Same FLOPs different runtime. Explanation? - python

For an m-by-n matrix, A, where m is much greater than n, the FLOPs to do QR factorization on A is 2mn^2. With another n-by-m matrix, B, the FLOPs to do B*A (matrix multiplication) is also 2mn^2. However, both MATLAB and Python show that matrix multiplication is faster than QR factorization, on my computer by a factor of about 6. I wonder how do we interpret this phenomenon correctly?
Below are my Python codes
import numpy as np
import time
t1 = t2 = 0
m = 5000
n = 100
for k in range(100):
A = np.random.rand(m,n)-0.5
B = np.random.rand(m,n)-0.5
tic = time.time()
Q,R = np.linalg.qr(A)
t1 += time.time()-tic
tic = time.time()
C = B.T # A
t2 += time.time()-tic
print('t1=%.3f, t2=%.3f'%(t1,t2))
Example outcome:
t1=2.246, t2=0.353

Related

making python code faster using numba, cache or any other optimization

I have defined the following function
def laplacian_2D_array(func_2D):
func_2nd_derv_x_fin2D = np.zeros((N,N))
for j in range (0,N):
func_CD2_x_list = []
for i in range (0,N):
value = func_2D[i][j] #func_2D is a NxN matrix
func_CD2_x_list.append(value)
func_CD2_x_array = np.array (func_CD2_x_list)[np.newaxis]
func_2nd_derv_x = matrix_R # (np.transpose(func_CD2_x_array))
func_2nd_derv_x_fin2D[j] = np.transpose (np.reshape(func_2nd_derv_x,[N,]))
func_2nd_derv_y_fin2D = np.zeros((N,N))
for i in range (0,N):
func_CD2_y_list = []
for j in range (0,N):
value = func_2D[i][j]
func_CD2_y_list.append(value)
func_CD2_y_array = np.array (func_CD2_y_list)[np.newaxis]
func_2nd_derv_y = matrix_S # (np.transpose(func_CD2_y_array))
func_2nd_derv_y_fin2D[i] = (np.reshape(func_2nd_derv_y,[N,]))
return (np.add(func_2nd_derv_x_fin2D, func_2nd_derv_y_fin2D))
In the above code a 2D matrix func_2Deach j row is extracted as column vector and multiplied with matrix_R and stored in jth column of func_2nd_derv_x_fin2D and similarly of 2nd block of code and finally function returns the addition of func_2nd_derv_x_fin2D and func_2nd_derv_y_fin2D
In this N = 401 and matrix_S and matrix_Rare also N X N matrices. This function is being called multiple times in a while loop and execution of single iteration is taking a lot of time. I have tried #njit to make it faster but I am not successful in doing so and getting errors. I have also tried using cache.
How can we optimise for lists and arrays in this and what are other ways to optimize the defined function?
I am showing the code where the function is used.
while (time<timemax):
#Analytical Solution----------------------------------------------------------------------------
exact_time = time/a_sec
omega_t = np.zeros((N,N))
psi_t = np.zeros((N,N))
for i in range (0,N):
for j in range (0,N):
psi_t[i][j] = np.sin(x_list[i]) * np.sin(y_list[j]) * np.exp((-2*exact_time)/Re)
omega_t[i][j] = 2*np.sin (x_list[i]) * np.sin(y_list[j]) * np.exp((-2*exact_time)/Re)
.
.
.
.
.
.
.
# BiCGSTAB algo
x0 = psi_0 #initial guess--> psi of previous time step
r0 = omega_0 - laplacian_2D_array(x0) # r0 = b-Ax0
r0_hat = r0
rho_0 = 1
alpha = 1
w0 = 1
v0 = np.zeros((N,N))
P_0 = np.zeros((N,N))
tol = 10 ** (-7)
iteration = 0
while ((np.max(np.abs(laplacian_2D_array(x0) - omega_0))) < tol):
rho_prev = rho_0
rho = np.dot ((np.reshape(r0_hat,(N**2,1))),(np.reshape(r0,(N**2,1))))
beta = (rho/rho_prev) * (alpha/w0)
P_0 = r0 + beta * (P_0 - w0 * v0)
v0 = laplacian_2D_array(P_0)
alpha = rho / np.dot ((np.reshape(r0_hat,(N**2,1))),(np.reshape(v0,(N**2,1))))
s = r0 - alpha * v0
t = laplacian_2D_array(s)
Any suggestions to fasten code is highly appreciable.
It turns out the complicated code of laplacian_2D_array can be simplified as the following implementation:
def laplacian_2D_array(func_2D):
return (matrix_R # func_2D + matrix_S # func_2D.T).T
This is 63 times faster on my machine on random matrices based on your provided inputs. Most of the time should be spent in the matrix multiplication (performed very efficiently in parallel if the installation of Numpy/Python/BLAS is done correctly on the target platform).

