temp = pl.sqrt((x[2*N+i]-x[2*N+j])**2+(x[3*N+i]-x[3*N+j])**2)
if r_temp < self.cutoff:
temp += (x[2*N+i]-x[2*N+j])/(r_temp)*24.0*(2.0/(r_temp**13) - 1.0/(r_temp**7))
# if periodic in x we are going to need to include all the wrap around forces
for gama in range(self.order):
r_temp = pl.sqrt((gama*self.xd-(x[2*N+i]-x[2*N+j]))**2+(x[3*N+i]-x[3*N+j])**2)
if r_temp < self.cutoff:
temp += -(gama*self.xd-(x[2*N+i]-x[2*N+j]))/(r_temp)*24.0*(2.0/(r_temp**13) - 1.0/(r_temp**7))
r_temp = pl.sqrt((gama*self.xd+(x[2*N+i]-x[2*N+j]))**2+(x[3*N+i]-x[3*N+j])**2)
if r_temp < self.cutoff:
temp += (gama*self.xd+(x[2*N+i]-x[2*N+j]))/(r_temp)*24.0*(2.0/(r_temp**13) - 1.0/(r_temp**7))
#temp -= self.beta*x[i]
xdot = pl.append(xdot,temp)
for i in range(N):
temp = 0.0
for j in range(N):
if i == j:
continue
#repulsive y interparticle force of j on i
r_temp = pl.sqrt((x[2*N+i]-x[2*N+j])**2+(x[3*N+i]-x[3*N+j])**2)
if r_temp < self.cutoff:
temp += (x[3*N+i]-x[3*N+j])/r_temp*24.0*(2.0/(r_temp**13)-1.0/(r_temp**7))
# force from same particle but in other direction becasue of periodic boundar
# conditions
for gama in range(self.order):
r_temp = pl.sqrt((x[2*N+i]-x[2*N+j])**2+(gama*self.yd-(x[3*N+i]-x[3*N+j]))**2)
if r_temp < self.cutoff:
temp += -(gama*self.yd-(x[3*N+i]-x[3*N+j]))/r_temp*24.0*(2.0/(r_temp**13)-1.0/(r_temp**7))
r_temp = pl.sqrt((x[2*N+i]-x[2*N+j])**2+(gama*self.yd+(x[3*N+i]-x[3*N+j]))**2)
if r_temp < self.cutoff:
temp += (gama*self.yd+(x[3*N+i]-x[3*N+j]))/r_temp*24.0*(2.0/(r_temp**13)-1.0/(r_temp**7))
#temp += -self.qq*(gama*self.yd-(x[3*N+i]-x[3*N+j]))/(pl.sqrt((gama*self.yd-(x[3*N+i]-x[3*N+j]))**2+(x[2*N+i]-x[2*N+j])**2)**3)
#temp += self.qq* (gama*self.yd+(x[3*N+i]-x[3*N+j]))/(pl.sqrt((gama*self.yd+(x[3*N+i]-x[3*N+j]))**2+(x[2*N+i]-x[2*N+j])**2)**3)
#temp -= self.beta*x[N+i]
xdot = pl.append(xdot,temp)
for i in range(N):
xdot = pl.append(xdot,x[i])
for i in range(N):
xdot = pl.append(xdot,x[N+i])
return xdot
def update_step(self, input_signal=None, teaching_signal=None):
"""update the network with the given input and teach_output, input_signal and teaching_signal must be a column vector
notice that input_signal is u(n+1) and output is output(n+1)
this step makes state(n) -> state(n+1)
the x_history is a list of state's state_history , every item is a row vector like (100L,)"""
if input_signal != None:
assert input_signal.shape == (self.input_unit_amount, 1)
if teaching_signal != None:
assert teaching_signal.shape == (self.output_unit_amount, 1)
if self.feedback_matrix != None and self.input_matrix != None:
self.state = self.unit_type_ufunc(sp.dot(self.input_matrix, input_signal) + sp.dot(self.internal_matrix, self.state) + sp.dot(self.feedback_matrix, self.output))
if teaching_signal == None:
self.output = sp.dot(self.output_matrix, sp.append(input_signal.T,self.state.T).T)
else:
self.output = teaching_signal
elif self.feedback_matrix != None:
self.state = self.unit_type_ufunc(sp.dot(self.internal_matrix, self.state) + sp.dot(self.feedback_matrix, self.output))
if teaching_signal == None:
self.output = sp.dot(self.output_matrix, self.state)
else:
self.output = teaching_signal
else:
self.state = self.unit_type_ufunc(sp.dot(self.input_matrix, input_signal) + sp.dot(self.internal_matrix, self.state))
if input_signal != None:
self.state_history.append(sp.append(input_signal.T, self.state.T))
else:
self.state_history.append(self.state.reshape(-1))
self.output_history.append(self.output)
def f(self,x,t):
N = len(x)/2
xdot = pl.array([])
# modulus the x for periodicity.
x[N:2*N]= x[N:2*N]%self.d
# HERE ---->> 1Dify
for i in range(N):
temp = 0.0
for j in range(N):
if i == j:
continue
#repulsive x interparticle force of j on i
temp += self.qq*(x[N+i]-x[N+j])/(pl.sqrt((x[N+i]-x[N+j])**2)**3)
# Add the forces from the two ancored charges
# First one at x=0
temp += self.qq*(x[N+i]-0.0)/(pl.sqrt((x[N+i]-0.0)**2)**3)
# Second one at the other boundary i.e. self.d
temp += self.qq*(x[N+i]-self.d)/(pl.sqrt((x[N+i]-self.d)**2)**3)
# periodic force on particle i
temp += self.As[i]*pl.sin(x[N+i])*pl.cos(t)
temp -= self.beta*x[i]
xdot = pl.append(xdot,temp)
for i in range(N):
xdot = pl.append(xdot,x[i])
return xdot
def __init__(self, x, y, z, f, boundary = 'natural', dx=0, dy=0, dz=0, bounds_error=True, fill_value=scipy.nan):
if dx != 0 or dy != 0 or dz != 0:
raise NotImplementedError(
"Trispline derivatives are not implemented, do not use tricubic "
"interpolation if you need to compute magnetic fields!"
