def plot_field(eng, mesh, val='u'):
Ne = mesh.Ne
it = FM.get_connections(mesh)
mat = []
for e in mesh.getElements():
mat.append(e.getMaterial().getID() + 1)
xyz = []
field = []
for n in mesh.getNodes():
xyz.append(n.getX().tolist())
if val == 'u':
for n in mesh.getNodes():
field.append(n.getU().tolist())
elif val == 'v':
for n in mesh.getNodes():
field.append(n.getV().tolist())
elif val == 'a':
for n in mesh.getNodes():
field.append(n.getU().tolist())
else:
return
#eng = matlab.engine.start_matlab()
IT = matlab.int64(it)
MAT = matlab.int64(mat)
XYZ = matlab.double(xyz)
Field = matlab.double(field)
eng.plot_field(IT, Field, XYZ, Ne, MAT, 0)
return eng
def convertLabels(self, inLabels):
convLabels = []
for stateID in inLabels.keys():
convLabels.append([stateID,'p1',matlab.int64(inLabels[stateID]['p1'][:])])
convLabels.append([stateID,'p2',matlab.int64(inLabels[stateID]['p2'][:])])
convLabels.append([stateID,'p3',matlab.int64(inLabels[stateID]['p3'][:])])
convLabels.append([stateID,'p4',matlab.int64(inLabels[stateID]['p4'][:])])
return convLabels
def interleave(eng, arrData_bin, nParam, strMethod=INTRLV_MATRIX):
"""
interleave data in a block way
"""
data_intrlv = None
nPadding = None
if(strMethod == INTRLV_MATRIX):
nCols = nParam
arrData_bin, nPadding = ct.zeroPadding(arrData_bin, nCols)
nRows = len(arrData_bin)/nCols
data = matlab.int64(list(arrData_bin))
data_intrlv = eng.matintrlv(data, nRows, nCols)
elif(strMethod == INTRLV_RANDOM):
nSeed = 4831
data = matlab.int64(list(arrData_bin))
data_intrlv = eng.randintrlv(data, nSeed)
else:
raise ValueError("Unsupported interleaving method: %s" % strMethod)
arrData_intrlv = np.array([i for i in data_intrlv[0]])
return arrData_intrlv, nPadding
def matlab_SurfStatLinMod(Y, M, surf=None, niter=1, thetalim=0.01, drlim=0.1):
from term import Term
from brainspace.mesh.mesh_elements import get_cells
from brainspace.vtk_interface.wrappers.data_object import BSPolyData
if isinstance(Y, np.ndarray):
Y = matlab.double(Y.tolist())
else:
Y = surfstat_eng.double(Y)
if isinstance(M, np.ndarray):
M = {'matrix': matlab.double(M.tolist())}
elif isinstance(M, Term):
M = surfstat_eng.term(matlab.double(M.matrix.values.tolist()),
M.matrix.columns.tolist())
else: # Random
M1 = matlab.double(M.mean.matrix.values.tolist())
V1 = matlab.double(M.variance.matrix.values.tolist())
M = surfstat_eng.random(V1, M1, surfstat_eng.cell(0),
surfstat_eng.cell(0), 1)
# Only require 'tri' or 'lat'
if surf is None:
k = None
surf = surfstat_eng.cell(0)
else:
if isinstance(surf,BSPolyData):
surf = {'tri': np.array(get_cells(surf))+1}
k = 'tri' if 'tri' in surf else 'lat'
s = surf[k]
surf = {k: matlab.int64(s.tolist())}
slm = surfstat_eng.SurfStatLinMod(Y, M, surf, niter, thetalim, drlim)
for key in ['SSE', 'coef']:
if key not in slm:
continue
slm[key] = np.atleast_2d(slm[key])
slm = {k: v if np.isscalar(v) else np.array(v) for k, v in slm.items()}
return slm
def matlab_SurfStatLinMod(Y, M, surf=None, niter=1, thetalim=0.01, drlim=0.1):
from term import Term
if isinstance(Y, np.ndarray):
Y = matlab.double(Y.tolist())
else:
Y = surfstat_eng.double(Y)
if isinstance(M, np.ndarray):
M = {'matrix': matlab.double(M.tolist())}
elif isinstance(M, Term):
M = surfstat_eng.term(matlab.double(M.matrix.values.tolist()),
M.matrix.columns.tolist())
else: # Random
M1 = matlab.double(M.mean.matrix.values.tolist())
V1 = matlab.double(M.variance.matrix.values.tolist())
M = surfstat_eng.random(V1, M1, surfstat_eng.cell(0),
surfstat_eng.cell(0), 1)
# Only require 'tri' or 'lat'
if surf is None or ('tri' not in surf and 'lat' not in surf):
k = None
surf = surfstat_eng.cell(0)
else:
k = 'tri' if 'tri' in surf else 'lat'
s = surf[k]
surf = {k: matlab.int64(s.tolist())}
slm = surfstat_eng.SurfStatLinMod(Y, M, surf, niter, thetalim, drlim)
for key in ['SSE', 'coef']:
if key not in slm:
continue
slm[key] = np.atleast_2d(slm[key])
slm = {k: v if np.isscalar(v) else np.array(v) for k, v in slm.items()}
return slm
def ndarray_to_matlab(numpy_array):
"""Conversion of a numpy array to matlab mlarray
The conversion is realised without copy for real data. First an empty initialization is realized.