Implementing a never ending matrix formula on python for curve fitting

I'm trying to write a program that can solve the general regression formula:
So I'm trying to implement this matrix equation, is there anyway to do this such as to let the user decide how big it can be, without me making more and more if conditions (so just one piece of code that collapses to the matrix that the user wishes for)?
Code:
#Solving the general matrix for the coefficients
if 3 == n:
a = np.array([[np.sum(np.multiply(FL[1],FL[1])),np.sum(np.multiply(FL[1],FL[2]))],
[np.sum(np.multiply(FL[1],FL[2])),np.sum(np.multiply(FL[2],FL[2]))]])
b = np.array([np.sum(np.multiply(FL[0],FL[1])),np.sum(np.multiply(FL[0],FL[2]))])
x = np.linalg.solve(a, b)
if 4 == n:
a = np.array([[np.sum(np.multiply(FL[1],FL[1])),np.sum(np.multiply(FL[1],FL[2])),np.sum(np.multiply(FL[1],FL[3]))],
[np.sum(np.multiply(FL[1],FL[2])),np.sum(np.multiply(FL[2],FL[2])),np.sum(np.multiply(FL[2],FL[3]))],
[np.sum(np.multiply(FL[1],FL[3])),np.sum(np.multiply(FL[2],FL[3])),np.sum(np.multiply(FL[3],FL[3]))]])
b = np.array([np.sum(np.multiply(FL[0],FL[1])),np.sum(np.multiply(FL[0],FL[2])),np.sum(np.multiply(FL[0],FL[3]))])
x = np.linalg.solve(a, b)
1 In this code Phi_0 corresponds to FL[i=1] and FL[0] corresponds to y.
You can make the algorithm independent of the order of the polynomial. The easiest way is using for loops, although these will be slow (since they don't exploit NumPy's vectorization).
Here is a reproducible example with random data:
import numpy as np
# Order of polynomial
n = 5
# Random seed for reproducibility
np.random.seed(1)
# Input arrays
phi = np.random.random((100,n))
y = np.random.random(100)
# Output arrays
a = np.zeros((n,n))
b = np.zeros(n)
for i in range(n):
b[i] = np.sum(y * phi[:,i])
for j in range(i,n):
# Exploit that matrix is diagonal
a[i,j] = a[j,i] = np.sum(phi[:,i] * phi[:,j])
# Coefficients array
x = np.linalg.solve(a,b)

