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qpms/qpms/qpms_c.pyx

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# Cythonized parts of QPMS here
# -----------------------------
import numpy as np
import cmath
from qpms_cdefs cimport *
cimport cython
from cython.parallel cimport parallel, prange
import enum
import warnings
# Here will be enum and dtype definitions; maybe move these to a separate file
class VSWFType(enum.IntEnum):
ELECTRIC = QPMS_VSWF_ELECTRIC
MAGNETIC = QPMS_VSWF_MAGNETIC
LONGITUDINAL = QPMS_VSWF_LONGITUDINAL
M = QPMS_VSWF_MAGNETIC
N = QPMS_VSWF_ELECTRIC
L = QPMS_VSWF_LONGITUDINAL
class VSWFNorm(enum.IntEnum):
#XU = QPMS_NORMALISATION_XU
#XU_CS = QPMS_NORMALISATION_XU_CS
NONE = QPMS_NORMALISATION_NONE
NONE_CS = QPMS_NORMALISATION_NONE_CS
POWER = QPMS_NORMALISATION_POWER
POWER_CS = QPMS_NORMALISATION_POWER_CS
SPHARM = QPMS_NORMALISATION_SPHARM
SPHARM_CS = QPMS_NORMALISATION_SPHARM_CS
UNDEF = QPMS_NORMALISATION_UNDEF
KRISTENSSON = QPMS_NORMALISATION_KRISTENSSON
KRISTENSSON_CS = QPMS_NORMALISATION_KRISTENSSON_CS
TAYLOR = QPMS_NORMALISATION_TAYLOR
TAYLOR_CS = QPMS_NORMALISATION_TAYLOR_CS
try:
class DebugFlags(enum.IntFlag): # Should be IntFlag if python version >= 3.6
MISC = QPMS_DBGMSG_MISC
THREADS = QPMS_DBGMSG_THREADS
has_IntFlag = True
except AttributeError: # For old versions of enum, use IntEnum instead
class DebugFlags(enum.IntEnum):
MISC = QPMS_DBGMSG_MISC
THREADS = QPMS_DBGMSG_THREADS
has_IntFlag = False
def dbgmsg_enable(qpms_dbgmsg_flags types):
flags = qpms_dbgmsg_enable(types)
return DebugFlags(flags) if has_IntFlag else flags
def dbgmsg_disable(qpms_dbgmsg_flags types):
flags = qpms_dbgmsg_disable(types)
return DebugFlags(flags) if has_IntFlag else flags
def dbgmsg_active():
flags = qpms_dbgmsg_enable(<qpms_dbgmsg_flags>0)
return DebugFlags(flags) if has_IntFlag else flags
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:
if 'lMax' in kwargs.keys(): # if only lMax is specified, create the 'usual' definition in ('E','M') order
lMax = kwargs['lMax']
my, ny = get_mn_y(lMax)
nelem = len(my)
tlist = nelem * (QPMS_VSWF_ELECTRIC,) + nelem * (QPMS_VSWF_MAGNETIC,)
mlist = 2*list(my)
llist = 2*list(ny)
ilist = tlm2uvswfi(tlist,llist,mlist)
else:
raise ValueError
else: # 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(ilist, 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?
if 'norm' in kwargs.keys():
self.s.norm = kwargs['norm']
else:
self.s.norm = QPMS_NORMALISATION_POWER_CS
# set the other metadata
cdef qpms_l_t l
self.s.lMax_L = -1
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
@staticmethod
def identity():
'''
An alias for the constructor without arguments; returns identity.
'''
return IRot3()
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
cdef class MaterialInterpolator:
'''
Wrapper over the qpms_permittivity_interpolator_t structure.
'''
cdef qpms_permittivity_interpolator_t *interp
cdef readonly double omegamin
cdef readonly double omegamax
def __cinit__(self, filename, *args, **kwargs):
'''Creates a permittivity interpolator.'''
cdef char *cpath = make_c_string(filename)
self.interp = qpms_permittivity_interpolator_from_yml(cpath, gsl_interp_cspline)
if not self.interp:
raise IOError("Could not load permittivity data from %s" % filename)
self.omegamin = qpms_permittivity_interpolator_omega_min(self.interp)
self.omegamax = qpms_permittivity_interpolator_omega_max(self.interp)
def __dealloc__(self):
qpms_permittivity_interpolator_free(self.interp)
def __call__(self, double freq):
'''Returns interpolated permittivity, corresponding to a given angular frequency.'''
if freq < self.omegamin or freq > self.omegamax:
raise ValueError("Input frequency %g is outside the interpolator domain (%g, %g)."
% (freq, self.minomega, self.freqs[self.maxomega]))
return qpms_permittivity_interpolator_eps_at_omega(self.interp, freq)
property freq_interval:
def __get__(self):
return [self.omegamin, self.omegamax]
cdef class TMatrixInterpolator:
'''
Wrapper over the qpms_tmatrix_interpolator_t structure.
'''
#cdef readonly np.ndarray m # Numpy array holding the matrix data
cdef readonly BaseSpec spec # Here we hold the base spec for the correct reference counting; TODO check if it gets copied
cdef qpms_tmatrix_t *tmatrices_array
cdef cdouble *tmdata
cdef double *freqs
cdef double *freqs_su
cdef size_t nfreqs
cdef qpms_tmatrix_interpolator_t *interp
def __cinit__(self, filename, BaseSpec bspec, *args, **kwargs):
'''Creates a T-matrix interpolator object from a scuff-tmatrix output'''
self.spec = bspec
cdef char * cpath = make_c_string(filename)
if QPMS_SUCCESS != qpms_load_scuff_tmatrix(cpath, self.spec.rawpointer(),
&(self.nfreqs), &(self.freqs), &(self.freqs_su),
&(self.tmatrices_array), &(self.tmdata)):
raise IOError("Could not read T-matrix from %s" % filename)
if 'symmetrise' in kwargs:
sym = kwargs['symmetrise']
if isinstance(sym, FinitePointGroup):
if QPMS_SUCCESS != qpms_symmetrise_tmdata_finite_group(
self.tmdata, self.nfreqs, self.spec.rawpointer(),
(<FinitePointGroup?>sym).rawpointer()):
raise Exception("This should not happen.")
atol = kwargs['atol'] if 'atol' in kwargs else 1e-16
qpms_czero_roundoff_clean(self.tmdata, self.nfreqs * len(bspec)**2, atol)
else:
warnings.warn('symmetrise argument type not supported; ignoring.')
self.interp = qpms_tmatrix_interpolator_create(self.nfreqs,
self.freqs, self.tmatrices_array, gsl_interp_cspline)
if not self.interp: raise Exception("Unexpected NULL at interpolator creation.")
def __call__(self, double freq):
'''Returns a TMatrix instance, corresponding to a given frequency.'''
if freq < self.freqs[0] or freq > self.freqs[self.nfreqs-1]:# FIXME here I assume that the input is already sorted
raise ValueError("input frequency %g is outside the interpolator domain (%g, %g)"
% (freq, self.freqs[0], self.freqs[self.nfreqs-1]))
# This is a bit stupid, I should rethink the CTMatrix constuctors
cdef qpms_tmatrix_t *t = qpms_tmatrix_interpolator_eval(self.interp, freq)
cdef CTMatrix res = CTMatrix(self.spec, <cdouble[:len(self.spec),:len(self.spec)]>(t[0].m))
qpms_tmatrix_free(t)
return res
def __dealloc__(self):
qpms_tmatrix_interpolator_free(self.interp)
free(self.tmatrices_array)
free(self.tmdata)
free(self.freqs_su)
free(self.freqs)
property freq_interval:
def __get__(self):
return [self.freqs[0], self.freqs[self.nfreqs-1]]
cdef class CTMatrix: # N.B. there is another type called TMatrix in tmatrices.py!
'''
Wrapper over the C qpms_tmatrix_t stucture.
'''
cdef readonly np.ndarray m # Numpy array holding the matrix data
cdef readonly BaseSpec spec # Here we hold the base spec for the correct reference counting; TODO check if it gets copied
cdef qpms_tmatrix_t t
def __cinit__(CTMatrix self, BaseSpec spec, matrix):
self.spec = spec
self.t.spec = self.spec.rawpointer();
if matrix is None or matrix == 0:
self.m = np.zeros((len(spec),len(spec)), dtype=complex, order='C')
else:
# The following will raise an exception if shape is wrong
self.m = np.array(matrix, dtype=complex, copy=True, order='C').reshape((len(spec), len(spec)))
#self.m.setflags(write=False) # checkme
cdef cdouble[:,:] m_memview = self.m
self.t.m = &(m_memview[0,0])
self.t.owns_m = False # Memory in self.t.m is "owned" by self.m, not by self.t...
cdef qpms_tmatrix_t *rawpointer(CTMatrix self):
'''Pointer to the qpms_tmatrix_t structure.
Don't forget to reference the BaseSpec object itself when storing the pointer anywhere!!!
'''
return &(self.t)
property rawpointer:
def __get__(self):
return <uintptr_t> &(self.t)
# Transparent access to the T-matrix elements.
def __getitem__(self, key):
return self.m[key]
def __setitem__(self, key, value):
self.m[key] = value
def as_ndarray(CTMatrix self):
''' Returns a copy of the T-matrix as a numpy array.'''
# Maybe not totally needed after all, as np.array(T[...]) should be equivalent and not longer
return np.array(self.m, copy=True)
def spherical_fill(CTMatrix self, double radius, cdouble k_int,
cdouble k_ext, cdouble mu_int = 1, cdouble mu_ext = 1):
''' Replaces the contents of the T-matrix with those of a spherical particle.'''
qpms_tmatrix_spherical_fill(&self.t, radius, k_int, k_ext, mu_int, mu_ext)
def spherical_perm_fill(CTMatrix self, double radius, double freq, cdouble epsilon_int,
cdouble epsilon_ext):
'''Replaces the contenst of the T-matrix with those of a spherical particle.'''
qpms_tmatrix_spherical_mu0_fill(&self.t, radius, freq, epsilon_int, epsilon_ext)
@staticmethod
def spherical(BaseSpec spec, double radius, cdouble k_int, cdouble k_ext,
cdouble mu_int = 1, cdouble mu_ext = 1):
''' Creates a T-matrix of a spherical nanoparticle. '''
tm = CTMatrix(spec, 0)
tm.spherical_fill(radius, k_int, k_ext, mu_int, mu_ext)
return tm
@staticmethod
def spherical_perm(BaseSpec spec, double radius, double freq, cdouble epsilon_int, cdouble epsilon_ext):
'''Creates a T-matrix of a spherical nanoparticle.'''
tm = CTMatrix(spec, 0)
tm.spherical_perm_fill(radius, freq, epsilon_int, epsilon_ext)
return tm
cdef char *make_c_string(pythonstring):
'''
Copies contents of a python string into a char[]
(allocating the memory with malloc())
'''
bytestring = pythonstring.encode('UTF-8')
cdef Py_ssize_t n = len(bytestring)
cdef Py_ssize_t i
cdef char *s
s = <char *>malloc(n+1)
if not s:
raise MemoryError
#s[:n] = bytestring # This segfaults; why?
for i in range(n): s[i] = bytestring[i]
s[n] = <char>0
return s
def string_c2py(const char* cstring):
return cstring.decode('UTF-8')
cdef class FinitePointGroup:
'''
Wrapper over the qpms_finite_group_t structure.