)
self._x = scipy.array(x,dtype=float)
self._y = scipy.array(y,dtype=float)
self._z = scipy.array(z,dtype=float)
self._xlim = scipy.array((x.min(), x.max()))
self._ylim = scipy.array((y.min(), y.max()))
self._zlim = scipy.array((z.min(), z.max()))
self.bounds_error = bounds_error
self.fill_value = fill_value
if f.shape != (self._x.size,self._y.size,self._z.size):
raise ValueError("dimensions do not match f")
if _tricub.ismonotonic(self._x) and _tricub.ismonotonic(self._y) and _tricub.ismonotonic(self._z):
self._x = scipy.insert(self._x,0,2*self._x[0]-self._x[1])
self._x = scipy.append(self._x,2*self._x[-1]-self._x[-2])
self._y = scipy.insert(self._y,0,2*self._y[0]-self._y[1])
self._y = scipy.append(self._y,2*self._y[-1]-self._y[-2])
self._z = scipy.insert(self._z,0,2*self._z[0]-self._z[1])
self._z = scipy.append(self._z,2*self._z[-1]-self._z[-2])
self._f = scipy.zeros(scipy.array(f.shape)+(2,2,2))
self._f[1:-1,1:-1,1:-1] = scipy.array(f) # place f in center, so that it is padded by unfilled values on all sides
if boundary == 'clamped':
# faces
self._f[(0,-1),1:-1,1:-1] = f[(0,-1),:,:]
self._f[1:-1,(0,-1),1:-1] = f[:,(0,-1),:]
self._f[1:-1,1:-1,(0,-1)] = f[:,:,(0,-1)]
#verticies
self._f[(0,0,-1,-1),(0,-1,0,-1),1:-1] = f[(0,0,-1,-1),(0,-1,0,-1),:]
self._f[(0,0,-1,-1),1:-1,(0,-1,0,-1)] = f[(0,0,-1,-1),:,(0,-1,0,-1)]
self._f[1:-1,(0,0,-1,-1),(0,-1,0,-1)] = f[:,(0,0,-1,-1),(0,-1,0,-1)]
#corners
self._f[(0,0,0,0,-1,-1,-1,-1),(0,0,-1,-1,0,0,-1,-1),(0,-1,0,-1,0,-1,0,-1)] = f[(0,0,0,0,-1,-1,-1,-1),(0,0,-1,-1,0,0,-1,-1),(0,-1,0,-1,0,-1,0,-1)]
elif boundary == 'natural':
# faces
self._f[(0,-1),1:-1,1:-1] = 2*f[(0,-1),:,:] - f[(1,-2),:,:]
self._f[1:-1,(0,-1),1:-1] = 2*f[:,(0,-1),:] - f[:,(1,-2),:]
self._f[1:-1,1:-1,(0,-1)] = 2*f[:,:,(0,-1)] - f[:,:,(1,-2)]
#verticies
self._f[(0,0,-1,-1),(0,-1,0,-1),1:-1] = 4*f[(0,0,-1,-1),(0,-1,0,-1),:] - f[(1,1,-2,-2),(0,-1,0,-1),:] - f[(0,0,-1,-1),(1,-2,1,-2),:] - f[(1,1,-2,-2),(1,-2,1,-2),:]
self._f[(0,0,-1,-1),1:-1,(0,-1,0,-1)] = 4*f[(0,0,-1,-1),:,(0,-1,0,-1)] - f[(1,1,-2,-2),:,(0,-1,0,-1)] - f[(0,0,-1,-1),:,(1,-2,1,-2)] - f[(1,1,-2,-2),:,(1,-2,1,-2)]
self._f[1:-1,(0,0,-1,-1),(0,-1,0,-1)] = 4*f[:,(0,0,-1,-1),(0,-1,0,-1)] - f[:,(1,1,-2,-2),(0,-1,0,-1)] - f[:,(0,0,-1,-1),(1,-2,1,-2)] - f[:,(1,1,-2,-2),(1,-2,1,-2)]
#corners
self._f[(0,0,0,0,-1,-1,-1,-1),(0,0,-1,-1,0,0,-1,-1),(0,-1,0,-1,0,-1,0,-1)] = 8*f[(0,0,0,0,-1,-1,-1,-1),(0,0,-1,-1,0,0,-1,-1),(0,-1,0,-1,0,-1,0,-1)] -f[(1,1,1,1,-2,-2,-2,-2),(0,0,-1,-1,0,0,-1,-1),(0,-1,0,-1,0,-1,0,-1)] -f[(0,0,0,0,-1,-1,-1,-1),(1,1,-2,-2,1,1,-2,-2),(0,-1,0,-1,0,-1,0,-1)] -f[(0,0,0,0,-1,-1,-1,-1),(0,0,-1,-1,0,0,-1,-1),(1,-2,1,-2,1,-2,1,-2)] -f[(1,1,1,1,-2,-2,-2,-2),(1,1,-2,-2,1,1,-2,-2),(0,-1,0,-1,0,-1,0,-1)] -f[(0,0,0,0,-1,-1,-1,-1),(1,1,-2,-2,1,1,-2,-2),(1,-2,1,-2,1,-2,1,-2)] -f[(1,1,1,1,-2,-2,-2,-2),(0,0,-1,-1,0,0,-1,-1),(1,-2,1,-2,1,-2,1,-2)] -f[(1,1,1,1,-2,-2,-2,-2),(1,1,-2,-2,1,1,-2,-2),(1,-2,1,-2,1,-2,1,-2)]
self._regular = False
if _tricub.isregular(self._x) and _tricub.isregular(self._y) and _tricub.isregular(self._z):
self._regular = True
def __init__(self, x, y, z, f, boundary = 'natural', dx=0, dy=0, dz=0, bounds_error=True, fill_value=scipy.nan):
if dx != 0 or dy != 0 or dz != 0:
raise NotImplementedError(
"Trispline derivatives are not implemented, do not use tricubic "
"interpolation if you need to compute magnetic fields!"
)
self._x = scipy.array(x,dtype=float)
self._y = scipy.array(y,dtype=float)
self._z = scipy.array(z,dtype=float)
self._xlim = scipy.array((x.min(), x.max()))
self._ylim = scipy.array((y.min(), y.max()))
self._zlim = scipy.array((z.min(), z.max()))
self.bounds_error = bounds_error
self.fill_value = fill_value
if f.shape != (self._x.size,self._y.size,self._z.size):
raise ValueError("dimensions do not match f")
if _tricub.ismonotonic(self._x) and _tricub.ismonotonic(self._y) and _tricub.ismonotonic(self._z):
self._x = scipy.insert(self._x,0,2*self._x[0]-self._x[1])
self._x = scipy.append(self._x,2*self._x[-1]-self._x[-2])
self._y = scipy.insert(self._y,0,2*self._y[0]-self._y[1])
self._y = scipy.append(self._y,2*self._y[-1]-self._y[-2])
self._z = scipy.insert(self._z,0,2*self._z[0]-self._z[1])
self._z = scipy.append(self._z,2*self._z[-1]-self._z[-2])
self._f = scipy.zeros(scipy.array(f.shape)+(2,2,2))
self._f[1:-1,1:-1,1:-1] = scipy.array(f) # place f in center, so that it is padded by unfilled values on all sides
if boundary == 'clamped':
# faces
self._f[(0,-1),1:-1,1:-1] = f[(0,-1),:,:]
self._f[1:-1,(0,-1),1:-1] = f[:,(0,-1),:]
self._f[1:-1,1:-1,(0,-1)] = f[:,:,(0,-1)]
#verticies
self._f[(0,0,-1,-1),(0,-1,0,-1),1:-1] = f[(0,0,-1,-1),(0,-1,0,-1),:]
self._f[(0,0,-1,-1),1:-1,(0,-1,0,-1)] = f[(0,0,-1,-1),:,(0,-1,0,-1)]
self._f[1:-1,(0,0,-1,-1),(0,-1,0,-1)] = f[:,(0,0,-1,-1),(0,-1,0,-1)]
#corners
self._f[(0,0,0,0,-1,-1,-1,-1),(0,0,-1,-1,0,0,-1,-1),(0,-1,0,-1,0,-1,0,-1)] = f[(0,0,0,0,-1,-1,-1,-1),(0,0,-1,-1,0,0,-1,-1),(0,-1,0,-1,0,-1,0,-1)]
elif boundary == 'natural':
# faces
self._f[(0,-1),1:-1,1:-1] = 2*f[(0,-1),:,:] - f[(1,-2),:,:]
self._f[1:-1,(0,-1),1:-1] = 2*f[:,(0,-1),:] - f[:,(1,-2),:]
self._f[1:-1,1:-1,(0,-1)] = 2*f[:,:,(0,-1)] - f[:,:,(1,-2)]
#verticies
self._f[(0,0,-1,-1),(0,-1,0,-1),1:-1] = 4*f[(0,0,-1,-1),(0,-1,0,-1),:] - f[(1,1,-2,-2),(0,-1,0,-1),:] - f[(0,0,-1,-1),(1,-2,1,-2),:] - f[(1,1,-2,-2),(1,-2,1,-2),:]