Optimize A*x = B solution for a tridiagonal coefficient matrix

I have a system of equations in the form of A*x = B where [A] is a tridiagonal coefficient matrix. Using the Numpy solver numpy.linalg.solve I can solve the system of equations for x.
See example below of how I develop the tridiagonal [A] martix. the {B} vector, and solve for x:
# Solve system of equations with a tridiagonal coefficient matrix
# uses numpy.linalg.solve
# use Python 3 print function
from __future__ import print_function
from __future__ import division
# modules
import numpy as np
import time
ti = time.clock()
#---- Build [A] array and {B} column vector
m = 1000 # size of array, make this 8000 to see time benefits
A = np.zeros((m, m)) # pre-allocate [A] array
B = np.zeros((m, 1)) # pre-allocate {B} column vector
A[0, 0] = 1
A[0, 1] = 2
B[0, 0] = 1
for i in range(1, m-1):
A[i, i-1] = 7 # node-1
A[i, i] = 8 # node
A[i, i+1] = 9 # node+1
B[i, 0] = 2
A[m-1, m-2] = 3
A[m-1, m-1] = 4
B[m-1, 0] = 3
print('A \n', A)
print('B \n', B)
#---- Solve using numpy.linalg.solve
x = np.linalg.solve(A, B) # solve A*x = B for x
print('x \n', x)
#---- Elapsed time for each approach
print('NUMPY time', time.clock()-ti, 'seconds')
So my question relates to two sections of the above example:
Since I am dealing with a tridiagonal matrix for [A], also called a banded matrix, is there a more efficient way to solve the system of equations instead of using numpy.linalg.solve?
Also, is there a better way to create the tridiagonal matrix instead of using a for-loop?
The above example runs on Linux in about 0.08 seconds according to the time.clock() function.
The numpy.linalg.solve function works fine, but I'm trying to find an approach that takes advantage of the tridiagonal form of [A] in hopes of speeding up the solution even further and then apply that approach to a more complicated example.
There are two immediate performance improvements (1) do not use a loop, (2) use scipy.linalg.solve_banded().
I would write the code something more like
import scipy.linalg as la
# Create arrays and set values
ab = np.zeros((3,m))
b = 2*ones(m)
ab[0] = 9
ab[1] = 8
ab[2] = 7
# Fix end points
ab[0,1] = 2
ab[1,0] = 1
ab[1,-1] = 4
ab[2,-2] = 3
b[0] = 1
b[-1] = 3
return la.solve_banded ((1,1),ab,b)
There may be more elegant ways to construct the matrix, but this works.
Using %timeit in ipython the original code took 112 ms for m=1000. This code takes 2.94 ms for m=10,000, an order of magnitude larger problem yet still almost two orders of magnitude faster! I did not have the patience to wait on the original code for m=10,000. Most of the time in the original may be in constructing the array, I did not test this. Regardless, for large arrays it is much more efficient to only store the non-zero values of the matrix.
There is a scipy.sparse matrix type called scipy.sparse.dia_matrix which captures the structure of your matrix well (it will store 3 arrays, in "positions" 0 (diagonal), 1 (above) and -1 (below)). Using this type of matrix you can try scipy.sparse.linalg.lsqr for solving. If your problem has an exact solution, it will be found, otherwise it will find the solution in least squares sense.
from scipy import sparse
A_sparse = sparse.dia_matrix(A)
ret_values = sparse.linalg.lsqr(A_sparse, C)
x = ret_values[0]
However, this may not be completely optimal in terms of exploiting the triadiagonal structure, there may be a theoretical way of making this faster. What this conversion does do for you is cut down the matrix multiplication expenses to the essential: Only the 3 bands are used. This, in combination with the iterative solver lsqr should already yield a speedup.
