diff options
Diffstat (limited to 'experiments/ml2.c')
| -rw-r--r-- | experiments/ml2.c | 2275 |
1 files changed, 1285 insertions, 990 deletions
diff --git a/experiments/ml2.c b/experiments/ml2.c index 572a8c5..a61a0d3 100644 --- a/experiments/ml2.c +++ b/experiments/ml2.c @@ -947,10 +947,39 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, int wraparound, int boundscheck); -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice( - PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop, - PyObject** py_start, PyObject** py_stop, PyObject** py_slice, - int has_cstart, int has_cstop, int wraparound); +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02070000 +static CYTHON_INLINE PyObject* __Pyx_PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name) { + PyObject *res; + PyTypeObject *tp = Py_TYPE(obj); +#if PY_MAJOR_VERSION < 3 + if (unlikely(PyInstance_Check(obj))) + return __Pyx_PyObject_GetAttrStr(obj, attr_name); +#endif + res = _PyType_Lookup(tp, attr_name); + if (likely(res)) { + descrgetfunc f = Py_TYPE(res)->tp_descr_get; + if (!f) { + Py_INCREF(res); + } else { + res = f(res, obj, (PyObject *)tp); + } + } else { + PyErr_SetObject(PyExc_AttributeError, attr_name); + } + return res; +} +#else +#define __Pyx_PyObject_LookupSpecial(o,n) __Pyx_PyObject_GetAttrStr(o,n) +#endif + +static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg); + +static CYTHON_INLINE PyObject* __Pyx_PyDict_Keys(PyObject* d); + +static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); + +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); @@ -1025,14 +1054,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); -static int __Pyx_Print(PyObject*, PyObject *, int); -#if CYTHON_COMPILING_IN_PYPY || PY_MAJOR_VERSION >= 3 -static PyObject* __pyx_print = 0; -static PyObject* __pyx_print_kwargs = 0; -#endif - -static int __Pyx_PrintOne(PyObject* stream, PyObject *o); - #if CYTHON_CCOMPLEX #ifdef __cplusplus #define __Pyx_CREAL(z) ((z).real()) @@ -1191,6 +1212,7 @@ int __pyx_module_is_main_ml2 = 0; /* Implementation of 'ml2' */ static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_sum; +static PyObject *__pyx_builtin_open; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_RuntimeError; @@ -1213,6 +1235,7 @@ static char __pyx_k_l[] = "l"; static char __pyx_k_q[] = "q"; static char __pyx_k_s[] = "s"; static char __pyx_k_t[] = "t"; +static char __pyx_k_w[] = "w"; static char __pyx_k_Zd[] = "Zd"; static char __pyx_k_Zf[] = "Zf"; static char __pyx_k_Zg[] = "Zg"; @@ -1223,14 +1246,16 @@ static char __pyx_k_w1[] = "w1"; static char __pyx_k_w2[] = "w2"; static char __pyx_k_w3[] = "w3"; static char __pyx_k_dts[] = "dts"; -static char __pyx_k_end[] = "end"; static char __pyx_k_inf[] = "-inf"; static char __pyx_k_ml2[] = "ml2"; +static char __pyx_k_s_s[] = "%s, %s\n"; static char __pyx_k_sum[] = "sum"; static char __pyx_k_dist[] = "dist"; -static char __pyx_k_file[] = "file"; +static char __pyx_k_exit[] = "__exit__"; +static char __pyx_k_keys[] = "keys"; static char __pyx_k_main[] = "__main__"; -static char __pyx_k_mean[] = "mean"; +static char __pyx_k_open[] = "open"; +static char __pyx_k_prnt[] = "prnt"; static char __pyx_k_prob[] = "prob"; static char __pyx_k_test[] = "__test__"; static char __pyx_k_DTYPE[] = "DTYPE"; @@ -1238,12 +1263,14 @@ static char __pyx_k_alpha[] = "alpha"; static char __pyx_k_delta[] = "delta"; static char __pyx_k_dists[] = "dists"; static char __pyx_k_dtype[] = "dtype"; +static char __pyx_k_enter[] = "__enter__"; static char __pyx_k_lmbda[] = "lmbda"; static char __pyx_k_numpy[] = "numpy"; -static char __pyx_k_print[] = "print"; +static char __pyx_k_prnts[] = "prnts"; static char __pyx_k_probs[] = "probs"; static char __pyx_k_range[] = "range"; static char __pyx_k_roots[] = "roots"; +static char __pyx_k_write[] = "write"; static char __pyx_k_zeros[] = "zeros"; static char __pyx_k_import[] = "__import__"; static char __pyx_k_float64[] = "float64"; @@ -1251,8 +1278,10 @@ static char __pyx_k_n_roots[] = "n_roots"; static char __pyx_k_parents[] = "parents"; static char __pyx_k_victims[] = "victims"; static char __pyx_k_failures[] = "failures"; +static char __pyx_k_infector[] = "infector"; static char __pyx_k_probs_nv[] = "probs_nv"; static char __pyx_k_enumerate[] = "enumerate"; +static char __pyx_k_infectors[] = "infectors"; static char __pyx_k_n_victims[] = "n_victims"; static char __pyx_k_successes[] = "successes"; static char __pyx_k_ValueError[] = "ValueError"; @@ -1263,6 +1292,8 @@ static char __pyx_k_non_victims[] = "non_victims"; static char __pyx_k_RuntimeError[] = "RuntimeError"; static char __pyx_k_parent_dists[] = "parent_dists"; static char __pyx_k_root_victims[] = "root_victims"; +static