self._f[(0,0,-1,-1),1:-1,(0,-1,0,-1)] = 4*f[(0,0,-1,-1),:,(0,-1,0,-1)] - f[(1,1,-2,-2),:,(0,-1,0,-1)] - f[(0,0,-1,-1),:,(1,-2,1,-2)] - f[(1,1,-2,-2),:,(1,-2,1,-2)]
self._f[1:-1,(0,0,-1,-1),(0,-1,0,-1)] = 4*f[:,(0,0,-1,-1),(0,-1,0,-1)] - f[:,(1,1,-2,-2),(0,-1,0,-1)] - f[:,(0,0,-1,-1),(1,-2,1,-2)] - f[:,(1,1,-2,-2),(1,-2,1,-2)]
#corners
self._f[(0,0,0,0,-1,-1,-1,-1),(0,0,-1,-1,0,0,-1,-1),(0,-1,0,-1,0,-1,0,-1)] = 8*f[(0,0,0,0,-1,-1,-1,-1),(0,0,-1,-1,0,0,-1,-1),(0,-1,0,-1,0,-1,0,-1)] -f[(1,1,1,1,-2,-2,-2,-2),(0,0,-1,-1,0,0,-1,-1),(0,-1,0,-1,0,-1,0,-1)] -f[(0,0,0,0,-1,-1,-1,-1),(1,1,-2,-2,1,1,-2,-2),(0,-1,0,-1,0,-1,0,-1)] -f[(0,0,0,0,-1,-1,-1,-1),(0,0,-1,-1,0,0,-1,-1),(1,-2,1,-2,1,-2,1,-2)] -f[(1,1,1,1,-2,-2,-2,-2),(1,1,-2,-2,1,1,-2,-2),(0,-1,0,-1,0,-1,0,-1)] -f[(0,0,0,0,-1,-1,-1,-1),(1,1,-2,-2,1,1,-2,-2),(1,-2,1,-2,1,-2,1,-2)] -f[(1,1,1,1,-2,-2,-2,-2),(0,0,-1,-1,0,0,-1,-1),(1,-2,1,-2,1,-2,1,-2)] -f[(1,1,1,1,-2,-2,-2,-2),(1,1,-2,-2,1,1,-2,-2),(1,-2,1,-2,1,-2,1,-2)]
self._regular = False
if _tricub.isregular(self._x) and _tricub.isregular(self._y) and _tricub.isregular(self._z):
self._regular = True
def read_mat_files(features_basename, labels_fname, camname_fname, actname_fname, partiname_fname):
"""docstring for read_mat_file"""
print "reading features"
tic = time.time()
f = h5py.File(features_basename + '_part1.mat', 'r')
ff = f["myData"]
features1 = ff[:,0:N_1STCHUNK].T
features2 = ff[:,N_1STCHUNK+1:N_2NDCHUNK].T
features3 = ff[:,N_2NDCHUNK+1:].T
features = sp.append(features1, features2,1)
features = sp.append(features, features3,1)
# features = sp.array(ff).T
import ipdb; ipdb.set_trace()
for nn in range(2,N_PARTS+1):
f = h5py.File(features_basename + '_part' + str(nn)+ '.mat', 'r')
import ipdb; ipdb.set_trace()
ff = f["myData"]
import ipdb; ipdb.set_trace()
temp = sp.array(ff).T
import ipdb; ipdb.set_trace()
features = sp.append(features, temp,1)
print nn
print "time taken :", time.time() - tic, 'seconds'
print "reading participant names"
tic = time.time()
partiNames = io.loadmat(partiname_fname)['myPartis']
partiNames = sp.array([str(partiNames[i][0][0]) for i in xrange(partiNames.shape[0])])
print "time taken :", time.time() - tic, 'seconds'
print "reading labels"
tic = time.time()
labels = io.loadmat(labels_fname)['labels']
labels = sp.array([str(labels[i][0][0]) for i in xrange(labels.shape[0])])
print "time taken :", time.time() - tic, 'seconds'
print "reading camera names"
tic = time.time()
camNames = io.loadmat(camname_fname)['myCams']
camNames = sp.array([str(camNames[i][0][0]) for i in xrange(camNames.shape[0])])
print "time taken :", time.time() - tic, 'seconds'
print "reading action names"
tic = time.time()
actNames = io.loadmat(actname_fname)['myActs']
actNames = sp.array([str(actNames[i][0][0]) for i in xrange(actNames.shape[0])])
print "time taken :", time.time() - tic, 'seconds'
# few sanity checks
#assert(not features.isnan().any())
#assert(not features.isinf().any())
return features, labels, camNames, actNames, partiNames
def point_append(self, p, k):
"""
Appends the lists of position and direction vectors with the position and the normalised direction vector.
"""
mag_k = sp.sqrt(sp.dot(k, k))
khat = k / mag_k
self.poslist = sp.append(self.poslist, sp.array([p]), axis=0)
self.dirlist = sp.append(self.dirlist, [khat], axis=0)
def onclick(self, event):
print 'button=%d, x=%d, y=%d, xdata=%f, ydata=%f' % (
event.button, event.x, event.y, event.xdata, event.ydata)
x = SP.append(self.x, event.xdata)
self.y = SP.append(self.y, event.ydata)
self.x = x[:, SP.newaxis]
self.on_show()
self.status_text.setText("New data point: x=%f, y=%f" %
(event.xdata, event.ydata))
def ConvolucionCircular(f,g):
# condicion para igualar convolucion lineal con circular
fog = len(f) + len(g) - 1
cerosX = fog - len(f)
cerosY = fog - len(g)
# agregando ceros
f = np.array(sp.append(f,sp.zeros(cerosX)))
g = np.array(sp.append(g,sp.zeros(cerosY)))
return np.real(sp.ifft(sp.fft(f) * sp.fft(g)))
def fitw(material, figurek):
# source_path = os.path.join("measurementData","2a.json")
# with open(source_path, "r") as ifile:
# idata = json.load(ifile)
# for k, material in enumerate(idata["materials"][:]):
# label = material["label"]
# print(label)
w = sp.array(material["w_sorption"])
# if type(material["w_sorption"]) == list:# and label == "D2":
RH = sp.array(material["w_sorption_RH"])
wmax = w[-1]
# 146/(1+(-8e-8*R_water*T_ref*rho_w*sp.log(phi))**1.6)**0.375
def fit_func(phi, a,b,c):
return wmax / (1+(a*sp.log(phi))**b)**c
def to_min(parms):
return (((w[:-1]-fit_func(RH[:-1], *parms))**2)**0.5).sum()
try:
popt, pcov = optimize.curve_fit(fit_func,
RH[:],
w[:],
[-2,
0.7,
2],
# [-67744.35379546453,
# 0.38825626197169383,
# 1.006448450321765]
)
except RuntimeError:
lb = [-1e4, 0,1]
ub = [0, 1, 3]
popt, fopt = pyswarm.pso(to_min, lb, ub,maxiter=1000 )
# print(fopt)
RHfit = sp.linspace(0,1,10000)
wfit=fit_func(RHfit, *popt)
RHfit = sp.append(RHfit, 1000)
wfit = sp.append(wfit, (w[-1] - w[-2])/(RH[-1] - RH[-2])* (RHfit[-1] - RHfit[-2]) )
# plt.figure(figurek)
# plt.plot(RH[:], w[:], "d")
# plt.plot(RHfit, wfit, "-")
# plt.xlim(0,1.1)
# plt.ylim(0,w.max()*1.3)
return RHfit, wfit
def matrix_rows(self):
if self.node==None or self.Phi==None:
raise NameError('DoF of point %(self.id)d has not been set.')
