def displace(self, load, x, ke, penal):
"""
FEA solver based on cvxopt.
See official document : https://cvxopt.org/userguide/index.html
Parameters
----------
load : object, child of the Load class
The load applied in the case.
x : 2-D array size(nely, nelx)
Current density distribution
ke : 2-D array size(8, 8)
Local stiffness matrix generated from lk(E, nu)
penal : float
The penalty exponent
Returns
-------
u : 1-D array
Displacement of all degree of freedom
Notes
-----
# cvxopt.matrix is for constructing matrix where each inner list
represents a column of the matrix.
# The spmatrix() function creates a sparse matrix from a
(value, row, column) triplet description.
# cvxopt.cholmod.linsolve(A,X) solves X in equation AX = B.
See : https://cvxopt.org/userguide/spsolvers.html
"""
freedofs = np.array(load.freedofs())
nely, nelx = x.shape
f = load.force()
Matrix_free = matrix(f[freedofs])
k_free = self.gk_freedofs(load, x, ke, penal).tocoo()
k_free = spmatrix(k_free.data, k_free.row, k_free.col)
u = np.zeros(load.dim * (nely + 1) * (nelx + 1))
linsolve(k_free, Matrix_free)
u[freedofs] = np.array(Matrix_free)[:, 0]
return u
def Lplus(L): try: nrow,ncol = L.shape Lcoo = L.tocoo() L = spmatrix(Lcoo.data.tolist(),Lcoo.row.tolist(),Lcoo.col.tolist()) except AttributeError: nrow,ncol = L.size ones = matrix(-1.0/nrow,(nrow,ncol)) ones+= spdiag(matrix(1.0,(1,nrow))) red = L[:-1,:-1] sol = ones[:-1,:] linsolve(red,sol,uplo='L') sol = array(sol) s = matrix(0.0,(1,ncol)) s[0,:]=sol.sum(0)/nrow lplus = zeros((nrow,ncol)) lplus[nrow-1,:] = -s[0,:] lplus[:-1,:] = sol-s return array(lplus)
def _calc(self, signal):
"""
Perform the ALS. Called from self.calculate (defined in
AbstractBaseline parent class)
Parameters
----------
signal : ndarray (>= 1D)
Input signal
Returns
-------
baseline : ndarray
Baseline of input signal
"""
# If asym_param is not a constant, it needs to be the same length as
# the FULL spectral axis, regardless of rng
if isinstance(self._asym_param, _np.ndarray):
if self._asym_param.size > 1:
assert self._asym_param.size == self.full_sig_spectral_size, \
'Asym parameter must be constant or same size as the full spectral axis'
asym_to_use = self.asym_param
# N signals to detrend
sig_n_to_detrend = int(signal.size / signal.shape[-1])
baseline_output = _np.zeros(self.redux_sig_shape)
# Cute linalg trick to create 2nd-order derivative transform matrix
difference_matrix = _np.diff(_np.eye(self.redux_sig_spectral_size),
n=self.order,
axis=0)
# Convert into sparse matrix
difference_matrix = _cvxopt.sparse(_cvxopt.matrix(difference_matrix))
for ct, coords in enumerate(_np.ndindex(signal.shape[0:-1])):
signal_current = signal[coords]
penalty_vector = _np.ones([self.redux_sig_spectral_size])
baseline_current = _np.zeros([self.redux_sig_spectral_size])
baseline_last = _np.zeros([self.redux_sig_spectral_size])
# Iterative asymmetric least squares smoothing
for ct_iter in range(self.max_iter):
penalty_matrix = _cvxopt.spdiag(list(penalty_vector))
minimazation_matrix = (
penalty_matrix +
_cvxopt.mul(self.smoothness_param, difference_matrix.T) *
difference_matrix)
x = _cvxopt.matrix(penalty_vector[:] * signal_current)
try:
# Cholesky factorization A = LL'
# Solve A * baseline_current = w_sp * Signal
_cholmod.linsolve(minimazation_matrix, x, uplo='U')
except:
print('Failure in Cholesky factorization')
break
else:
if ct_iter > 0:
baseline_last = baseline_current
baseline_current = _np.array(x).squeeze()
if ct_iter > 0: # Difference check b/w iterations
differ = _np.abs(
_np.sum(baseline_current - baseline_last, axis=0))
if differ < self.min_diff:
break
# Apply asymmetric penalization
penalty_vector = _np.squeeze(