Then the numpy array is affected to the _data field. Thus the data field is not really an
array.array but a numpy array. Matlab doesn't see anything...
For complex data, the strides seems to not work properly with matlab.double.
Paramerters
-----------
numpy_array : numpy array
the array to convert
Returns
-------
matlab_array : mlarray
the converted array that can be passe to matlab
Examples
--------
>>> npi=numpy.array([[1,2,3],[4,5,6],[7,8,9],[10,11,12]],dtype=numpy.int64,order='C')
>>> ndarray_to_matlab(npi)
matlab.int64([[1,2,3],[4,5,6],[7,8,9],[10,11,12]])
>>> npif=numpy.array([[1,2,3],[4,5,6],[7,8,9],[10,11,12]],dtype=numpy.int64,order='F')
>>> ndarray_to_matlab(npif)
matlab.int64([[1,2,3],[4,5,6],[7,8,9],[10,11,12]])
>>> npcf=numpy.array([[1,2+0.2j,3],[4,5,6],[7,8,9],[10+0.1j,11,12]],dtype=numpy.complex,order='F')
>>> ndarray_to_matlab(npcf)
matlab.double([[(1+0j),(2+0.2j),(3+0j)],[(4+0j),(5+0j),(6+0j)],[(7+0j),(8+0j),(9+0j)],[(10+0.1j),(11+0j),(12+0j)]], is_complex=True)
References
-----------
https://scipy-lectures.org/advanced/advanced_numpy/ (strides)
"""
if "ndarray" not in str(type(numpy_array)): # check numpy
raise TypeError(f"Expect numpy.ndarray. Got {type(numpy_array)}")
shape = numpy_array.shape # get shape
num_elements = numpy.prod(shape) # number of elements
if numpy_array.flags.f_contiguous: # compute strides (real case)
strides = get_strides_f(shape)
order = "F"
else:
strides = get_strides_c(shape)
order = "C"
if numpy.iscomplexobj(numpy_array): # complex case
matlab_array = matlab.double(
initializer=None, size=(1, num_elements), is_complex=True
) # create empty matlab.mlarray
# associate the data
"""
# associate the data (no copy), works on 2D array only...
matlab_array._real=numpy_array.ravel(order=order) # allow to map real and imaginary part continuously!
"""
cpx = numpy_array.ravel(order="F") # copy except for fortran like array
matlab_array._real = (
cpx.real.ravel()
) # second ravel to correct the strides 18->8
matlab_array._imag = cpx.imag.ravel()
matlab_array.reshape(shape)
# matlab_array._strides=strides
else: # real case # create empty matlab.mlarray
if numpy_array.dtype == numpy.float64:
matlab_array = matlab.double(
initializer=None, size=(1, num_elements), is_complex=False
)
elif numpy_array.dtype == numpy.int64:
matlab_array = matlab.int64(initializer=None, size=(1, num_elements))
elif numpy_array.dtype == numpy.bool:
matlab_array = matlab.logical(initializer=None, size=(1, num_elements))
else:
raise TypeError(f"Type {numpy_array.dtype} is missing")
matlab_array._data = numpy_array.ravel(order=order) # associate the data
# print(matlab_array._data.flags,matlab_array._data,'\n') # control owner
matlab_array.reshape(shape) # back to original shape
if (
len(shape) > 1
): # array strides are in number of cell (numpy strides are in bytes)
# if len(shape)==1 no need to change. Format pb because _stride expect (1,1) and stride = (1,)
matlab_array._strides = (
strides # change stride (matlab use 'F' order ie [nc,1] )
)
return matlab_array
def decompose(self, r, method='tensorly') -> 'DecomposedFactor':
"""
Decompose this factor into r rank-1 components using non-negative CP decomposition. In certain trivial cases,
returns a decomposition with one component rather than r.
:param method: Library to use to compute CP decomposition, either 'tensorly' or 'matlab' (see note about MATLAB
support at the top of this file).