char __pyx_k_infectors_file[] = "infectors_file"; +static char __pyx_k_Results_infectors_csv[] = "../../Results/infectors.csv"; static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; static char __pyx_k_Users_ben_Documents_Cascade_Pro[] = "/Users/ben/Documents/Cascade Project/criminal_cascades/experiments/ml2.pyx"; static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; @@ -1274,6 +1305,7 @@ static PyObject *__pyx_n_s_DTYPE; static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2; static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; +static PyObject *__pyx_kp_s_Results_infectors_csv; static PyObject *__pyx_n_s_RuntimeError; static PyObject *__pyx_kp_s_Users_ben_Documents_Cascade_Pro; static PyObject *__pyx_n_s_ValueError; @@ -1284,20 +1316,23 @@ static PyObject *__pyx_n_s_dists; static PyObject *__pyx_n_s_dt; static PyObject *__pyx_n_s_dts; static PyObject *__pyx_n_s_dtype; -static PyObject *__pyx_n_s_end; +static PyObject *__pyx_n_s_enter; static PyObject *__pyx_n_s_enumerate; +static PyObject *__pyx_n_s_exit; static PyObject *__pyx_n_s_failures; -static PyObject *__pyx_n_s_file; static PyObject *__pyx_n_s_float64; static PyObject *__pyx_n_s_i; static PyObject *__pyx_n_s_import; static PyObject *__pyx_kp_s_inf; +static PyObject *__pyx_n_s_infector; +static PyObject *__pyx_n_s_infectors; +static PyObject *__pyx_n_s_infectors_file; static PyObject *__pyx_n_s_itervalues; +static PyObject *__pyx_n_s_keys; static PyObject *__pyx_n_s_l; static PyObject *__pyx_n_s_ll; static PyObject *__pyx_n_s_lmbda; static PyObject *__pyx_n_s_main; -static PyObject *__pyx_n_s_mean; static PyObject *__pyx_n_s_ml2; static PyObject *__pyx_n_s_n_roots; static PyObject *__pyx_n_s_n_victims; @@ -1306,10 +1341,12 @@ static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; static PyObject *__pyx_n_s_non_victims; static PyObject *__pyx_n_s_np; static PyObject *__pyx_n_s_numpy; +static PyObject *__pyx_n_s_open; static PyObject *__pyx_n_s_parent_dists; static PyObject *__pyx_n_s_parent_dts; static PyObject *__pyx_n_s_parents; -static PyObject *__pyx_n_s_print; +static PyObject *__pyx_n_s_prnt; +static PyObject *__pyx_n_s_prnts; static PyObject *__pyx_n_s_prob; static PyObject *__pyx_n_s_probs; static PyObject *__pyx_n_s_probs_fail; @@ -1318,20 +1355,21 @@ static PyObject *__pyx_n_s_range; static PyObject *__pyx_n_s_root_victims; static PyObject *__pyx_n_s_roots; static PyObject *__pyx_n_s_s; +static PyObject *__pyx_kp_s_s_s; static PyObject *__pyx_n_s_successes; static PyObject *__pyx_n_s_sum; static PyObject *__pyx_n_s_t; static PyObject *__pyx_n_s_test; static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; static PyObject *__pyx_n_s_victims; +static PyObject *__pyx_n_s_w; static PyObject *__pyx_n_s_w1; static PyObject *__pyx_n_s_w2; static PyObject *__pyx_n_s_w3; +static PyObject *__pyx_n_s_write; static PyObject *__pyx_n_s_zeros; -static PyObject *__pyx_int_1; -static PyObject *__pyx_int_100; -static PyObject *__pyx_slice_; -static PyObject *__pyx_slice__2; +static PyObject *__pyx_tuple_; +static PyObject *__pyx_tuple__2; static PyObject *__pyx_tuple__3; static PyObject *__pyx_tuple__4; static PyObject *__pyx_tuple__5; @@ -1349,7 +1387,7 @@ static PyObject *__pyx_codeobj__10; * """weight for successful infection, exponential time model""" */ -static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(CYTHON_UNUSED int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, __pyx_t_3ml2_DTYPE_t __pyx_v_lmbda, __pyx_t_3ml2_DTYPE_t __pyx_v_w1, __pyx_t_3ml2_DTYPE_t __pyx_v_w2, __pyx_t_3ml2_DTYPE_t __pyx_v_w3) { +static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_lmbda, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w3) { __pyx_t_3ml2_DTYPE_t __pyx_v_structural; __pyx_t_3ml2_DTYPE_t __pyx_v_temporal; __pyx_t_3ml2_DTYPE_t __pyx_v_result; @@ -1357,26 +1395,26 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(CYTHON_UNUSED int __pyx_ __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("weight_success", 0); - /* "ml2.pyx":14 + /* "ml2.pyx":13 + * """weight for successful infection, exponential time model""" * cdef DTYPE_t structural, temporal, result - * # structural = delta ** dist - * structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) # <<<<<<<<<<<<<< + * structural = delta ** dist # <<<<<<<<<<<<<< + * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) * temporal = log(exp(alpha)-1.) - alpha*dt - * # temporal = 1 - exp(-alpha*dt) */ - __pyx_v_structural = (__pyx_v_delta / (((1. + (1. / (__pyx_v_w1 * __pyx_v_lmbda))) + (1. / (__pyx_v_w2 * __pyx_v_lmbda))) + (1. / (__pyx_v_w3 * __pyx_v_lmbda)))); + __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_3ml2_DTYPE_t)__pyx_v_dist)); /* "ml2.pyx":15 - * # structural = delta ** dist - * structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) + * structural = delta ** dist + * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) * temporal = log(exp(alpha)-1.) - alpha*dt # <<<<<<<<<<<<<< - * # temporal = 1 - exp(-alpha*dt) - * # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' + * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 + * result = log(structural) + temporal */ __pyx_v_temporal = (log((exp(__pyx_v_alpha) - 1.)) - (__pyx_v_alpha * __pyx_v_dt)); - /* "ml2.pyx":19 - * # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' + /* "ml2.pyx":17 + * temporal = log(exp(alpha)-1.) - alpha*dt * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 * result = log(structural) + temporal # <<<<<<<<<<<<<< * # print 'st', structural, temporal @@ -1384,7 +1422,7 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(CYTHON_UNUSED int __pyx_ */ __pyx_v_result = (log(__pyx_v_structural) + __pyx_v_temporal); - /* "ml2.pyx":21 + /* "ml2.pyx":19 * result = log(structural) + temporal * # print 'st', structural, temporal * return result # <<<<<<<<<<<<<< @@ -1408,7 +1446,7 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(CYTHON_UNUSED int __pyx_ return __pyx_r; } -/* "ml2.pyx":23 +/* "ml2.pyx":21 * return result * * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, # <<<<<<<<<<<<<< @@ -1416,7 +1454,7 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(CYTHON_UNUSED int __pyx_ * """weight for failed infection, exponential time model""" */ -static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(CYTHON_UNUSED int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, __pyx_t_3ml2_DTYPE_t __pyx_v_lmbda, __pyx_t_3ml2_DTYPE_t __pyx_v_w1, __pyx_t_3ml2_DTYPE_t __pyx_v_w2, __pyx_t_3ml2_DTYPE_t __pyx_v_w3) { +static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_lmbda, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w3) { __pyx_t_3ml2_DTYPE_t __pyx_v_structural; __pyx_t_3ml2_DTYPE_t __pyx_v_temporal; __pyx_t_3ml2_DTYPE_t __pyx_v_result; @@ -1424,25 +1462,25 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(CYTHON_UNUSED int __pyx_ __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("weight_failure", 0); - /* "ml2.pyx":28 + /* "ml2.pyx":25 + * """weight for failed infection, exponential time model""" * cdef DTYPE_t structural, temporal, result - * # structural = delta ** dist - * structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) # <<<<<<<<<<<<<< + * structural = delta ** dist # <<<<<<<<<<<<<< + * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) * temporal = exp(-alpha * dt) - * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 */ - __pyx_v_structural = (__pyx_v_delta / (((1. + (1. / (__pyx_v_w1 * __pyx_v_lmbda))) + (1. / (__pyx_v_w2 * __pyx_v_lmbda))) + (1. / (__pyx_v_w3 * __pyx_v_lmbda)))); + __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_3ml2_DTYPE_t)__pyx_v_dist)); - /* "ml2.pyx":29 - * # structural = delta ** dist - * structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) + /* "ml2.pyx":27 + * structural = delta ** dist + * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) * temporal = exp(-alpha * dt) # <<<<<<<<<<<<<< * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 * result = log(1. - structural + structural * temporal) */ __pyx_v_temporal = exp(((-__pyx_v_alpha) * __pyx_v_dt)); - /* "ml2.pyx":31 + /* "ml2.pyx":29 * temporal = exp(-alpha * dt) * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 * result = log(1. - structural + structural * temporal) # <<<<<<<<<<<<<< @@ -1451,7 +1489,7 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(CYTHON_UNUSED int __pyx_ */ __pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal))); - /* "ml2.pyx":33 + /* "ml2.pyx":31 * result = log(1. - structural + structural * temporal) * # print 'stnv', structural, temporal * return result # <<<<<<<<<<<<<< @@ -1461,7 +1499,7 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(CYTHON_UNUSED int __pyx_ __pyx_r = __pyx_v_result; goto __pyx_L0; - /* "ml2.pyx":23 + /* "ml2.pyx":21 * return result * * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, # <<<<<<<<<<<<<< @@ -1475,7 +1513,7 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(CYTHON_UNUSED int __pyx_ return __pyx_r; } -/* "ml2.pyx":35 +/* "ml2.pyx":33 * return result * * def ml2(dict root_victims, dict victims, dict non_victims, # <<<<<<<<<<<<<< @@ -1523,31 +1561,31 @@ static PyObject *__pyx_pw_3ml2_1ml2(PyObject *__pyx_self, PyObject *__pyx_args, case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_victims)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_non_victims)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_alpha)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_delta)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_lmbda)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml2") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml2") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 6) { goto __pyx_L5_argtuple_error; @@ -1562,21 +1600,21 @@ static PyObject *__pyx_pw_3ml2_1ml2(PyObject *__pyx_self, PyObject *__pyx_args, __pyx_v_root_victims = ((PyObject*)values[0]); __pyx_v_victims = ((PyObject*)values[1]); __pyx_v_non_victims = ((PyObject*)values[2]); - __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_delta = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_lmbda = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_lmbda == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_delta = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_lmbda = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_lmbda == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("ml2.ml2", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_root_victims), (&PyDict_Type), 1, "root_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_victims), (&PyDict_Type), 1, "victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_non_victims), (&PyDict_Type), 1, "non_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_root_victims), (&PyDict_Type), 1, "root_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_victims), (&PyDict_Type), 1, "victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_non_victims), (&PyDict_Type), 1, "non_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3ml2_ml2(__pyx_self, __pyx_v_root_victims, __pyx_v_victims, __pyx_v_non_victims, __pyx_v_alpha, __pyx_v_delta, __pyx_v_lmbda); /* function exit code */ @@ -1605,13 +1643,20 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject PyArrayObject *__pyx_v_probs_nv = 0; PyArrayObject *__pyx_v_parent_dists = 0; PyArrayObject *__pyx_v_parent_dts = 0; + PyArrayObject *__pyx_v_infectors = 0; PyObject *__pyx_v_dists = NULL; PyObject *__pyx_v_dts = NULL; + PyObject *__pyx_v_prnts = NULL; PyObject *__pyx_v_s = NULL; PyObject *__pyx_v_prob = NULL; + PyObject *__pyx_v_infectors_file = NULL; + PyObject *__pyx_v_infector = NULL; + PyObject *__pyx_v_prnt = NULL; PyObject *__pyx_v_w1 = NULL; PyObject *__pyx_v_w2 = NULL; PyObject *__pyx_v_w3 = NULL; + __Pyx_LocalBuf_ND __pyx_pybuffernd_infectors; + __Pyx_Buffer __pyx_pybuffer_infectors; __Pyx_LocalBuf_ND __pyx_pybuffernd_parent_dists; __Pyx_Buffer __pyx_pybuffer_parent_dists; __Pyx_LocalBuf_ND __pyx_pybuffernd_parent_dts; @@ -1635,29 +1680,39 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject PyArrayObject *__pyx_t_9 = NULL; PyArrayObject *__pyx_t_10 = NULL; PyArrayObject *__pyx_t_11 = NULL; - int __pyx_t_12; + PyArrayObject *__pyx_t_12 = NULL; int __pyx_t_13; int __pyx_t_14; - Py_ssize_t __pyx_t_15; - PyObject *__pyx_t_16 = NULL; + int __pyx_t_15; + Py_ssize_t __pyx_t_16; PyObject *__pyx_t_17 = NULL; PyObject *__pyx_t_18 = NULL; PyObject *__pyx_t_19 = NULL; PyObject *__pyx_t_20 = NULL; PyObject *__pyx_t_21 = NULL; - PyObject *(*__pyx_t_22)(PyObject *); - int __pyx_t_23; - __pyx_t_3ml2_DTYPE_t __pyx_t_24; - __pyx_t_3ml2_DTYPE_t __pyx_t_25; + PyObject *__pyx_t_22 = NULL; + PyObject *__pyx_t_23 = NULL; + PyObject *(*__pyx_t_24)(PyObject *); + int __pyx_t_25; __pyx_t_3ml2_DTYPE_t __pyx_t_26; - int __pyx_t_27; - double __pyx_t_28; + __pyx_t_3ml2_DTYPE_t __pyx_t_27; + __pyx_t_3ml2_DTYPE_t __pyx_t_28; int __pyx_t_29; - int __pyx_t_30; + double __pyx_t_30; int __pyx_t_31; int __pyx_t_32; int __pyx_t_33; int __pyx_t_34; + int __pyx_t_35; + int __pyx_t_36; + int __pyx_t_37; + PyObject *__pyx_t_38 = NULL; + PyObject *__pyx_t_39 = NULL; + PyObject *__pyx_t_40 = NULL; + PyObject *__pyx_t_41 = NULL; + PyObject *(*__pyx_t_42)(PyObject *); + PyObject *__pyx_t_43 = NULL; + int __pyx_t_44; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -1682,8 +1737,12 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_pybuffer_parent_dts.refcount = 0; __pyx_pybuffernd_parent_dts.data = NULL; __pyx_pybuffernd_parent_dts.rcbuffer = &__pyx_pybuffer_parent_dts; + __pyx_pybuffer_infectors.pybuffer.buf = NULL; + __pyx_pybuffer_infectors.refcount = 0; + __pyx_pybuffernd_infectors.data = NULL; + __pyx_pybuffernd_infectors.rcbuffer = &__pyx_pybuffer_infectors; - /* "ml2.pyx":41 + /* "ml2.pyx":39 * DTYPE_t ll * list parents, failures, successes * n_roots, n_victims = len(root_victims), len(victims) # <<<<<<<<<<<<<< @@ -1692,54 +1751,54 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject */ if (unlikely(__pyx_v_root_victims == Py_None)) { PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (unlikely(__pyx_v_victims == Py_None)) { PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_n_roots = __pyx_t_1; __pyx_v_n_victims = __pyx_t_2; - /* "ml2.pyx":43 + /* "ml2.pyx":41 * n_roots, n_victims = len(root_victims), len(victims) * cdef: * np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE) # <<<<<<<<<<<<<< * np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] probs_nv = np.zeros(len(non_victims), dtype=DTYPE) */ - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_7 = ((PyArrayObject *)__pyx_t_6); { __Pyx_BufFmt_StackElem __pyx_stack[1]; if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_probs.rcbuffer->pybuffer, (PyObject*)__pyx_t_7, &__Pyx_TypeInfo_nn___pyx_t_3ml2_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) { __pyx_v_probs = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_probs.diminfo[0].strides = __pyx_pybuffernd_probs.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_probs.diminfo[0].shape = __pyx_pybuffernd_probs.rcbuffer->pybuffer.shape[0]; } } @@ -1747,43 +1806,43 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_v_probs = ((PyArrayObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "ml2.pyx":44 + /* "ml2.pyx":42 * cdef: * np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE) # <<<<<<<<<<<<<< * np.ndarray[DTYPE_t] probs_nv = np.zeros(len(non_victims), dtype=DTYPE) * np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE) */ - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_zeros); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_zeros); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_8 = ((PyArrayObject *)__pyx_t_4); { __Pyx_BufFmt_StackElem 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* np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] probs_nv = np.zeros(len(non_victims), dtype=DTYPE) # <<<<<<<<<<<<<< * np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] parent_dts = np.zeros(n_victims, dtype=DTYPE) */ - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_zeros); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_zeros); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (unlikely(__pyx_v_non_victims == Py_None)) { PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_2 = PyDict_Size(__pyx_v_non_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_4 = PyInt_FromSsize_t(__pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyDict_Size(__pyx_v_non_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; 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__pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_10 = ((PyArrayObject *)__pyx_t_6); { __Pyx_BufFmt_StackElem __pyx_stack[1]; if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_parent_dists.rcbuffer->pybuffer, (PyObject*)__pyx_t_10, 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__pyx_k_infectors, sizeof(__pyx_k_infectors), 0, 0, 1, 1}, + {&__pyx_n_s_infectors_file, __pyx_k_infectors_file, sizeof(__pyx_k_infectors_file), 0, 0, 1, 1}, {&__pyx_n_s_itervalues, __pyx_k_itervalues, sizeof(__pyx_k_itervalues), 0, 0, 1, 1}, + {&__pyx_n_s_keys, __pyx_k_keys, sizeof(__pyx_k_keys), 0, 0, 1, 1}, {&__pyx_n_s_l, __pyx_k_l, sizeof(__pyx_k_l), 0, 0, 1, 1}, {&__pyx_n_s_ll, __pyx_k_ll, sizeof(__pyx_k_ll), 0, 0, 1, 1}, {&__pyx_n_s_lmbda, __pyx_k_lmbda, sizeof(__pyx_k_lmbda), 0, 0, 1, 1}, {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1}, - {&__pyx_n_s_mean, __pyx_k_mean, sizeof(__pyx_k_mean), 0, 0, 1, 1}, {&__pyx_n_s_ml2, __pyx_k_ml2, sizeof(__pyx_k_ml2), 0, 0, 1, 1}, {&__pyx_n_s_n_roots, __pyx_k_n_roots, sizeof(__pyx_k_n_roots), 0, 0, 1, 1}, {&__pyx_n_s_n_victims, __pyx_k_n_victims, sizeof(__pyx_k_n_victims), 0, 0, 1, 1}, @@ -5136,10 +5547,12 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_non_victims, __pyx_k_non_victims, 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= { {&__pyx_n_s_root_victims, __pyx_k_root_victims, sizeof(__pyx_k_root_victims), 0, 0, 1, 1}, {&__pyx_n_s_roots, __pyx_k_roots, sizeof(__pyx_k_roots), 0, 0, 1, 1}, {&__pyx_n_s_s, __pyx_k_s, sizeof(__pyx_k_s), 0, 0, 1, 1}, + {&__pyx_kp_s_s_s, __pyx_k_s_s, sizeof(__pyx_k_s_s), 0, 0, 1, 0}, {&__pyx_n_s_successes, __pyx_k_successes, sizeof(__pyx_k_successes), 0, 0, 1, 1}, {&__pyx_n_s_sum, __pyx_k_sum, sizeof(__pyx_k_sum), 0, 0, 1, 1}, {&__pyx_n_s_t, __pyx_k_t, sizeof(__pyx_k_t), 0, 0, 1, 1}, {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1}, {&__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_k_unknown_dtype_code_in_numpy_pxd, sizeof(__pyx_k_unknown_dtype_code_in_numpy_pxd), 0, 1, 0, 0}, {&__pyx_n_s_victims, __pyx_k_victims, sizeof(__pyx_k_victims), 0, 0, 1, 1}, + {&__pyx_n_s_w, __pyx_k_w, sizeof(__pyx_k_w), 0, 0, 1, 1}, {&__pyx_n_s_w1, __pyx_k_w1, sizeof(__pyx_k_w1), 0, 0, 1, 1}, {&__pyx_n_s_w2, __pyx_k_w2, sizeof(__pyx_k_w2), 0, 0, 1, 1}, {&__pyx_n_s_w3, __pyx_k_w3, sizeof(__pyx_k_w3), 0, 0, 1, 1}, + {&__pyx_n_s_write, __pyx_k_write, sizeof(__pyx_k_write), 0, 0, 1, 1}, {&__pyx_n_s_zeros, __pyx_k_zeros, sizeof(__pyx_k_zeros), 0, 0, 1, 1}, {0, 0, 0, 0, 0, 0, 0} }; static int __Pyx_InitCachedBuiltins(void) { - __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_sum = __Pyx_GetBuiltinName(__pyx_n_s_sum); if (!