diff options
Diffstat (limited to 'experiments/ml2.c')
| -rw-r--r-- | experiments/ml2.c | 816 |
1 files changed, 425 insertions, 391 deletions
diff --git a/experiments/ml2.c b/experiments/ml2.c index 9deccbc..572a8c5 100644 --- a/experiments/ml2.c +++ b/experiments/ml2.c @@ -695,7 +695,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; * DTYPE = np.float64 * ctypedef np.float_t DTYPE_t # <<<<<<<<<<<<<< * - * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): + * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, */ typedef __pyx_t_5numpy_float_t __pyx_t_3ml2_DTYPE_t; #if CYTHON_CCOMPLEX @@ -1182,8 +1182,8 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, cha /* Module declarations from 'libc.math' */ /* Module declarations from 'ml2' */ -static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(int, int, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t); /*proto*/ -static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(int, int, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t); /*proto*/ +static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(int, int, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t); /*proto*/ +static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(int, int, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t); /*proto*/ static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_3ml2_DTYPE_t = { "DTYPE_t", NULL, sizeof(__pyx_t_3ml2_DTYPE_t), { 0 }, 0, 'R', 0, 0 }; #define __Pyx_MODULE_NAME "ml2" int __pyx_module_is_main_ml2 = 0; @@ -1194,7 +1194,7 @@ static PyObject *__pyx_builtin_sum; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_RuntimeError; -static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_age, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta); /* proto */ +static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, __pyx_t_3ml2_DTYPE_t __pyx_v_lmbda); /* proto */ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ static char __pyx_k_B[] = "B"; @@ -1222,16 +1222,15 @@ static char __pyx_k_np[] = "np"; static char __pyx_k_w1[] = "w1"; static char __pyx_k_w2[] = "w2"; static char __pyx_k_w3[] = "w3"; -static char __pyx_k_age[] = "age"; 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_sum[] = "sum"; -static char __pyx_k_beta[] = "beta"; static char __pyx_k_dist[] = "dist"; static char __pyx_k_file[] = "file"; static char __pyx_k_main[] = "__main__"; +static char __pyx_k_mean[] = "mean"; static char __pyx_k_prob[] = "prob"; static char __pyx_k_test[] = "__test__"; static char __pyx_k_DTYPE[] = "DTYPE"; @@ -1239,6 +1238,7 @@ 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_lmbda[] = "lmbda"; static char __pyx_k_numpy[] = "numpy"; static char __pyx_k_print[] = "print"; static char __pyx_k_probs[] = "probs"; @@ -1277,9 +1277,7 @@ static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; static PyObject *__pyx_n_s_RuntimeError; static PyObject *__pyx_kp_s_Users_ben_Documents_Cascade_Pro; static PyObject *__pyx_n_s_ValueError; -static PyObject *__pyx_n_s_age; static PyObject *__pyx_n_s_alpha; -static PyObject *__pyx_n_s_beta; static PyObject *__pyx_n_s_delta; static PyObject *__pyx_n_s_dist; static PyObject *__pyx_n_s_dists; @@ -1297,7 +1295,9 @@ static PyObject *__pyx_kp_s_inf; static PyObject *__pyx_n_s_itervalues; 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; @@ -1344,49 +1344,12 @@ static PyObject *__pyx_codeobj__10; /* "ml2.pyx":9 * ctypedef np.float_t DTYPE_t * - * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): # <<<<<<<<<<<<<< - * return 1./(1. + exp(-weight/delta)) - * - */ - -static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_plogis(__pyx_t_3ml2_DTYPE_t __pyx_v_weight, __pyx_t_3ml2_DTYPE_t __pyx_v_delta) { - __pyx_t_3ml2_DTYPE_t __pyx_r; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("plogis", 0); - - /* "ml2.pyx":10 - * - * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): - * return 1./(1. + exp(-weight/delta)) # <<<<<<<<<<<<<< - * - * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, - */ - __pyx_r = (1. / (1. + exp(((-__pyx_v_weight) / __pyx_v_delta)))); - goto __pyx_L0; - - /* "ml2.pyx":9 - * ctypedef np.float_t DTYPE_t - * - * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): # <<<<<<<<<<<<<< - * return 1./(1. + exp(-weight/delta)) - * - */ - - /* function exit code */ - __pyx_L0:; - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - -/* "ml2.pyx":12 - * return 1./(1. + exp(-weight/delta)) - * - * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< + * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, # <<<<<<<<<<<<<< * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): * """weight for successful infection, exponential time model""" */ -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_w1, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w3) { +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) { __pyx_t_3ml2_DTYPE_t __pyx_v_structural; __pyx_t_3ml2_DTYPE_t __pyx_v_temporal; __pyx_t_3ml2_DTYPE_t __pyx_v_result; @@ -1394,47 +1357,47 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(int __pyx_v_dist, int __ __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("weight_success", 0); - /* "ml2.pyx":16 - * """weight for successful infection, exponential time model""" + /* "ml2.pyx":14 * cdef DTYPE_t structural, temporal, result - * structural = dist * log(delta) # <<<<<<<<<<<<<< - * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) + * # 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_dist * log(__pyx_v_delta)); + __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)))); - /* "ml2.pyx":18 - * structural = dist * log(delta) - * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) + /* "ml2.pyx":15 + * # 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' */ __pyx_v_temporal = (log((exp(__pyx_v_alpha) - 1.)) - (__pyx_v_alpha * __pyx_v_dt)); - /* "ml2.pyx":22 + /* "ml2.pyx":19 * # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 - * result = structural + temporal # <<<<<<<<<<<<<< + * result = log(structural) + temporal # <<<<<<<<<<<<<< * # print 'st', structural, temporal * return result */ - __pyx_v_result = (__pyx_v_structural + __pyx_v_temporal); + __pyx_v_result = (log(__pyx_v_structural) + __pyx_v_temporal); - /* "ml2.pyx":24 - * result = structural + temporal + /* "ml2.pyx":21 + * result = log(structural) + temporal * # print 'st', structural, temporal * return result # <<<<<<<<<<<<<< * - * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, + * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, */ __pyx_r = __pyx_v_result; goto __pyx_L0; - /* "ml2.pyx":12 - * return 1./(1. + exp(-weight/delta)) + /* "ml2.pyx":9 + * ctypedef np.float_t DTYPE_t * - * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< + * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, # <<<<<<<<<<<<<< * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): * """weight for successful infection, exponential time model""" */ @@ -1445,15 +1408,15 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(int __pyx_v_dist, int __ return __pyx_r; } -/* "ml2.pyx":26 +/* "ml2.pyx":23 * return result * - * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< + * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, # <<<<<<<<<<<<<< * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): * """weight for failed infection, exponential time model""" */ -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_w1, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w3) { +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) { __pyx_t_3ml2_DTYPE_t __pyx_v_structural; __pyx_t_3ml2_DTYPE_t __pyx_v_temporal; __pyx_t_3ml2_DTYPE_t __pyx_v_result; @@ -1461,25 +1424,25 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(int __pyx_v_dist, int __ __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("weight_failure", 0); - /* "ml2.pyx":30 - * """weight for failed infection, exponential time model""" + /* "ml2.pyx":28 * cdef DTYPE_t structural, temporal, result - * structural = delta ** dist # <<<<<<<<<<<<<< - * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) + * # 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 = pow(__pyx_v_delta, ((__pyx_t_3ml2_DTYPE_t)__pyx_v_dist)); + __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)))); - /* "ml2.pyx":32 - * structural = delta ** dist - * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) + /* "ml2.pyx":29 + * # 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":34 + /* "ml2.pyx":31 * temporal = exp(-alpha * dt) * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 * result = log(1. - structural + structural * temporal) # <<<<<<<<<<<<<< @@ -1488,20 +1451,20 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(int __pyx_v_dist, int __ */ __pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal))); - /* "ml2.pyx":36 + /* "ml2.pyx":33 * result = log(1. - structural + structural * temporal) * # print 'stnv', structural, temporal * return result # <<<<<<<<<<<<<< * - * def ml2(dict root_victims, dict victims, dict non_victims, DTYPE_t age, + * def ml2(dict root_victims, dict victims, dict non_victims, */ __pyx_r = __pyx_v_result; goto __pyx_L0; - /* "ml2.pyx":26 + /* "ml2.pyx":23 * return result * - * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< + * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, # <<<<<<<<<<<<<< * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): * """weight for failed infection, exponential time model""" */ @@ -1512,11 +1475,11 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(int __pyx_v_dist, int __ return __pyx_r; } -/* "ml2.pyx":38 +/* "ml2.pyx":35 * return result * - * def ml2(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< - * DTYPE_t alpha, DTYPE_t delta): + * def ml2(dict root_victims, dict victims, dict non_victims, # <<<<<<<<<<<<<< + * DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda): * cdef: */ @@ -1527,9 +1490,9 @@ static PyObject *__pyx_pw_3ml2_1ml2(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_v_root_victims = 0; PyObject *__pyx_v_victims = 0; PyObject *__pyx_v_non_victims = 0; - CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_age; __pyx_t_3ml2_DTYPE_t __pyx_v_alpha; __pyx_t_3ml2_DTYPE_t __pyx_v_delta; + __pyx_t_3ml2_DTYPE_t __pyx_v_lmbda; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -1537,7 +1500,7 @@ static PyObject *__pyx_pw_3ml2_1ml2(PyObject *__pyx_self, PyObject *__pyx_args, __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ml2 (wrapper)", 0); { - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_root_victims,&__pyx_n_s_victims,&__pyx_n_s_non_victims,&__pyx_n_s_age,&__pyx_n_s_alpha,&__pyx_n_s_delta,0}; + static PyObject **__pyx_pyargnames[] = {&__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,0}; PyObject* values[6] = {0,0,0,0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -1560,31 +1523,31 @@ 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 = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __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 = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: - if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_age)) != 0)) kw_args--; + 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 = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: - if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_alpha)) != 0)) kw_args--; + 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 = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: - if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_delta)) != 0)) kw_args--; + 