cols = scipy.array([i*3 for i in self.nodes])
data = scipy.array([phi for phi in self.Phi])
cols = scipy.append(cols, 3*self.node)
data = self.binding_weight*scipy.append(data, -1)
return [[cols, data]], [0,1,2], None
def AddPeople(space, ratio):
init1 = sci.zeros(100)
init2 = sci.ones(100)
init3 = sci.append(init1, init2)
init4 = sci.array([100] * ratio)
initialize = sci.append(init3, init4)
for i in range(1, rows - 1):
for j in range(1, cols - 1):
space[i, j] = sci.random.choice(initialize)
return space
def matrix_rows(self):
if self.node == None or self.Phi == None:
raise NameError(
'DoF of point %(self.id)d has not been set.')
cols = scipy.array([i * 3 for i in self.nodes])
data = scipy.array([phi for phi in self.Phi])
cols = scipy.append(cols, 3 * self.node)
data = self.binding_weight * scipy.append(data, -1)
return [[cols, data]], [0, 1, 2], None
def readScatteringFactorFile(self, tablefile): flag_header = True for line in open(tablefile): if flag_header: flag_header = False else: cols = line.split() self.array_energy_eV = scipy.append(self.array_energy_eV, float(cols[0])) self.array_energy_keV = scipy.append(self.array_energy_keV, 0.001*float(cols[0])) self.array_f1 = scipy.append(self.array_f1, float(cols[1])) self.array_f2 = scipy.append(self.array_f2, float(cols[2])) self.interpolateScatteringFactor()
def f(self,x,t):
# the 4.0 only works for 2D
N = len(x)/4
xdot = pl.array([])
# modulus the x component to keep periodicity right.
x[2*N:3*N]= x[2*N:3*N]%self.diameter
for i in range(N):
temp = 0.0
for j in range(N):
if i == j:
continue
#repulsive x interparticle force of j on i
temp += self.qq*(x[2*N+i]-x[2*N+j])/(pl.sqrt((x[2*N+i]-x[2*N+j])**2+(x[3*N+i]-x[3*N+j])**2)**3)
# force from same particle but in other direction becasue of periodic boundar
# conditions
temp += -self.qq*(self.diameter-(x[2*N+i]-x[2*N+j]))/(pl.sqrt((self.diameter-(x[2*N+i]-x[2*N+j]))**2+(x[3*N+i]-x[3*N+j])**2)**3)
# could do this forever but for now just include one more of force going around in
# same direction as first. draw a diagam if you need to
temp += self.qq*(self.diameter+(x[2*N+i]-x[2*N+j]))/(pl.sqrt((self.diameter+(x[2*N+i]-x[2*N+j]))**2+(x[3*N+i]-x[3*N+j])**2)**3)
# EC x force on particle i
temp += self.A*(self.square_wave(t))*(-2*(pl.cosh(self.d-x[3*N+i]) + \
pl.cosh(x[3*N+i]))*(pl.cos(x[2*N+i])**2 - \
pl.cosh(self.d-x[3*N+i])*pl.cosh(x[3*N+i]))*pl.sin(x[2*N+i]))/((pl.cos(x[2*N+i])\
- pl.cosh(self.d-x[3*N+i]))*(pl.cos(x[2*N+i]) + pl.cosh(self.d - \
x[3*N+i]))*(pl.cos(x[2*N+i]) - pl.cosh(x[3*N+i]))*(pl.cos(x[2*N+i]) + \
pl.cosh(x[3*N+i]))) - self.beta*x[i]
xdot = pl.append(xdot,temp)
for i in range(N):
temp = 0.0
for j in range(N):
if i == j:
continue
#repulsive y interparticle force of j on i
temp += self.qq*(x[3*N+i]-x[3*N+j])/(pl.sqrt((x[2*N+i]-x[2*N+j])**2+(x[3*N+i]-x[3*N+j])**2)**3)
# force from same particle but in other direction becasue of periodic boundar
# conditions
temp += self.qq*(x[3*N+i]-x[3*N+j])/(pl.sqrt((self.diameter-(x[2*N+i]-x[2*N+j]))**2+(x[3*N+i]-x[3*N+j])**2)**3)
# EC y force on particle i
temp += self.A*(self.square_wave(t))*(2*pl.cos(x[2*N+i])*(pl.sinh(self.d - x[3*N+i]) - \
pl.sinh(x[3*N+i]))*(-pl.sin(x[2*N+i])**2 + pl.sinh(self.d - \
x[3*N+i])*pl.sinh(x[3*N+i])))/((pl.cos(x[2*N+i]) - pl.cosh(self.d - \
x[3*N+i]))*(pl.cos(x[2*N+i]) + pl.cosh(self.d - x[3*N+i]))*(pl.cos(x[2*N+i]) \
- pl.cosh(x[3*N+i]))*(pl.cos(x[2*N+i]) + \
pl.cosh(x[3*N+i])))-self.beta*x[N+i]
# quadropole restoring force to center of electric curtains
temp += -self.quadA*(pl.cos(200.0*t)+0.1)*(x[3*N+i]-self.d/2.0)
xdot = pl.append(xdot,temp)
for i in range(N):
xdot = pl.append(xdot,x[i])
for i in range(N):
xdot = pl.append(xdot,x[N+i])
return xdot
def TOBEFIXED_build_k_coo_sub(self):
import scipy
import scipy.sparse as ss
import alg3dpy.scipy_sparse as assparse
#FIXME not considering pos to build the matrix!!!
self.k_coo_sub = {}
for sub in self.subcases.values():
dim = 6*len( self.k_pos ) - \
len( self.index_to_delete[ sub.id ] )
data = scipy.zeros(0, dtype='float64')
row = scipy.zeros(0, dtype='int64')
col = scipy.zeros(0, dtype='int64')
for elem in self.elemdict.values():
numg = len(elem.grids)
for i in xrange(numg):
gi = elem.grids[i]
offseti = gi.k_offset[sub.id]
consi = set([])
if sub.id in gi.cons.keys():
consi = gi.cons[sub.id]
for j in xrange(numg):
gj = elem.grids[j]
offsetj = gj.k_offset[sub.id]
consj = set([])
if sub.id in gj.cons.keys():
consj = gj.cons[sub.id]
cons = consi | consj
index_to_delete = [(c - 1) for c in cons]
k_grid = assparse.in_sparse(elem.k, i * 6, i * 6 + 5,
j * 6, j * 6 + 5)
if len(index_to_delete) < 6:
k = k_grid
for d, r, c, in zip(k.data, k.row, k.col):
#FIXME remove the search below
if not r in index_to_delete:
sub_r = 0
for k in index_to_delete:
if r > k:
sub_r += 1
if not c in index_to_delete:
sub_c = 0
for m in index_to_delete:
if c > m:
sub_c += 1
newr = r + gi.pos * 6 - offseti - sub_r
newc = c + gj.pos * 6 - offsetj - sub_c
data = scipy.append(data, d)
row = scipy.append(row, newr)
col = scipy.append(col, newc)
k_coo = ss.coo_matrix((data, (row, col)), shape=(dim, dim))
self.k_coo_sub[sub.id] = k_coo
def generate_dummy_data():
xw1 = norm(loc=0.3, scale=.15).rvs(20)
yw1 = norm(loc=0.3, scale=.15).rvs(20)
xw2 = norm(loc=0.7, scale=.15).rvs(20)
yw2 = norm(loc=0.7, scale=.15).rvs(20)
xw3 = norm(loc=0.2, scale=.15).rvs(20)
yw3 = norm(loc=0.8, scale=.15).rvs(20)
x = scipy.append(scipy.append(xw1, xw2), xw3)
y = scipy.append(scipy.append(yw1, yw2), yw3)
return x, y
def set_cur_mzvalues_and_intensities(self, act_scan_number):
self.set_cur_scan(act_scan_number)
if self.is_profile_bool:
if len(self.cur_scan.profile) != 0:
self.cur_mzvals = self.cur_scan.profile[:, 0]
self.cur_intensities = self.cur_scan.profile[:, 1]
else:
self.cur_mzvals = sp.array([])
self.cur_intensities = sp.array([])
for i in self.cur_scan.peaklist:
self.cur_mzvals = sp.append(self.cur_mzvals, i.mz)
self.cur_intensities = sp.append(self.cur_intensities,
i.intensity)
def prob3():
rate1, sig1 = wavfile.read('chopinw.wav')
n = sig1.shape[0]
rate2, sig2 = wavfile.read('balloon.wav')
m = sig2.shape[0]
sig1 = sp.append(sig1, sp.zeros((m, 2)))
sig2 = sp.append(sig2, sp.zeros((n, 2)))
f1 = sp.fft(sig1)
f2 = sp.fft(sig2)
out = sp.ifft((f1 * f2))
out = sp.real(out)
scaled = sp.int16(out / sp.absolute(out).max() * 32767)
wavfile.write('test.wav', rate1, scaled)
def prob3():
rate1,sig1 = wavfile.read('chopinw.wav')
n = sig1.shape[0]
rate2,sig2 = wavfile.read('balloon.wav')
m = sig2.shape[0]
sig1 = sp.append(sig1,sp.zeros((m,2)))
sig2 = sp.append(sig2,sp.zeros((n,2)))
f1 = sp.fft(sig1)
f2 = sp.fft(sig2)
out = sp.ifft((f1*f2))
out = sp.real(out)
scaled = sp.int16(out/sp.absolute(out).max() * 32767)
wavfile.write('test.wav',rate1,scaled)
def f(self,x,t):
# for now masses just = 1.0
# the 4.0 only works for 2D
N = len(x)/4
xdot = pl.array([])