__pyx_builtin_sum) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_sum = __Pyx_GetBuiltinName(__pyx_n_s_sum); if (!__pyx_builtin_sum) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_open = __Pyx_GetBuiltinName(__pyx_n_s_open); if (!__pyx_builtin_open) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -5175,27 +5592,19 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); - /* "ml2.pyx":86 - * roots = n_roots - * # print n_nodes, n_roots, n_victims, max_i, roots - * print parent_dists[1:100] # <<<<<<<<<<<<<< - * print parent_dts[1:100] - * print np.mean(parent_dists) - */ - __pyx_slice_ = PySlice_New(__pyx_int_1, __pyx_int_100, Py_None); if (unlikely(!__pyx_slice_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_slice_); - __Pyx_GIVEREF(__pyx_slice_); - - /* "ml2.pyx":87 - * # print n_nodes, n_roots, n_victims, max_i, roots - * print parent_dists[1:100] - * print parent_dts[1:100] # <<<<<<<<<<<<<< - * print np.mean(parent_dists) - * print np.mean(parent_dts) + /* "ml2.pyx":94 + * # print np.mean(parent_dts) + * + * with open('../../Results/infectors.csv', 'w') as infectors_file: # <<<<<<<<<<<<<< + * for i, infector in enumerate(infectors): + * infectors_file.write("%s, %s\n" % ((victims.keys())[i], infector)) */ - __pyx_slice__2 = PySlice_New(__pyx_int_1, __pyx_int_100, Py_None); if (unlikely(!__pyx_slice__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_slice__2); - __Pyx_GIVEREF(__pyx_slice__2); + __pyx_tuple_ = PyTuple_Pack(2, __pyx_kp_s_Results_infectors_csv, __pyx_n_s_w); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple_); + __Pyx_GIVEREF(__pyx_tuple_); + __pyx_tuple__2 = PyTuple_Pack(3, Py_None, Py_None, Py_None); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__2); + __Pyx_GIVEREF(__pyx_tuple__2); /* "../../../../Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) @@ -5263,17 +5672,17 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__8); __Pyx_GIVEREF(__pyx_tuple__8); - /* "ml2.pyx":35 + /* "ml2.pyx":33 * return result * * def ml2(dict root_victims, dict victims, dict non_victims, # <<<<<<<<<<<<<< * DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda): * cdef: */ - __pyx_tuple__9 = PyTuple_Pack(30, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_lmbda, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_roots, __pyx_n_s_i, __pyx_n_s_dist, __pyx_n_s_dt, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_ll, __pyx_n_s_parents, __pyx_n_s_failures, __pyx_n_s_successes, __pyx_n_s_probs, __pyx_n_s_probs_fail, __pyx_n_s_probs_nv, __pyx_n_s_parent_dists, __pyx_n_s_parent_dts, __pyx_n_s_dists, __pyx_n_s_dts, __pyx_n_s_s, __pyx_n_s_prob, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3); if (unlikely(!__pyx_tuple__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__9 = PyTuple_Pack(35, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_lmbda, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_roots, __pyx_n_s_i, __pyx_n_s_dist, __pyx_n_s_dt, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_ll, __pyx_n_s_parents, __pyx_n_s_failures, __pyx_n_s_successes, __pyx_n_s_probs, __pyx_n_s_probs_fail, __pyx_n_s_probs_nv, __pyx_n_s_parent_dists, __pyx_n_s_parent_dts, __pyx_n_s_infectors, __pyx_n_s_dists, __pyx_n_s_dts, __pyx_n_s_prnts, __pyx_n_s_s, __pyx_n_s_prob, __pyx_n_s_infectors_file, __pyx_n_s_infector, __pyx_n_s_prnt, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3); if (unlikely(!__pyx_tuple__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__9); __Pyx_GIVEREF(__pyx_tuple__9); - __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(6, 0, 30, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml2, 35, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(6, 0, 35, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml2, 33, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -5283,8 +5692,6 @@ static int __Pyx_InitCachedConstants(void) { static int __Pyx_InitGlobals(void) { if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; - __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_int_100 = PyInt_FromLong(100); if (unlikely(!