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 = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __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 = 38; __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 = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 6) { goto __pyx_L5_argtuple_error; @@ -1599,22 +1562,22 @@ 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_age = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_age == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_delta = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __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 = 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;} } 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 = 38; __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 = 35; __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 = 38; __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 = 38; __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 = 38; __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_age, __pyx_v_alpha, __pyx_v_delta); + 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;} + __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 */ goto __pyx_L0; @@ -1625,7 +1588,7 @@ static PyObject *__pyx_pw_3ml2_1ml2(PyObject *__pyx_self, PyObject *__pyx_args, return __pyx_r; } -static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_age, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta) { +static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, __pyx_t_3ml2_DTYPE_t __pyx_v_lmbda) { int __pyx_v_n_roots; int __pyx_v_n_victims; int __pyx_v_roots; @@ -1633,7 +1596,6 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject int __pyx_v_dist; int __pyx_v_dt; int __pyx_v_l; - __pyx_t_3ml2_DTYPE_t __pyx_v_beta; __pyx_t_3ml2_DTYPE_t __pyx_v_ll; PyObject *__pyx_v_parents = 0; PyObject *__pyx_v_failures = 0; @@ -1721,8 +1683,8 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_pybuffernd_parent_dts.data = NULL; __pyx_pybuffernd_parent_dts.rcbuffer = &__pyx_pybuffer_parent_dts; - /* "ml2.pyx":44 - * DTYPE_t beta, ll + /* "ml2.pyx":41 + * DTYPE_t ll * list parents, failures, successes * n_roots, n_victims = len(root_victims), len(victims) # <<<<<<<<<<<<<< * cdef: @@ -1730,54 +1692,54 @@ 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 = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__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 = 44; __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;} 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 = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__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 = 44; __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_v_n_roots = __pyx_t_1; __pyx_v_n_victims = __pyx_t_2; - /* "ml2.pyx":46 + /* "ml2.pyx":43 * 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 = 46; __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 = 43; __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 = 46; __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 = 43; __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 = 46; __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 = 43; __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 = 46; __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 = 43; __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 = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __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_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 = 46; __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 = 43; __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 = 46; __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 = 43; __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 = 46; __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 = 43; __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 = 43; __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 = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __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]; } } @@ -1785,43 +1747,43 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_v_probs = ((PyArrayObject *)__pyx_t_6); __pyx_t_6 = 0; 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if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __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 = 44; __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 = 47; __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 = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_8 = ((PyArrayObject *)__pyx_t_4); { __Pyx_BufFmt_StackElem __pyx_stack[1]; if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_probs_fail.rcbuffer->pybuffer, (PyObject*)__pyx_t_8, &__Pyx_TypeInfo_nn___pyx_t_3ml2_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) { __pyx_v_probs_fail = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_probs_fail.diminfo[0].strides = __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_probs_fail.diminfo[0].shape = __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.shape[0]; } } @@ -1829,48 +1791,48 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_v_probs_fail = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "ml2.pyx":48 + /* "ml2.pyx":45 * 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 = 48; __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 = 45; __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 = 48; __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 = 45; __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 = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__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 = 48; __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 = 