diff options
Diffstat (limited to 'experiments/ml.c')
| -rw-r--r-- | experiments/ml.c | 772 |
1 files changed, 425 insertions, 347 deletions
diff --git a/experiments/ml.c b/experiments/ml.c index 67e5cd1..1ae9098 100644 --- a/experiments/ml.c +++ b/experiments/ml.c @@ -773,12 +773,12 @@ struct __pyx_obj_2ml___pyx_scope_struct__ml { }; -/* "ml.pyx":71 - * successes = [weight_success(dist, dt, alpha, delta, gamma) - * for (dist, dt) in parents] +/* "ml.pyx":74 + * for (dist, dt, w1, w2, w3) in parents] + * # find parent that maximizes p/\tilde{p} * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) # <<<<<<<<<<<<<< - * probs_fail[i] = all_failures * + * # loop through non-victims */ struct __pyx_obj_2ml___pyx_scope_struct_1_genexpr { PyObject_HEAD @@ -1284,6 +1284,9 @@ static char __pyx_k_dt[] = "dt"; static char __pyx_k_ll[] = "ll"; static char __pyx_k_ml[] = "ml"; 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_end[] = "end"; static char __pyx_k_max[] = "max"; @@ -1331,7 +1334,6 @@ static char __pyx_k_itervalues[] = "itervalues"; static char __pyx_k_probs_fail[] = "probs_fail"; static char __pyx_k_non_victims[] = "non_victims"; static char __pyx_k_RuntimeError[] = "RuntimeError"; -static char __pyx_k_all_failures[] = "all_failures"; static char __pyx_k_root_victims[] = "root_victims"; static char __pyx_k_ml_locals_genexpr[] = "ml.<locals>.genexpr"; static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; @@ -1350,7 +1352,6 @@ 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_all_failures; static PyObject *__pyx_n_s_alpha; static PyObject *__pyx_kp_s_alpha_0_delta_1_Everyone_is_a_ro; static PyObject *__pyx_n_s_args; @@ -1405,6 +1406,9 @@ static PyObject *__pyx_n_s_test; static PyObject *__pyx_n_s_throw; static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; static PyObject *__pyx_n_s_victims; +static PyObject *__pyx_n_s_w1; +static PyObject *__pyx_n_s_w2; +static PyObject *__pyx_n_s_w3; static PyObject *__pyx_n_s_xrange; static PyObject *__pyx_n_s_zeros; static PyObject *__pyx_int_neg_1; @@ -1815,12 +1819,12 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py } static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */ -/* "ml.pyx":71 - * successes = [weight_success(dist, dt, alpha, delta, gamma) - * for (dist, dt) in parents] +/* "ml.pyx":74 + * for (dist, dt, w1, w2, w3) in parents] + * # find parent that maximizes p/\tilde{p} * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) # <<<<<<<<<<<<<< - * probs_fail[i] = all_failures * + * # loop through non-victims */ static PyObject *__pyx_pf_2ml_2ml_genexpr(PyObject *__pyx_self) { @@ -1841,7 +1845,7 @@ static PyObject *__pyx_pf_2ml_2ml_genexpr(PyObject *__pyx_self) { __Pyx_INCREF(((PyObject *)__pyx_cur_scope->__pyx_outer_scope)); __Pyx_GIVEREF(__pyx_cur_scope->__pyx_outer_scope); { - __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_2ml_2ml_2generator, (PyObject *) __pyx_cur_scope, __pyx_n_s_genexpr, __pyx_n_s_ml_locals_genexpr); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_2ml_2ml_2generator, (PyObject *) __pyx_cur_scope, __pyx_n_s_genexpr, __pyx_n_s_ml_locals_genexpr); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_cur_scope); __Pyx_RefNannyFinishContext(); return (PyObject *) gen; @@ -1879,16 +1883,16 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera return NULL; } __pyx_L3_first_run:; - if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_1 = 0; - if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_successes)) { __Pyx_RaiseClosureNameError("successes"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } + if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_successes)) { __Pyx_RaiseClosureNameError("successes"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_2 = __pyx_cur_scope->__pyx_outer_scope->__pyx_v_successes; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0; for (;;) { if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_4); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_4); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif __Pyx_XGOTREF(__pyx_cur_scope->__pyx_v_s); __Pyx_XDECREF_SET(__pyx_cur_scope->__pyx_v_s, __pyx_t_4); @@ -1896,14 +1900,14 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera __pyx_t_4 = 0; __pyx_cur_scope->__pyx_v_l = __pyx_t_1; __pyx_t_1 = (__pyx_t_1 + 1); - if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures)) { __Pyx_RaiseClosureNameError("failures"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } + if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures)) { __Pyx_RaiseClosureNameError("failures"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } if (unlikely(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_4 = __Pyx_GetItemInt_List(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures, __pyx_cur_scope->__pyx_v_l, Py_ssize_t, 1, PyInt_FromSsize_t, 1, 1, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_4 = __Pyx_GetItemInt_List(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures, __pyx_cur_scope->__pyx_v_l, Py_ssize_t, 1, PyInt_FromSsize_t, 1, 1, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = PyNumber_Subtract(__pyx_cur_scope->__pyx_v_s, __pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyNumber_Subtract(__pyx_cur_scope->__pyx_v_s, __pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_r = __pyx_t_5; @@ -1923,7 +1927,7 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera __pyx_cur_scope->__pyx_t_1 = 0; __Pyx_XGOTREF(__pyx_t_2); __pyx_t_3 = __pyx_cur_scope->__pyx_t_2; - if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -1961,13 +1965,15 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ int __pyx_v_dist; int __pyx_v_dt; __pyx_t_2ml_DTYPE_t __pyx_v_beta; - __pyx_t_2ml_DTYPE_t __pyx_v_all_failures; __pyx_t_2ml_DTYPE_t __pyx_v_ll; PyObject *__pyx_v_parents = 0; PyArrayObject *__pyx_v_probs = 0; PyArrayObject *__pyx_v_probs_fail = 0; PyArrayObject *__pyx_v_probs_nv = 0; PyArrayObject *__pyx_v_cums = 0; + CYTHON_UNUSED PyObject *__pyx_v_w1 = NULL; + CYTHON_UNUSED PyObject *__pyx_v_w2 = NULL; + CYTHON_UNUSED PyObject *__pyx_v_w3 = NULL; __Pyx_LocalBuf_ND __pyx_pybuffernd_cums; __Pyx_Buffer __pyx_pybuffer_cums; __Pyx_LocalBuf_ND __pyx_pybuffernd_probs; @@ -1994,16 +2000,19 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ PyObject *__pyx_t_14 = NULL; PyObject *__pyx_t_15 = NULL; PyObject *__pyx_t_16 = NULL; - PyObject *(*__pyx_t_17)(PyObject *); - int __pyx_t_18; - __pyx_t_2ml_DTYPE_t __pyx_t_19; - int __pyx_t_20; + PyObject *__pyx_t_17 = NULL; + PyObject *__pyx_t_18 = NULL; + PyObject *__pyx_t_19 = NULL; + PyObject *(*__pyx_t_20)(PyObject *); int __pyx_t_21; - PyObject *__pyx_t_22 = NULL; - PyObject *__pyx_t_23 = NULL; - PyObject *__pyx_t_24 = NULL; - PyArrayObject *__pyx_t_25 = NULL; - int __pyx_t_26; + __pyx_t_2ml_DTYPE_t __pyx_t_22; + int __pyx_t_23; + int __pyx_t_24; + PyObject *__pyx_t_25 = NULL; + PyObject *__pyx_t_26 = NULL; + PyObject *__pyx_t_27 = NULL; + PyArrayObject *__pyx_t_28 = NULL; + int __pyx_t_29; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -2032,10 +2041,10 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_pybuffernd_cums.rcbuffer = &__pyx_pybuffer_cums; /* "ml.pyx":56 - * DTYPE_t beta, all_failures, ll, beta2 + * DTYPE_t beta, ll, beta2 * list parents, failures, successes * n_roots, n_victims = len(root_victims), len(victims) # <<<<<<<<<<<<<< - * n_nodes = n_victims + len(non_victims) + n_roots + * n_nodes = n_roots + n_victims + len(non_victims) * cdef: */ if (unlikely(__pyx_v_root_victims == Py_None)) { @@ -2054,7 +2063,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ /* "ml.pyx":57 * list parents, failures, successes * n_roots, n_victims = len(root_victims), len(victims) - * n_nodes = n_victims + len(non_victims) + n_roots # <<<<<<<<<<<<<< + * n_nodes = n_roots + n_victims + len(non_victims) # <<<<<<<<<<<<<< * cdef: * np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE) */ @@ -2063,10 +2072,10 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __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 = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_n_nodes = ((__pyx_v_n_victims + __pyx_t_2) + __pyx_v_n_roots); + __pyx_v_n_nodes = ((__pyx_v_n_roots + __pyx_v_n_victims) + __pyx_t_2); /* "ml.pyx":59 - * n_nodes = n_victims + len(non_victims) + n_roots + * n_nodes = n_roots + n_victims + len(non_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) @@ -2114,7 +2123,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ * 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) - * for i, parents in enumerate(victims.itervalues()): + * */ __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); @@ -2157,8 +2166,8 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ * 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) # <<<<<<<<<<<<<< - * for i, parents in enumerate(victims.itervalues()): - * # for each victim node i, compute the probability that all its parents + * + * # loop through victims */ __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); @@ -2202,9 +2211,9 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_v_probs_nv = ((PyArrayObject *)__pyx_t_3); __pyx_t_3 = 0; - /* "ml.pyx":62 - * 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) + /* "ml.pyx":64 + * + * # loop through victims * for i, parents in enumerate(victims.itervalues()): # <<<<<<<<<<<<<< * # for each victim node i, compute the probability that all its parents * # fail to infect it, also computes the probability that its most @@ -2213,9 +2222,9 @@ static PyObject *__pyx_pf_2ml_ml(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 = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_4 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_11)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_11)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = __pyx_t_4; @@ -2223,42 +2232,42 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ while (1) { __pyx_t_12 = __Pyx_dict_iter_next(__pyx_t_3, __pyx_t_1, &__pyx_t_2, NULL, &__pyx_t_4, NULL, __pyx_t_11); if (unlikely(__pyx_t_12 == 0)) break; - if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - if (!(likely(PyList_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_4)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(PyList_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_4)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_XDECREF_SET(__pyx_v_parents, ((PyObject*)__pyx_t_4)); __pyx_t_4 = 0; __pyx_v_i = __pyx_t_10; __pyx_t_10 = (__pyx_t_10 + 1); - /* "ml.pyx":66 + /* "ml.pyx":68 * # fail to infect it, also computes the probability that its most * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, gamma) # <<<<<<<<<<<<<< - * for (dist, dt) in parents] - * all_failures = sum(failures) + * for (dist, dt, w1, w2, w3) in parents] + * probs_fail[i] = sum(failures) */ - __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - /* "ml.pyx":67 + /* "ml.pyx":69 * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, gamma) - * for (dist, dt) in parents] # <<<<<<<<<<<<<< - * all_failures = sum(failures) + * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< + * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, gamma) */ if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_5 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_5); __pyx_t_13 = 0; for (;;) { if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_5)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_6 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; 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_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_6 = PySequence_ITEM(__pyx_t_5, __pyx_t_13); __pyx_t_13++; 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_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) { PyObject* sequence = __pyx_t_6; @@ -2267,73 +2276,95 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ #else Py_ssize_t size = PySequence_Size(sequence); #endif - if (unlikely(size != 2)) { - if (size > 2) __Pyx_RaiseTooManyValuesError(2); + if (unlikely(size != 5)) { + if (size > 5) __Pyx_RaiseTooManyValuesError(5); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { __pyx_t_14 = PyTuple_GET_ITEM(sequence, 0); __pyx_t_15 = PyTuple_GET_ITEM(sequence, 1); + __pyx_t_16 = PyTuple_GET_ITEM(sequence, 2); + __pyx_t_17 = PyTuple_GET_ITEM(sequence, 3); + __pyx_t_18 = PyTuple_GET_ITEM(sequence, 4); } else { __pyx_t_14 = PyList_GET_ITEM(sequence, 0); __pyx_t_15 = PyList_GET_ITEM(sequence, 1); + __pyx_t_16 = PyList_GET_ITEM(sequence, 2); + __pyx_t_17 = PyList_GET_ITEM(sequence, 3); + __pyx_t_18 = PyList_GET_ITEM(sequence, 4); } __Pyx_INCREF(__pyx_t_14); __Pyx_INCREF(__pyx_t_15); + __Pyx_INCREF(__pyx_t_16); + __Pyx_INCREF(__pyx_t_17); + __Pyx_INCREF(__pyx_t_18); #else - __pyx_t_14 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_14); - __pyx_t_15 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_15); + { + Py_ssize_t i; + PyObject** temps[5] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_16,&__pyx_t_17,&__pyx_t_18}; + for (i=0; i < 5; i++) { + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(item); + *(temps[i]) = item; + } + } #endif __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; } else { Py_ssize_t index = -1; - __pyx_t_16 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_16); + PyObject** temps[5] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_16,&__pyx_t_17,&__pyx_t_18}; + __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_19); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_17 = Py_TYPE(__pyx_t_16)->tp_iternext; - index = 0; __pyx_t_14 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_14)) goto __pyx_L7_unpacking_failed; - __Pyx_GOTREF(__pyx_t_14); - index = 1; __pyx_t_15 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_15)) goto __pyx_L7_unpacking_failed; - __Pyx_GOTREF(__pyx_t_15); - if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_16), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_17 = NULL; - __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0; + __pyx_t_20 = Py_TYPE(__pyx_t_19)->tp_iternext; + for (index=0; index < 5; index++) { + PyObject* item = __pyx_t_20(__pyx_t_19); if (unlikely(!item)) goto __pyx_L7_unpacking_failed; + __Pyx_GOTREF(item); + *(temps[index]) = item; + } + if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_20 = NULL; + __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; goto __pyx_L8_unpacking_done; __pyx_L7_unpacking_failed:; - __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0; - __pyx_t_17 = NULL; + __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; + __pyx_t_20 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L8_unpacking_done:; } - __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; - __pyx_t_18 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_18 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_21 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_21 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0; __pyx_v_dist = __pyx_t_12; - __pyx_v_dt = __pyx_t_18; + __pyx_v_dt = __pyx_t_21; + __Pyx_XDECREF_SET(__pyx_v_w1, __pyx_t_16); + __pyx_t_16 = 0; + __Pyx_XDECREF_SET(__pyx_v_w2, __pyx_t_17); + __pyx_t_17 = 0; + __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_18); + __pyx_t_18 = 0; - /* "ml.pyx":66 + /* "ml.pyx":68 * # fail to infect it, also computes the probability that its most * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, gamma) # <<<<<<<<<<<<<< - * for (dist, dt) in parents] - * all_failures = sum(failures) + * for (dist, dt, w1, w2, w3) in parents] + * probs_fail[i] = sum(failures) */ - __pyx_t_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_gamma)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_gamma)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_4, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_4, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "ml.pyx":67 + /* "ml.pyx":69 * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, gamma) - * for (dist, dt) in parents] # <<<<<<<<<<<<<< - * all_failures = sum(failures) + * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< + * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, gamma) */ } @@ -2343,53 +2374,55 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GIVEREF(__pyx_t_4); __pyx_t_4 = 0; - /* "ml.pyx":68 + /* "ml.pyx":70 * failures = [weight_failure(dist, dt, alpha, delta, gamma) - * for (dist, dt) in parents] - * all_failures = sum(failures) # <<<<<<<<<<<<<< + * for (dist, dt, w1, w2, w3) in parents] + * probs_fail[i] = sum(failures) # <<<<<<<<<<<<<< * successes = [weight_success(dist, dt, alpha, delta, gamma) - * for (dist, dt) in parents] + * for (dist, dt, w1, w2, w3) in parents] */ - __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_INCREF(__pyx_cur_scope->__pyx_v_failures); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_cur_scope->__pyx_v_failures); __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_failures); - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_19 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_19 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_v_all_failures = __pyx_t_19; + __pyx_t_21 = __pyx_v_i; + if (__pyx_t_21 < 0) __pyx_t_21 += __pyx_pybuffernd_probs_fail.diminfo[0].shape; + *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_probs_fail.diminfo[0].strides) = __pyx_t_22; - /* "ml.pyx":69 - * for (dist, dt) in parents] - * all_failures = sum(failures) + /* "ml.pyx":71 + * for (dist, dt, w1, w2, w3) in parents] + * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, gamma) # <<<<<<<<<<<<<< - * for (dist, dt) in parents] - * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) + * for (dist, dt, w1, w2, w3) in parents] + * # find parent that maximizes p/\tilde{p} */ - __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __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 = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - /* "ml.pyx":70 - * all_failures = sum(failures) + /* "ml.pyx":72 + * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, gamma) - * for (dist, dt) in parents] # <<<<<<<<<<<<<< + * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< + * # find parent that maximizes p/\tilde{p} * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) - * probs_fail[i] = all_failures */ if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_4 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_4); __pyx_t_13 = 0; for (;;) { if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_4)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_6 = PySequence_ITEM(__pyx_t_4, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PySequence_ITEM(__pyx_t_4, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) { PyObject* sequence = __pyx_t_6; @@ -2398,74 +2431,96 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ #else Py_ssize_t size = PySequence_Size(sequence); #endif - if (unlikely(size != 2)) { - if (size > 2) __Pyx_RaiseTooManyValuesError(2); + if (unlikely(size != 5)) { + if (size > 5) __Pyx_RaiseTooManyValuesError(5); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { - __pyx_t_15 = PyTuple_GET_ITEM(sequence, 0); - __pyx_t_14 = PyTuple_GET_ITEM(sequence, 1); + __pyx_t_18 = PyTuple_GET_ITEM(sequence, 0); + __pyx_t_17 = PyTuple_GET_ITEM(sequence, 1); + __pyx_t_16 = PyTuple_GET_ITEM(sequence, 2); + __pyx_t_15 = PyTuple_GET_ITEM(sequence, 3); + __pyx_t_14 = PyTuple_GET_ITEM(sequence, 4); } else { - __pyx_t_15 = PyList_GET_ITEM(sequence, 0); - __pyx_t_14 = PyList_GET_ITEM(sequence, 1); + __pyx_t_18 = PyList_GET_ITEM(sequence, 0); + __pyx_t_17 = PyList_GET_ITEM(sequence, 1); + __pyx_t_16 = PyList_GET_ITEM(sequence, 2); + __pyx_t_15 = PyList_GET_ITEM(sequence, 3); + __pyx_t_14 = PyList_GET_ITEM(sequence, 4); } + __Pyx_INCREF(__pyx_t_18); + __Pyx_INCREF(__pyx_t_17); + __Pyx_INCREF(__pyx_t_16); __Pyx_INCREF(__pyx_t_15); __Pyx_INCREF(__pyx_t_14); #else - __pyx_t_15 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_15); - __pyx_t_14 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_14); + { + Py_ssize_t i; + PyObject** temps[5] = {&__pyx_t_18,&__pyx_t_17,&__pyx_t_16,&__pyx_t_15,&__pyx_t_14}; + for (i=0; i < 5; i++) { + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(item); + *(temps[i]) = item; + } + } #endif __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; } else { Py_ssize_t index = -1; - __pyx_t_16 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_16); + PyObject** temps[5] = {&__pyx_t_18,&__pyx_t_17,&__pyx_t_16,&__pyx_t_15,&__pyx_t_14}; + __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_19); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_17 = Py_TYPE(__pyx_t_16)->tp_iternext; - index = 0; __pyx_t_15 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_15)) goto __pyx_L11_unpacking_failed; - __Pyx_GOTREF(__pyx_t_15); - index = 1; __pyx_t_14 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_14)) goto __pyx_L11_unpacking_failed; - __Pyx_GOTREF(__pyx_t_14); - if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_16), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_17 = NULL; - __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0; + __pyx_t_20 = Py_TYPE(__pyx_t_19)->tp_iternext; + for (index=0; index < 5; index++) { + PyObject* item = __pyx_t_20(__pyx_t_19); if (unlikely(!item)) goto __pyx_L11_unpacking_failed; + __Pyx_GOTREF(item); + *(temps[index]) = item; + } + if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_20 = NULL; + __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; goto __pyx_L12_unpacking_done; __pyx_L11_unpacking_failed:; - __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0; - __pyx_t_17 = NULL; + __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; + __pyx_t_20 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L12_unpacking_done:; } - __pyx_t_18 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_18 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0; - __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; - __pyx_v_dist = __pyx_t_18; - __pyx_v_dt = __pyx_t_12; + __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_18); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 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 = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0; + __pyx_v_dist = __pyx_t_12; + __pyx_v_dt = __pyx_t_23; + __Pyx_XDECREF_SET(__pyx_v_w1, __pyx_t_16); + __pyx_t_16 = 0; + __Pyx_XDECREF_SET(__pyx_v_w2, __pyx_t_15); + __pyx_t_15 = 0; + __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_14); + __pyx_t_14 = 0; - /* "ml.pyx":69 - * for (dist, dt) in parents] - * all_failures = sum(failures) + /* "ml.pyx":71 + * for (dist, dt, w1, w2, w3) in parents] + * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, gamma) # <<<<<<<<<<<<<< - * for (dist, dt) in parents] - * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) + * for (dist, dt, w1, w2, w3) in parents] + * # find parent that maximizes p/\tilde{p} */ - __pyx_t_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_success(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_gamma)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_success(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_gamma)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "ml.pyx":70 - * all_failures = sum(failures) + /* "ml.pyx":72 + * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, gamma) - * for (dist, dt) in parents] # <<<<<<<<<<<<<< + * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< + * # find parent that maximizes p/\tilde{p} * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) - * probs_fail[i] = all_failures */ } __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -2474,45 +2529,34 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = 0; - /* "ml.pyx":71 - * successes = [weight_success(dist, dt, alpha, delta, gamma) - * for (dist, dt) in parents] + /* "ml.pyx":74 + * for (dist, dt, w1, w2, w3) in parents] + * # find parent that maximizes p/\tilde{p} * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) # <<<<<<<<<<<<<< - * probs_fail[i] = all_failures * + * # loop through non-victims */ - __pyx_t_5 = __pyx_pf_2ml_2ml_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __pyx_pf_2ml_2ml_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_max, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_max, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_19 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_19 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_12 = __pyx_v_i; - if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_probs.diminfo[0].shape; - *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_probs.diminfo[0].strides) = __pyx_t_19; - - /* "ml.pyx":72 - * for (dist, dt) in parents] - * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) - * probs_fail[i] = all_failures # <<<<<<<<<<<<<< - * - * for i, parents in enumerate(non_victims.itervalues()): - */ - __pyx_t_18 = __pyx_v_i; - if (__pyx_t_18 < 0) __pyx_t_18 += __pyx_pybuffernd_probs_fail.diminfo[0].shape; - *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_probs_fail.diminfo[0].strides) = __pyx_v_all_failures; + __pyx_t_23 = __pyx_v_i; + if (__pyx_t_23 < 0) __pyx_t_23 += __pyx_pybuffernd_probs.diminfo[0].shape; + *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_23, __pyx_pybuffernd_probs.diminfo[0].strides) = __pyx_t_22; } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "ml.pyx":74 - * probs_fail[i] = all_failures + /* "ml.pyx":77 * + * # loop through non-victims * for i, parents in enumerate(non_victims.itervalues()): # <<<<<<<<<<<<<< * # for each non victim node, compute the probability that all its * # parents fail to infect it @@ -2521,52 +2565,52 @@ static PyObject *__pyx_pf_2ml_ml(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 = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __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_11)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __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_11)); 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_XDECREF(__pyx_t_3); __pyx_t_3 = __pyx_t_5; __pyx_t_5 = 0; while (1) { - __pyx_t_20 = __Pyx_dict_iter_next(__pyx_t_3, __pyx_t_2, &__pyx_t_1, NULL, &__pyx_t_5, NULL, __pyx_t_11); - if (unlikely(__pyx_t_20 == 0)) break; - if (unlikely(__pyx_t_20 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_12 = __Pyx_dict_iter_next(__pyx_t_3, __pyx_t_2, &__pyx_t_1, NULL, &__pyx_t_5, NULL, __pyx_t_11); + if (unlikely(__pyx_t_12 == 0)) break; + if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __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 = 74; __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 = 77; __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_10; __pyx_t_10 = (__pyx_t_10 + 1); - /* "ml.pyx":77 + /* "ml.pyx":80 * # for each non victim node, compute the probability that all its * # parents fail to infect it * failures = [weight_failure(dist, dt, alpha, delta, gamma) # <<<<<<<<<<<<<< - * for (dist, dt) in parents] + * 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 = 77; __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 = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - /* "ml.pyx":78 + /* "ml.pyx":81 * # parents fail to infect it * failures = [weight_failure(dist, dt, alpha, delta, gamma) - * for (dist, dt) in