__pyx_int_100)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} return 0; __pyx_L1_error:; return -1; @@ -5414,16 +5821,16 @@ PyMODINIT_FUNC PyInit_ml2(void) if (PyDict_SetItem(__pyx_d, __pyx_n_s_DTYPE, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "ml2.pyx":35 + /* "ml2.pyx":33 * return result * * def ml2(dict root_victims, dict victims, dict non_victims, # <<<<<<<<<<<<<< * DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda): * cdef: */ - __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_3ml2_1ml2, NULL, __pyx_n_s_ml2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_3ml2_1ml2, NULL, __pyx_n_s_ml2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml2, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml2, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; /* "ml2.pyx":1 @@ -6671,101 +7078,130 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); } -static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice( - PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop, - PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, - int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) { +static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) { + PyObject *method, *result = NULL; + method = __Pyx_PyObject_GetAttrStr(obj, method_name); + if (unlikely(!method)) goto bad; #if CYTHON_COMPILING_IN_CPYTHON - PyMappingMethods* mp; -#if PY_MAJOR_VERSION < 3 - PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence; - if (likely(ms && ms->sq_slice)) { - if (!has_cstart) { - if (_py_start && (*_py_start != Py_None)) { - cstart = __Pyx_PyIndex_AsSsize_t(*_py_start); - if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; - } else - cstart = 0; - } - if (!has_cstop) { - if (_py_stop && (*_py_stop != Py_None)) { - cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop); - if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; - } else - cstop = PY_SSIZE_T_MAX; - } - if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) { - Py_ssize_t l = ms->sq_length(obj); - if (likely(l >= 0)) { - if (cstop < 0) { - cstop += l; - if (cstop < 0) cstop = 0; - } - if (cstart < 0) { - cstart += l; - if (cstart < 0) cstart = 0; - } - } else { - if (PyErr_ExceptionMatches(PyExc_OverflowError)) - PyErr_Clear(); - else - goto bad; - } + if (likely(PyMethod_Check(method))) { + PyObject *self = PyMethod_GET_SELF(method); + if (likely(self)) { + PyObject *args; + PyObject *function = PyMethod_GET_FUNCTION(method); + args = PyTuple_New(2); + if (unlikely(!args)) goto bad; + Py_INCREF(self); + PyTuple_SET_ITEM(args, 0, self); + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 1, arg); + Py_INCREF(function); + Py_DECREF(method); method = NULL; + result = __Pyx_PyObject_Call(function, args, NULL); + Py_DECREF(args); + Py_DECREF(function); + return result; } - return ms->sq_slice(obj, cstart, cstop); } #endif - mp = Py_TYPE(obj)->tp_as_mapping; - if (likely(mp && mp->mp_subscript)) + result = __Pyx_PyObject_CallOneArg(method, arg); +bad: + Py_XDECREF(method); + return result; +} + +static CYTHON_INLINE PyObject* __Pyx_PyDict_Keys(PyObject* d) { + if (PY_MAJOR_VERSION >= 3) + return __Pyx_PyObject_CallMethod1((PyObject*)&PyDict_Type, __pyx_n_s_keys, d); + else + return PyDict_Keys(d); +} + +static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->exc_type; + *value = tstate->exc_value; + *tb = tstate->exc_traceback; + Py_XINCREF(*type); + Py_XINCREF(*value); + Py_XINCREF(*tb); +#else + PyErr_GetExcInfo(type, value, tb); #endif - { - PyObject* result; - PyObject *py_slice, *py_start, *py_stop; - if (_py_slice) { - py_slice = *_py_slice; - } else { - PyObject* owned_start = NULL; - PyObject* owned_stop = NULL; - if (_py_start) { - py_start = *_py_start; - } else { - if (has_cstart) { - owned_start = py_start = PyInt_FromSsize_t(cstart); - if (unlikely(!py_start)) goto bad; - } else - py_start = Py_None; - } - if (_py_stop) { - py_stop = *_py_stop; - } else { - if (has_cstop) { - owned_stop = py_stop = PyInt_FromSsize_t(cstop); - if (unlikely(!py_stop)) { - Py_XDECREF(owned_start); - goto bad; - } - } else - py_stop = Py_None; - } - py_slice = PySlice_New(py_start, py_stop, Py_None); - Py_XDECREF(owned_start); - Py_XDECREF(owned_stop); - if (unlikely(!py_slice)) goto bad; - } +} +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON - result = mp->mp_subscript(obj, py_slice); + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = type; + tstate->exc_value = value; + tstate->exc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); #else - result = PyObject_GetItem(obj, py_slice); + PyErr_SetExcInfo(type, value, tb); #endif - if (!