QPMS
/
qpms
1
0
Fork 0
Code Issues Pull Requests Projects Releases Wiki Activity
qpms/qpms/qpms_c.pyx

1067 lines
39 KiB
Cython
Raw Blame History

# Cythonized parts of QPMS here
# -----------------------------
import numpy as np
import cmath
from qpms_cdefs cimport *
cimport cython
from cython.parallel cimport parallel, prange
import math # for copysign in crep methods
#import re # TODO for crep methods?
#cimport openmp
#openmp.omp_set_dynamic(1)
## Auxillary function for retrieving the "meshgrid-like" indices; inc. nmax
@cython.boundscheck(False)
def get_mn_y(int nmax):
"""
Auxillary function for retreiving the 'meshgrid-like' indices from the flat indexing;
inc. nmax.
('y to mn' conversion)
Parameters
----------
nmax : int
The maximum order to which the VSWFs / Legendre functions etc. will be evaluated.
Returns
-------
output : (m, n)
Tuple of two arrays of type np.array(shape=(nmax*nmax + 2*nmax), dtype=np.int),
where [(m[y],n[y]) for y in range(nmax*nmax + 2*nma)] covers all possible
integer pairs n >= 1, -n <= m <= n.
"""
cdef Py_ssize_t nelems = nmax * nmax + 2 * nmax
cdef np.ndarray[np.int_t,ndim=1] m_arr = np.empty([nelems], dtype=np.int)
cdef np.ndarray[np.int_t,ndim=1] n_arr = np.empty([nelems], dtype=np.int)
cdef Py_ssize_t i = 0
cdef np.int_t n, m
for n in range(1,nmax+1):
for m in range(-n,n+1):
m_arr[i] = m
n_arr[i] = n
i = i + 1
return (m_arr, n_arr)
def get_nelem(unsigned int lMax):
return lMax * (lMax + 2)
def get_y_mn_unsigned(int nmax):
"""
Auxillary function for mapping 'unsigned m', n indices to the flat y-indexing.
For use with functions as scipy.special.lpmn, which have to be evaluated separately
for positive and negative m.
Parameters
----------
nmax : int
The maximum order to which the VSWFs / Legendre functions etc. will be evaluated.
output : (ymn_plus, ymn_minus)
Tuple of two arrays of shape (nmax+1,nmax+1), containing the flat y-indices corresponding
to the respective (m,n) and (-m,n). The elements for which |m| > n are set to -1.
(Therefore, the caller must not use those elements equal to -1.)
"""
cdef np.ndarray[np.intp_t, ndim=2] ymn_plus = np.full((nmax+1,nmax+1),-1, dtype=np.intp)
cdef np.ndarray[np.intp_t, ndim=2] ymn_minus = np.full((nmax+1,nmax+1),-1, dtype=np.intp)
cdef Py_ssize_t i = 0
cdef np.int_t n, m
for n in range(1,nmax+1):
for m in range(-n,0):
ymn_minus[-m,n] = i
i = i + 1
for m in range(0,n+1):
ymn_plus[m,n] = i
i = i + 1
return(ymn_plus, ymn_minus)
cdef int q_max(int m, int n, int mu, int nu):
return min(n,nu,(n+nu-abs(m+mu)//2))
"""
Now we generate our own universal functions to be used with numpy.
Good way to see how this is done is to look at scipy/scipy/special/generate_ufuncs.py
and scipy/scipy/special/generate_ufuncs.py
In simple words, it works like this:
- Let's have a single element function. This can be function which returns or a "subroutine".
- Then we need a loop function; this is a wrapper that gets bunch of pointers from numpy and
has to properly call the single element function.
- From those two, we build a python object using PyUFunc_FromFuncAndData.
* If the ufunc is supposed to work on different kinds of input/output types,
then a pair of single-element and loop functions is o be provided for
each combination of types. However, the single-element function can be reused if
the corresponding loop functions do the proper casting.
"""
## as in scipy/special/_ufuncs_cxx.pyx
##-------------------------------------
#cdef extern from "numpy/ufuncobject.h":
# int PyUFunc_getfperr() nogil
#
#cdef public int wrap_PyUFunc_getfperr() nogil:
# """
# Call PyUFunc_getfperr in a context where PyUFunc_API array is initialized;
#
# """
# return PyUFunc_getfperr()
#
#cimport sf_error
#-------------------------------------
cdef void loop_D_iiiidddii_As_D_lllldddbl(char **args, np.npy_intp *dims, np.npy_intp *steps, void *data) nogil:
cdef np.npy_intp i, n = dims[0]
cdef void *func = (<void**>data)#[0]
#cdef char *func_name= <char*>(<void**>data)[1] # i am not using this, nor have I saved func_name to data
cdef char *ip0 = args[0]
cdef char *ip1 = args[1]
cdef char *ip2 = args[2]
cdef char *ip3 = args[3]
cdef char *ip4 = args[4]
cdef char *ip5 = args[5]
cdef char *ip6 = args[6]
cdef char *ip7 = args[7]
cdef char *ip8 = args[8]
cdef char *op0 = args[9]
cdef cdouble ov0
for i in range(n): # iterating over dimensions
ov0 = (<double complex(*)(int, int, int, int, double, double, double, int, int) nogil>func)(
<int>(<np.npy_long*>ip0)[0],
<int>(<np.npy_long*>ip1)[0],
<int>(<np.npy_long*>ip2)[0],
<int>(<np.npy_long*>ip3)[0],
<double>(<np.npy_double*>ip4)[0],
<double>(<np.npy_double*>ip5)[0],
<double>(<np.npy_double*>ip6)[0],
<int>(<np.npy_bool*>ip7)[0],
<int>(<np.npy_long*>ip8)[0],
)
(<cdouble *>op0)[0] = <cdouble>ov0
ip0 += steps[0]
ip1 += steps[1]
ip2 += steps[2]
ip3 += steps[3]
ip4 += steps[4]
ip5 += steps[5]
ip6 += steps[6]
ip7 += steps[7]
ip8 += steps[8]
op0 += steps[9]
# FIXME ERROR HANDLING!!! requires correct import and different data passed (see scipy's generated ufuncs)
# sf_error.check_fpe(func_name)
# Module initialisation
# ---------------------
np.import_array() # not sure whether this is really needed
np.import_ufunc()
# Arrays passed to PyUFunc_FromFuncAndData()
# ------------------------------------------
# BTW, aren't there anonymous arrays in cython?
cdef np.PyUFuncGenericFunction trans_X_taylor_loop_func[1]
cdef void *trans_A_taylor_elementwise_funcs[1]
cdef void *trans_B_taylor_elementwise_funcs[1]
trans_X_taylor_loop_func[0] = loop_D_iiiidddii_As_D_lllldddbl
# types to be used for all of the single-type translation
# coefficient retrieval ufuncs called like
# coeff = func(m, n, mu, nu, r, theta, phi, r_ge_d, J)
# currently supported signatures: (D_lllldddbl)
cdef char ufunc__get_either_trans_coeff_types[10]
ufunc__get_either_trans_coeff_types[0] = np.NPY_LONG
ufunc__get_either_trans_coeff_types[1] = np.NPY_LONG
ufunc__get_either_trans_coeff_types[2] = np.NPY_LONG
ufunc__get_either_trans_coeff_types[3] = np.NPY_LONG
ufunc__get_either_trans_coeff_types[4] = np.NPY_DOUBLE
ufunc__get_either_trans_coeff_types[5] = np.NPY_DOUBLE
ufunc__get_either_trans_coeff_types[6] = np.NPY_DOUBLE
ufunc__get_either_trans_coeff_types[7] = np.NPY_BOOL
ufunc__get_either_trans_coeff_types[8] = np.NPY_LONG
ufunc__get_either_trans_coeff_types[9] = np.NPY_CDOUBLE
# types to be used for all of the both-type translation
# coefficient retrieval ufuncs called like
# errval = func(m, n, mu, nu, r, theta, phi, r_ge_d, J, &A, &B)
# currently supported signatures: (lllldddbl_DD)
cdef char ufunc__get_both_coeff_types[11]
ufunc__get_both_coeff_types[0] = np.NPY_LONG
ufunc__get_both_coeff_types[1] = np.NPY_LONG
ufunc__get_both_coeff_types[2] = np.NPY_LONG
ufunc__get_both_coeff_types[3] = np.NPY_LONG
ufunc__get_both_coeff_types[4] = np.NPY_DOUBLE
ufunc__get_both_coeff_types[5] = np.NPY_DOUBLE
ufunc__get_both_coeff_types[6] = np.NPY_DOUBLE
ufunc__get_both_coeff_types[7] = np.NPY_BOOL
ufunc__get_both_coeff_types[8] = np.NPY_LONG
ufunc__get_both_coeff_types[9] = np.NPY_CDOUBLE
ufunc__get_both_coeff_types[10] = np.NPY_CDOUBLE
trans_A_taylor_elementwise_funcs[0] = <void*> qpms_trans_single_A_Taylor_ext
trans_B_taylor_elementwise_funcs[0] = <void*> qpms_trans_single_B_Taylor_ext
trans_A_Taylor = np.PyUFunc_FromFuncAndData(
trans_X_taylor_loop_func, # func
trans_A_taylor_elementwise_funcs, #data
ufunc__get_either_trans_coeff_types, # types
1, # ntypes: number of supported input types
9, # nin: number of input args
1, # nout: number of output args
0, # identity element, unused
"trans_A_Taylor", # name
"""
TODO computes the E-E or M-M translation coefficient in Taylor's normalisation
""", # doc
0 # unused, for backward compatibility of numpy c api
)
trans_B_Taylor = np.PyUFunc_FromFuncAndData(
trans_X_taylor_loop_func,
trans_B_taylor_elementwise_funcs,
ufunc__get_either_trans_coeff_types,
1, # number of supported input types
9, # number of input args
1, # number of output args
0, # identity element, unused
"trans_B_Taylor",
"""
TODO computes the E-E or M-M translation coefficient in Taylor's normalisation
""",
0 # unused
)
# ---------------------------------------------
# Wrapper for the qpms_trans_calculator "class"
# ---------------------------------------------
ctypedef struct trans_calculator_get_X_data_t:
qpms_trans_calculator* c
void* cmethod
cdef void trans_calculator_loop_D_Ciiiidddii_As_D_lllldddbl(char **args, np.npy_intp *dims, np.npy_intp *steps, void *data) nogil:
cdef np.npy_intp i, n = dims[0]
cdef void *func = (<trans_calculator_get_X_data_t*>data)[0].cmethod
#cdef cdouble (*func)(qpms_trans_calculator*, int, int, int, int, double, double, double, int, int) nogil = (<trans_calculator_get_X_data_t*>data)[0].cmethod
cdef qpms_trans_calculator* c = (<trans_calculator_get_X_data_t*>data)[0].c
#cdef char *func_name= <char*>(<void**>data)[1] # i am not using this, nor have I saved func_name to data
cdef char *ip0 = args[0]
cdef char *ip1 = args[1]
cdef char *ip2 = args[2]
cdef char *ip3 = args[3]
cdef char *ip4 = args[4]
cdef char *ip5 = args[5]
cdef char *ip6 = args[6]
cdef char *ip7 = args[7]
cdef char *ip8 = args[8]
cdef char *op0 = args[9]
cdef cdouble ov0
for i in range(n): # iterating over dimensions
#ov0 = func(
ov0 = (<double complex(*)(qpms_trans_calculator*, int, int, int, int, double, double, double, int, int) nogil>func)(
c,
<int>(<np.npy_long*>ip0)[0],
<int>(<np.npy_long*>ip1)[0],
<int>(<np.npy_long*>ip2)[0],
<int>(<np.npy_long*>ip3)[0],
<double>(<np.npy_double*>ip4)[0],
<double>(<np.npy_double*>ip5)[0],
<double>(<np.npy_double*>ip6)[0],
<int>(<np.npy_bool*>ip7)[0],
<int>(<np.npy_long*>ip8)[0],
)
(<cdouble *>op0)[0] = <cdouble>ov0
ip0 += steps[0]
ip1 += steps[1]
ip2 += steps[2]
ip3 += steps[3]
ip4 += steps[4]
ip5 += steps[5]
ip6 += steps[6]
ip7 += steps[7]
ip8 += steps[8]
op0 += steps[9]
# FIXME ERROR HANDLING!!! requires correct import and different data passed (see scipy's generated ufuncs)
# sf_error.check_fpe(func_name)
cdef void trans_calculator_loop_E_C_DD_iiiidddii_As_lllldddbl_DD(char **args, np.npy_intp *dims, np.npy_intp *steps, void *data) nogil:
# E stands for error value (int), C for qpms_trans_calculator*
cdef np.npy_intp i, n = dims[0]
cdef void *func = (<trans_calculator_get_X_data_t*>data)[0].cmethod
#cdef complex double (*func)(qpms_trans_calculator*, double complex *, double complex *, int, int, int, int, double, double, double, int, int) nogil = (<trans_calculator_get_X_data_t*>data)[0].cmethod
cdef qpms_trans_calculator* c = (<trans_calculator_get_X_data_t*>data)[0].c
#cdef char *func_name= <char*>(<void**>data)[1] # i am not using this, nor have I saved func_name to data
cdef char *ip0 = args[0]
cdef char *ip1 = args[1]
cdef char *ip2 = args[2]
cdef char *ip3 = args[3]
cdef char *ip4 = args[4]
cdef char *ip5 = args[5]
cdef char *ip6 = args[6]
cdef char *ip7 = args[7]
cdef char *ip8 = args[8]
cdef char *op0 = args[9]
cdef char *op1 = args[10]
cdef cdouble ov0
cdef int errval
for i in range(n): # iterating over dimensions
#errval = func(
errval = (<int(*)(qpms_trans_calculator*, double complex *, double complex *, int, int, int, int, double, double, double, int, int) nogil>func)(
c,
<cdouble *> op0,
<cdouble *> op1,
<int>(<np.npy_long*>ip0)[0],
<int>(<np.npy_long*>ip1)[0],
<int>(<np.npy_long*>ip2)[0],
<int>(<np.npy_long*>ip3)[0],
<double>(<np.npy_double*>ip4)[0],
<double>(<np.npy_double*>ip5)[0],
<double>(<np.npy_double*>ip6)[0],
<int>(<np.npy_bool*>ip7)[0],
<int>(<np.npy_long*>ip8)[0],
)
ip0 += steps[0]
ip1 += steps[1]
ip2 += steps[2]
ip3 += steps[3]
ip4 += steps[4]
ip5 += steps[5]
ip6 += steps[6]
ip7 += steps[7]
ip8 += steps[8]
op0 += steps[9]
op1 += steps[10]
# TODO if (errval != 0): ...
# FIXME ERROR HANDLING!!! requires correct import and different data passed (see scipy's generated ufuncs)
# sf_error.check_fpe(func_name)
@cython.boundscheck(False)
@cython.wraparound(False)
cdef void trans_calculator_parallel_loop_E_C_DD_iiiidddii_As_lllldddbl_DD(char **args, np.npy_intp *dims, np.npy_intp *steps, void *data) nogil:
# E stands for error value (int), C for qpms_trans_calculator*
cdef np.npy_intp i, n = dims[0]
cdef void *func = (<trans_calculator_get_X_data_t*>data)[0].cmethod
#cdef complex double (*func)(qpms_trans_calculator*, double complex *, double complex *, int, int, int, int, double, double, double, int, int) nogil = (<trans_calculator_get_X_data_t*>data)[0].cmethod
cdef qpms_trans_calculator* c = (<trans_calculator_get_X_data_t*>data)[0].c
#cdef char *func_name= <char*>(<void**>data)[1] # i am not using this, nor have I saved func_name to data
cdef char *ip0
cdef char *ip1
cdef char *ip2
cdef char *ip3
cdef char *ip4
cdef char *ip5
cdef char *ip6
cdef char *ip7
cdef char *ip8
cdef char *op0
cdef char *op1
cdef int errval
for i in prange(n): # iterating over dimensions
ip0 = args[0] + i * steps[0]
ip1 = args[1] + i * steps[1]
ip2 = args[2] + i * steps[2]
ip3 = args[3] + i * steps[3]
ip4 = args[4] + i * steps[4]
ip5 = args[5] + i * steps[5]
ip6 = args[6] + i * steps[6]
ip7 = args[7] + i * steps[7]
ip8 = args[8] + i * steps[8]
op0 = args[9] + i * steps[9]
op1 = args[10] + i * steps[10]
#errval = func(
errval = (<int(*)(qpms_trans_calculator*, double complex *, double complex *, int, int, int, int, double, double, double, int, int) nogil>func)(
c,
<cdouble *> op0,
<cdouble *> op1,
<int>(<np.npy_long*>ip0)[0],
<int>(<np.npy_long*>ip1)[0],
<int>(<np.npy_long*>ip2)[0],
<int>(<np.npy_long*>ip3)[0],
<double>(<np.npy_double*>ip4)[0],
<double>(<np.npy_double*>ip5)[0],
<double>(<np.npy_double*>ip6)[0],
<int>(<np.npy_bool*>ip7)[0],
<int>(<np.npy_long*>ip8)[0],
)
# TODO if (errval != 0): ...
# FIXME ERROR HANDLING!!! requires correct import and different data passed (see scipy's generated ufuncs)
# sf_error.check_fpe(func_name)
cdef np.PyUFuncGenericFunction trans_calculator_get_X_loop_funcs[1]
trans_calculator_get_X_loop_funcs[0] = trans_calculator_loop_D_Ciiiidddii_As_D_lllldddbl
cdef np.PyUFuncGenericFunction trans_calculator_get_AB_loop_funcs[1]
#trans_calculator_get_AB_loop_funcs[0] = trans_calculator_parallel_loop_E_C_DD_iiiidddii_As_lllldddbl_DD
trans_calculator_get_AB_loop_funcs[0] = trans_calculator_loop_E_C_DD_iiiidddii_As_lllldddbl_DD
cdef void *trans_calculator_get_AB_elementwise_funcs[1]
trans_calculator_get_AB_elementwise_funcs[0] = <void *>qpms_trans_calculator_get_AB_p_ext
'''
cdef extern from "numpy/ndarrayobject.h":
struct PyArrayInterface:
int itemsize
np.npy_uintp *shape
np.npy_uintp *strides
void *data
'''
from libc.stdlib cimport malloc, free, calloc, abort
cdef class trans_calculator:
cdef qpms_trans_calculator* c
cdef trans_calculator_get_X_data_t get_A_data[1]
cdef trans_calculator_get_X_data_t* get_A_data_p[1]
cdef trans_calculator_get_X_data_t get_B_data[1]
cdef trans_calculator_get_X_data_t* get_B_data_p[1]
cdef trans_calculator_get_X_data_t get_AB_data[1]
cdef trans_calculator_get_X_data_t* get_AB_data_p[1]
cdef public: # TODO CHECK FOR CORRECT REFERENCE COUNTING AND LEAKS
# have to be cdef public in order that __init__ can set these attributes
object get_A, get_B, get_AB
def __cinit__(self, int lMax, int normalization = 1):
if (lMax <= 0):
raise ValueError('lMax has to be greater than 0.')
self.c = qpms_trans_calculator_init(lMax, normalization)
if self.c is NULL:
raise MemoryError
def __init__(self, int lMax, int normalization = 1):
if self.c is NULL:
raise MemoryError()
self.get_A_data[0].c = self.c
self.get_A_data[0].cmethod = <void *>qpms_trans_calculator_get_A_ext
self.get_A_data_p[0] = &(self.get_A_data[0])
self.get_A = <object>np.PyUFunc_FromFuncAndData(# TODO CHECK FOR CORRECT REFERENCE COUNTING AND LEAKS
trans_calculator_get_X_loop_funcs, # func
<void **>self.get_A_data_p, #data
ufunc__get_either_trans_coeff_types, #types
1, # ntypes: number of supported input types
9, # nin: number of input args
1, # nout: number of output args
0, # identity element, unused
"get_A", #name
"""
TODO doc
""", # doc
0 # unused
)
self.get_B_data[0].c = self.c
self.get_B_data[0].cmethod = <void *>qpms_trans_calculator_get_B_ext
self.get_B_data_p[0] = &(self.get_B_data[0])
self.get_B = <object>np.PyUFunc_FromFuncAndData(# TODO CHECK FOR CORRECT REFERENCE COUNTING AND LEAKS
trans_calculator_get_X_loop_funcs, # func
<void **>self.get_B_data_p, #data
ufunc__get_either_trans_coeff_types, #types
1, # ntypes: number of supported input types
9, # nin: number of input args
1, # nout: number of output args
0, # identity element, unused
"get_B", #name
"""
TODO doc
""", # doc
0 # unused
)
self.get_AB_data[0].c = self.c
self.get_AB_data[0].cmethod = <void *>qpms_trans_calculator_get_AB_p_ext
self.get_AB_data_p[0] = &(self.get_AB_data[0])
self.get_AB = <object>np.PyUFunc_FromFuncAndData(# TODO CHECK FOR CORRECT REFERENCE COUNTING AND LEAKS
trans_calculator_get_AB_loop_funcs, # func
<void **>self.get_AB_data_p, #data
ufunc__get_both_coeff_types, #types
1, # ntypes: number of supported input types
9, # nin: number of input args
2, # nout: number of output args
0, # identity element, unused
"get_AB", #name
"""
TODO doc
""", # doc
0 # unused
)
def __dealloc__(self):
if self.c is not NULL:
qpms_trans_calculator_free(self.c)