TODO more functionality to make it better usable in Python
(group element class at least)
'''
cdef readonly bint owns_data
cdef qpms_finite_group_t *G
def __cinit__(self, info):
'''Constructs a FinitePointGroup from PointGroupInfo'''
# TODO maybe I might use a try..finally statement to avoid leaks
# First, generate all basic data from info
permlist = info.deterministic_elemlist()
cdef int order = len(permlist)
permindices = {perm: i for i, perm in enumerate(permlist)} # 'invert' permlist
identity = info.permgroup.identity
# We use calloc to avoid calling free to unitialized pointers
self.G = <qpms_finite_group_t *>calloc(1,sizeof(qpms_finite_group_t))
if not self.G: raise MemoryError
self.G[0].name = make_c_string(info.name)
self.G[0].order = order
self.G[0].idi = permindices[identity]
self.G[0].mt = <qpms_gmi_t *>malloc(sizeof(qpms_gmi_t) * order * order)
if not self.G[0].mt: raise MemoryError
for i in range(order):
for j in range(order):
self.G[0].mt[i*order + j] = permindices[permlist[i] * permlist[j]]
self.G[0].invi = <qpms_gmi_t *>malloc(sizeof(qpms_gmi_t) * order)
if not self.G[0].invi: raise MemoryError
for i in range(order):
self.G[0].invi[i] = permindices[permlist[i]**-1]
self.G[0].ngens = len(info.permgroupgens)
self.G[0].gens = <qpms_gmi_t *>malloc(sizeof(qpms_gmi_t) * self.G[0].ngens)
if not self.G[0].gens: raise MemoryError
for i in range(self.G[0].ngens):
self.G[0].gens[i] = permindices[info.permgroupgens[i]]
self.G[0].permrep = <char **>calloc(order, sizeof(char *))
if not self.G[0].permrep: raise MemoryError
for i in range(order):
self.G[0].permrep[i] = make_c_string(str(permlist[i]))
if not self.G[0].permrep[i]: raise MemoryError
self.G[0].permrep_nelem = info.permgroup.degree
if info.rep3d is not None:
self.G[0].rep3d = <qpms_irot3_t *>malloc(order * sizeof(qpms_irot3_t))
for i in range(order):
self.G[0].rep3d[i] = info.rep3d[permlist[i]].qd
self.G[0].nirreps = len(info.irreps)
self.G[0].irreps = <qpms_finite_group_irrep_t *>calloc(self.G[0].nirreps, sizeof(qpms_finite_group_irrep_t))
if not self.G[0].irreps: raise MemoryError
cdef int dim
for iri, irname in enumerate(sorted(info.irreps.keys())):
irrep = info.irreps[irname]
is1d = isinstance(irrep[identity], (int, float, complex))
dim = 1 if is1d else irrep[identity].shape[0]
self.G[0].irreps[iri].dim = dim
self.G[0].irreps[iri].name = <char *>make_c_string(irname)
if not self.G[0].irreps[iri].name: raise MemoryError
self.G[0].irreps[iri].m = <cdouble *>malloc(dim*dim*sizeof(cdouble)*order)
if not self.G[0].irreps[iri].m: raise MemoryError
if is1d:
for i in range(order):
self.G[0].irreps[iri].m[i] = irrep[permlist[i]]
else:
for i in range(order):
for row in range(dim):
for col in range(dim):
self.G[0].irreps[iri].m[i*dim*dim + row*dim + col] = irrep[permlist[i]][row,col]
self.G[0].elemlabels = <char **> 0 # Elem labels not yet implemented
self.owns_data = True
def __dealloc__(self):
cdef qpms_gmi_t order
if self.owns_data:
if self.G:
order = self.G[0].order
free(self.G[0].name)
free(self.G[0].mt)
free(self.G[0].invi)
free(self.G[0].gens)
if self.G[0].permrep:
for i in range(order): free(self.G[0].permrep[i])
free(self.G[0].permrep)
if self.G[0].elemlabels: # this is not even contructed right now
for i in range(order): free(self.G[0].elemlabels[i])
if self.G[0].irreps:
for iri in range(self.G[0].nirreps):
free(self.G[0].irreps[iri].name)
free(self.G[0].irreps[iri].m)
free(self.G[0].irreps)
free(self.G)
self.G = <qpms_finite_group_t *>0
self.owns_data = False
cdef qpms_finite_group_t *rawpointer(self):
return self.G
cdef class FinitePointGroupElement:
'''TODO'''
cdef readonly FinitePointGroup G
cdef readonly qpms_gmi_t gmi
def __cinit__(self, FinitePointGroup G, qpms_gmi_t gmi):
self.G = G
self.gmi = gmi
cdef class Particle:
'''
Wrapper over the qpms_particle_t structure.