"""
assert method in ['tensorly', 'matlab']
if method == 'matlab':
assert with_matlab, 'MATLAB Python API not detected'
# Variables with cardinality 1 cause problems with tensorly non_negative_decomp, so we only decompose the
# nontrivial dimensions of the table (and set the matrices for trivial dimensions to [[1, ..., 1]]).
table_nt = np.squeeze(self.table)
if table_nt.ndim == 1:
# If the nontrivial table has just one variable, the resulting decomposition has just one term (not r terms)
# and we don't call the decomposition algorithm at all
n_terms = 1
weights = np.ones(n_terms)
# Reshape is to change np.array([1,2,3]) to np.array([[1],[2],[3]])
matrices_nt = [table_nt.reshape(table_nt.shape[0], 1)]
else:
n_terms = r
if method == 'tensorly':
if 'tensorly' not in sys.modules:
if verbosity == 3:
import_tensorly()
else:
with SuppressOutput():
import_tensorly()
weights = np.ones(n_terms)
matrices_nt = None
table_nt_orig = table_nt
i = 0
while not matrices_nt:
try:
matrices_nt = tensorly.decomposition.non_negative_parafac(
table_nt, n_terms)
except LinAlgError:
i += 1
status(
"Warning: singular matrix encountered, perturbing tensor and attempting decomposition "
"again ({})".format(i), 3)
table_nt = perturb(table_nt_orig)
elif method == 'matlab':
# Initialise MATLAB
global eng
if not eng:
eng = matlab.engine.start_matlab()
eng.addpath(MATLAB_PATH)
w, T = eng.cp_kolda(matlab.double(
table_nt.flatten(order='F').tolist()),
matlab.int64(table_nt.shape),
r,
nargout=2)
matrices_nt = [np.array(t) for t in T]
weights = np.array(w).flatten()
# Add the trivial dimensions back in
matrices = []
j = 0
for i in range(self.n_vars):
if self.cardinalities[i] == 1:
matrices.append(np.ones((1, n_terms)))
else:
matrices.append(matrices_nt[j])
j += 1
assert matrices[i].shape == (self.cardinalities[i], n_terms)
assert j == len(matrices_nt)
df = DecomposedFactor(self.vars, weights, matrices)
# Make sure the decomposition is close to the original factor
# diff = df.expand().table - self.table
# print("Reconstruction error: norm=%s, largest=%s" % (
# np.linalg.norm(diff),
# np.max(diff),
# ))
return df
def asiduj_test():
"""
Test of the module
It runs the doctest and create other tests with matlab engine calls."""
import scipy.linalg as spl
print("Run matlab engine...")
if len(matlab.engine.find_matlab()) == 0:
# si aucune session share, run
eng = matlab.engine.start_matlab()
else:
# connect to a session
eng = matlab.engine.connect_matlab(matlab.engine.find_matlab()[0])
print("connected...")
print("Further tests....\n")
# create matlab data
# ------------------------------------------------------------------------
mf = eng.rand(3)
mc = matlab.double([[1 + 1j, 0.3, 1j], [1.2j - 1, 0, 1 + 1j]],
is_complex=True)
mi64 = matlab.int64([1, 2, 3])
mi8 = matlab.int8([1, 2, 3])
mb = matlab.logical([True, True, False])
# Test conversion from matlab to numpy
# ------------------------------------------------------------------------
npf = matlab_to_ndarray(mf) # no copy, if mf is changed, npf change!
npc = matlab_to_ndarray(mc) # still copy for complex (only)
npi64 = matlab_to_ndarray(mi64)
npi8 = matlab_to_ndarray(mi8)
npb = matlab_to_ndarray(mb)
# Test conversion from numpy to matlab
# ------------------------------------------------------------------------
npi = numpy.array([[1, 2, 3], [4, 5, 6], [7, 8, 9], [10, 11, 12]],
dtype=numpy.int64,
order="F")
mi = ndarray_to_matlab(npi)
mc2 = ndarray_to_matlab(npc)
mf2 = ndarray_to_matlab(
npf) # copy, because npf has 'F' order (comes from mlarray)
mi64_2 = ndarray_to_matlab(npi)
mb2 = ndarray_to_matlab(npb)
# test orientation in the matlab workspace
# ------------------------------------------------------------------------
eng.workspace["mi"] = mi64_2
eng.workspace["mc2"] = mc2
# check results
# ------------------------------------------------------------------------
npcc = numpy.array(
[
[1.0, 1.1 + 1j],
[
1.12 + 0.13j,
22.1,
],
],
dtype=numpy.complex,
) # assume C
mcc = ndarray_to_matlab(npcc)
npcc_inv = spl.inv(npcc)
mcc_inv = eng.inv(mcc)
print("Are the inverse of matrix equal ?")
print(mcc_inv)
print(npcc_inv)
# # no copy check
# # ------------------------------------------------------------------------
# # complex
#
# npcc[0,0]=0.25
# print("Are the data reuse ?", ", OWNDATA =", mcc._real.flags.owndata,
# "same base =", mcc._real.base is npcc,
# ', If one is modified, the other is modified =', mcc._real[0]==npcc[0,0])
#
# test sparse matrix requiert Recast4py.m
K1, K2 = eng.sptest(3.0, nargout=2)
Ksp1 = dict_to_sparse(K1)
Ksp2 = dict_to_sparse(K2)
def np2mlarray(npa):
""" Conversion of a numpy array to matlab mlarray
The conversion is realised without copy for real data. First an empty initialization is realized.