# TODO Reference counts to get_A, get_B, get_AB?
def lMax(self):
return self.c[0].lMax
def nelem(self):
return self.c[0].nelem
def get_AB_arrays(self, r, theta, phi, r_ge_d, int J,
destaxis=None, srcaxis=None, expand=True):
"""
Returns arrays of translation coefficients, inserting two new nelem-sized axes
(corresponding to the destination and source axes of the translation matrix,
respectively).
By default (expand==True), it inserts the new axes. or it can be provided with
the resulting shape (with the corresponding axes dimensions equal to one).
The provided axes positions are for the resulting array.
If none axis positions are provided, destaxis and srcaxis will be the second-to-last
and last, respectively.
"""
# TODO CHECK (and try to cast) INPUT ARRAY TYPES (now is done)
# BIG FIXME: make skalars valid arguments, now r, theta, phi, r_ge_d have to be ndarrays
cdef:
int daxis, saxis, smallaxis, bigaxis, resnd, i, j, d, ax, errval
np.npy_intp sstride, dstride, longi
int *local_indices
char *r_p
char *theta_p
char *phi_p
char *r_ge_d_p
char *a_p
char *b_p
# Process the array shapes
baseshape = np.broadcast(r,theta,phi,r_ge_d).shape # nope, does not work as needed
'''
cdef int r_orignd = r.ndim if hasattr(r, "ndim") else 0
cdef int theta_orignd = theta.ndim if hasattr(theta, "ndim") else 0
cdef int phi_orignd = phi.ndim if hasattr(phi, "ndim") else 0
cdef int r_ge_d_orignd = r_ge_d.ndim if hasattr(r_ge_d, "__len__") else 0
cdef int basend = max(r_orignd, theta_orignd, phi_orignd, r_ge_d_orignd)
baseshape = list()
for d in range(basend):
baseshape.append(max(
r.shape[d+r_orignd-basend] if d+r_orignd-basend >= 0 else 1,
theta.shape[d+theta_orignd-basend] if d+theta_orignd-basend >= 0 else 1,
phi.shape[d+phi_orignd-basend] if d+phi_orignd-basend >= 0 else 1,
r_ge_d.shape[d+r_ge_d_orignd-basend] if d+r_ge_d_orignd-basend >= 0 else 1,
))
baseshape = tuple(baseshape)
'''
if not expand:
resnd = len(baseshape)
if resnd < 2:
raise ValueError('Translation matrix arrays must have at least 2 dimensions!')
daxis = (resnd-2) if destaxis is None else destaxis
saxis = (resnd-1) if srcaxis is None else srcaxis
if daxis < 0:
daxis = resnd + daxis
if saxis < 0:
saxis = resnd + saxis
if daxis < 0 or saxis < 0 or daxis >= resnd or saxis >= resnd or daxis == saxis:
raise ValueError('invalid axes provided (destaxis = %d, srcaxis = %d, # of axes: %d'
% (daxis, saxis, resnd))
if baseshape[daxis] != 1 or baseshape[saxis] != 1:
raise ValueError('dimension mismatch (input argument dimensions have to be 1 both at'
'destaxis (==%d) and srcaxis (==%d) but are %d and %d' %
(daxis, saxis, baseshape[daxis], baseshape[saxis]))
resultshape = list(baseshape)
else:
resnd = len(baseshape)+2
daxis = (resnd-2) if destaxis is None else destaxis
saxis = (resnd-1) if srcaxis is None else srcaxis
if daxis < 0:
daxis = resnd + daxis
if saxis < 0:
saxis = resnd + saxis
if daxis < 0 or saxis < 0 or daxis >= resnd or saxis >= resnd or daxis == saxis:
raise ValueError('invalid axes provided') # TODO better error formulation
resultshape = list(baseshape)
if daxis > saxis:
smallaxis = saxis
bigaxis = daxis
else:
smallaxis = daxis
bigaxis = saxis
resultshape.insert(smallaxis,1)
resultshape.insert(bigaxis,1)
r = np.expand_dims(np.expand_dims(r.astype(np.float_, copy=False), smallaxis), bigaxis)
theta = np.expand_dims(np.expand_dims(theta.astype(np.float_, copy=False), smallaxis), bigaxis)
phi = np.expand_dims(np.expand_dims(phi.astype(np.float_, copy=False), smallaxis), bigaxis)
r_ge_d = np.expand_dims(np.expand_dims(r_ge_d.astype(np.bool_, copy=False), smallaxis), bigaxis)
resultshape[daxis] = self.c[0].nelem
resultshape[saxis] = self.c[0].nelem
cdef np.ndarray r_c = np.broadcast_to(r,resultshape)
cdef np.ndarray theta_c = np.broadcast_to(theta,resultshape)
cdef np.ndarray phi_c = np.broadcast_to(phi,resultshape)
cdef np.ndarray r_ge_d_c = np.broadcast_to(r_ge_d, resultshape)
cdef np.ndarray a = np.empty(resultshape, dtype=complex)
cdef np.ndarray b = np.empty(resultshape, dtype=complex)
dstride = a.strides[daxis]
sstride = a.strides[saxis]
with nogil:
errval = qpms_cython_trans_calculator_get_AB_arrays_loop(
self.c, J, resnd,
daxis, saxis,
a.data, a.shape, a.strides,
b.data, b.shape, b.strides,
r_c.data, r_c.shape, r_c.strides,
theta_c.data, theta_c.shape, theta_c.strides,
phi_c.data, phi_c.shape, phi_c.strides,
r_ge_d_c.data, r_ge_d_c.shape, r_ge_d_c.strides
)
return a, b
# TODO make possible to access the attributes (to show normalization etc)
def complex_crep(complex c, parentheses = False, shortI = True, has_Imaginary = False):
'''
Return a C-code compatible string representation of a (python) complex number.