48; __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_GOTREF(__pyx_t_4); - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_dtype, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; 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__pyx_t_3 = 0; - /* "ml2.pyx":49 + /* "ml2.pyx":46 * 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_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __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 = 46; __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 = 49; __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]; 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if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __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 = 46; __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 = 49; __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 = 46; __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, &__Pyx_TypeInfo_nn___pyx_t_3ml2_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) { __pyx_v_parent_dists = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_parent_dists.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_parent_dists.diminfo[0].strides = __pyx_pybuffernd_parent_dists.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_parent_dists.diminfo[0].shape = __pyx_pybuffernd_parent_dists.rcbuffer->pybuffer.shape[0]; } } @@ -1922,43 +1884,43 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_v_parent_dists = ((PyArrayObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "ml2.pyx":50 + /* "ml2.pyx":47 * 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) # <<<<<<<<<<<<<< * * # loop through victims */ - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __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 = 47; __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 = 50; __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 = 47; __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 = 50; __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 = 47; __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 = 50; __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 = 47; __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 = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __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 = 50; __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 = 47; __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 = 50; __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 = 47; __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 = 50; __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 = 47; __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 = 50; __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 = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_11 = ((PyArrayObject *)__pyx_t_4); { __Pyx_BufFmt_StackElem __pyx_stack[1]; if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_parent_dts.rcbuffer->pybuffer, (PyObject*)__pyx_t_11, &__Pyx_TypeInfo_nn___pyx_t_3ml2_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) { __pyx_v_parent_dts = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_parent_dts.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_parent_dts.diminfo[0].strides = __pyx_pybuffernd_parent_dts.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_parent_dts.diminfo[0].shape = __pyx_pybuffernd_parent_dts.rcbuffer->pybuffer.shape[0]; } } @@ -1966,7 +1928,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_v_parent_dts = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "ml2.pyx":53 + /* "ml2.pyx":50 * * # loop through victims * for i, parents in enumerate(victims.itervalues()): # <<<<<<<<<<<<<< @@ -1977,9 +1939,9 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_t_2 = 0; if (unlikely(__pyx_v_victims == Py_None)) { PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "itervalues"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_6 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_13)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_13)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = __pyx_t_6; @@ -1987,42 +1949,42 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject while (1) { __pyx_t_14 = __Pyx_dict_iter_next(__pyx_t_4, __pyx_t_1, &__pyx_t_2, NULL, &__pyx_t_6, NULL, __pyx_t_13); if (unlikely(__pyx_t_14 == 0)) break; - if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (!(likely(PyList_CheckExact(__pyx_t_6))||((__pyx_t_6) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_6)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(PyList_CheckExact(__pyx_t_6))||((__pyx_t_6) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_6)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_XDECREF_SET(__pyx_v_parents, ((PyObject*)__pyx_t_6)); __pyx_t_6 = 0; __pyx_v_i = __pyx_t_12; __pyx_t_12 = (__pyx_t_12 + 1); - /* "ml2.pyx":57 + /* "ml2.pyx":54 * # fail to infect it, also computes the probability that its most * # likely parent infects it - * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< + * failures = [weight_failure(dist, dt, alpha, delta, lmbda, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) */ - __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - /* "ml2.pyx":58 + /* "ml2.pyx":55 * # likely parent infects it - * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) + * failures = [weight_failure(dist, dt, alpha, delta, lmbda, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< * probs_fail[i] = sum(failures) - * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) + * successes = [weight_success(dist, dt, alpha, delta, lmbda, w1, w2, w3) */ if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_5 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_5); __pyx_t_15 = 0; for (;;) { if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_5)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_3 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_3 = PySequence_ITEM(__pyx_t_5, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PySequence_ITEM(__pyx_t_5, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) { PyObject* sequence = __pyx_t_3; @@ -2034,7 +1996,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject if (unlikely(size != 5)) { if (size > 5) __Pyx_RaiseTooManyValuesError(5); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -2060,7 +2022,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject Py_ssize_t i; PyObject** temps[5] = {&__pyx_t_16,&__pyx_t_17,&__pyx_t_18,&__pyx_t_19,&__pyx_t_20}; for (i=0; i < 5; i++) { - PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(item); *(temps[i]) = item; } @@ -2070,7 +2032,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject } else { Py_ssize_t index = -1; PyObject** temps[5] = {&__pyx_t_16,&__pyx_t_17,&__pyx_t_18,&__pyx_t_19,&__pyx_t_20}; - __pyx_t_21 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_21 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_21); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_22 = Py_TYPE(__pyx_t_21)->tp_iternext; @@ -2079,7 +2041,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_GOTREF(item); *(temps[index]) = item; } - if (__Pyx_IternextUnpackEndCheck(__pyx_t_22(__pyx_t_21), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_22(__pyx_t_21), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_22 = NULL; __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0; goto __pyx_L8_unpacking_done; @@ -2087,12 +2049,12 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0; __pyx_t_22 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L8_unpacking_done:; } - __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_16); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_16); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0; - __pyx_t_23 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_23 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_23 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_23 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0; __pyx_v_dist = __pyx_t_14; __pyx_v_dt = __pyx_t_23; @@ -2103,82 +2065,82 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_20); __pyx_t_20 = 0; - /* "ml2.pyx":57 + /* "ml2.pyx":54 * # fail to infect it, also computes the probability that its most * # likely parent infects it - * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< + * failures = [weight_failure(dist, dt, alpha, delta, lmbda, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) */ - __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w1); 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__pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_26 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyFloat_FromDouble(__pyx_f_3ml2_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_lmbda, __pyx_t_24, __pyx_t_25, __pyx_t_26)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_6, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_6, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; 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__pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_26 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_23 = __pyx_v_i; if (__pyx_t_23 < 0) __pyx_t_23 += __pyx_pybuffernd_probs_fail.diminfo[0].shape; *__Pyx_BufPtrStrided1d(__pyx_t_3ml2_DTYPE_t *, __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.buf, __pyx_t_23, __pyx_pybuffernd_probs_fail.diminfo[0].strides) = __pyx_t_26; - /* "ml2.pyx":60 + /* "ml2.pyx":57 * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) - * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< + * successes = [weight_success(dist, dt, alpha, delta, lmbda, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * dists = [dist for (dist, dt, w1, w2, w3) in parents] */ - __pyx_t_5 = PyList_New(0); 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if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0; - __pyx_t_27 = __Pyx_PyInt_As_int(__pyx_t_19); if (unlikely((__pyx_t_27 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_27 = __Pyx_PyInt_As_int(__pyx_t_19); if (unlikely((__pyx_t_27 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; __pyx_v_dist = __pyx_t_14; __pyx_v_dt = __pyx_t_27; @@ -2259,24 +2221,24 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_16); __pyx_t_16 = 0; - /* "ml2.pyx":60 + /* "ml2.pyx":57 * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) - * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< + * successes = [weight_success(dist, dt, alpha, delta, lmbda, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * dists = [dist for (dist, dt, w1, w2, w3) in parents] */ - __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_v_w1); 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__pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyFloat_FromDouble(__pyx_f_3ml2_weight_success(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_lmbda, __pyx_t_26, __pyx_t_25, __pyx_t_24)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "ml2.pyx":61 + /* "ml2.pyx":58 * probs_fail[i] = sum(failures) - * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) + * successes = [weight_success(dist, dt, alpha, delta, lmbda, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< * dists = [dist for (dist, dt, w1, w2, w3) in parents] * dts = [dt for (dist, dt, w1, w2, w3) in parents] @@ -2286,26 +2248,26 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_XDECREF_SET(__pyx_v_successes, ((PyObject*)__pyx_t_5)); __pyx_t_5 = 0; - /* "ml2.pyx":62 - * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) + /* "ml2.pyx":59 + * successes = [weight_success(dist, dt, alpha, delta, lmbda, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] * dists = [dist for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< * dts = [dt for (dist, dt, w1, w2, w3) in parents] * # find parent that maximizes log(p) - log(\tilde{p}) */ - __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_6 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_6); __pyx_t_15 = 0; for (;;) { if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_6)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) { PyObject* sequence = __pyx_t_3; @@ -2317,7 +2279,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject if (unlikely(size != 5)) { if (size > 5) __Pyx_RaiseTooManyValuesError(5); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; 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if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_21 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_21); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_22 = Py_TYPE(__pyx_t_21)->tp_iternext; @@ -2362,7 +2324,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_GOTREF(item); *(temps[index]) = item; } - if (__Pyx_IternextUnpackEndCheck(__pyx_t_22(__pyx_t_21), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_22(__pyx_t_21), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_22 = NULL; __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0; goto __pyx_L16_unpacking_done; @@ -2370,12 +2332,12 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_DECREF(__pyx_t_21); 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if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0; __pyx_v_dist = __pyx_t_27; __pyx_v_dt = __pyx_t_14; @@ -2385,35 +2347,35 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_t_19 = 0; __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_20); __pyx_t_20 = 0; - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_dist); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_dist); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; 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__pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_6 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_6); __pyx_t_15 = 0; for (;;) { if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_6)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) { PyObject* sequence = __pyx_t_3; @@ -2425,7 +2387,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject if (unlikely(size != 5)) { if (size > 5) __Pyx_RaiseTooManyValuesError(5); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -2451,7 +2413,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject Py_ssize_t i; PyObject** temps[5] = {&__pyx_t_20,&__pyx_t_19,&__pyx_t_18,&__pyx_t_17,&__pyx_t_16}; for (i=0; i < 5; i++) { - PyObject* item = PySequence_ITEM(sequence, i); 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__Pyx_INCREF(__pyx_t_6); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_15); __Pyx_INCREF(__pyx_t_6); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_6 = PySequence_ITEM(__pyx_t_5, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PySequence_ITEM(__pyx_t_5, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif __Pyx_XDECREF_SET(__pyx_v_s, __pyx_t_6); __pyx_t_6 = 0; __pyx_v_l = __pyx_t_14; __pyx_t_14 = (__pyx_t_14 + 1); - /* "ml2.pyx":68 + /* "ml2.pyx":65 * probs[i] = float("-inf") * for l, s in enumerate(successes): * prob = s - failures[l] # <<<<<<<<<<<<<< * if prob > probs[i]: * probs[i] = prob */ - __pyx_t_6 = __Pyx_GetItemInt_List(__pyx_v_failures, __pyx_v_l, int, 1, __Pyx_PyInt_From_int, 1, 1, 0); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_6 = __Pyx_GetItemInt_List(__pyx_v_failures, __pyx_v_l, int, 1, __Pyx_PyInt_From_int, 1, 1, 0); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_6); - __pyx_t_3 = PyNumber_Subtract(__pyx_v_s, __pyx_t_6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyNumber_Subtract(__pyx_v_s, __pyx_t_6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_XDECREF_SET(__pyx_v_prob, __pyx_t_3); __pyx_t_3 = 0; - /* "ml2.pyx":69 + /* "ml2.pyx":66 * for l, s in enumerate(successes): * prob = s - failures[l] * if prob > probs[i]: # <<<<<<<<<<<<<< @@ -2559,51 +2521,51 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject */ __pyx_t_29 = __pyx_v_i; if (__pyx_t_29 < 0) __pyx_t_29 += __pyx_pybuffernd_probs.diminfo[0].shape; - __pyx_t_3 = PyFloat_FromDouble((*__Pyx_BufPtrStrided1d(__pyx_t_3ml2_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_probs.diminfo[0].strides))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyFloat_FromDouble((*__Pyx_BufPtrStrided1d(__pyx_t_3ml2_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_probs.diminfo[0].strides))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_6 = PyObject_RichCompare(__pyx_v_prob, __pyx_t_3, Py_GT); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyObject_RichCompare(__pyx_v_prob, __pyx_t_3, Py_GT); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_30 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_30 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_30 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_30 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; if (__pyx_t_30) { - /* "ml2.pyx":70 + /* "ml2.pyx":67 * prob = s - failures[l] * if prob > probs[i]: * probs[i] = prob # <<<<<<<<<<<<<< * parent_dists[i] = dists[l] * parent_dts[i] = dts[l] */ - __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_prob); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_prob); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_31 = __pyx_v_i; if (__pyx_t_31 < 0) __pyx_t_31 += __pyx_pybuffernd_probs.diminfo[0].shape; *__Pyx_BufPtrStrided1d(__pyx_t_3ml2_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_31, __pyx_pybuffernd_probs.diminfo[0].strides) = __pyx_t_24; - /* "ml2.pyx":71 + /* "ml2.pyx":68 * if prob > probs[i]: * probs[i] = prob * parent_dists[i] = dists[l] # <<<<<<<<<<<<<< * parent_dts[i] = dts[l] * */ - __pyx_t_6 = __Pyx_GetItemInt_List(__pyx_v_dists, __pyx_v_l, int, 1, __Pyx_PyInt_From_int, 1, 1, 0); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_6 = __Pyx_GetItemInt_List(__pyx_v_dists, __pyx_v_l, int, 1, __Pyx_PyInt_From_int, 1, 1, 0); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_6); - __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_6); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_6); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_32 = __pyx_v_i; if (__pyx_t_32 < 0) __pyx_t_32 += __pyx_pybuffernd_parent_dists.diminfo[0].shape; *__Pyx_BufPtrStrided1d(__pyx_t_3ml2_DTYPE_t *, __pyx_pybuffernd_parent_dists.rcbuffer->pybuffer.buf, __pyx_t_32, __pyx_pybuffernd_parent_dists.diminfo[0].strides) = __pyx_t_24; - /* "ml2.pyx":72 + /* "ml2.pyx":69 * probs[i] = prob * parent_dists[i] = dists[l] * parent_dts[i] = dts[l] # <<<<<<<<<<<<<< * * # loop through non-victims */ - __pyx_t_6 = __Pyx_GetItemInt_List(__pyx_v_dts, __pyx_v_l, int, 1, __Pyx_PyInt_From_int, 1, 1, 0); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_6 = __Pyx_GetItemInt_List(__pyx_v_dts, __pyx_v_l, int, 1, __Pyx_PyInt_From_int, 1, 1, 0); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_6); - __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_6); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_6); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_33 = __pyx_v_i; if (__pyx_t_33 < 0) __pyx_t_33 += __pyx_pybuffernd_parent_dts.diminfo[0].shape; @@ -2612,7 +2574,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject } __pyx_L23:; - /* "ml2.pyx":67 + /* "ml2.pyx":64 * # probs[i] = max(s - failures[l] for l, s in enumerate(successes)) * probs[i] = float("-inf") * for l, s in enumerate(successes): # <<<<<<<<<<<<<< @@ -2624,7 +2586,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject } __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - /* "ml2.pyx":75 + /* "ml2.pyx":72 * * # loop through non-victims * for i, parents in enumerate(non_victims.itervalues()): # <<<<<<<<<<<<<< @@ -2635,9 +2597,9 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_t_1 = 0; if (unlikely(__pyx_v_non_victims == Py_None)) { PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "itervalues"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_5 = __Pyx_dict_iterator(__pyx_v_non_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_2), (&__pyx_t_13)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_dict_iterator(__pyx_v_non_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_2), (&__pyx_t_13)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = __pyx_t_5; @@ -2645,42 +2607,42 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject while (1) { __pyx_t_14 = __Pyx_dict_iter_next(__pyx_t_4, __pyx_t_2, &__pyx_t_1, NULL, &__pyx_t_5, NULL, __pyx_t_13); if (unlikely(__pyx_t_14 == 0)) break; - if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - if (!(likely(PyList_CheckExact(__pyx_t_5))||((__pyx_t_5) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_5)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(PyList_CheckExact(__pyx_t_5))||((__pyx_t_5) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_5)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_XDECREF_SET(__pyx_v_parents, ((PyObject*)__pyx_t_5)); __pyx_t_5 = 0; __pyx_v_i = __pyx_t_12; __pyx_t_12 = (__pyx_t_12 + 1); - /* "ml2.pyx":78 + /* "ml2.pyx":75 * # for each non victim node, compute the probability that all its * # parents fail to infect it - * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< + * failures = [weight_failure(dist, dt, alpha, delta, lmbda, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * probs_nv[i] = sum(failures) */ - __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - /* "ml2.pyx":79 + /* "ml2.pyx":76 * # parents fail to infect it - * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) + * failures = [weight_failure(dist, dt, alpha, delta, lmbda, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< * probs_nv[i] = sum(failures) * */ if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_6 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_6); __pyx_t_15 = 0; for (;;) { if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_6)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) { PyObject* sequence = __pyx_t_3; @@ -2692,7 +2654,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject if (unlikely(size != 5)) { if (size > 5) __Pyx_RaiseTooManyValuesError(5); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -2718,7 +2680,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject Py_ssize_t i; PyObject** temps[5] = {&__pyx_t_16,&__pyx_t_17,&__pyx_t_18,&__pyx_t_19,&__pyx_t_20}; for (i=0; i < 5; i++) { - PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(item); *(temps[i]) = item; } @@ -2728,7 +2690,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject } else { Py_ssize_t index = -1; PyObject** temps[5] = {&__pyx_t_16,&__pyx_t_17,&__pyx_t_18,&__pyx_t_19,&__pyx_t_20}; - __pyx_t_21 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_21 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_21); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_22 = Py_TYPE(__pyx_t_21)->tp_iternext; @@ -2737,7 +2699,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_GOTREF(item); *(temps[index]) = item; } - if (__Pyx_IternextUnpackEndCheck(__pyx_t_22(__pyx_t_21), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_22(__pyx_t_21), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_22 = NULL; __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0; goto __pyx_L29_unpacking_done; @@ -2745,12 +2707,12 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0; __pyx_t_22 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L29_unpacking_done:; } - __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_16); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_16); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0; - __pyx_t_34 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_34 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_34 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_34 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0; __pyx_v_dist = __pyx_t_14; __pyx_v_dt = __pyx_t_34; @@ -2761,24 +2723,24 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_20); __pyx_t_20 = 0; - /* "ml2.pyx":78 + /* "ml2.pyx":75 * # for each non victim node, compute the probability that all its * # parents fail to infect it - * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< + * failures = [weight_failure(dist, dt, alpha, delta, lmbda, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * probs_nv[i] = sum(failures) */ - __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w1); 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__pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_26 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyFloat_FromDouble(__pyx_f_3ml2_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_lmbda, __pyx_t_24, __pyx_t_25, __pyx_t_26)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "ml2.pyx":79 + /* "ml2.pyx":76 * # parents fail to infect it - * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) + * failures = [weight_failure(dist, dt, alpha, delta, lmbda, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< * probs_nv[i] = sum(failures) * @@ -2788,22 +2750,22 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_XDECREF_SET(__pyx_v_failures, ((PyObject*)__pyx_t_5)); __pyx_t_5 = 0; - /* "ml2.pyx":80 - * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) + /* "ml2.pyx":77 + * failures = [weight_failure(dist, dt, alpha, delta, lmbda, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] * probs_nv[i] = sum(failures) # <<<<<<<<<<<<<< * - * # print successes + * # calculate log likelihood */ - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __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 = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_INCREF(__pyx_v_failures); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_failures); __Pyx_GIVEREF(__pyx_v_failures); - __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_5, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_5, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_t_6); if (unlikely((__pyx_t_26 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_t_6); if (unlikely((__pyx_t_26 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_34 = __pyx_v_i; if (__pyx_t_34 < 0) __pyx_t_34 += __pyx_pybuffernd_probs_nv.diminfo[0].shape; @@ -2811,14 +2773,14 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject } __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - /* "ml2.pyx":90 - * # cdef: - * # np.ndarray[DTYPE_t] cums = probs.cumsum() + /* "ml2.pyx":80 + * + * # calculate log likelihood * ll = probs_fail.sum() # add probability that all edges to victims fail # <<<<<<<<<<<<<< * ll += probs_nv.sum() # add probability that all edges to non_victims fail * ll += probs.sum() # add probability for realized edges and subtract probability these edges fail */ - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs_fail), __pyx_n_s_sum); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs_fail), __pyx_n_s_sum); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __pyx_t_5 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_6))) { @@ -2831,27 +2793,27 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject } } if (__pyx_t_5) { - __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } else { - __pyx_t_4 = __Pyx_PyObject_CallNoArg(__pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_CallNoArg(__pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_t_4); if (unlikely((__pyx_t_26 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_t_4); if (unlikely((__pyx_t_26 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_v_ll = __pyx_t_26; - /* "ml2.pyx":91 - * # np.ndarray[DTYPE_t] cums = probs.cumsum() + /* "ml2.pyx":81 + * # calculate log likelihood * ll = probs_fail.sum() # add probability that all edges to victims fail * ll += probs_nv.sum() # add probability that all edges to non_victims fail # <<<<<<<<<<<<<< * ll += probs.sum() # add probability for realized edges and subtract probability these edges fail * */ - __pyx_t_4 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs_nv), __pyx_n_s_sum); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs_nv), __pyx_n_s_sum); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_3 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_5))) { @@ -2864,31 +2826,31 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject } } if (__pyx_t_3) { - __pyx_t_6 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; } else { - __pyx_t_6 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_t_4, __pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_t_4, __pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_26 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_26 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_v_ll = __pyx_t_26; - /* "ml2.pyx":92 + /* "ml2.pyx":82 * ll = probs_fail.sum() # add probability that all edges to victims fail * ll += probs_nv.sum() # add probability that all edges to non_victims fail * ll += probs.sum() # add probability for realized edges and subtract probability these edges fail # <<<<<<<<<<<<<< * * roots = n_roots */ - __pyx_t_5 = PyFloat_FromDouble(__pyx_v_ll); 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