parents] # <<<<<<<<<<<<<< + * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< * probs_nv[i] = sum(failures) - * probs.sort() + * */ if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_4 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_4); __pyx_t_13 = 0; for (;;) { if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_4)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_6 = PySequence_ITEM(__pyx_t_4, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PySequence_ITEM(__pyx_t_4, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) { PyObject* sequence = __pyx_t_6; @@ -2575,74 +2619,96 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ #else Py_ssize_t size = PySequence_Size(sequence); #endif - if (unlikely(size != 2)) { - if (size > 2) __Pyx_RaiseTooManyValuesError(2); + if (unlikely(size != 5)) { + if (size > 5) __Pyx_RaiseTooManyValuesError(5); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { __pyx_t_14 = PyTuple_GET_ITEM(sequence, 0); __pyx_t_15 = PyTuple_GET_ITEM(sequence, 1); + __pyx_t_16 = PyTuple_GET_ITEM(sequence, 2); + __pyx_t_17 = PyTuple_GET_ITEM(sequence, 3); + __pyx_t_18 = PyTuple_GET_ITEM(sequence, 4); } else { __pyx_t_14 = PyList_GET_ITEM(sequence, 0); __pyx_t_15 = PyList_GET_ITEM(sequence, 1); + __pyx_t_16 = PyList_GET_ITEM(sequence, 2); + __pyx_t_17 = PyList_GET_ITEM(sequence, 3); + __pyx_t_18 = PyList_GET_ITEM(sequence, 4); } __Pyx_INCREF(__pyx_t_14); __Pyx_INCREF(__pyx_t_15); + __Pyx_INCREF(__pyx_t_16); + __Pyx_INCREF(__pyx_t_17); + __Pyx_INCREF(__pyx_t_18); #else - __pyx_t_14 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_14); - __pyx_t_15 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_15); + { + Py_ssize_t i; + PyObject** temps[5] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_16,&__pyx_t_17,&__pyx_t_18}; + for (i=0; i < 5; i++) { + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(item); + *(temps[i]) = item; + } + } #endif __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; } else { Py_ssize_t index = -1; - __pyx_t_16 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_16); + PyObject** temps[5] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_16,&__pyx_t_17,&__pyx_t_18}; + __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_19); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_17 = Py_TYPE(__pyx_t_16)->tp_iternext; - index = 0; __pyx_t_14 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_14)) goto __pyx_L17_unpacking_failed; - __Pyx_GOTREF(__pyx_t_14); - index = 1; __pyx_t_15 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_15)) goto __pyx_L17_unpacking_failed; - __Pyx_GOTREF(__pyx_t_15); - if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_16), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_17 = NULL; - __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0; + __pyx_t_20 = Py_TYPE(__pyx_t_19)->tp_iternext; + for (index=0; index < 5; index++) { + PyObject* item = __pyx_t_20(__pyx_t_19); if (unlikely(!item)) goto __pyx_L17_unpacking_failed; + __Pyx_GOTREF(item); + *(temps[index]) = item; + } + if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_20 = NULL; + __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; goto __pyx_L18_unpacking_done; __pyx_L17_unpacking_failed:; - __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0; - __pyx_t_17 = NULL; + __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; + __pyx_t_20 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L18_unpacking_done:; } - __pyx_t_20 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_20 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; - __pyx_t_21 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_21 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_24 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0; - __pyx_v_dist = __pyx_t_20; - __pyx_v_dt = __pyx_t_21; + __pyx_v_dist = __pyx_t_12; + __pyx_v_dt = __pyx_t_24; + __Pyx_XDECREF_SET(__pyx_v_w1, __pyx_t_16); + __pyx_t_16 = 0; + __Pyx_XDECREF_SET(__pyx_v_w2, __pyx_t_17); + __pyx_t_17 = 0; + __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_18); + __pyx_t_18 = 0; - /* "ml.pyx":77 + /* "ml.pyx":80 * # for each non victim node, compute the probability that all its * # parents fail to infect it * failures = [weight_failure(dist, dt, alpha, delta, gamma) # <<<<<<<<<<<<<< - * for (dist, dt) in parents] + * for (dist, dt, w1, w2, w3) in parents] * probs_nv[i] = sum(failures) */ - __pyx_t_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_gamma)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_gamma)); 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); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "ml.pyx":78 + /* "ml.pyx":81 * # parents fail to infect it * failures = [weight_failure(dist, dt, alpha, delta, gamma) - * for (dist, dt) in parents] # <<<<<<<<<<<<<< + * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< * probs_nv[i] = sum(failures) - * probs.sort() + * */ } __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -2651,37 +2717,37 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = 0; - /* "ml.pyx":79 + /* "ml.pyx":82 * failures = [weight_failure(dist, dt, alpha, delta, gamma) - * for (dist, dt) in parents] + * for (dist, dt, w1, w2, w3) in parents] * probs_nv[i] = sum(failures) # <<<<<<<<<<<<<< - * probs.sort() - * probs = probs[::-1] + * + * # calculate log likelihood */ - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __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 = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_INCREF(__pyx_cur_scope->__pyx_v_failures); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_cur_scope->__pyx_v_failures); __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_failures); - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_5, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_5, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_19 = __pyx_PyFloat_AsDouble(__pyx_t_4); if (unlikely((__pyx_t_19 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_t_4); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_21 = __pyx_v_i; - if (__pyx_t_21 < 0) __pyx_t_21 += __pyx_pybuffernd_probs_nv.diminfo[0].shape; - *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs_nv.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_probs_nv.diminfo[0].strides) = __pyx_t_19; + __pyx_t_24 = __pyx_v_i; + if (__pyx_t_24 < 0) __pyx_t_24 += __pyx_pybuffernd_probs_nv.diminfo[0].shape; + *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs_nv.rcbuffer->pybuffer.buf, __pyx_t_24, __pyx_pybuffernd_probs_nv.diminfo[0].strides) = __pyx_t_22; } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "ml.pyx":80 - * for (dist, dt) in parents] - * probs_nv[i] = sum(failures) - * probs.sort() # <<<<<<<<<<<<<< - * probs = probs[::-1] + /* "ml.pyx":85 + * + * # calculate log likelihood + * probs.sort(); probs = probs[::-1] # sort probs in descending order # <<<<<<<<<<<<<< * cdef: + * np.ndarray[DTYPE_t] cums = probs.cumsum() */ - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs), __pyx_n_s_sort); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs), __pyx_n_s_sort); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_5 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_4))) { @@ -2694,54 +2760,46 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } } if (__pyx_t_5) { - __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } else { - __pyx_t_3 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - - /* "ml.pyx":81 - * probs_nv[i] = sum(failures) - * probs.sort() - * probs = probs[::-1] # <<<<<<<<<<<<<< - * cdef: - * np.ndarray[DTYPE_t] cums = probs.cumsum() - */ - __pyx_t_3 = PyObject_GetItem(((PyObject *)__pyx_v_probs), __pyx_slice_); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_3 = PyObject_GetItem(((PyObject *)__pyx_v_probs), __pyx_slice_); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_3); - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __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]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_7 = ((PyArrayObject *)__pyx_t_3); { __Pyx_BufFmt_StackElem __pyx_stack[1]; __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_probs.rcbuffer->pybuffer); __pyx_t_10 = __Pyx_GetBufferAndValidate(&__pyx_pybuffernd_probs.rcbuffer->pybuffer, (PyObject*)__pyx_t_7, &__Pyx_TypeInfo_nn___pyx_t_2ml_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack); if (unlikely(__pyx_t_10 < 0)) { - PyErr_Fetch(&__pyx_t_22, &__pyx_t_23, &__pyx_t_24); + PyErr_Fetch(&__pyx_t_25, &__pyx_t_26, &__pyx_t_27); if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_probs.rcbuffer->pybuffer, (PyObject*)__pyx_v_probs, &__Pyx_TypeInfo_nn___pyx_t_2ml_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) { - Py_XDECREF(__pyx_t_22); Py_XDECREF(__pyx_t_23); Py_XDECREF(__pyx_t_24); + Py_XDECREF(__pyx_t_25); Py_XDECREF(__pyx_t_26); Py_XDECREF(__pyx_t_27); __Pyx_RaiseBufferFallbackError(); } else { - PyErr_Restore(__pyx_t_22, __pyx_t_23, __pyx_t_24); + PyErr_Restore(__pyx_t_25, __pyx_t_26, __pyx_t_27); } } __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]; - if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_7 = 0; __Pyx_DECREF_SET(__pyx_v_probs, ((PyArrayObject *)__pyx_t_3)); __pyx_t_3 = 0; - /* "ml.pyx":83 - * probs = probs[::-1] + /* "ml.pyx":87 + * probs.sort(); probs = probs[::-1] # sort probs in descending order * cdef: * np.ndarray[DTYPE_t] cums = probs.cumsum() # <<<<<<<<<<<<<< * ll = probs_fail.sum() * ll += probs_nv.sum() */ - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs), __pyx_n_s_cumsum); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs), __pyx_n_s_cumsum); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_5 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_4))) { @@ -2754,35 +2812,35 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } } if (__pyx_t_5) { - __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } else { - __pyx_t_3 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_GOTREF(__pyx_t_3); __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 = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_25 = ((PyArrayObject *)__pyx_t_3); + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_28 = ((PyArrayObject *)__pyx_t_3); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_cums.rcbuffer->pybuffer, (PyObject*)__pyx_t_25, &__Pyx_TypeInfo_nn___pyx_t_2ml_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_cums.rcbuffer->pybuffer, (PyObject*)__pyx_t_28, &__Pyx_TypeInfo_nn___pyx_t_2ml_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) { __pyx_v_cums = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_cums.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_cums.diminfo[0].strides = __pyx_pybuffernd_cums.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_cums.diminfo[0].shape = __pyx_pybuffernd_cums.rcbuffer->pybuffer.shape[0]; } } - __pyx_t_25 = 0; + __pyx_t_28 = 0; __pyx_v_cums = ((PyArrayObject *)__pyx_t_3); __pyx_t_3 = 0; - /* "ml.pyx":84 + /* "ml.pyx":88 * cdef: * np.ndarray[DTYPE_t] cums = probs.cumsum() * ll = probs_fail.sum() # <<<<<<<<<<<<<< * ll += probs_nv.sum() * */ - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs_fail), __pyx_n_s_sum); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs_fail), __pyx_n_s_sum); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_5 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_4))) { @@ -2795,27 +2853,27 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } } if (__pyx_t_5) { - __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } else { - __pyx_t_3 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_19 = __pyx_PyFloat_AsDouble(__pyx_t_3); if (unlikely((__pyx_t_19 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_t_3); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_v_ll = __pyx_t_19; + __pyx_v_ll = __pyx_t_22; - /* "ml.pyx":85 + /* "ml.pyx":89 * np.ndarray[DTYPE_t] cums = probs.cumsum() * ll = probs_fail.sum() * ll += probs_nv.sum() # <<<<<<<<<<<<<< * * for i in xrange(n_victims - 1, 0, -1): */ - __pyx_t_3 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __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 = 85; __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 = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_6 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_5))) { @@ -2828,22 +2886,22 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } } if (__pyx_t_6) { - __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; } else { - __pyx_t_4 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_19 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_19 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_v_ll = __pyx_t_19; + __pyx_v_ll = __pyx_t_22; - /* "ml.pyx":87 + /* "ml.pyx":91 * ll += probs_nv.sum() * * for i in xrange(n_victims - 1, 0, -1): # <<<<<<<<<<<<<< @@ -2853,38 +2911,50 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ for (__pyx_t_10 = (__pyx_v_n_victims - 1); __pyx_t_10 > 0; __pyx_t_10-=1) { __pyx_v_i = __pyx_t_10; - /* "ml.pyx":89 + /* "ml.pyx":93 * for i in xrange(n_victims - 1, 0, -1): * # iterate over all victim nodes to find the optimal threshold * roots = n_roots + n_victims - 1 - i # <<<<<<<<<<<<<< - * beta = 1. / (1. + exp(-probs[i])) - * if beta > float(roots) / age: + * beta = exp(probs[i])#1. / (1. + exp(-probs[i])) + * print beta */ __pyx_v_roots = (((__pyx_v_n_roots + __pyx_v_n_victims) - 1) - __pyx_v_i); - /* "ml.pyx":90 + /* "ml.pyx":94 * # iterate over all victim nodes to find the optimal threshold * roots = n_roots + n_victims - 1 - i - * beta = 1. / (1. + exp(-probs[i])) # <<<<<<<<<<<<<< + * beta = exp(probs[i])#1. / (1. + exp(-probs[i])) # <<<<<<<<<<<<<< + * print beta * if beta > float(roots) / age: - * break */ __pyx_t_11 = __pyx_v_i; if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_pybuffernd_probs.diminfo[0].shape; - __pyx_v_beta = (1. / (1. + exp((-(*__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_probs.diminfo[0].strides)))))); + __pyx_v_beta = exp((*__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_probs.diminfo[0].strides))); - /* "ml.pyx":91 + /* "ml.pyx":95 * roots = n_roots + n_victims - 1 - i - * beta = 1. / (1. + exp(-probs[i])) + * beta = exp(probs[i])#1. / (1. + exp(-probs[i])) + * print beta # <<<<<<<<<<<<<< + * if beta > float(roots) / age: + * break + */ + __pyx_t_5 = PyFloat_FromDouble(__pyx_v_beta); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + if (__Pyx_PrintOne(0, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + + /* "ml.pyx":96 + * beta = exp(probs[i])#1. / (1. + exp(-probs[i])) + * print beta * if beta > float(roots) / age: # <<<<<<<<<<<<<< * break * else: */ - __pyx_t_26 = ((__pyx_v_beta > (((double)__pyx_v_roots) / __pyx_v_age)) != 0); - if (__pyx_t_26) { + __pyx_t_29 = ((__pyx_v_beta > (((double)__pyx_v_roots) / __pyx_v_age)) != 0); + if (__pyx_t_29) { - /* "ml.pyx":92 - * beta = 1. / (1. + exp(-probs[i])) + /* "ml.pyx":97 + * print beta * if beta > float(roots) / age: * break # <<<<<<<<<<<<<< * else: @@ -2895,50 +2965,50 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } /*else*/ { - /* "ml.pyx":94 + /* "ml.pyx":99 * break * else: * print "alpha: {0}, delta: {1}. Everyone is a root".format(alpha, delta) # <<<<<<<<<<<<<< * roots = n_victims + n_roots * i = -1 */ - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_alpha_0_delta_1_Everyone_is_a_ro, __pyx_n_s_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_alpha_0_delta_1_Everyone_is_a_ro, __pyx_n_s_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = PyFloat_FromDouble(__pyx_v_alpha); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyFloat_FromDouble(__pyx_v_alpha); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_6 = PyFloat_FromDouble(__pyx_v_delta); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyFloat_FromDouble(__pyx_v_delta); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_15 = NULL; + __pyx_t_18 = NULL; __pyx_t_2 = 0; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_4))) { - __pyx_t_15 = PyMethod_GET_SELF(__pyx_t_4); - if (likely(__pyx_t_15)) { + __pyx_t_18 = PyMethod_GET_SELF(__pyx_t_4); + if (likely(__pyx_t_18)) { PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); - __Pyx_INCREF(__pyx_t_15); + __Pyx_INCREF(__pyx_t_18); __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_4, function); __pyx_t_2 = 1; } } - __pyx_t_14 = PyTuple_New(2+__pyx_t_2); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_14); - if (__pyx_t_15) { - PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_t_15); __Pyx_GIVEREF(__pyx_t_15); __pyx_t_15 = NULL; + __pyx_t_17 = PyTuple_New(2+__pyx_t_2); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_17); + if (__pyx_t_18) { + PyTuple_SET_ITEM(__pyx_t_17, 0, __pyx_t_18); __Pyx_GIVEREF(__pyx_t_18); __pyx_t_18 = NULL; } - PyTuple_SET_ITEM(__pyx_t_14, 0+__pyx_t_2, __pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_17, 0+__pyx_t_2, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); - PyTuple_SET_ITEM(__pyx_t_14, 1+__pyx_t_2, __pyx_t_6); + PyTuple_SET_ITEM(__pyx_t_17, 1+__pyx_t_2, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __pyx_t_3 = 0; __pyx_t_6 = 0; - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_14, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_17, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; + __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - if (__Pyx_PrintOne(0, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_PrintOne(0, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "ml.pyx":95 + /* "ml.pyx":100 * else: * print "alpha: {0}, delta: {1}. Everyone is a root".format(alpha, delta) * roots = n_victims + n_roots # <<<<<<<<<<<<<< @@ -2947,7 +3017,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ */ __pyx_v_roots = (__pyx_v_n_victims + __pyx_v_n_roots); - /* "ml.pyx":96 + /* "ml.pyx":101 * print "alpha: {0}, delta: {1}. Everyone is a root".format(alpha, delta) * roots = n_victims + n_roots * i = -1 # <<<<<<<<<<<<<< @@ -2958,7 +3028,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } __pyx_L20_break:; - /* "ml.pyx":97 + /* "ml.pyx":102 * roots = n_victims + n_roots * i = -1 * beta = float(roots) / age # <<<<<<<<<<<<<< @@ -2967,7 +3037,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ */ __pyx_v_beta = (((double)__pyx_v_roots) / __pyx_v_age); - /* "ml.pyx":98 + /* "ml.pyx":103 * i = -1 * beta = float(roots) / age * for i in xrange(n_victims - 1, 0, -1): # <<<<<<<<<<<<<< @@ -2977,19 +3047,19 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ for (__pyx_t_10 = (__pyx_v_n_victims - 1); __pyx_t_10 > 0; __pyx_t_10-=1) { __pyx_v_i = __pyx_t_10; - /* "ml.pyx":99 + /* "ml.pyx":104 * beta = float(roots) / age * for i in xrange(n_victims - 1, 0, -1): * if probs[i] >= log(beta/(1.- beta)): # <<<<<<<<<<<<<< * break * ll += age * log(1 - beta) */ - __pyx_t_20 = __pyx_v_i; - if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_pybuffernd_probs.diminfo[0].shape; - __pyx_t_26 = (((*__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_probs.diminfo[0].strides)) >= log((__pyx_v_beta / (1. - __pyx_v_beta)))) != 0); - if (__pyx_t_26) { + __pyx_t_12 = __pyx_v_i; + if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_probs.diminfo[0].shape; + __pyx_t_29 = (((*__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_probs.diminfo[0].strides)) >= log((__pyx_v_beta / (1. - __pyx_v_beta)))) != 0); + if (__pyx_t_29) { - /* "ml.pyx":100 + /* "ml.pyx":105 * for i in xrange(n_victims - 1, 0, -1): * if probs[i] >= log(beta/(1.- beta)): * break # <<<<<<<<<<<<<< @@ -3001,7 +3071,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } __pyx_L23_break:; - /* "ml.pyx":101 + /* "ml.pyx":106 * if probs[i] >= log(beta/(1.