'''
return ( ('(' if parentheses else '')
+ repr(c.real)
+ ('+' if math.copysign(1, c.imag) >= 0 else '')
+ repr(c.imag)
+ ('*I' if shortI else '*_Imaginary_I' if has_Imaginary else '*_Complex_I')
+ (')' if parentheses else '')
)
cdef class basespec:
'''Cython wrapper over qpms_vswf_set_spec_t.
It should be kept immutable. The memory is managed by numpy/cython, not directly by the C functions, therefore
whenever used in other wrapper classes that need the pointer
to qpms_vswf_set_spec_t, remember to set a (private, probably immutable) reference to qpms.basespec to ensure
correct reference counting and garbage collection.
'''
cdef qpms_vswf_set_spec_t s
cdef np.ndarray __ilist
#cdef const qpms_uvswfi_t[:] __ilist
def __cinit__(self, *args, **kwargs):
cdef const qpms_uvswfi_t[:] ilist_memview
if len(args) > 0:
ilist = args[0]
#self.__ilist = np.array(args[0], dtype=qpms_uvswfi_t, order='C', copy=True) # FIXME define the dtypes at qpms_cdef.pxd level
self.__ilist = np.array(args[0], dtype=np.ulonglong, order='C', copy=True)
self.__ilist.setflags(write=False)
ilist_memview = self.__ilist
self.s.ilist = &ilist_memview[0]
self.s.n = len(self.__ilist)
self.s.capacity = 0 # is this the best way?
else:
raise ValueError
if 'norm' in kwargs.keys():
self.s.norm = kwargs['norm']
else:
self.s.norm = QPMS_NORMALISATION_POWER
# set the other metadata
cdef qpms_l_t l
cdef qpms_m_t m
cdef qpms_vswf_type_t t
for i in range(self.s.n):
if(qpms_uvswfi2tmn(ilist_memview[i], &t, &m, &l) != QPMS_SUCCESS):
raise ValueError("Invalid uvswf index")
if (t == QPMS_VSWF_ELECTRIC):
self.s.lMax_N = max(self.s.lMax_N, l)
elif (t == QPMS_VSWF_MAGNETIC):
self.s.lMax_M = max(self.s.lMax_M, l)
elif (t == QPMS_VSWF_LONGITUDINAL):
self.s.lMax.L = max(self.s.lMax_L, l)
else:
raise ValueError # If this happens, it's probably a bug, as it should have failed already at qpms_uvswfi2tmn
self.s.lMax = max(self.s.lMax, l)
def tlm(self):
cdef const qpms_uvswfi_t[:] ilist_memview = <qpms_uvswfi_t[:self.s.n]> self.s.ilist
#cdef qpms_vswf_type_t[:] t = np.empty(shape=(self.s.n,), dtype=qpms_vswf_type_t) # does not work, workaround:
cdef size_t i
cdef np.ndarray ta = np.empty(shape=(self.s.n,), dtype=np.intc)
cdef int[:] t = ta
#cdef qpms_l_t[:] l = np.empty(shape=(self.s.n,), dtype=qpms_l_t) # FIXME explicit dtype again
cdef np.ndarray la = np.empty(shape=(self.s.n,), dtype=np.intc)
cdef qpms_l_t[:] l = la
#cdef qpms_m_t[:] m = np.empty(shape=(self.s.n,), dtype=qpms_m_t) # FIXME explicit dtype again
cdef np.ndarray ma = np.empty(shape=(self.s.n,), dtype=np.intc)
cdef qpms_m_t[:] m = ma
for i in range(self.s.n):
qpms_uvswfi2tmn(self.s.ilist[i], <qpms_vswf_type_t*>&t[i], &m[i], &l[i])
return (ta, la, ma)
def m(self): # ugly
return self.tlm()[2]
def t(self): # ugly
return self.tlm()[0]
def l(self): # ugly
return self.tlm()[1]
def __len__(self):
return self.s.n
def __getitem__(self, key):
# TODO raise correct errors (TypeError on bad type of key, IndexError on exceeding index)
return self.__ilist[key]
property ilist:
def __get__(self):
return self.__ilist
cdef qpms_vswf_set_spec_t *rawpointer(basespec self):
'''Pointer to the qpms_vswf_set_spec_t structure.
Don't forget to reference the basespec object itself when storing the pointer anywhere!!!
'''
return &(self.s)
property rawpointer:
def __get__(self):
return <uintptr_t> &(self.s)
# Quaternions from wigner.h
# (mainly for testing; use moble's quaternions in python)
cdef class cquat:
'''
Wrapper of the qpms_quat_t object, with the functionality
to evaluate Wigner D-matrix elements.
'''
cdef readonly qpms_quat_t q
def __cinit__(self, double w, double x, double y, double z):
cdef qpms_quat4d_t p
p.c1 = w
p.ci = x
p.cj = y
p.ck = z
self.q = qpms_quat_2c_from_4d(p)
def copy(self):
res = cquat(0,0,0,0)
res.q = self.q
return res
def __repr__(self): # TODO make this look like a quaternion with i,j,k
return repr(self.r)
def __add__(cquat self, cquat other):
# TODO add real numbers
res = cquat(0,0,0,0)
res.q = qpms_quat_add(self.q, other.q)
return res
def __mul__(self, other):
res = cquat(0,0,0,0)
if isinstance(self, cquat):
if isinstance(other, cquat):
res.q = qpms_quat_mult(self.q, other.q)
elif isinstance(other, (int, float)):
res.q = qpms_quat_rscale(other, self.q)
else: return NotImplemented
elif isinstance(self, (int, float)):
if isinstance(other, cquat):
res.q = qpms_quat_rscale(self, other.q)
else: return NotImplemented
return res
def __neg__(cquat self):
res = cquat(0,0,0,0)
res.q = qpms_quat_rscale(-1, self.q)
return res
def __sub__(cquat self, cquat other):
res = cquat(0,0,0,0)
res.q = qpms_quat_add(self.q, qpms_quat_rscale(-1,other.q))
return res
def __abs__(self):
return qpms_quat_norm(self.q)
def norm(self):
return qpms_quat_norm(self.q)
def imnorm(self):
return qpms_quat_imnorm(self.q)
def exp(self):
res = cquat(0,0,0,0)
res.q = qpms_quat_exp(self.q)
return res
def log(self):
res = cquat(0,0,0,0)
res.q = qpms_quat_exp(self.q)
return res
def __pow__(cquat self, double other, _):
res = cquat(0,0,0,0)
res.q = qpms_quat_pow(self.q, other)
return res
def normalise(self):
res = cquat(0,0,0,0)
res.q = qpms_quat_normalise(self.q)
return res
def isclose(cquat self, cquat other, rtol=1e-5, atol=1e-8):
'''
Checks whether two quaternions are "almost equal".
'''
return abs(self - other) <= (atol + rtol * abs(other))
property c:
'''
Quaternion representation as two complex numbers
'''
def __get__(self):
return (self.q.a, self.q.b)
def __set__(self, RaRb):
self.q.a = RaRb[0]
self.q.b = RaRb[1]
property r:
'''
Quaternion representation as four real numbers
'''
def __get__(self):
cdef qpms_quat4d_t p
p = qpms_quat_4d_from_2c(self.q)
return (p.c1, p.ci, p.cj, p.ck)
def __set__(self, wxyz):
cdef qpms_quat4d_t p
p.c1 = wxyz[0]
p.ci = wxyz[1]
p.cj = wxyz[2]
p.ck = wxyz[3]
self.q = qpms_quat_2c_from_4d(p)
def crepr(self):
'''
Returns a string that can be used in C code to initialise a qpms_irot3_t
'''
return '{' + complex_crep(self.q.a) + ', ' + complex_crep(self.q.b) + '}'
def wignerDelem(self, qpms_l_t l, qpms_m_t mp, qpms_m_t m):
'''
Returns an element of a bosonic Wigner matrix.
'''
# don't crash on bad l, m here
if (abs(m) > l or abs(mp) > l):
return 0
return qpms_wignerD_elem(self.q, l, mp, m)
cdef class irot3:
'''
Wrapper over the C type qpms_irot3_t.
'''
cdef readonly qpms_irot3_t qd
def __cinit__(self, *args):
'''
TODO doc
'''
# TODO implement a constructor with
# - tuple as argument ...?
if (len(args) == 0): # no args, return identity
self.qd.rot.a = 1
self.qd.rot.b = 0
self.qd.det = 1
elif (len(args) == 2 and isinstance(args[0], cquat) and isinstance(args[1], (int, float))):
# The original __cinit__(self, cquat q, short det) constructor
q = args[0]
det = args[1]
if (det != 1 and det != -1):
raise ValueError("Improper rotation determinant has to be 1 or -1")
self.qd.rot = q.normalise().q
self.qd.det = det
elif (len(args) == 1 and isinstance(args[0], irot3)):
# Copy
self.qd = args[0].qd
elif (len(args) == 1 and isinstance(args[0], cquat)):
# proper rotation from a quaternion
q = args[0]
det = 1
self.qd.rot = q.normalise().q
self.qd.det = det
else:
raise ValueError('Unsupported constructor arguments')
def copy(self):
res = irot3(cquat(1,0,0,0),1)
res.qd = self.qd
return res
property rot:
'''
The proper rotation part of the irot3 type.