Then the numpy array is affected to the _data field. Thus the data field is not really an
array.array but a numpy array. Matlab doesn't see anything...
For complex data, the strides seems to not work properly with matlab.double.
Paramerters
-----------
npa : numpy array
the array to convert
Returns
-------
ma : mlarray
the converted array that can be passe to matlab
Examples
--------
>>> npi=np.array([[1,2,3],[4,5,6],[7,8,9],[10,11,12]],dtype=np.int64,order='C')
>>> np2mlarray(npi)
matlab.int64([[1,2,3],[4,5,6],[7,8,9],[10,11,12]])
>>> npif=np.array([[1,2,3],[4,5,6],[7,8,9],[10,11,12]],dtype=np.int64,order='F')
>>> np2mlarray(npif)
matlab.int64([[1,2,3],[4,5,6],[7,8,9],[10,11,12]])
>>> npcf=np.array([[1,2+0.2j,3],[4,5,6],[7,8,9],[10+0.1j,11,12]],dtype=np.complex,order='F')
>>> np2mlarray(npcf)
matlab.double([[(1+0j),(2+0.2j),(3+0j)],[(4+0j),(5+0j),(6+0j)],[(7+0j),(8+0j),(9+0j)],[(10+0.1j),(11+0j),(12+0j)]], is_complex=True)
References
-----------
https://scipy-lectures.org/advanced/advanced_numpy/ (strides)
"""
# check numpy
if 'ndarray' not in str(type(npa)):
raise TypeError('Expect numpy.ndarray. Got %s' % type(npa))
# get shape
shape = npa.shape
# number of elements
N = np.prod(shape)
# compute strides (real case)
if npa.flags.f_contiguous == True:
strides = _getStridesF(shape) # pour la sortie
order = 'F'
else:
strides = _getStridesC(shape) # ok, garde le même
order = 'C'
# complex case
if npa.dtype in (np.complex128, np.complex):
# create empty matlab.mlarray
ma = matlab.double(initializer=None, size=(1, N), is_complex=True)
# associate the data
"""
# associate the data (no copy), works on 2D array only...
ma._real=npa.ravel(order=order) # allow to map real and imaginary part continuously!
"""
cpx = npa.ravel(order='F') # copy except for fortran like array
ma._real = cpx.real.ravel(
) # second ravel to correct the strides 18->8
ma._imag = cpx.imag.ravel()
ma.reshape(shape)
# ma._strides=strides
# real case
else:
# create empty matlab.mlarray
if npa.dtype == np.float64:
ma = matlab.double(initializer=None, size=(1, N), is_complex=False)
elif npa.dtype == np.int64:
ma = matlab.int64(initializer=None, size=(1, N))
elif npa.dtype == np.bool:
ma = matlab.logical(initializer=None, size=(1, N))
else:
raise TypeError('Type %s is missing' % npa.dtype)
# associate the data
ma._data = npa.ravel(order=order)
# print(ma._data.flags,ma._data,'\n') # control owner
# back to original shape
ma.reshape(shape)
# array strides are in number of cell (numpy strides are in bytes)
# if len(shape)==1 no need to change. Format pb because _stride expect (1,1) and stride = (1,)
if len(shape) > 1:
ma._strides = strides # change stride (matlab use 'F' order ie [nc,1] )
return ma
eng = matlab.engine.start_matlab()
else:
# connect to a session
eng = matlab.engine.connect_matlab(matlab.engine.find_matlab()[0])
print('connected...')
else:
print('Matlab engine is already runnig...')
print('Further tests....\n')
# create matlab data
# ------------------------------------------------------------------------
mf = eng.rand(3)
mc = matlab.double([[1 + 1j, 0.3, 1j], [1.2j - 1, 0, 1 + 1j]],
is_complex=True)
mi64 = matlab.int64([1, 2, 3])
mi8 = matlab.int8([1, 2, 3])
mb = matlab.logical([True, True, False])
# Test conversion from matlab to numpy
# ------------------------------------------------------------------------
npf = mlarray2np(mf) # no copy, if mf is changed, npf change!
npc = mlarray2np(mc) # still copy for complex (only)
npi64 = mlarray2np(mi64)
npi8 = mlarray2np(mi8)
npb = mlarray2np(mb)
# Test conversion from numpy to matlab
# ------------------------------------------------------------------------
npi = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9], [10, 11, 12]],
dtype=np.int64,