asym_to_use * (signal_current >= baseline_current) +
(1 - asym_to_use) *
(signal_current < baseline_current))
if self.fix_end_points:
penalty_vector[0] = 1
penalty_vector[-1] = 1
if self.fix_rng is not None:
penalty_vector[self.fix_rng] = self.fix_const
baseline_output[coords] = baseline_current
if self.verbose:
print('Number of iterations to converge: {}'.format(ct_iter))
print('Finished detrending spectra {}/{}'.format(
ct + 1, sig_n_to_detrend))
return baseline_output
def _calc(self, signal):
"""
Perform the ALS. Called from self.calculate (defined in
AbstractBaseline parent class)
Parameters
----------
signal : ndarray (>= 1D)
Input signal
Returns
-------
baseline : ndarray
Baseline of input signal
"""
# If asym_param is not a constant, it needs to be the same length as
# the FULL spectral axis, regardless of rng
if isinstance(self._asym_param, _np.ndarray):
if self._asym_param.size > 1:
assert self._asym_param.size == self.full_sig_spectral_size, \
'Asym parameter must be constant or same size as the full spectral axis'
asym_to_use = self.asym_param
# N signals to detrend
sig_n_to_detrend = int(signal.size/signal.shape[-1])
baseline_output = _np.zeros(self.redux_sig_shape)
# Cute linalg trick to create 2nd-order derivative transform matrix
difference_matrix = _np.diff(_np.eye(self.redux_sig_spectral_size),
n=self.order, axis=0)
# Convert into sparse matrix
difference_matrix = _cvxopt.sparse(_cvxopt.matrix(difference_matrix))
for ct, coords in enumerate(_np.ndindex(signal.shape[0:-1])):
signal_current = signal[coords]
penalty_vector = _np.ones([self.redux_sig_spectral_size])
baseline_current = _np.zeros([self.redux_sig_spectral_size])
baseline_last = _np.zeros([self.redux_sig_spectral_size])
# Iterative asymmetric least squares smoothing
for ct_iter in range(self.max_iter):
penalty_matrix = _cvxopt.spdiag(list(penalty_vector))
minimazation_matrix = (penalty_matrix +
_cvxopt.mul(self.smoothness_param,
difference_matrix.T) *
difference_matrix)
x = _cvxopt.matrix(penalty_vector[:]*signal_current)
try:
# Cholesky factorization A = LL'
# Solve A * baseline_current = w_sp * Signal
_cholmod.linsolve(minimazation_matrix,x,uplo='U')
except:
print('Failure in Cholesky factorization')
break
else:
if ct_iter > 0:
baseline_last = baseline_current
baseline_current = _np.array(x).squeeze()
if ct_iter > 0: # Difference check b/w iterations
differ = _np.abs(_np.sum(baseline_current -
baseline_last, axis=0))
if differ < self.min_diff:
break
# Apply asymmetric penalization
penalty_vector = _np.squeeze(asym_to_use *
(signal_current >=
baseline_current) +
(1-asym_to_use) *
(signal_current <
baseline_current))
if self.fix_end_points:
penalty_vector[0] = 1
penalty_vector[-1] = 1
if self.fix_rng is not None:
penalty_vector[self.fix_rng] = self.fix_const
baseline_output[coords] = baseline_current
if self.verbose:
print('Number of iterations to converge: {}'.format(ct_iter))
print('Finished detrending spectra {}/{}'.format(ct + 1,
sig_n_to_detrend))
return baseline_output
def cholsolve(A, B):
B = matrix(B)
cholmod.linsolve(A, B)
return B
def _calc(self, signal):
# Shut-off over-flow warning temporarily
_np.seterr(over = 'ignore')
sig_shape = signal.shape # Shape of input signal
# sig_ndim = signal.ndim # N Signal dimensions
sig_size = signal.shape[-1] # Length of spectral axis
# N signals to detrend
sig_n_to_detrend = int(signal.size/signal.shape[-1])
baseline_output = _np.zeros(sig_shape)
# Cute linalg trick to create 2nd-order derivative transform matrix
difference_matrix = _np.diff(_np.eye(sig_size),
n=self.order, axis=0)
# Convert into sparse matrix
difference_matrix = _cvxopt.sparse(_cvxopt.matrix(difference_matrix))