# modulus the y component to keep periodicity right.
x[3*N:4*N]= x[3*N:4*N]%self.yd
# x too
if self.x_periodic:
x[2*N:3*N]= x[2*N:3*N]%self.xd
for i in range(N):
temp = 0.0
for j in range(N):
if i == j:
continue
#repulsive x interparticle force of j on i
temp += self.qq*(x[2*N+i]-x[2*N+j])/(pl.sqrt((x[2*N+i]-x[2*N+j])**2+(x[3*N+i]-x[3*N+j])**2)**3)
# if periodic in x we are going to need to include all the wrap around forces
if self.x_periodic:
#repulsive y interparticle force of j on i
temp += self.qq*(x[2*N+i]-x[2*N+j])/(pl.sqrt((x[2*N+i]-x[2*N+j])**2+(x[3*N+i]-x[3*N+j])**2)**3)
for gama in range(self.order):
temp += -self.qq*(gama*self.xd-(x[2*N+i]-x[2*N+j]))/(pl.sqrt((gama*self.xd-(x[2*N+i]-x[2*N+j]))**2+(x[3*N+i]-x[3*N+j])**2)**3)
temp += self.qq* (gama*self.xd+(x[2*N+i]-x[2*N+j]))/(pl.sqrt((gama*self.xd+(x[2*N+i]-x[2*N+j]))**2+(x[3*N+i]-x[3*N+j])**2)**3)
# EC x force on particle i
# surface set to 1.0
for a in range(2):
temp+=self.As[i]*pl.sin(x[2*N+i]-a*pl.pi)*pl.cos(t-a*pl.pi)/(pl.cosh(1.0)-pl.cos(x[2*N+i]-a*pl.pi))
temp -= self.beta*x[i]
xdot = pl.append(xdot,temp)
for i in range(N):
temp = 0.0
for j in range(N):
if i == j:
continue
#repulsive y interparticle force of j on i
temp += self.qq*(x[3*N+i]-x[3*N+j])/(pl.sqrt((x[2*N+i]-x[2*N+j])**2+(x[3*N+i]-x[3*N+j])**2)**3)
# force from same particle but in other direction becasue of periodic boundar
# conditions
for gama in range(self.order):
temp += -self.qq*(gama*self.yd-(x[3*N+i]-x[3*N+j]))/(pl.sqrt((gama*self.yd-(x[3*N+i]-x[3*N+j]))**2+(x[2*N+i]-x[2*N+j])**2)**3)
temp += self.qq* (gama*self.yd+(x[3*N+i]-x[3*N+j]))/(pl.sqrt((gama*self.yd+(x[3*N+i]-x[3*N+j]))**2+(x[2*N+i]-x[2*N+j])**2)**3)
temp -= self.beta*x[N+i]
xdot = pl.append(xdot,temp)
for i in range(N):
xdot = pl.append(xdot,x[i])
for i in range(N):
xdot = pl.append(xdot,x[N+i])
return xdot
def TOBEFIXED_build_k_coo_sub(self):
import scipy
import scipy.sparse as ss
import alg3dpy.scipy_sparse as assparse
#FIXME not considering pos to build the matrix!!!
self.k_coo_sub = {}
for sub in self.subcases.values():
dim = 6*len( self.k_pos ) - \
len( self.index_to_delete[ sub.id ] )
data = scipy.zeros(0, dtype='float64')
row = scipy.zeros(0, dtype='int64')
col = scipy.zeros(0, dtype='int64')
for elem in self.elemdict.values():
numg = len( elem.grids )
for i in xrange( numg ):
gi = elem.grids[ i ]
offseti = gi.k_offset[ sub.id ]
consi = set( [] )
if sub.id in gi.cons.keys():
consi = gi.cons[ sub.id ]
for j in xrange( numg ):
gj = elem.grids[ j ]
offsetj = gj.k_offset[ sub.id ]
consj = set( [] )
if sub.id in gj.cons.keys():
consj = gj.cons[ sub.id ]
cons = consi | consj
index_to_delete = [ (c-1) for c in cons ]
k_grid = assparse.in_sparse(elem.k,i*6,i*6+5,j*6,j*6+5)
if len(index_to_delete) < 6:
k = k_grid
for d, r, c, in zip( k.data , k.row, k.col ):
#FIXME remove the search below
if not r in index_to_delete:
sub_r = 0
for k in index_to_delete:
if r > k:
sub_r += 1
if not c in index_to_delete:
sub_c = 0
for m in index_to_delete:
if c > m:
sub_c += 1
newr = r + gi.pos * 6 - offseti - sub_r
newc = c + gj.pos * 6 - offsetj - sub_c
data = scipy.append( data , d )
row = scipy.append( row , newr )
col = scipy.append( col , newc )
k_coo = ss.coo_matrix(( data, (row,col) ), shape=(dim,dim))
self.k_coo_sub[sub.id] = k_coo
def createNormalizedDataSets():
xw1 = norm(loc=0.3, scale=.15).rvs(20)
yw1 = norm(loc=0.3, scale=.15).rvs(20)
xw2 = norm(loc=0.7, scale=.15).rvs(20)
yw2 = norm(loc=0.7, scale=.15).rvs(20)
xw3 = norm(loc=0.2, scale=.15).rvs(20)
yw3 = norm(loc=0.8, scale=.15).rvs(20)
x = sp.append(sp.append(xw1, xw2), xw3)
y = sp.append(sp.append(yw1, yw2), yw3)
return x, y
def shift(self, items):
"""Shift all buffers up or down a defined number of items on offset axis.