Note: I am not proposing scipy.sparse.linalg.spsolve, because it converts your matrix to csr format. However, replacing lsqr with spsolve is worth a try, especially because spsolve can bind UMFPACK, see relevant doc on spsolve. Also, it may be of interest to take a look at this stackoverflow question and answer relating to UMFPACK
You could use scipy.linalg.solveh_banded.
EDIT: You CANNOT used the above as your matrix is not symmetric and I thought it was. However, as was mentioned above in the comment, the Thomas algorithm is great for this
a = [7] * ( m - 2 ) + [3]
b = [1] + [8] * ( m - 2 ) + [4]
c = [2] + [9] * ( m - 2 )
d = [1] + [2] * ( m - 2 ) + [3]
# This is taken directly from the Wikipedia page also cited above
# this overwrites b and d
def TDMASolve(a, b, c, d):
n = len(d) # n is the numbers of rows, a and c has length n-1
for i in xrange(n-1):
d[i+1] -= 1. * d[i] * a[i] / b[i]
b[i+1] -= 1. * c[i] * a[i] / b[i]
for i in reversed(xrange(n-1)):
d[i] -= d[i+1] * c[i] / b[i+1]
return [d[i] / b[i] for i in xrange(n)]
This code is not optimize nor does it use np, but if I (or any of the other fine folks here) have time, I will edit it so that it does those thing. It currently times at ~10 ms for m=10000.
This probably will help
There is a function creates_tridiagonal which will create tridiagonal matrix. There is another function which converts a matrix into diagonal ordered form as requested by SciPy solve_banded function.
import numpy as np
def lu_decomp3(a):
"""
c,d,e = lu_decomp3(a).
LU decomposition of tridiagonal matrix a = [c\d\e]. On output
{c},{d} and {e} are the diagonals of the decomposed matrix a.
"""
n = np.diagonal(a).size
assert(np.all(a.shape ==(n,n))) # check if square matrix
d = np.copy(np.diagonal(a)) # without copy (assignment destination is read-only) error is raised
e = np.copy(np.diagonal(a, 1))
c = np.copy(np.diagonal(a, -1))
for k in range(1,n):
lam = c[k-1]/d[k-1]
d[k] = d[k] - lam*e[k-1]
c[k-1] = lam
return c,d,e
def lu_solve3(c,d,e,b):
"""
x = lu_solve(c,d,e,b).
Solves [c\d\e]{x} = {b}, where {c}, {d} and {e} are the
vectors returned from lu_decomp3.
"""
n = len(d)
y = np.zeros_like(b)
y[0] = b[0]
for k in range(1,n):
y[k] = b[k] - c[k-1]*y[k-1]
x = np.zeros_like(b)
x[n-1] = y[n-1]/d[n-1] # there is no x[n] out of range
for k in range(n-2,-1,-1):
x[k] = (y[k] - e[k]*x[k+1])/d[k]
return x
from scipy.sparse import diags
def create_tridiagonal(size = 4):
diag = np.random.randn(size)*100
diag_pos1 = np.random.randn(size-1)*10
diag_neg1 = np.random.randn(size-1)*10
a = diags([diag_neg1, diag, diag_pos1], offsets=[-1, 0, 1],shape=(size,size)).todense()
return a
a = create_tridiagonal(4)
b = np.random.randn(4)*10
print('matrix a is\n = {} \n\n and vector b is \n {}'.format(a, b))
c, d, e = lu_decomp3(a)
x = lu_solve3(c, d, e, b)
print("x from our function is {}".format(x))
print("check is answer correct ({})".format(np.allclose(np.dot(a, x), b)))
## Test Scipy
from scipy.linalg import solve_banded
def diagonal_form(a, upper = 1, lower= 1):
"""
a is a numpy square matrix
this function converts a square matrix to diagonal ordered form
returned matrix in ab shape which can be used directly for scipy.linalg.solve_banded
"""
n = a.shape[1]
assert(np.all(a.shape ==(n,n)))
ab = np.zeros((2*n-1, n))
for i in range(n):
ab[i,(n-1)-i:] = np.diagonal(a,(n-1)-i)
for i in range(n-1):
ab[(2*n-2)-i,:i+1] = np.diagonal(a,i-(n-1))
mid_row_inx = int(ab.shape[0]/2)
upper_rows = [mid_row_inx - i for i in range(1, upper+1)]
upper_rows.reverse()
upper_rows.append(mid_row_inx)
lower_rows = [mid_row_inx + i for i in range(1, lower+1)]
keep_rows = upper_rows+lower_rows
ab = ab[keep_rows,:]
return ab
ab = diagonal_form(a, upper=1, lower=1) # for tridiagonal matrix upper and lower = 1
x_sp = solve_banded((1,1), ab, b)
print("is our answer the same as scipy answer ({})".format(np.allclose(x, x_sp)))