for ct, coords in enumerate(_np.ndindex(signal.shape[0:-1])):
signal_current = signal[coords]
penalty_vector = _np.ones([sig_size])
baseline_current = _np.zeros([sig_size])
# baseline_last = _np.zeros([sig_size])
# Iterative asymmetric least squares smoothing
for ct_iter in range(self.max_iter):
penalty_matrix = _cvxopt.spdiag(list(penalty_vector))
minimazation_matrix = (penalty_matrix +
_cvxopt.mul(self.smoothness_param,
difference_matrix.T) *
difference_matrix)
x = _cvxopt.matrix(penalty_vector[:]*signal_current)
# Cholesky factorization A = LL'
# Solve A * baseline_current = w_sp * Signal
_cholmod.linsolve(minimazation_matrix,x,uplo='U')
# if ct_iter > 0:
# baseline_last = baseline_current
baseline_current = _np.array(x).squeeze()
signal_baseline_differ = signal_current - baseline_current
neg_signal_baseline_differ = signal_baseline_differ[signal_baseline_differ < 0]
mean_neg_signal_baseline_differ = _np.mean(neg_signal_baseline_differ)
std_neg_signal_baseline_differ = _np.std(neg_signal_baseline_differ)
penalty_vector_temp = 1 / (1 +
_np.exp(2*(signal_baseline_differ -
(2*std_neg_signal_baseline_differ -
mean_neg_signal_baseline_differ)) /
std_neg_signal_baseline_differ))
if ct_iter > 0:
norm_differ = (_np.linalg.norm(penalty_vector -
penalty_vector_temp) /
_np.linalg.norm(penalty_vector))
# print('Norm differ: {:.2f}'.format(norm_differ))
# print(norm_differ)
# print('norm: {:.6e}'.format(_np.linalg.norm(penalty_vector)))
if (norm_differ < self.min_diff) | (_np.isnan(norm_differ)):
break
penalty_vector = penalty_vector_temp
if self.fix_end_points:
penalty_vector[0] = 1
penalty_vector[-1] = 1
if self.verbose:
print('Number of iterations to converge: {}'.format(ct_iter))
baseline_output[coords] = baseline_current
if self.verbose:
print('Finished detrending spectra {}/{}'.format(ct + 1,
sig_n_to_detrend))
return baseline_output
def solve_system(K, nodemap, D, forces, con_dof):
# we want to solve the matrix equation
# |Kqq Kqr||xq| = |fq |
# |Krq Krr||xr| |fr+c|
# Where K, xr, fq, and fr are known.
#First step is to organize K, x, and f into that form
#(we will use nodemap)
spl_dex = K.size[0] - con_dof
K = nodemap * K * nodemap
forces = nodemap * forces
D = nodemap * D
'''
for nmap in nodemap:
swap_Matrix_Rows(K,nmap[0],nmap[1])
swap_Matrix_Cols(K,nmap[0],nmap[1])
swap_Vector_Vals(forces,nmap[0],nmap[1])
swap_Vector_Vals(D,nmap[0],nmap[1])
'''
#splitting the reorganized matrix up into the partially solved equations
[Kqq, Kqr, Krq, Krr] = [
K[:spl_dex, :spl_dex], K[:spl_dex, spl_dex:], K[spl_dex:, :spl_dex],
K[spl_dex:, spl_dex:]
]
#K1 = np.hsplit(K,np.array([spl_dex]))
#[Kqq,Krq] = np.vsplit(K1[0],np.array([spl_dex]))
#[Kqr,Krr] = np.vsplit(K1[1],np.array([spl_dex]))
#print(Kqq)
#Knew = np.hstack((np.vstack((Kqq,Krq)),np.vstack((Kqr,Krr))))
#for row in K-Knew:
# print(row)
[xq, xr] = [D[:spl_dex], D[spl_dex:]] #np.split(D,[spl_dex])
[fq, fr] = [forces[:spl_dex],
forces[spl_dex:]] #np.split(forces,[spl_dex])
#xq = co.matrix(xq)
#xr = co.matrix(xr)
#fq = co.matrix(fq)
#fr = co.matrix(fr)
#Now we want to solve the equation
# Kqq xq + Kqr xr = fq
#print(size(co.matrix(Kqr,Kqr.size)))
#Kqr = co.matrix(Kqr,Kqr.size)
Kqr_xr = Kqr * xr
b = fq - Kqr_xr
#print(b,fq,Kqr_xr,Kqq)
try:
#tKqq = np.array(co.matrix(Kqq))
#tb = np.array(co.matrix(b))
#tC = sp.linalg.cho_factor(tKqq)
#xq = sp.linalg.cho_solve(tC,tb)
# Sparse Solver- using the CVXOPT cholesky solver
cholmod.linsolve(Kqq, b)
xq = b
except Exception, e:
print(type(e))
print(e)
print("Warning: Cholesky did not work")
#If Cholesky dies (perhaps the matrix is not pos-def and symmetric)
#We switch over to the sad scipy solver. very slow.
xq = sp.linalg.solve(Kqq, fq - Kqr_xr)
def als_baseline_cvxopt(signal_input, smoothness_param=1e3, asym_param=1e-4, print_iteration=False):
"""
als_baseline_cvxopt(signal_input [,smoothness_param , asym_param]
Compute the baseline_current of signal_input using an asymmetric least squares
algorithm designed by P. H. C. Eilers. This implementation uses
CHOLMOD through the cvxopt toolkit wrapper.
Parameters
----------
signal_input : ndarray (1D)
smoothness_param : float, optional (default, 1e3)
Smoothness parameter
asym_param : float, optional (default, 1e-4)
Assymetry parameter
Returns
-------
out : ndarray
Baseline vector
Notes
-----
This is the first attempt at converting MATLAB (Mathworks, Inc)
scripts into Python code; thus, there will be bugs, the efficiency
will be low(-ish), and I appreciate any useful suggestions or
bug-finds.
References
----------
[1] P. H. C. Eilers, "A perfect smoother," Anal. Chem. 75,
3631-3636 (2003).
[2] P. H. C. Eilers and H. F. M. Boelens, "Baseline correction with
asymmetric least squares smoothing," Report. October 21, 2005.
[3] C. H. Camp Jr, Y. J. Lee, and M. T. Cicerone, "Quantitative,
Comparable Coherent Anti-Stokes Raman Scattering (CARS)
Spectroscopy: Correcting Errors in Phase Retrieval"
"""
# print('Print iteration: {}'.format(print_iteration))
signal_shape_orig = signal_input.shape
signal_length = signal_shape_orig[-1]
dim = _np.ndim(signal_input)
assert dim <= 3, "The input signal_input needs to be 1D, 2D, or 3D"
if dim == 1:
num_to_detrend = 1
elif dim == 2:
num_to_detrend = signal_input.shape[0]
else:
space_shp = list(signal_shape_orig)[0:-1]
num_to_detrend = signal_input.shape[0]*signal_input.shape[1]
baseline_output = _np.zeros(_np.shape(signal_input))
difference_matrix = _cvxopt.sparse(_cvxopt.matrix(_scipy.diff(_np.eye(signal_length),\
n=ORDER,axis=0)))
for count_spectra in range(num_to_detrend):
if dim == 1:
signal_current = signal_input
elif dim == 2:
signal_current = signal_input[count_spectra,:]
else:
# Calculate equivalent row- and column-count
rc, cc = _row_col_from_lin(count_spectra, space_shp)
signal_current = signal_input[rc, cc, :]
if count_spectra == 0:
penalty_vector = _np.ones(signal_length)
baseline_current = _np.zeros([signal_length])
baseline_last = _np.zeros([signal_length])
else: # Start with the previous spectral baseline to seed
penalty_vector = _np.squeeze(asym_param*(signal_current >=\
baseline_current)+(1-asym_param)*\
(signal_current < baseline_current))
# Iterative asymmetric least squares smoothing
for count_iterate in range(MAX_ITER):
penalty_matrix = _cvxopt.spdiag(list(penalty_vector))
minimazation_matrix = penalty_matrix + \
_cvxopt.mul(smoothness_param,difference_matrix.T)*\
difference_matrix
x = _cvxopt.matrix(penalty_vector[:]*signal_current);
# Cholesky factorization A = LL'
# Solve A * baseline_current = w_sp * Signal
_cvxopt_cholmod.linsolve(minimazation_matrix,x,uplo='U')
if (count_iterate > 0 or count_spectra > 0):
baseline_last = baseline_current
baseline_current = _np.array(x).squeeze()
if count_iterate > 0 or count_spectra > 0: # Difference check b/w iterations
differ = _np.abs(_np.sum(baseline_current - baseline_last,axis=0))
if differ < MIN_DIFF:
break
# Apply asymmetric penalization
penalty_vector = _np.squeeze(asym_param*(signal_current >=\
baseline_current)+(1-asym_param)*\
(signal_current < baseline_current))
if dim == 1:
baseline_output = baseline_current
elif dim == 2:
baseline_output[count_spectra,:] = baseline_current
else:
baseline_output[rc, cc, :] = baseline_current
if print_iteration:
if dim < 3:
print('Finished detrending spectra {}/{}'.format(
count_spectra + 1, num_to_detrend))
elif rc + 1 == space_shp[0]:
print('Finished detrending spectra {}/{}'.format(
count_spectra + 1, num_to_detrend))
return baseline_output
def solve_system(K,nodemap,D,forces,con_dof):
# we want to solve the matrix equation
# |Kqq Kqr||xq| = |fq |
# |Krq Krr||xr| |fr+c|
# Where K, xr, fq, and fr are known.
#First step is to organize K, x, and f into that form
#(we will use nodemap)
spl_dex = K.size[0]-con_dof
K = nodemap*K*nodemap
forces = nodemap*forces
D = nodemap*D
'''
for nmap in nodemap:
swap_Matrix_Rows(K,nmap[0],nmap[1])
swap_Matrix_Cols(K,nmap[0],nmap[1])
swap_Vector_Vals(forces,nmap[0],nmap[1])
swap_Vector_Vals(D,nmap[0],nmap[1])
'''
#splitting the reorganized matrix up into the partially solved equations
[Kqq,Kqr,Krq,Krr] = [K[:spl_dex,:spl_dex],K[:spl_dex,spl_dex:],K[spl_dex:,:spl_dex],K[spl_dex:,spl_dex:]]
#K1 = np.hsplit(K,np.array([spl_dex]))
#[Kqq,Krq] = np.vsplit(K1[0],np.array([spl_dex]))
#[Kqr,Krr] = np.vsplit(K1[1],np.array([spl_dex]))
#print(Kqq)
#Knew = np.hstack((np.vstack((Kqq,Krq)),np.vstack((Kqr,Krr))))
#for row in K-Knew:
# print(row)
[xq,xr] = [D[:spl_dex],D[spl_dex:]]#np.split(D,[spl_dex])
[fq,fr] = [forces[:spl_dex],forces[spl_dex:]]#np.split(forces,[spl_dex])
#xq = co.matrix(xq)
#xr = co.matrix(xr)
#fq = co.matrix(fq)
#fr = co.matrix(fr)
#Now we want to solve the equation
# Kqq xq + Kqr xr = fq
#print(size(co.matrix(Kqr,Kqr.size)))
#Kqr = co.matrix(Kqr,Kqr.size)
Kqr_xr = Kqr*xr
b = fq-Kqr_xr
#print(b,fq,Kqr_xr,Kqq)
try:
#tKqq = np.array(co.matrix(Kqq))
#tb = np.array(co.matrix(b))
#tC = sp.linalg.cho_factor(tKqq)
#xq = sp.linalg.cho_solve(tC,tb)
# Sparse Solver- using the CVXOPT cholesky solver
cholmod.linsolve(Kqq,b)
xq = b
except Exception,e:
print(type(e))
print(e)
print("Warning: Cholesky did not work")
#If Cholesky dies (perhaps the matrix is not pos-def and symmetric)
#We switch over to the sad scipy solver. very slow.