Negative values indicate backward shift."""
if items == 0:
return
self.offset += items
for buffername, _ in self.bufferlist:
buf = getattr(self, buffername)
assert abs(items) <= len(buf), "Cannot shift further than length of buffer."
fill = zeros((abs(items), len(buf[0])))
if items < 0:
buf[:] = append(buf[-items:], fill, 0)
else:
buf[:] = append(fill ,buf[0:-items] , 0)
def center_orbit(sol,N,Dim):
how_much = 20
#sol[:,N:(2*N)]=sol[:,N:(2*N)]%(2.0*sp.pi)
print('looking for orbit for with smallest velocity amplitude. This only works for 1D systems')
# make an array of the mean velocity squared values. The array will be orderd as the solution is
# ordered
mean_vel_arr = sp.array([])
# we also need an array of mean_positions to figure out where these things are
mean_pos_arr = sp.array([])
count = 0
while count < N:
mean_vel_arr = sp.append(mean_vel_arr,(sol[(-len(sol)/how_much):,count]**2).mean())
print('mean vel appended: ' +str((sol[(-len(sol)/how_much):,count]**2).mean()))
# so this is a little trickey...
# We also need the standard deveation becuase if the paticle is oscilating at the boundary
# so it is right around 0 AND 2pi then its mean position is pi. We can use the standard
# deviation to tell weather or not it is actualy at pi or at the boundary. The standard
# deveation should certinaly be less than pi/2 unless there is only 1 particle.
cur_mean_pos = (sol[(-len(sol)/how_much):,N+count]).mean()
cur_mean_std = (sol[(-len(sol)/how_much):,N+count]).std()
if (cur_mean_std > 3.0):
print('foud particle oscilating at boundary')
print('standard deviation: ' +str(cur_mean_std))
cur_mean_pos = 0.0
mean_pos_arr = sp.append(mean_pos_arr,cur_mean_pos)
print('mean pos appended: ' +str(cur_mean_pos))
count+=1
print('mean pos arr: ' +str(mean_pos_arr))
print('mean vel arr: ' +str(mean_vel_arr))
# which particle is the one with the smallest v^2 trajectory? the_one will be the index of this
# particle
the_one = sp.argmin(mean_vel_arr)
print('orbit with smallest velocity amplitued: '+str(the_one))
print('mean vel of the_one: ' +str(mean_vel_arr[the_one]))
print('mean pos of the_one: ' +str(mean_pos_arr[the_one]))
# Now we need to shift everything to get it into the center.
# there are a few ways to do this. We are going to try this one but it might not be the best one
shift = sp.pi-mean_pos_arr[the_one]
# now shift everything by the right amount
sol[:,N:] = (sol[:,N:]+shift)%(2.0*sp.pi)
return sol
def square_wave(self,input):
if type(input)==float:
if input%(2.0*pl.pi)<= pl.pi:
output = 1.0
if input%(2.0*pl.pi)> pl.pi:
output = -1.0
if (type(input)==pl.ndarray)or(type(input)==list):
output = pl.array([])
for i,j in enumerate(input):
if j%(2.0*pl.pi)<= pl.pi:
output = pl.append(output,1.0)
if j%(2.0*pl.pi)> pl.pi:
output = pl.append(output,-1.0)
print('square wave output: ' + str(output))
return output
def position(xyzsource, xyzobserver):
'''
Calculates the norm and angle between a set of points
'''
S = np.array([])
thetas = np.array([])
for xyz in xyzsource:
distance = np.linalg.norm(np.array(xyz) - np.array(xyzobserver))
opposite = xyz[0] - xyzobserver[0]
adjacent = xyz[1] - xyzobserver[1]
angle = np.arctan2(opposite, adjacent)
S = np.append(S, distance / 0.3048)
thetas = np.append(thetas, angle)
return S, thetas
def generation_CommonRare(common, rare, annotation, h2_anno, h2_r, h2_c, pi):
# first deal with NA in the genoytype matrix
common = common.fillna(common.mean()).values
rare = rare.fillna(rare.mean()).values
rare = (rare - rare.mean()) / rare.std()
common = (common - common.mean()) / common.std()
geno = sp.hstack((rare, common))
G = []
R = rare.shape[1]
N = common.shape[0]
C = common.shape[1]
###real parameters
# number of SNPs being causal
p_causal = math.floor(pi * R)
sigma_r = h2_r / p_causal
sigma_b = h2_anno / (annotation.shape[1] - 1)
b = sp.random.normal(0, math.sqrt(sigma_b), annotation.shape[1] - 1)
# first determine random noise in the annotation layer
anno_error = ((1 - h2_anno) / h2_anno) * annotation[:, 0:-1].dot(b).var()
b = b / math.sqrt(anno_error)
sigma_b = h2_anno / (annotation.shape[1] - 1) / anno_error
# determine the intercept based on how many values larger than 0
anno_noise = sp.random.normal(0, 1, R)
anno_val = annotation[:, 0:-1].dot(b) + anno_noise
anno_intercept = -sorted(anno_val, reverse=True)[p_causal]
b = sp.append(b, anno_intercept)
w = annotation.dot(b) + anno_noise
gamma = sp.zeros(shape=R)
beta_rare = sp.zeros(shape=R)
gamma[w > 0] = 1
beta_rare[w > 0] = sp.random.normal(0, math.sqrt(sigma_r), sum(w > 0))
sigma_c = h2_c / C
beta_common = sp.random.normal(0, math.sqrt(sigma_c), C)
sigma_e = (1 - h2_c - h2_r) / (h2_c + h2_r) * (
rare.dot(beta_rare) + common.dot(beta_common)).var()
noise = sp.random.normal(0, math.sqrt(sigma_e), N)
noise < -noise / noise.std() * math.sqrt(sigma_e)
beta = sp.append(beta_rare, beta_common)
G = geno.dot(beta) + noise
return G, common, rare, gamma, beta, sigma_r, sigma_c, sigma_e, sigma_b, b, w
def __init__(self, body_model, body_controller, final_height, max_velocity,
acceleration):
logger.info("New path.",
path_name="TrapezoidalSitStand",
final_height=final_height,
max_velocity=max_velocity,
acceleration=acceleration)
self.model = body_model
self.controller = body_controller
self.final_foot_positions = self.model.getFootPositions()
self.feet_path = []
for i in range(NUM_LEGS):
self.final_foot_positions[i][2] = final_height
for i in range(NUM_LEGS):
self.feet_path = append(
self.feet_path,
TrapezoidalFootMove(self.model.getLegs()[i],
self.controller.getLimbControllers()[i],
self.final_foot_positions[i], max_velocity,
acceleration))
self.done = False
def on_click():
f = file.File(inFile1, mode='r')
ptcloud = np.vstack((f.x, f.y, f.z)).transpose()
f.close()
# Centred the data
ptcloud_centred = ptcloud - np.mean(ptcloud, 0)
# Simulate an intensity information between 0 and 1
ptcloud_centred = sc.append(ptcloud_centred,
np.zeros((ptcloud.shape[0], 1)),
axis=1) # Ajout d'une ligne (axis=0)
for i in range(ptcloud_centred.shape[0] - 1):
ptcloud_centred[i, 3] = random.random()
p = pcl.PointCloud_PointXYZI()
p.from_array(np.array(ptcloud_centred, dtype=np.float32))
visual = pcl_visualization.CloudViewing()