Gradient Descent

So I am writing a program that handles gradient descent. Im using this method to solve equations of the form
Ax = b
where A is a random 10x10 matrix and b is a random 10x1 matrix
Here is my code:
import numpy as np
import math
import random
def steepestDistance(A,b,xO, e):
xPrev = xO
dPrev = -((A * xPrev) - b)
magdPrev = np.linalg.norm(dPrev)
danger = np.asscalar(((magdPrev * magdPrev)/(np.dot(dPrev.T,A * dPrev))))
xNext = xPrev + (danger * dPrev)
step = 1
while (np.linalg.norm((A * xNext) - b) >= e and np.linalg.norm((A * xNext) - b) < math.pow(10,4)):
xPrev = xNext
dPrev = -((A * xPrev) - b)
magdPrev = np.linalg.norm(dPrev)
danger = np.asscalar((math.pow(magdPrev,2))/(np.dot(dPrev.T,A * dPrev)))
xNext = xPrev + (danger * dPrev)
step = step + 1
return xNext
##print(steepestDistance(np.matrix([[5,2],[2,1]]),np.matrix([[1],[1]]),np.matrix([[0.5],[0]]), math.pow(10,-5)))
def chooseRandMatrix():
matrix = np.zeros(shape = (10,10))
for i in range(10):
for a in range(10):
matrix[i][a] = random.randint(0,100)
return matrix.T * matrix
def chooseRandColArray():
arra = np.zeros(shape = (10,1))
for i in range(10):
arra[i][0] = random.randint(0,100)
return arra
for i in range(4):
matrix = np.asmatrix(chooseRandMatrix())
array = np.asmatrix(chooseRandColArray())
print(steepestDistance(matrix, array, np.asmatrix(chooseRandColArray()),math.pow(10,-5)))
When I run the method steepestDistance on the random matrix and column, I keep getting an infinite loop. It works fine when simple 2x2 matrices are used for A, but it loops indefinitely for 10x10 matrices. The problem is in np.linalg.norm((A * xNext) - b); it keeps growing indefinitely. Thats why I put an upper bound on it; Im not supposed to do it for the algorithm however. Can someone tell me what the problem is?
Solving a linear system Ax=b with gradient descent means to minimize the quadratic function
f(x) = 0.5*x^t*A*x - b^t*x.
This only works if the matrix A is symmetric, A=A^t, since the derivative or gradient of f is
f'(x)^t = 0.5*(A+A^t)*x - b,
and additionally A must be positive definite. If there are negative eigenvalues,then the descent will proceed to minus infinity, there is no minimum to be found.
One work-around is to replace b by A^tb and A by a^t*A, that is to minimize the function
f(x) = 0.5*||A*x-b||^2
= 0.5*x^t*A^t*A*x - b^t*A*x + 0.5*b^t*b
with gradient
f'(x)^t = A^t*A*x - A^t*b
But for large matrices A this is not recommended since the condition number of A^t*A is about the square of the condition number of A.