'''
cdef qpms_particle_t p
cdef readonly CTMatrix t # We hold the reference to the T-matrix to ensure correct reference counting
def __cinit__(Particle self, pos, CTMatrix t):
if(len(pos)>=2 and len(pos) < 4):
self.p.pos.x = pos[0]
self.p.pos.y = pos[1]
self.p.pos.z = pos[2] if len(pos)==3 else 0
else:
raise ValueError("Position argument has to contain 3 or 2 cartesian coordinates")
self.t = t
self.p.tmatrix = self.t.rawpointer()
cdef qpms_particle_t *rawpointer(Particle self):
'''Pointer to the qpms_particle_p structure.
'''
return &(self.p)
property rawpointer:
def __get__(self):
return <uintptr_t> &(self.p)
cdef qpms_particle_t cval(Particle self):
'''Provides a copy for assigning in cython code'''
return self.p
property x:
def __get__(self):
return self.p.pos.x
def __set__(self,x):
self.p.pos.x = x
property y:
def __get__(self):
return self.p.pos.y
def __set__(self,y):
self.p.pos.y = y
property z:
def __get__(self):
return self.p.pos.z
def __set__(self,z):
self.p.pos.z = z
property pos:
def __get__(self):
return (self.p.pos.x, self.p.pos.y, self.p.pos.z)
def __set__(self, pos):
if(len(pos)>=2 and len(pos) < 4):
self.p.pos.x = pos[0]
self.p.pos.y = pos[1]
self.p.pos.z = pos[2] if len(pos)==3 else 0
else:
raise ValueError("Position argument has to contain 3 or 2 cartesian coordinates")
cpdef void scatsystem_set_nthreads(long n):
qpms_scatsystem_set_nthreads(n)
return
cdef class ScatteringSystem:
'''
Wrapper over the C qpms_scatsys_t structure.
'''
cdef list basespecs # Here we keep the references to occuring basespecs
#cdef list Tmatrices # Here we keep the references to occuring T-matrices
cdef qpms_scatsys_t *s
def __cinit__(self, particles, FinitePointGroup sym):
'''TODO doc.