- beta)): * break * ll += age * log(1 - beta) # <<<<<<<<<<<<<< @@ -3010,17 +3080,17 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ */ __pyx_v_ll = (__pyx_v_ll + (__pyx_v_age * log((1.0 - __pyx_v_beta)))); - /* "ml.pyx":102 + /* "ml.pyx":107 * break * ll += age * log(1 - beta) * if i >= 0: # <<<<<<<<<<<<<< * ll += cums[i] * if roots > 0: */ - __pyx_t_26 = ((__pyx_v_i >= 0) != 0); - if (__pyx_t_26) { + __pyx_t_29 = ((__pyx_v_i >= 0) != 0); + if (__pyx_t_29) { - /* "ml.pyx":103 + /* "ml.pyx":108 * ll += age * log(1 - beta) * if i >= 0: * ll += cums[i] # <<<<<<<<<<<<<< @@ -3034,17 +3104,17 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } __pyx_L25:; - /* "ml.pyx":104 + /* "ml.pyx":109 * if i >= 0: * ll += cums[i] * if roots > 0: # <<<<<<<<<<<<<< * ll += roots * log(beta) - roots * log(1 - beta) * return (beta, roots, ll) */ - __pyx_t_26 = ((__pyx_v_roots > 0) != 0); - if (__pyx_t_26) { + __pyx_t_29 = ((__pyx_v_roots > 0) != 0); + if (__pyx_t_29) { - /* "ml.pyx":105 + /* "ml.pyx":110 * ll += cums[i] * if roots > 0: * ll += roots * log(beta) - roots * log(1 - beta) # <<<<<<<<<<<<<< @@ -3055,29 +3125,29 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } __pyx_L26:; - /* "ml.pyx":106 + /* "ml.pyx":111 * if roots > 0: * ll += roots * log(beta) - roots * log(1 - beta) * return (beta, roots, ll) # <<<<<<<<<<<<<< */ __Pyx_XDECREF(__pyx_r); - __pyx_t_5 = PyFloat_FromDouble(__pyx_v_beta); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 106; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyFloat_FromDouble(__pyx_v_beta); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_roots); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 106; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_roots); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_14 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 106; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_14); - __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 106; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_17 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_17); + __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); - PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_14); - __Pyx_GIVEREF(__pyx_t_14); + PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_17); + __Pyx_GIVEREF(__pyx_t_17); __pyx_t_5 = 0; __pyx_t_4 = 0; - __pyx_t_14 = 0; + __pyx_t_17 = 0; __pyx_r = __pyx_t_6; __pyx_t_6 = 0; goto __pyx_L0; @@ -3099,6 +3169,9 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF(__pyx_t_14); __Pyx_XDECREF(__pyx_t_15); __Pyx_XDECREF(__pyx_t_16); + __Pyx_XDECREF(__pyx_t_17); + __Pyx_XDECREF(__pyx_t_18); + __Pyx_XDECREF(__pyx_t_19); { PyObject *__pyx_type, *__pyx_value, *__pyx_tb; __Pyx_ErrFetch(&__pyx_type, &__pyx_value, &__pyx_tb); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_cums.rcbuffer->pybuffer); @@ -3120,6 +3193,9 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF((PyObject *)__pyx_v_probs_fail); __Pyx_XDECREF((PyObject *)__pyx_v_probs_nv); __Pyx_XDECREF((PyObject *)__pyx_v_cums); + __Pyx_XDECREF(__pyx_v_w1); + __Pyx_XDECREF(__pyx_v_w2); + __Pyx_XDECREF(__pyx_v_w3); __Pyx_DECREF(((PyObject *)__pyx_cur_scope)); __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); @@ -5386,7 +5462,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_k_Users_ben_Documents_Cascade_Pro, sizeof(__pyx_k_Users_ben_Documents_Cascade_Pro), 0, 0, 1, 0}, {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1}, {&__pyx_n_s_age, __pyx_k_age, sizeof(__pyx_k_age), 0, 0, 1, 1}, - {&__pyx_n_s_all_failures, __pyx_k_all_failures, sizeof(__pyx_k_all_failures), 0, 0, 1, 1}, {&__pyx_n_s_alpha, __pyx_k_alpha, sizeof(__pyx_k_alpha), 0, 0, 1, 1}, {&__pyx_kp_s_alpha_0_delta_1_Everyone_is_a_ro, __pyx_k_alpha_0_delta_1_Everyone_is_a_ro, sizeof(__pyx_k_alpha_0_delta_1_Everyone_is_a_ro), 0, 0, 1, 0}, {&__pyx_n_s_args, __pyx_k_args, sizeof(__pyx_k_args), 0, 0, 1, 1}, @@ -5441,18 +5516,21 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_throw, __pyx_k_throw, sizeof(__pyx_k_throw), 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_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_xrange, __pyx_k_xrange, sizeof(__pyx_k_xrange), 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 = 62; __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 = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_max = __Pyx_GetBuiltinName(__pyx_n_s_max); if (!__pyx_builtin_max) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __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 = 64; __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 = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_max = __Pyx_GetBuiltinName(__pyx_n_s_max); if (!__pyx_builtin_max) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if PY_MAJOR_VERSION >= 3 - __pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_xrange); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_xrange); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif __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;} @@ -5466,14 +5544,14 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); - /* "ml.pyx":81 - * probs_nv[i] = sum(failures) - * probs.sort() - * probs = probs[::-1] # <<<<<<<<<<<<<< + /* "ml.pyx":85 + * + * # calculate log likelihood + * probs.sort(); probs = probs[::-1] # sort probs in descending order # <<<<<<<<<<<<<< * cdef: * np.ndarray[DTYPE_t] cums = probs.cumsum() */ - __pyx_slice_ = PySlice_New(Py_None, Py_None, __pyx_int_neg_1); if (unlikely(!__pyx_slice_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_slice_ = PySlice_New(Py_None, Py_None, __pyx_int_neg_1); if (unlikely(!__pyx_slice_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_slice_); __Pyx_GIVEREF(__pyx_slice_); @@ -5550,10 +5628,10 @@ static int __Pyx_InitCachedConstants(void) { * DTYPE_t alpha, DTYPE_t delta, DTYPE_t gamma=10): * cdef: */ - __pyx_tuple__8 = PyTuple_Pack(29, __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, __pyx_n_s_gamma, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_n_nodes, __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_beta, __pyx_n_s_all_failures, __pyx_n_s_ll, __pyx_n_s_beta2, __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_cums, __pyx_n_s_genexpr, __pyx_n_s_genexpr); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__8 = PyTuple_Pack(31, __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, __pyx_n_s_gamma, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_n_nodes, __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_beta, __pyx_n_s_ll, __pyx_n_s_beta2, __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_cums, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3, __pyx_n_s_genexpr, __pyx_n_s_genexpr); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__8); __Pyx_GIVEREF(__pyx_tuple__8); - __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(7, 0, 29, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__8, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml, 50, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(7, 0, 31, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__8, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml, 50, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -5653,7 +5731,7 @@ PyMODINIT_FUNC PyInit_ml(void) if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct__ml) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type_2ml___pyx_scope_struct__ml.tp_print = 0; __pyx_ptype_2ml___pyx_scope_struct__ml = &__pyx_type_2ml___pyx_scope_struct__ml; - if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type_2ml___pyx_scope_struct_1_genexpr.tp_print = 0; __pyx_ptype_2ml___pyx_scope_struct_1_genexpr = &__pyx_type_2ml___pyx_scope_struct_1_genexpr; /*--- Type import code ---*/ |