visual.ShowGrayCloud(p)
def check_was_stopped():
visual.WasStopped()
root.after(100, check_was_stopped)
check_was_stopped()
def coordinates_to_voxel_idx(coords_xyz, masker): # transform to homogeneous coordinates coords_h_xyz = sp.append(coords_xyz, ones([1,coords_xyz.shape[1]]),axis=0) # apply inverse affine transformation to get homogeneous coordinates in voxel space inv_transf = sp.linalg.inv(masker.volume.get_affine()) coords_h_voxel_space = inv_transf.dot(coords_h_xyz) coords_h_voxel_space = sp.rint(coords_h_voxel_space).astype(int) # remove homogeneous dimension coords_voxel_space = coords_h_voxel_space[0:-1,:] # convert coordinates to idcs in a flattened voxel space flattened_idcs = sp.ravel_multi_index(coords_voxel_space, masker.dims) # check if there is any study data for the flattened idcs voxel_idcs = sp.zeros((1,len(flattened_idcs)),dtype=int64) for i in range(0,len(flattened_idcs)): idcs = find(masker.in_mask == flattened_idcs[i]) if len(idcs > 0): voxel_idcs[0,i] = find(masker.in_mask == flattened_idcs[i]) else: voxel_idcs[0,i] = nan return voxel_idcs
def orbitVel(self, r, t, antiCW): #legacy
#velocity for a circular orbit around body at vector r
#Anticlockwise is default, enter -1 for clockwise
v = sp.sqrt(G * self.mass / mag(self.orbitPos(t), r)) #mag v=(GM/R)^0.5
rHat = sp.append(unitV(self.orbitPos(t), r), 0) #make it 3D
vHat = antiCW * sp.cross(zHat, rHat)[:2] #return to 2D
return v * vHat
def get_scan_nums_in_orderd_array(self):
if len(self.scan_number_array) == 0:
count = 0
#print self.scan_list
for i in self.scan_list:
self.act_scan_number_array = sp.append(
self.act_scan_number_array, i)
self.scan_number_array = sp.append(self.scan_number_array,
count)
#print("i['retentionTime']")
#print(self.scan_list[i]['retentionTime'])
self.rt_arr = sp.append(self.rt_arr,
self.scan_list[i]['retentionTime'])
count += 1
self.rt_arr.sort()
def plot_delta():
beta = 0.99
N = 1000
u = lambda c: sp.sqrt(c)
W = sp.linspace(0,1,N)
X, Y = sp.meshgrid(W,W)
Wdiff = sp.transpose(X-Y)
index = Wdiff <0
Wdiff[index] = 0
util_grid = u(Wdiff)
util_grid[index] = -10**10
Vprime = sp.zeros((N,1))
delta = sp.ones(1)
tol = 10**-9
it = 0
max_iter = 500
while (delta[-1] >= tol) and (it < max_iter):
V = Vprime
it += 1;
print(it)
val = util_grid + beta*sp.transpose(V)
Vprime = sp.amax(val, axis = 1)
Vprime = Vprime.reshape((N,1))
delta = sp.append(delta,sp.dot(sp.transpose(Vprime - V),Vprime-V))
plt.figure()
plt.plot(delta[1:])
plt.ylabel(r'$\delta_k$')
plt.xlabel('iteration')
plt.savefig('convergence.pdf')
def GP_plotpred(xpred, x, y, cov_par, cov_func = None, cov_typ = 'SE',
MF = None, MF_par = None, MF_args = None, MF_args_pred = None, \
WhiteNoise = False, plot_color = None):
'''
Wrapper for GP_predict that takes care of merging the
covariance and mean function parameters, and (optionally) plots
the predictive distribution (as well as returning it)
'''
if MF != None:
merged_par = scipy.append(cov_par, MF_par)
n_MF_par = len(MF_par)
else:
merged_par = cov_par[:]
n_MF_par = 0
fpred, fpred_err = GP_predict(merged_par, xpred, x, y, \
cov_func = cov_func, cov_typ = cov_typ, \
MF = MF, n_MF_par = n_MF_par, \
MF_args = MF_args, MF_args_pred = MF_args_pred, \
WhiteNoise = WhiteNoise)
xpl = scipy.array(xpred[:,0]).flatten()
if plot_color != None:
pylab.fill_between(xpl, fpred + 2 * fpred_err, fpred - 2 * fpred_err, \
color = plot_color, alpha = 0.1)
pylab.fill_between(xpl, fpred + fpred_err, fpred - fpred_err, \
color = plot_color, alpha = 0.1)
pylab.plot(xpl, fpred, '-', color = plot_color)
return fpred, fpred_err
def heun(f, u0, T, h):
t0 = T[0]
te = T[1]
# Anfangswert ggf. auf Zeilenvektor transformieren
u0 = array(u0).flatten()
tv = t0
uv = u0.T
# eigentliches Verfahren
t = t0
u = u0
ttol = 1e-8 * h
while t < te:
tn = t + h
if tn > te - ttol:
tn = te
h = tn - t
# Euler-Schritt
un = u + h / 2 * (f(u, t) + f(u + h * f(u, t), tn))
t = tn
u = un
tv = append(tv, t)
uv = vstack((uv, u))
return (uv, tv)
def main():
import pcl
# laspy librairy, read las file
f = file.File('28XXX10000075-18.las', mode='r')
# Store pointcloud in array
ptcloud = np.vstack((f.x, f.y, f.z)).transpose()
f.close()
# cloud = pcl.load('./examples/pcldata/tutorials/table_scene_mug_stereo_textured.pcd')
# ptcloud = cloud.to_list()
# Centred the data
ptcloud_centred = ptcloud - np.mean(ptcloud, 0)
# Simulate an intensity information between 0 and 1
ptcloud_centred = sc.append(ptcloud_centred,
np.zeros((ptcloud.shape[0], 1)),
axis=1)
for i in range(ptcloud_centred.shape[0] - 1):
ptcloud_centred[i, 3] = random.random()
p = pcl.PointCloud_PointXYZI()
p.from_array(np.array(ptcloud_centred, dtype=np.float32))
# Visualization
visual = pcl_visualization.CloudViewing()
visual.ShowGrayCloud(p, b'cloud')
v = True
while v:
v = not (visual.WasStopped())
def unique_rows(array, index = None, counts = False):
"""Make array unique by rows"""
if array.shape[0] == 0:
if index == True:
return (array, [])
else:
return (array)
if len(array.shape) == 1:
if index == True:
return (array, [0])
else:
return array
(array_s, s_idx) = sort_rows(array, True)
tmp = [False]
tmp.extend([sp.all(array_s[i-1, :] == array_s[i, :]) for i in range(1, array.shape[0])])
k_idx = sp.where(~sp.array(tmp, dtype='bool'))[0]
if index == True:
if counts:
uidx = s_idx[k_idx]
dist = sp.append((uidx[1:] - uidx[:-1]), array.shape[0] - uidx[-1])
return (array[s_idx[k_idx], :], s_idx[k_idx], dist)
else:
return (array[s_idx[k_idx], :], s_idx[k_idx])
else:
return array[s_idx[k_idx], :]
def clean(probs,
deckSize,
locked=[0, 1],
maxNum=array([24, 60, 40, 30] + [10] * 10) * .7):
if sum(probs) - sum(probs[locked]) == 0:
return probs / sum(probs) if sum(probs) else array(probs)
probs = probs / sum(probs)
lockedProbs = probs[locked]
probs *= deckSize
probs = array([round(p) for p in probs])
maxed = []
maxedProbs = array([])
for i in xrange(len(probs)):
if probs[i] > maxNum[i] and i not in locked:
maxed += [i]
maxedProbs = append(maxedProbs, 1. * maxNum[i] / deckSize)
if (sum(probs) - sum(probs[locked]) - sum(probs[maxed])) == 0:
probs[locked] = lockedProbs
probs[maxed] = maxedProbs
return probs
probs = probs / (sum(probs) - sum(probs[locked]) - sum(probs[maxed])) * (