Simultaneously diagonalize matrices with numpy

I have a m × n × n numpy.ndarray of m simultaneously diagonalizable square matrices and would like to use numpy to obtain their simultaneous eigenvalues.
For example, if I had
from numpy import einsum, diag, array, linalg, random
U = linalg.svd(random.random((3,3)))[2]
M = einsum(
"ij, ajk, lk",
U, [diag([2,2,0]), diag([1,-1,1])], U)
the two matrices in M are simultaneously diagonalizable, and I am looking for a way to obtain the array
array([[2., 1.],
[2., -1.],
[0., 1.]])
(up to permutation of the lines) from M. Is there a built-in or easy way to get this?
There is a fairly simple and very elegant simultaneous diagonalization algorithm based on Givens rotation that was published by Cardoso and Soulomiac in 1996:
Cardoso, J., & Souloumiac, A. (1996). Jacobi Angles for Simultaneous Diagonalization. SIAM Journal on Matrix Analysis and Applications, 17(1), 161–164. doi:10.1137/S0895479893259546
I've attached a numpy implementation of the algorithm at the end of this response. Caveat: It turns out simultaneous diagonalization is a bit of a tricky numerical problem, with no algorithm (to the best of my knowledge) that guarantees global convergence. However, the cases in which it does not work (see the paper) are degenerate and in practice I have never had the Jacobi angles algorithm fail on me.
#!/usr/bin/env python2.7
# -*- coding: utf-8 -*-
"""
Routines for simultaneous diagonalization
Arun Chaganty <arunchaganty#gmail.com>
"""
import numpy as np
from numpy import zeros, eye, diag
from numpy.linalg import norm
def givens_rotate( A, i, j, c, s ):
"""
Rotate A along axis (i,j) by c and s
"""
Ai, Aj = A[i,:], A[j,:]
A[i,:], A[j,:] = c * Ai + s * Aj, c * Aj - s * Ai
return A
def givens_double_rotate( A, i, j, c, s ):
"""
Rotate A along axis (i,j) by c and s
"""
Ai, Aj = A[i,:], A[j,:]
A[i,:], A[j,:] = c * Ai + s * Aj, c * Aj - s * Ai
A_i, A_j = A[:,i], A[:,j]
A[:,i], A[:,j] = c * A_i + s * A_j, c * A_j - s * A_i
return A
def jacobi_angles( *Ms, **kwargs ):
r"""
Simultaneously diagonalize using Jacobi angles
#article{SC-siam,
HTML = "ftp://sig.enst.fr/pub/jfc/Papers/siam_note.ps.gz",
author = "Jean-Fran\c{c}ois Cardoso and Antoine Souloumiac",
journal = "{SIAM} J. Mat. Anal. Appl.",
title = "Jacobi angles for simultaneous diagonalization",
pages = "161--164",
volume = "17",
number = "1",
month = jan,
year = {1995}}
(a) Compute Givens rotations for every pair of indices (i,j) i < j
- from eigenvectors of G = gg'; g = A_ij - A_ji, A_ij + A_ji
- Compute c, s as \sqrt{x+r/2r}, y/\sqrt{2r(x+r)}
(b) Update matrices by multiplying by the givens rotation R(i,j,c,s)
(c) Repeat (a) until stopping criterion: sin theta < threshold for all ij pairs
"""
assert len(Ms) > 0
m, n = Ms[0].shape
assert m == n
sweeps = kwargs.get('sweeps', 500)
threshold = kwargs.get('eps', 1e-8)
rank = kwargs.get('rank', m)
R = eye(m)
for _ in xrange(sweeps):
done = True
for i in xrange(rank):
for j in xrange(i+1, m):
G = zeros((2,2))
for M in Ms:
g = np.array([ M[i,i] - M[j,j], M[i,j] + M[j,i] ])
G += np.outer(g,g) / len(Ms)
# Compute the eigenvector directly
t_on, t_off = G[0,0] - G[1,1], G[0,1] + G[1,0]
theta = 0.5 * np.arctan2( t_off, t_on + np.sqrt( t_on*t_on + t_off * t_off) )
c, s = np.cos(theta), np.sin(theta)
if abs(s) > threshold:
done = False
# Update the matrices and V
for M in Ms:
givens_double_rotate(M, i, j, c, s)
#assert M[i,i] > M[j, j]
R = givens_rotate(R, i, j, c, s)
if done:
break
R = R.T
L = np.zeros((m, len(Ms)))