'''
def __get__(self):
res = cquat(0,0,0,0)
res.q = self.qd.rot
return res
def __set__(self, cquat r):
# TODO check for non-zeroness and throw an exception if norm is zero
self.qd.rot = r.normalise().q
property det:
'''
The determinant of the improper rotation.
'''
def __get__(self):
return self.qd.det
def __set__(self, d):
d = int(d)
if (d != 1 and d != -1):
raise ValueError("Improper rotation determinant has to be 1 or -1")
self.qd.det = d
def __repr__(self): # TODO make this look like a quaternion with i,j,k
return '(' + repr(self.rot) + ', ' + repr(self.det) + ')'
def crepr(self):
'''
Returns a string that can be used in C code to initialise a qpms_irot3_t
'''
return '{' + self.rot.crepr() + ', ' + repr(self.det) + '}'
def __mul__(irot3 self, irot3 other):
res = irot3(cquat(1,0,0,0), 1)
res.qd = qpms_irot3_mult(self.qd, other.qd)
return res
def __pow__(irot3 self, n, _):
cdef int nint
if (n % 1 == 0):
nint = n
else:
raise ValueError("The exponent of an irot3 has to have an integer value.")
res = irot3(cquat(1,0,0,0), 1)
res.qd = qpms_irot3_pow(self.qd, n)
return res
def isclose(irot3 self, irot3 other, rtol=1e-5, atol=1e-8):
'''
Checks whether two (improper) rotations are "almost equal".
Returns always False if the determinants are different.
'''
if self.det != other.det:
return False
return (self.rot.isclose(other.rot, rtol=rtol, atol=atol)
# unit quaternions are a double cover of SO(3), i.e.
# minus the same quaternion represents the same rotation
or self.rot.isclose(-(other.rot), rtol=rtol, atol=atol)
)
# Several 'named constructors' for convenience
@staticmethod
def inversion():
'''
Returns an irot3 object representing the 3D spatial inversion.
'''
r = irot3()
r.det = -1
return r
@staticmethod
def zflip():
'''
Returns an irot3 object representing the 3D xy-plane mirror symmetry (z axis sign flip).
'''
r = irot3()
r.rot = cquat(0,0,0,1) # π-rotation around z-axis
r.det = -1 # inversion
return r
@staticmethod
def yflip():
'''
Returns an irot3 object representing the 3D xz-plane mirror symmetry (y axis sign flip).
'''
r = irot3()
r.rot = cquat(0,0,1,0) # π-rotation around y-axis
r.det = -1 # inversion
return r
@staticmethod
def xflip():
'''
Returns an irot3 object representing the 3D yz-plane mirror symmetry (x axis sign flip).
'''
r = irot3()
r.rot = cquat(0,1,0,0) # π-rotation around x-axis
r.det = -1 # inversion
return r
@staticmethod
def zrotN(int n):
'''
Returns an irot3 object representing a \f$ C_n $\f rotation (around the z-axis).
'''
r = irot3()
r.rot = cquat(math.cos(math.pi/n),0,0,math.sin(math.pi/n))
return r
def as_uvswf_matrix(irot3 self, basespec bspec):
'''
Returns the uvswf representation of the current transform as a numpy array
'''
cdef ssize_t sz = len(bspec)
cdef np.ndarray m = np.empty((sz, sz), dtype=complex, order='C') # FIXME explicit dtype
cdef cdouble[:, ::1] view = m
qpms_irot3_uvswfi_dense(&view[0,0], bspec.rawpointer(), self.qd)
return m
def tlm2uvswfi(t, l, m):
''' TODO doc
'''
# Very low-priority TODO: add some types / cythonize
if isinstance(t, int) and isinstance(l, int) and isinstance(m, int):
return qpms_tmn2uvswfi(t, m, l)
elif len(t) == len(l) and len(t) == len(m):
u = list()
for i in range(len(t)):
if not (isinstance(t[i], int) and isinstance(l[i], int) and isinstance(m[i], int)): # not the best check possible, though
raise ValueError # TODO error message
u.append(qpms_tmn2uvswfi(t[i],m[i],l[i]))
return u
else:
raise ValueError # TODO error message
def uvswfi2tlm(u):
''' TODO doc
'''
cdef qpms_vswf_type_t t
cdef qpms_l_t l
cdef qpms_m_t m
cdef size_t i
if isinstance(u, (int, np.ulonglong)):
if (qpms_uvswfi2tmn(u, &t, &m, &l) != QPMS_SUCCESS):
raise ValueError("Invalid uvswf index")
return (t, l, m)
else:
ta = list()
la = list()
ma = list()
for i in range(len(u)):
if (qpms_uvswfi2tmn(u[i], &t, &m, &l) != QPMS_SUCCESS):
raise ValueError("Invalid uvswf index")
ta.append(t)
la.append(l)
ma.append(m)
return (ta, la, ma)
Reference in New Issue View Git Blame Copy Permalink