xq = sp.linalg.solve(Kqq,fq-Kqr_xr)
def _calc(self, signal):
# Shut-off over-flow warning temporarily
_np.seterr(over='ignore')
sig_shape = signal.shape # Shape of input signal
# sig_ndim = signal.ndim # N Signal dimensions
sig_size = signal.shape[-1] # Length of spectral axis
# N signals to detrend
sig_n_to_detrend = int(signal.size / signal.shape[-1])
baseline_output = _np.zeros(sig_shape)
# Cute linalg trick to create 2nd-order derivative transform matrix
difference_matrix = _np.diff(_np.eye(sig_size), n=self.order, axis=0)
# Convert into sparse matrix
difference_matrix = _cvxopt.sparse(_cvxopt.matrix(difference_matrix))
for ct, coords in enumerate(_np.ndindex(signal.shape[0:-1])):
signal_current = signal[coords]
penalty_vector = _np.ones([sig_size])
baseline_current = _np.zeros([sig_size])
# baseline_last = _np.zeros([sig_size])
# Iterative asymmetric least squares smoothing
for ct_iter in range(self.max_iter):
penalty_matrix = _cvxopt.spdiag(list(penalty_vector))
minimazation_matrix = (
penalty_matrix +
_cvxopt.mul(self.smoothness_param, difference_matrix.T) *
difference_matrix)
x = _cvxopt.matrix(penalty_vector[:] * signal_current)
# Cholesky factorization A = LL'
# Solve A * baseline_current = w_sp * Signal
_cholmod.linsolve(minimazation_matrix, x, uplo='U')
# if ct_iter > 0:
# baseline_last = baseline_current
baseline_current = _np.array(x).squeeze()
signal_baseline_differ = signal_current - baseline_current
neg_signal_baseline_differ = signal_baseline_differ[
signal_baseline_differ < 0]
mean_neg_signal_baseline_differ = _np.mean(
neg_signal_baseline_differ)
std_neg_signal_baseline_differ = _np.std(
neg_signal_baseline_differ)
penalty_vector_temp = 1 / (
1 + _np.exp(2 * (signal_baseline_differ -
(2 * std_neg_signal_baseline_differ -
mean_neg_signal_baseline_differ)) /
std_neg_signal_baseline_differ))
if ct_iter > 0:
norm_differ = (
_np.linalg.norm(penalty_vector - penalty_vector_temp) /
_np.linalg.norm(penalty_vector))
# print('Norm differ: {:.2f}'.format(norm_differ))
# print(norm_differ)
# print('norm: {:.6e}'.format(_np.linalg.norm(penalty_vector)))
if (norm_differ <
self.min_diff) | (_np.isnan(norm_differ)):
break
penalty_vector = penalty_vector_temp
if self.fix_end_points:
penalty_vector[0] = 1
penalty_vector[-1] = 1
if self.verbose:
print('Number of iterations to converge: {}'.format(ct_iter))
baseline_output[coords] = baseline_current
if self.verbose:
print('Finished detrending spectra {}/{}'.format(
ct + 1, sig_n_to_detrend))
return baseline_output
def als_baseline_cvxopt(signal_input, smoothness_param=1e3, asym_param=1e-4, print_iteration=False):
"""
als_baseline_cvxopt(signal_input [,smoothness_param , asym_param]
Compute the baseline_current of signal_input using an asymmetric least squares
algorithm designed by P. H. C. Eilers. This implementation uses
CHOLMOD through the cvxopt toolkit wrapper.
Parameters
----------
signal_input : ndarray (1D)
smoothness_param : float, optional (default, 1e3)
Smoothness parameter
asym_param : float, optional (default, 1e-4)
Assymetry parameter
Returns
-------
out : ndarray
Baseline vector
Note
----
This is the first attempt at converting MATLAB (Mathworks, Inc)
scripts into Python code; thus, there will be bugs, the efficiency
will be low(-ish), and I appreciate any useful suggestions or
bug-finds.
References
----------
P. H. C. Eilers, "A perfect smoother," Anal. Chem. 75,
3631-3636 (2003).
P. H. C. Eilers and H. F. M. Boelens, "Baseline correction with
asymmetric least squares smoothing," Report. October 21, 2005.