1 - sum(lockedProbs) - sum(maxedProbs))
probs[locked] = lockedProbs
probs[maxed] = maxedProbs
if array([
round(probs[i] * deckSize) > maxNum[i] for i in xrange(len(probs))
if i not in locked
]).any():
return clean(probs, deckSize, locked=locked + maxed)
return probs
def get_indices(code_country):
indices_country = scipy.array(0)
for i in code_country:
tmp = c_shape_df[c_shape_df.COWCODE == i].index.tolist()
indices_country = scipy.append(indices_country, tmp)
return indices_country.reshape(len(indices_country), 1)
def PathSPCA(A, k):
M, N = A.shape
# Loop through variables
As = ((A * A).sum(axis=0))
vmax = As.max()
vp = As.argmax()
subset = [vp]
vars = []
res = subset
rhos = [(A[:, vp] * A[:, vp]).sum()]
Stemp = array([rhos])
for i in range(1, k):
lev, v = la.eig(Stemp)
vars.append(real(lev).max())
vp = real(lev).argmax()
x = dot(A[:, subset], v[:, vp])
x = x / la.norm(x)
seto = list(range(0, N))
for j in subset:
seto.remove(j)
vals = dot(x.T, A[:, seto])
vals = vals * vals
rhos.append(vals.max())
vpo = seto[vals.argmax()]
Stemp = column_stack((Stemp, dot(A[:, subset].T, A[:, vpo])))
vbuf = append(dot(A[:, vpo].T, A[:, subset]),
array([(A[:, vpo] * A[:, vpo]).sum()]))
Stemp = row_stack((Stemp, vbuf))
subset.append(vpo)
lev, v = la.eig(Stemp)
vars.append(real(lev).max())
return vars, res, rhos
def E_gliding(s_glide, V_glide, t=np.array([0]), E=np.array([0]), P_arr=np.array([0])):
'''
Calculates energy for gliding
'''
t_begin = t[-1]
x = np.array([0])
dt = 0.1
while x[-1]<s_glide:
x = np.append(x,x[-1]+V_glide*dt)
E = np.append(E, E[-1]+E_sensors(dt))
t = np.append(t,t[-1]+dt)
P_arr = np.append(P_arr,25.25)
return E, E[-1], t, t[-1]-t_begin, P_arr
def initialize(self, state, chain):
params = {}
for key in self.scan_range.keys():
# Check for single range
if len(self.scan_range[key]) == 2:
params[key] = sp.rand() * (self.scan_range[key][1] - self.scan_range[key][0]) + self.scan_range[key][0]
else:
# calculate weights of sub_regions
sub_size = sp.array([])
# Determine weights of region
for i in range(0, len(self.scan_range[key]), 2):
sub_size = sp.append(sub_size, self.scan_range[key][i + 1] - self.scan_range[key][i])
self.range_weight[key] = sub_size / float(sp.sum(sub_size))
# sample region based on size
i_sel = 2 * sp.searchsorted(sp.cumsum(self.range_weight[key]), sp.rand())
# sample point
params[key] = (
sp.rand() * (self.scan_range[key][i_sel + 1] - self.scan_range[key][i_sel])
+ self.scan_range[key][i_sel]
)
# params=dict([(key,sp.rand()*(self.scan_range[key][1]-self.scan_range[key][0])+self.scan_range[key][0]) for key in self.scan_range.keys() if type(self.scan_range[key])==list])
# Add constant parameters
for key in self.constants.keys():
params[key] = self.constants[key]
for key in self.functions.keys():
params[key] = self.functions[key](params)
modelid = "%i%01i" % (self.rank, 0) + "%i" % chain.accepted
return params, modelid
def read_data(filename_, flag=True):
"""Reads the odometry and sensor readings from a file.
Args:
filename_: string containing file location
Returns:
output: A FburgData class which contains the odometry
and/or sensor data
Raises:
NameError: incorrect filepath
"""
output = {'sensor':[],'odometry':[]}
data = scipy.genfromtxt(filename_, dtype='object')
idx = scipy.squeeze(data[:,0] == 'ODOMETRY')
for inp in data[idx,1:].astype(float):
output['odometry'] += [{'r1':inp[0],
't':inp[1],
'r2':inp[2]}]
idxarray = scipy.where(idx)
idxarray = scipy.append(idxarray,[len(idx)])
for i in xrange(len(idxarray) - 1):
temp = []
for j in scipy.arange(idxarray[i] + 1, idxarray[i + 1]):
temp += [{'id':int(data[j,1]) - 1,
'range':float(data[j,2]),
'bearing':float(data[j,3])}]
output['sensor'] += [temp]
return output
def nullSpaceBasis(A):
"""
This funciton will find the basis of the null space of the matrix A.
Inputs:
A: The matrix you want the basis for
Outputs:
A numpy matrix containing the vectors as row vectors.
Notes:
If A is an empty matrix, an empty matrix is returned.
"""
if A:
U,s, Vh = la.svd(A)
vecs = np.array([])
toAppend = A.shape[1] -s.size
s = sp.append(s,sp.zeros((1,toAppend)))
for i in range(0,s.size):
if s[i]==0:
vecs = Vh[-toAppend:,:]
if vecs.size ==0:
vecs = sp.zeros((1,A.shape[1]))
return sp.mat(vecs)
else:
return sp.zeros((0,0))
def get_hand_props(self):
"""Initializes self.handarea [sqmeters], self.handrad [m],
self.handslope [-], and self.handstage [ft]"""
# ************
# This is the next big to-do item. Need to pass in hand_props file
# (see details in 'mannings.py') and parse through with hand_props_idx
# to collect data needed for querying mannings_n() on all xs discharges
# for every stage-height for any given comid.
# ************
handc = self.hand_props.variables['COMID']
handslope = self.hand_props.variables['Slope'] # So
handstage = self.hand_props.variables[
'StageHeight'] # h values for each Aw and Hr
handarea = self.hand_props.variables['WetArea'] # Aw
handrad = self.hand_props.variables['HydraulicRadius'] # Hr
if handc[self.hand_props_idx] == self.comid:
self.handarea = handarea[
self.hand_props_idx] * 10.7639 # Convert sqm to sqft
self.handrad = handrad[
self.hand_props_idx] * 3.28084 # Convert m to ft
self.handslope = handslope[self.hand_props_idx] # unitless
handstagenew = scipy.array([])
for i in handstage:
handstagenew = scipy.append(handstagenew, handstage)
self.handstage = handstagenew
self.handstage = self.handstage[:] * 3.28084 # Convert m to ft # cutoff - [:49]
self.handstage = scipy.rint(
self.handstage) # Round to nearest int, to clean up conversion
def plot_delta():
beta = 0.99
N = 1000
u = lambda c: sp.sqrt(c)
W = sp.linspace(0,1,N)
X, Y = sp.meshgrid(W,W)
Wdiff = sp.transpose(X-Y)
index = Wdiff <0
Wdiff[index] = 0
util_grid = u(Wdiff)
util_grid[index] = -10**10
Vprime = sp.zeros((N,1))
delta = sp.ones(1)
tol = 10**-9
it = 0
max_iter = 500
while (delta[-1] >= tol) and (it < max_iter):
V = Vprime
it += 1;
print(it)
val = util_grid + beta*sp.transpose(V)
Vprime = sp.amax(val, axis = 1)
Vprime = Vprime.reshape((N,1))
delta = sp.append(delta,sp.dot(sp.transpose(Vprime - V),Vprime-V))
plt.figure()
plt.plot(delta[1:])
plt.ylabel(r'$\delta_k$')
plt.xlabel('iteration')
plt.savefig('convergence.pdf')
