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The calculator module now works in python 

Former-commit-id: 928dc98f6960bd53317a861c2787e197dcb87c88
This commit is contained in:
Marek Nečada 2017-04-26 14:12:29 +03:00
parent 816771be8d
commit c41c0d80ff
6 changed files with 277 additions and 26 deletions
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14
qpms/assert_cython_workaround.h Normal file
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@ -0,0 +1,14 @@
// The purpose of this file is to enable assertions in cython modules.
// By default, cython includes -DNDEBUG argument when running gcc and
// it seems this can not be disabled. Therefore, we force undefining
// NDEBUG in the code if DISABLE_NDEBUG is defined.
#ifndef ASSERT_CYTHON_H
#define ASSERT_CYTHON_H
#ifdef DISABLE_NDEBUG
#undef NDEBUG
#endif
#include <assert.h>
#endif // ASSERT_CYTHON_H

2
qpms/gaunt.c
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@ -11,7 +11,7 @@ void gaunt_xu(int m, int n, int mu, int nu, int qmax, double *v_aq, int *err) {
//#include <stdlib.h>
#include <math.h>
#include <stdio.h>
#include <assert.h>
#include "assert_cython_workaround.h"
#define ZERO_THRESHOLD 1.e-8
#define BF_PREC 1.e-10

256
qpms/qpms_c.pyx
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@ -4,6 +4,7 @@
import numpy as np
cimport numpy as np
cimport cython
from cython.parallel cimport parallel, prange
## Auxillary function for retrieving the "meshgrid-like" indices; inc. nmax
@cython.boundscheck(False)
@ -162,6 +163,20 @@ cdef extern from "translations.h":
double r, double th, double ph, int r_ge_d, int J) nogil
cdouble qpms_trans_single_B_Taylor_ext(int m, int n, int mu, int nu,
double r, double th, double ph, int r_ge_d, int J) nogil
struct qpms_trans_calculator:
pass
enum qpms_normalization_t:
pass
qpms_trans_calculator* qpms_trans_calculator_init(int lMax, int nt) # should be qpms_normalization_t
void qpms_trans_calculator_free(qpms_trans_calculator* c)
cdouble qpms_trans_calculator_get_A_ext(const qpms_trans_calculator* c,
int m, int n, int mu, int nu, double kdlj_r, double kdlj_th, double kdlj_phi,
int r_ge_d, int J)
cdouble qpms_trans_calculator_get_B_ext(const qpms_trans_calculator* c,
int m, int n, int mu, int nu, double kdlj_r, double kdlj_th, double kdlj_phi,
int r_ge_d, int J)
# Module initialisation
# ---------------------
@ -174,31 +189,53 @@ np.import_ufunc()
# BTW, aren't there anonymous arrays in cython?
cdef np.PyUFuncGenericFunction loop_func[1]
cdef char input_output_types[10]
cdef void *elementwise_funcs_A[1]
cdef void *elementwise_funcs_B[1]
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]
loop_func[0] = loop_D_iiiidddii_As_D_lllldddbl
trans_X_taylor_loop_func[0] = loop_D_iiiidddii_As_D_lllldddbl
input_output_types[0] = np.NPY_LONG
input_output_types[1] = np.NPY_LONG
input_output_types[2] = np.NPY_LONG
input_output_types[3] = np.NPY_LONG
input_output_types[4] = np.NPY_DOUBLE
input_output_types[5] = np.NPY_DOUBLE
input_output_types[6] = np.NPY_DOUBLE
input_output_types[7] = np.NPY_BOOL
input_output_types[8] = np.NPY_LONG
input_output_types[9] = np.NPY_CDOUBLE
# 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
elementwise_funcs_A[0] = <void*> qpms_trans_single_A_Taylor_ext
elementwise_funcs_B[0] = <void*> qpms_trans_single_B_Taylor_ext
# 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(
loop_func, # func
elementwise_funcs_A, #data
input_output_types, # types
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
@ -211,9 +248,9 @@ trans_A_Taylor = np.PyUFunc_FromFuncAndData(
)
trans_B_Taylor = np.PyUFunc_FromFuncAndData(
loop_func,
elementwise_funcs_B,
input_output_types,
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
@ -225,3 +262,176 @@ trans_B_Taylor = np.PyUFunc_FromFuncAndData(
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)
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
#TODO
#cdef np.PyUFuncGenericFunction trans_calculator_get_AB_loop_funcs[1]
#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] = qpms_trans_calculator_get_AB_p_ext
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
object get_A, get_B, #get_AB
def __cinit__(self, int lMax, int normalization = 1):
self.c = qpms_trans_calculator_init(lMax, normalization)
def __init__(self, int lMax, int normalization = 1):
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
)
def __dealloc__(self):
qpms_trans_calculator_free(self.c)
# TODO make possible to access the attributes (to show normalization etc)