C. H. Camp Jr, Y. J. Lee, and M. T. Cicerone, "Quantitative,
Comparable Coherent Anti-Stokes Raman Scattering (CARS)
Spectroscopy: Correcting Errors in Phase Retrieval"
===================================
Original Python branch: Feb 16 2015
@author: ("Charles H Camp Jr")
@email: ("*****@*****.**")
@date: ("Fri Jun 19 2015")
@version: ("0.1_1")
"""
signal_length = signal_input.shape[0]
dim = signal_input.ndim
assert dim <= 3, "The input signal_input needs to be 1D, 2D, or 3D"
if dim == 1:
num_to_detrend = 1
elif dim == 2:
num_to_detrend = signal_input.shape[1]
else:
num_to_detrend = signal_input.shape[1]*signal_input.shape[2]
signal_input = signal_input.reshape([signal_length,num_to_detrend])
baseline_output = _np.zeros(_np.shape(signal_input))
difference_matrix = _cvxopt.sparse(_cvxopt.matrix(_scipy.diff(_np.eye(signal_length),\
n=ORDER,axis=0)))
for count_spectra in range(num_to_detrend):
if dim == 1:
signal_current = signal_input
else:
signal_current = signal_input[:,count_spectra]
if count_spectra == 0:
penalty_vector = _np.ones(signal_length)
baseline_current = _np.zeros([signal_length])
baseline_last = _np.zeros([signal_length])
else: # Start with the previous spectral baseline to seed
penalty_vector = _np.squeeze(asym_param*(signal_current >=\
baseline_current)+(1-asym_param)*\
(signal_current < baseline_current))
# Iterative asymmetric least squares smoothing
for count_iterate in range(MAX_ITER):
penalty_matrix = _cvxopt.spdiag(list(penalty_vector))
minimazation_matrix = penalty_matrix + \
_cvxopt.mul(smoothness_param,difference_matrix.T)*\
difference_matrix
x = _cvxopt.matrix(penalty_vector[:]*signal_current);
# Cholesky factorization A = LL'
# Solve A * baseline_current = w_sp * Signal
_cvxopt_cholmod.linsolve(minimazation_matrix,x,uplo='U')
if (count_iterate > 0 or count_spectra > 0):
baseline_last = baseline_current
baseline_current = _np.array(x).squeeze()
if count_iterate > 0 or count_spectra > 0: # Difference check b/w iterations
differ = _np.abs(_np.sum(baseline_current - baseline_last,axis=0))
if differ < MIN_DIFF:
break
# Apply asymmetric penalization
penalty_vector = _np.squeeze(asym_param*(signal_current >=\
baseline_current)+(1-asym_param)*\
(signal_current < baseline_current))
if print_iteration == True:
print("Finished detrending in %d iteration" % (count_iterate + 1))
if dim > 1:
baseline_output[:,count_spectra] = baseline_current
elif dim:
baseline_output = baseline_current
return baseline_output.reshape(signal_input.shape)
I = [0, 1, 0, 2, 4, 1, 2, 3, 4, 2, 1, 4] J = [0, 0, 1, 1, 1, 2, 2, 2, 2, 3, 4, 4] A = spmatrix(VA, I, J) B = spmatrix(VB, I, J) x = matrix(1.0, (5, 1)) Fs = umfpack.symbolic(A) FA = umfpack.numeric(A, Fs) FB = umfpack.numeric(B, Fs) umfpack.solve(A, FA, x) umfpack.solve(B, FB, x) umfpack.solve(A, FA, x, trans='T') print(x) A = spmatrix([10, 3, 5, -2, 5, 2], [0, 2, 1, 3, 2, 3], [0, 0, 1, 1, 2, 3]) X = matrix(range(8), (4, 2), 'd') cholmod.linsolve(A, X) print(X) X = cholmod.splinsolve(A, spmatrix(1.0, range(4), range(4))) print(X) X = matrix(range(8), (4, 2), 'd') F = cholmod.symbolic(A) cholmod.numeric(A, F) cholmod.solve(F, X) print(X) F = cholmod.symbolic(A) cholmod.numeric(A, F) print(2.0 * sum(log(cholmod.diag(F)))) options['supernodal'] = 0
def als_baseline_cvxopt(signal_input,
smoothness_param=1e3,
asym_param=1e-4,
print_iteration=False):
"""
als_baseline_cvxopt(signal_input [,smoothness_param , asym_param]
Compute the baseline_current of signal_input using an asymmetric least squares
algorithm designed by P. H. C. Eilers. This implementation uses
CHOLMOD through the cvxopt toolkit wrapper.
Parameters
----------
signal_input : ndarray (1D)
smoothness_param : float, optional (default, 1e3)
Smoothness parameter
asym_param : float, optional (default, 1e-4)
Assymetry parameter
Returns
-------
out : ndarray
Baseline vector
Note
----
This is the first attempt at converting MATLAB (Mathworks, Inc)
scripts into Python code; thus, there will be bugs, the efficiency
will be low(-ish), and I appreciate any useful suggestions or
bug-finds.
References
----------
P. H. C. Eilers, "A perfect smoother," Anal. Chem. 75,
3631-3636 (2003).
P. H. C. Eilers and H. F. M. Boelens, "Baseline correction with
asymmetric least squares smoothing," Report. October 21, 2005.
C. H. Camp Jr, Y. J. Lee, and M. T. Cicerone, "Quantitative,
Comparable Coherent Anti-Stokes Raman Scattering (CARS)
Spectroscopy: Correcting Errors in Phase Retrieval"
===================================
Original Python branch: Feb 16 2015
@author: ("Charles H Camp Jr")
@email: ("*****@*****.**")
@date: ("Fri Jun 19 2015")
@version: ("0.1_1")
"""
signal_length = signal_input.shape[0]
dim = signal_input.ndim
assert dim <= 3, "The input signal_input needs to be 1D, 2D, or 3D"
if dim == 1:
num_to_detrend = 1
elif dim == 2:
num_to_detrend = signal_input.shape[1]
else:
num_to_detrend = signal_input.shape[1] * signal_input.shape[2]
signal_input = signal_input.reshape([signal_length, num_to_detrend])
baseline_output = _np.zeros(_np.shape(signal_input))
difference_matrix = _cvxopt.sparse(_cvxopt.matrix(_scipy.diff(_np.eye(signal_length),\
n=ORDER,axis=0)))
for count_spectra in range(num_to_detrend):
if dim == 1:
signal_current = signal_input
else:
signal_current = signal_input[:, count_spectra]
if count_spectra == 0:
penalty_vector = _np.ones(signal_length)
baseline_current = _np.zeros([signal_length])
baseline_last = _np.zeros([signal_length])
else: # Start with the previous spectral baseline to seed
penalty_vector = _np.squeeze(asym_param*(signal_current >=\
baseline_current)+(1-asym_param)*\
(signal_current < baseline_current))
# Iterative asymmetric least squares smoothing
for count_iterate in range(MAX_ITER):
penalty_matrix = _cvxopt.spdiag(list(penalty_vector))
minimazation_matrix = penalty_matrix + \
_cvxopt.mul(smoothness_param,difference_matrix.T)*\
difference_matrix
x = _cvxopt.matrix(penalty_vector[:] * signal_current)
# Cholesky factorization A = LL'
# Solve A * baseline_current = w_sp * Signal
_cvxopt_cholmod.linsolve(minimazation_matrix, x, uplo='U')
if (count_iterate > 0 or count_spectra > 0):
baseline_last = baseline_current
baseline_current = _np.array(x).squeeze()
if count_iterate > 0 or count_spectra > 0: # Difference check b/w iterations
differ = _np.abs(
_np.sum(baseline_current - baseline_last, axis=0))
if differ < MIN_DIFF:
break
# Apply asymmetric penalization
penalty_vector = _np.squeeze(asym_param*(signal_current >=\
baseline_current)+(1-asym_param)*\
(signal_current < baseline_current))
if print_iteration == True:
print("Finished detrending in %d iteration" % (count_iterate + 1))
if dim > 1:
baseline_output[:, count_spectra] = baseline_current
elif dim:
baseline_output = baseline_current
return baseline_output.reshape(signal_input.shape)