err = 0
for i, M in enumerate(Ms):
# The off-diagonal elements of M should be 0
L[:,i] = diag(M)
err += norm(M - diag(diag(M)))
return R, L, err
I am not aware of any direct solution. But why not just getting the eigenvalues and the eigenvectors of the first matrix, and using the eigenvectors to transform all other matrices to the diagonal form? Something like:
eigvals, eigvecs = np.linalg.eig(matrix1)
eigvals2 = np.diagonal(np.dot(np.dot(transpose(eigvecs), matrix2), eigvecs))
You can the add the columns to an array via hstack if you like.
UPDATE: As pointed out below, this is only valid if no degenerate eigenvalues occur. Otherwise one would have to check first for the degenerate eigenvalues, then transform the 2nd matrix to a blockdiagonal form, and diagonalize eventual blocks bigger than 1x1 separately.
I am sure there is significant room for improvement in my solution, but I have come up with the following set of three functions doing the calculation for me in a semi-robust way.
def clusters(array,
orig_indices = None,
start = 0,
rtol=numpy.allclose.__defaults__[0],
atol=numpy.allclose.__defaults__[1]):
"""For an array, return a permutation that sorts the numbers and the sizes of the resulting blocks of identical numbers."""
array = numpy.asarray(array)
if not len(array):
return numpy.array([]),[]
if orig_indices is None:
orig_indices = numpy.arange(len(array))
x = array[0]
close = abs(array-x) <= (atol + rtol*abs(x))
first = sum(close)
r_perm, r_sizes = clusters(
array[~close],
orig_indices[~close],
start+first,
rtol, atol)
r_sizes.insert(0, first)
return numpy.concatenate((orig_indices[close], r_perm)), r_sizes
def permutation_matrix(permutation, dtype=dtype):
n = len(permutation)
P = numpy.zeros((n,n), dtype)
for i,j in enumerate(permutation):
P[j,i]=1
return P
def simultaneously_diagonalize(tensor, atol=numpy.allclose.__defaults__[1]):
tensor = numpy.asarray(tensor)
old_shape = tensor.shape
size = old_shape[-1]
tensor = tensor.reshape((-1, size, size))
diag_mask = 1-numpy.eye(size)
eigvalues, diagonalizer = numpy.linalg.eig(tensor[0])
diagonalization = numpy.dot(
numpy.dot(
matrix.linalg.inv(diagonalizer),
tensor).swapaxes(0,-2),
diagonalizer)
if numpy.allclose(diag_mask*diagonalization, 0):
return diagonalization.diagonal(axis1=-2, axis2=-1).reshape(old_shape[:-1])
else:
perm, cluster_sizes = clusters(diagonalization[0].diagonal())
perm_matrix = permutation_matrix(perm)
diagonalization = numpy.dot(
numpy.dot(
perm_matrix.T,
diagonalization).swapaxes(0,-2),
perm_matrix)
mask = 1-scipy.linalg.block_diag(
*list(
numpy.ones((blocksize, blocksize))
for blocksize in cluster_sizes))
print(diagonalization)
assert(numpy.allclose(
diagonalization*mask,
0)) # Assert that the matrices are co-diagonalizable
blocks = numpy.cumsum(cluster_sizes)
start = 0
other_part = []
for block in blocks:
other_part.append(
simultaneously_diagonalize(
diagonalization[1:, start:block, start:block]))
start = block
return numpy.vstack(
(diagonalization[0].diagonal(axis1=-2, axis2=-1),
numpy.hstack(other_part)))
If you know something about the size of the eigenvalues of the two matrices in advance, you can diagonalize a linear combination of the two matrices, with coefficients chosen to break the degeneracy. For example, if the eigenvalues of both lie between -10 and 10, you could diagonalize 100*M1 + M2. There's a slight loss of precision, but for many purposes it's good enough--and quick and easy!

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