Takes the particles (which have to be a sequence of instances of Particle),
fills them together with their t-matrices to the "proto-qpms_scatsys_t"
orig and calls qpms_scatsys_apply_symmetry
(and then cleans orig)
'''
cdef qpms_scatsys_t orig # This should be automatically init'd to 0 (CHECKME)
cdef qpms_ss_pi_t p_count = len(particles)
cdef qpms_ss_tmi_t tm_count = 0
tmindices = dict()
tmobjs = list()
self.basespecs=list()
for p in particles: # find and enumerate unique t-matrices
if id(p.t) not in tmindices:
tmindices[id(p.t)] = tm_count
tmobjs.append(p.t)
tm_count += 1
orig.tm_count = tm_count
orig.p_count = p_count
for tm in tmobjs: # create references to BaseSpec objects
self.basespecs.append(tm.spec)
try:
orig.tm = <qpms_tmatrix_t **>malloc(orig.tm_count * sizeof(orig.tm[0]))
if not orig.tm: raise MemoryError
orig.p = <qpms_particle_tid_t *>malloc(orig.p_count * sizeof(orig.p[0]))
if not orig.p: raise MemoryError
for tmi in range(tm_count):
orig.tm[tmi] = (<CTMatrix?>(tmobjs[tmi])).rawpointer()
for pi in range(p_count):
orig.p[pi].pos = (<Particle?>(particles[pi])).cval().pos
orig.p[pi].tmatrix_id = tmindices[id(particles[pi].t)]
self.s = qpms_scatsys_apply_symmetry(&orig, sym.rawpointer())
finally:
free(orig.tm)
free(orig.p)
def __dealloc__(self):
qpms_scatsys_free(self.s)
def particles_tmi(self):
r = list()
cdef qpms_ss_pi_t pi
for pi in range(self.s[0].p_count):
r.append(self.s[0].p[pi])
return r
property fecv_size:
def __get__(self): return self.s[0].fecv_size
property saecv_sizes:
def __get__(self):
return [self.s[0].saecv_sizes[i]
for i in range(self.s[0].sym[0].nirreps)]
property irrep_names:
def __get__(self):
return [string_c2py(self.s[0].sym[0].irreps[iri].name)
if (self.s[0].sym[0].irreps[iri].name) else None
for iri in range(self.s[0].sym[0].nirreps)]
property nirreps:
def __get__(self): return self.s[0].sym[0].nirreps
def pack_vector(self, vect, iri):
if len(vect) != self.fecv_size:
raise ValueError("Length of a full vector has to be %d, not %d"
% (self.fecv_size, len(vect)))
vect = np.array(vect, dtype=complex, copy=False, order='C')
cdef cdouble[::1] vect_view = vect;
cdef np.ndarray[np.complex_t, ndim=1] target_np = np.empty(
(self.saecv_sizes[iri],), dtype=complex, order='C')
cdef cdouble[::1] target_view = target_np
qpms_scatsys_irrep_pack_vector(&target_view[0], &vect_view[0], self.s, iri)
return target_np
def unpack_vector(self, packed, iri):
if len(packed) != self.saecv_sizes[iri]:
raise ValueError("Length of %d. irrep-packed vector has to be %d, not %d"
% (iri, self.saecv_sizes, len(packed)))
packed = np.array(packed, dtype=complex, copy=False, order='C')
cdef cdouble[::1] packed_view = packed
cdef np.ndarray[np.complex_t, ndim=1] target_np = np.empty(
(self.fecv_size,), dtype=complex)
cdef cdouble[::1] target_view = target_np
qpms_scatsys_irrep_unpack_vector(&target_view[0], &packed_view[0],
self.s, iri, 0)
return target_np
def pack_matrix(self, fullmatrix, iri):
cdef size_t flen = self.s[0].fecv_size
cdef size_t rlen = self.saecv_sizes[iri]
fullmatrix = np.array(fullmatrix, dtype=complex, copy=False, order='C')
if fullmatrix.shape != (flen, flen):
raise ValueError("Full matrix shape should be (%d,%d), is %s."
% (flen, flen, repr(fullmatrix.shape)))
cdef cdouble[:,::1] fullmatrix_view = fullmatrix
cdef np.ndarray[np.complex_t, ndim=2] target_np = np.empty(
(rlen, rlen), dtype=complex, order='C')
cdef cdouble[:,::1] target_view = target_np
qpms_scatsys_irrep_pack_matrix(&target_view[0][0], &fullmatrix_view[0][0],
self.s, iri)
return target_np
def unpack_matrix(self, packedmatrix, iri):
cdef size_t flen = self.s[0].fecv_size
cdef size_t rlen = self.saecv_sizes[iri]
packedmatrix = np.array(packedmatrix, dtype=complex, copy=False, order='C')
if packedmatrix.shape != (rlen, rlen):
raise ValueError("Packed matrix shape should be (%d,%d), is %s."
% (rlen, rlen, repr(packedmatrix.shape)))
cdef cdouble[:,::1] packedmatrix_view = packedmatrix
cdef np.ndarray[np.complex_t, ndim=2] target_np = np.empty(
(flen, flen), dtype=complex, order='C')
cdef cdouble[:,::1] target_view = target_np
qpms_scatsys_irrep_unpack_matrix(&target_view[0][0], &packedmatrix_view[0][0],
self.s, iri, 0)
return target_np
def modeproblem_matrix_full(self, double k):
cdef size_t flen = self.s[0].fecv_size
cdef np.ndarray[np.complex_t, ndim=2] target = np.empty(
(flen,flen),dtype=complex, order='C')
cdef cdouble[:,::1] target_view = target
qpms_scatsys_build_modeproblem_matrix_full(&target_view[0][0], self.s, k)
return target
def modeproblem_matrix_packed(self, double k, qpms_iri_t iri, version='pR'):
cdef size_t rlen = self.saecv_sizes[iri]
cdef np.ndarray[np.complex_t, ndim=2] target = np.empty(
(rlen,rlen),dtype=complex, order='C')
cdef cdouble[:,::1] target_view = target
if (version == 'R'):
qpms_scatsys_build_modeproblem_matrix_irrep_packed_orbitorderR(&target_view[0][0], self.s, iri, k)
elif (version == 'pR'):
with nogil:
qpms_scatsys_build_modeproblem_matrix_irrep_packed_parallelR(&target_view[0][0], self.s, iri, k)
else:
qpms_scatsys_build_modeproblem_matrix_irrep_packed(&target_view[0][0], self.s, iri, k)
return target
def translation_matrix_full(self, double k):
cdef size_t flen = self.s[0].fecv_size
cdef np.ndarray[np.complex_t, ndim=2] target = np.empty(
(flen,flen),dtype=complex, order='C')
cdef cdouble[:,::1] target_view = target
qpms_scatsys_build_translation_matrix_full(&target_view[0][0], self.s, k)
return target
def fullvec_psizes(self):
cdef np.ndarray[int32_t, ndim=1] ar = np.empty((self.s[0].p_count,), dtype=np.int32)
cdef int32_t[::1] ar_view = ar
for pi in range(self.s[0].p_count):
ar_view[pi] = self.s[0].tm[self.s[0].p[pi].tmatrix_id].spec[0].n
return ar
def fullvec_poffsets(self):
cdef np.ndarray[intptr_t, ndim=1] ar = np.empty((self.s[0].p_count,), dtype=np.intp)
cdef intptr_t[::1] ar_view = ar
cdef intptr_t offset = 0
for pi in range(self.s[0].p_count):
ar_view[pi] = offset
offset += self.s[0].tm[self.s[0].p[pi].tmatrix_id].spec[0].n
return ar
def positions(self):
cdef np.ndarray[np.double_t, ndim=2] ar = np.empty((self.s[0].p_count, 3), dtype=float)
cdef np.double_t[:,::1] ar_view = ar
for pi in range(self.s[0].p_count):
ar_view[pi,0] = self.s[0].p[pi].pos.x
ar_view[pi,1] = self.s[0].p[pi].pos.y
ar_view[pi,2] = self.s[0].p[pi].pos.z
return ar
def tlm2uvswfi(t, l, m):
''' TODO doc
And TODO this should rather be an ufunc.
'''
# 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 (t[i] % 1 == 0 and l[i] % 1 == 0 and m[i] % 1 == 0): # maybe not the best check possible, though
raise ValueError # TODO error message
u.append(qpms_tmn2uvswfi(t[i],m[i],l[i]))
return u
else:
print(len(t), len(l), len(m))
raise ValueError("Lengths of the t,l,m arrays must be equal, but they are %d, %d, %d."
% (len(t), len(l), len(m)))
def uvswfi2tlm(u):
''' TODO doc
and TODO this should rather be an ufunc.
'''
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)
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