18
qpms/translations.c
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@ -4,7 +4,7 @@
#include <stdbool.h>
#include <gsl/gsl_sf_legendre.h>
#include <gsl/gsl_sf_bessel.h>
#include <assert.h>
#include "assert_cython_workaround.h"
static const double sqrtpi = 1.7724538509055160272981674833411451827975494561223871;
@ -498,6 +498,22 @@ complex double qpms_trans_calculator_get_B(const qpms_trans_calculator *c,
bes,leg);
}
complex double qpms_trans_calculator_get_A_ext(const qpms_trans_calculator *c,
int m, int n, int mu, int nu,
double kdlj_r, double kdlj_theta, double kdlj_phi,
int r_ge_d, int J) {
sph_t kdlj = {kdlj_r, kdlj_theta, kdlj_phi};
return qpms_trans_calculator_get_A(c,m,n,mu,nu,kdlj,r_ge_d,J);
}
complex double qpms_trans_calculator_get_B_ext(const qpms_trans_calculator *c,
int m, int n, int mu, int nu,
double kdlj_r, double kdlj_theta, double kdlj_phi,
int r_ge_d, int J) {
sph_t kdlj = {kdlj_r, kdlj_theta, kdlj_phi};
return qpms_trans_calculator_get_B(c,m,n,mu,nu,kdlj,r_ge_d,J);
}
#if 0
int qpms_trans_calculator_get_AB_p(const qpms_trans_calculator *c,
complex double *Adest, complex double *Bdest,

9
qpms/translations.h
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@ -52,6 +52,15 @@ complex double qpms_trans_calculator_get_A(const qpms_trans_calculator *c,
complex double qpms_trans_calculator_get_B(const qpms_trans_calculator *c,
int m, int n, int mu, int nu, sph_t kdlj,
bool r_ge_d, qpms_bessel_t J);
complex double qpms_trans_calculator_get_A_ext(const qpms_trans_calculator *c,
int m, int n, int mu, int nu, double kdlj_r,
double kdlj_th, double kdlj_phi, int r_ge_d, int J);
complex double qpms_trans_calculator_get_B_ext(const qpms_trans_calculator *c,
int m, int n, int mu, int nu, double kdlj_r,
double kdlj_th, double kdlj_phi, int r_ge_d, int J);
#if 0
int qpms_trans_calculator_get_AB_p(const qpms_trans_calculator *c,
complex double *Adest, complex double *Bdest,

4
setup.py
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@ -20,7 +20,9 @@ qpms_c = Extension('qpms_c',
sources = ['qpms/qpms_c.pyx','qpms/gaunt.c',#'qpms/gaunt.h','qpms/vectors.h','qpms/translations.h',
# FIXME http://stackoverflow.com/questions/4259170/python-setup-script-extensions-how-do-you-include-a-h-file
'qpms/translations.c'],
extra_compile_args=['-std=c99','-ggdb','-O3'],
extra_compile_args=['-std=c99','-ggdb','-O3',
'-DDISABLE_NDEBUG', # uncomment to enable assertions in the modules
],
libraries=['gsl', 'blas'],
runtime_library_dirs=os.environ['LD_LIBRARY_PATH'].split(':')
)