_py_slice) { - Py_DECREF(py_slice); - } - return result; +} + +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { + PyObject *local_type, *local_value, *local_tb; +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + local_type = tstate->curexc_type; + local_value = tstate->curexc_value; + local_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(&local_type, &local_value, &local_tb); +#endif + PyErr_NormalizeException(&local_type, &local_value, &local_tb); +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(tstate->curexc_type)) +#else + if (unlikely(PyErr_Occurred())) +#endif + goto bad; + #if PY_MAJOR_VERSION >= 3 + if (local_tb) { + if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) + goto bad; } - PyErr_Format(PyExc_TypeError, - "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name); + #endif + Py_XINCREF(local_tb); + Py_XINCREF(local_type); + Py_XINCREF(local_value); + *type = local_type; + *value = local_value; + *tb = local_tb; +#if CYTHON_COMPILING_IN_CPYTHON + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = local_type; + tstate->exc_value = local_value; + tstate->exc_traceback = local_tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(local_type, local_value, local_tb); +#endif + return 0; bad: - return NULL; + *type = 0; + *value = 0; + *tb = 0; + Py_XDECREF(local_type); + Py_XDECREF(local_value); + Py_XDECREF(local_tb); + return -1; } static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { @@ -7351,147 +7787,6 @@ raise_neg_overflow: return (int) -1; } -#if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3 -static PyObject *__Pyx_GetStdout(void) { - PyObject *f = PySys_GetObject((char *)"stdout"); - if (!f) { - PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout"); - } - return f; -} -static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) { - int i; - if (!f) { - if (!(f = __Pyx_GetStdout())) - return -1; - } - Py_INCREF(f); - for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) { - PyObject* v; - if (PyFile_SoftSpace(f, 1)) { - if (PyFile_WriteString(" ", f) < 0) - goto error; - } - v = PyTuple_GET_ITEM(arg_tuple, i); - if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0) - goto error; - if (PyString_Check(v)) { - char *s = PyString_AsString(v); - Py_ssize_t len = PyString_Size(v); - if (len > 0) { - switch (s[len-1]) { - case ' ': break; - case '\f': case '\r': case '\n': case '\t': case '\v': - PyFile_SoftSpace(f, 0); - break; - default: break; - } - } - } - } - if (newline) { - if (PyFile_WriteString("\n", f) < 0) - goto error; - PyFile_SoftSpace(f, 0); - } - Py_DECREF(f); - return 0; -error: - Py_DECREF(f); - return -1; -} -#else -static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) { - PyObject* kwargs = 0; - PyObject* result = 0; - PyObject* end_string; - if (unlikely(!__pyx_print)) { - __pyx_print = PyObject_GetAttr(__pyx_b, __pyx_n_s_print); - if (!__pyx_print) - return -1; - } - if (stream) { - kwargs = PyDict_New(); - if (unlikely(!kwargs)) - return -1; - if (unlikely(PyDict_SetItem(kwargs, __pyx_n_s_file, stream) < 0)) - goto bad; - if (!newline) { - end_string = PyUnicode_FromStringAndSize(" ", 1); - if (unlikely(!end_string)) - goto bad; - if (PyDict_SetItem(kwargs, __pyx_n_s_end, end_string) < 0) { - Py_DECREF(end_string); - goto bad; - } - Py_DECREF(end_string); - } - } else if (!newline) { - if (unlikely(!__pyx_print_kwargs)) { - __pyx_print_kwargs = PyDict_New(); - if (unlikely(!__pyx_print_kwargs)) - return -1; - end_string = PyUnicode_FromStringAndSize(" ", 1); - if (unlikely(!end_string)) - return -1; - if (PyDict_SetItem(__pyx_print_kwargs, __pyx_n_s_end, end_string) < 0) { - Py_DECREF(end_string); - return -1; - } - Py_DECREF(end_string); - } - kwargs = __pyx_print_kwargs; - } - result = PyObject_Call(__pyx_print, arg_tuple, kwargs); - if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs)) - Py_DECREF(kwargs); - if (!result) - return -1; - Py_DECREF(result); - return 0; -bad: - if (kwargs != __pyx_print_kwargs) - Py_XDECREF(kwargs); - return -1; -} -#endif - -#if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3 -static int __Pyx_PrintOne(PyObject* f, PyObject *o) { - if (!f) { - if (!(f = __Pyx_GetStdout())) - return -1; - } - Py_INCREF(f); - if (PyFile_SoftSpace(f, 0)) { - if (PyFile_WriteString(" ", f) < 0) - goto error; - } - if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0) - goto error; - if (PyFile_WriteString("\n", f) < 0) - goto error; - Py_DECREF(f); - return 0; -error: - Py_DECREF(f); - return -1; - /* the line below is just to avoid C compiler - * warnings about unused functions */ - return __Pyx_Print(f, NULL, 0); -} -#else -static int __Pyx_PrintOne(PyObject* stream, PyObject *o) { - int res; - PyObject* arg_tuple = PyTuple_Pack(1, o); - if (unlikely(!arg_tuple)) - return -1; - res = __Pyx_Print(stream, arg_tuple, 1); - Py_DECREF(arg_tuple); - return res; -} -#endif - #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { |