diff options
Diffstat (limited to 'experiments/ml2.c')
| -rw-r--r-- | experiments/ml2.c | 642 |
1 files changed, 208 insertions, 434 deletions
diff --git a/experiments/ml2.c b/experiments/ml2.c index fe1b1f6..af1134b 100644 --- a/experiments/ml2.c +++ b/experiments/ml2.c @@ -773,7 +773,7 @@ struct __pyx_obj_3ml2___pyx_scope_struct__ml2 { }; -/* "ml2.pyx":62 +/* "ml2.pyx":61 * for (dist, dt, w1, w2, w3) in parents] * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) # <<<<<<<<<<<<<< @@ -871,13 +871,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject static PyObject *__Pyx_GetBuiltinName(PyObject *name); -static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); -static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); - -static void __Pyx_WriteUnraisable(const char *name, int clineno, - int lineno, const char *filename, - int full_traceback); - static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); @@ -978,6 +971,9 @@ static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { #endif #define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0) +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); + static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); #if PY_MAJOR_VERSION >= 3 @@ -1046,14 +1042,6 @@ static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); -static int __Pyx_Print(PyObject*, PyObject *, int); -#if CYTHON_COMPILING_IN_PYPY || PY_MAJOR_VERSION >= 3 -static PyObject* __pyx_print = 0; -static PyObject* __pyx_print_kwargs = 0; -#endif - -static int __Pyx_PrintOne(PyObject* stream, PyObject *o); - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); @@ -1288,14 +1276,12 @@ 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"; static char __pyx_k_ml2[] = "ml2"; static char __pyx_k_sum[] = "sum"; static char __pyx_k_args[] = "args"; 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_send[] = "send"; static char __pyx_k_test[] = "__test__"; @@ -1305,7 +1291,6 @@ static char __pyx_k_close[] = "close"; static char __pyx_k_delta[] = "delta"; static char __pyx_k_dtype[] = "dtype"; static char __pyx_k_numpy[] = "numpy"; -static char __pyx_k_print[] = "print"; static char __pyx_k_probs[] = "probs"; static char __pyx_k_range[] = "range"; static char __pyx_k_roots[] = "roots"; @@ -1314,7 +1299,6 @@ static char __pyx_k_zeros[] = "zeros"; static char __pyx_k_import[] = "__import__"; static char __pyx_k_float64[] = "float64"; static char __pyx_k_genexpr[] = "genexpr"; -static char __pyx_k_n_nodes[] = "n_nodes"; static char __pyx_k_n_roots[] = "n_roots"; static char __pyx_k_parents[] = "parents"; static char __pyx_k_victims[] = "victims"; @@ -1329,7 +1313,6 @@ 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_root_victims[] = "root_victims"; -static char __pyx_k_UNDERFLOW_ERROR[] = "UNDERFLOW ERROR"; static char __pyx_k_ml2_locals_genexpr[] = "ml2.<locals>.genexpr"; static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; static char __pyx_k_Users_ben_Documents_Cascade_Pro[] = "/Users/ben/Documents/Cascade Project/criminal_cascades/experiments/ml2.pyx"; @@ -1343,7 +1326,6 @@ static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2; static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; static PyObject *__pyx_n_s_RuntimeError; -static PyObject *__pyx_kp_s_UNDERFLOW_ERROR; static PyObject *__pyx_kp_s_Users_ben_Documents_Cascade_Pro; static PyObject *__pyx_n_s_ValueError; static PyObject *__pyx_n_s_age; @@ -1355,10 +1337,8 @@ static PyObject *__pyx_n_s_delta; static PyObject *__pyx_n_s_dist; static PyObject *__pyx_n_s_dt; static PyObject *__pyx_n_s_dtype; -static PyObject *__pyx_n_s_end; static PyObject *__pyx_n_s_enumerate; static PyObject *__pyx_n_s_failures; -static PyObject *__pyx_n_s_file; static PyObject *__pyx_n_s_float64; static PyObject *__pyx_n_s_genexpr; static PyObject *__pyx_n_s_i; @@ -1370,7 +1350,6 @@ static PyObject *__pyx_n_s_main; static PyObject *__pyx_n_s_max; static PyObject *__pyx_n_s_ml2; static PyObject *__pyx_n_s_ml2_locals_genexpr; -static PyObject *__pyx_n_s_n_nodes; static PyObject *__pyx_n_s_n_roots; static PyObject *__pyx_n_s_n_victims; static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; @@ -1379,7 +1358,6 @@ static PyObject *__pyx_n_s_non_victims; static PyObject *__pyx_n_s_np; static PyObject *__pyx_n_s_numpy; static PyObject *__pyx_n_s_parents; -static PyObject *__pyx_n_s_print; static PyObject *__pyx_n_s_probs; static PyObject *__pyx_n_s_probs_fail; static PyObject *__pyx_n_s_probs_nv; @@ -1458,55 +1436,37 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(int __pyx_v_dist, int __ __pyx_t_3ml2_DTYPE_t __pyx_v_result; __pyx_t_3ml2_DTYPE_t __pyx_r; __Pyx_RefNannyDeclarations - int __pyx_t_1; - int __pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; __Pyx_RefNannySetupContext("weight_success", 0); /* "ml2.pyx":16 * """weight for successful infection, exponential time model""" * cdef DTYPE_t structural, temporal, result - * structural = delta ** dist # <<<<<<<<<<<<<< + * structural = dist * log(delta) # <<<<<<<<<<<<<< * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) - * temporal = exp(-alpha*dt) * (exp(alpha)-1.) + * temporal = log(exp(alpha)-1.) - alpha*dt */ - __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_3ml2_DTYPE_t)__pyx_v_dist)); + __pyx_v_structural = (__pyx_v_dist * log(__pyx_v_delta)); /* "ml2.pyx":18 - * structural = delta ** dist + * structural = dist * log(delta) * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) - * temporal = exp(-alpha*dt) * (exp(alpha)-1.) # <<<<<<<<<<<<<< + * temporal = log(exp(alpha)-1.) - alpha*dt # <<<<<<<<<<<<<< * # temporal = 1 - exp(-alpha*dt) - * if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' + * # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' */ - __pyx_v_temporal = (exp(((-__pyx_v_alpha) * __pyx_v_dt)) * (exp(__pyx_v_alpha) - 1.)); - - /* "ml2.pyx":20 - * temporal = exp(-alpha*dt) * (exp(alpha)-1.) - * # temporal = 1 - exp(-alpha*dt) - * if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' # <<<<<<<<<<<<<< - * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 - * result = log(structural * temporal) - */ - __pyx_t_1 = ((exp(((-__pyx_v_alpha) * __pyx_v_dt)) == 0.) != 0); - if (__pyx_t_1) { - if (__Pyx_PrintOne(0, __pyx_kp_s_UNDERFLOW_ERROR) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; - } - __pyx_L3:; + __pyx_v_temporal = (log((exp(__pyx_v_alpha) - 1.)) - (__pyx_v_alpha * __pyx_v_dt)); /* "ml2.pyx":22 - * if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' + * # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 - * result = log(structural * temporal) # <<<<<<<<<<<<<< + * result = structural + temporal # <<<<<<<<<<<<<< * # print 'st', structural, temporal * return result */ - __pyx_v_result = log((__pyx_v_structural * __pyx_v_temporal)); + __pyx_v_result = (__pyx_v_structural + __pyx_v_temporal); /* "ml2.pyx":24 - * result = log(structural * temporal) + * result = structural + temporal * # print 'st', structural, temporal * return result # <<<<<<<<<<<<<< * @@ -1524,9 +1484,6 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(int __pyx_v_dist, int __ */ /* function exit code */ - __pyx_L1_error:; - __Pyx_WriteUnraisable("ml2.weight_success", __pyx_clineno, __pyx_lineno, __pyx_filename, 0); - __pyx_r = 0; __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; @@ -1713,7 +1670,7 @@ static PyObject *__pyx_pw_3ml2_1ml2(PyObject *__pyx_self, PyObject *__pyx_args, } static PyObject *__pyx_gb_3ml2_3ml2_2generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */ -/* "ml2.pyx":62 +/* "ml2.pyx":61 * for (dist, dt, w1, w2, w3) in parents] * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) # <<<<<<<<<<<<<< @@ -1739,7 +1696,7 @@ static PyObject *__pyx_pf_3ml2_3ml2_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_3ml2_3ml2_2generator, (PyObject *) __pyx_cur_scope, __pyx_n_s_genexpr, __pyx_n_s_ml2_locals_genexpr); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_3ml2_3ml2_2generator, (PyObject *) __pyx_cur_scope, __pyx_n_s_genexpr, __pyx_n_s_ml2_locals_genexpr); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_cur_scope); __Pyx_RefNannyFinishContext(); return (PyObject *) gen; @@ -1777,16 +1734,16 @@ static PyObject *__pyx_gb_3ml2_3ml2_2generator(__pyx_GeneratorObject *__pyx_gene return NULL; } __pyx_L3_first_run:; - if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __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 = 62; __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 = 61; __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 = 62; __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 = 61; __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 = 62; __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 = 61; __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); @@ -1794,14 +1751,14 @@ static PyObject *__pyx_gb_3ml2_3ml2_2generator(__pyx_GeneratorObject *__pyx_gene __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 = 62; __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 = 61; __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 = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __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 = 62; __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 = 61; __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 = 62; __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 = 61; __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; @@ -1821,7 +1778,7 @@ static PyObject *__pyx_gb_3ml2_3ml2_2generator(__pyx_GeneratorObject *__pyx_gene __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 = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -1853,7 +1810,6 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject struct __pyx_obj_3ml2___pyx_scope_struct__ml2 *__pyx_cur_scope; int __pyx_v_n_roots; int __pyx_v_n_victims; - CYTHON_UNUSED int __pyx_v_n_nodes; int __pyx_v_roots; int __pyx_v_i; int __pyx_v_dist; @@ -1928,8 +1884,8 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject * DTYPE_t beta, ll * list parents, failures, successes * n_roots, n_victims = len(root_victims), len(victims) # <<<<<<<<<<<<<< - * n_nodes = 100 * cdef: + * np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE) */ if (unlikely(__pyx_v_root_victims == Py_None)) { PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); @@ -1944,52 +1900,43 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_v_n_roots = __pyx_t_1; __pyx_v_n_victims = __pyx_t_2; - /* "ml2.pyx":45 - * list parents, failures, successes + /* "ml2.pyx":46 * n_roots, n_victims = len(root_victims), len(victims) - * n_nodes = 100 # <<<<<<<<<<<<<< - * cdef: - * np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE) - */ - __pyx_v_n_nodes = 100; - - /* "ml2.pyx":47 - * n_nodes = 100 * 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 = 47; __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 = 47; __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 = 46; __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 = 47; __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 = 46; __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 = 47; __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 = 46; __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 = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __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_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 = 47; __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 = 46; __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 = 47; __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 = 46; __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 = 47; __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 = 47; __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_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 = 47; __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_probs.diminfo[0].strides = __pyx_pybuffernd_probs.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_probs.diminfo[0].shape = __pyx_pybuffernd_probs.rcbuffer->pybuffer.shape[0]; } } @@ -1997,43 +1944,43 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_v_probs = ((PyArrayObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "ml2.pyx":48 + /* "ml2.pyx":47 * 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_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __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 = 48; __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 = 48; __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 = 48; __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 = 48; __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 = 48; __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]; 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__pyx_lineno = 48; __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_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 = 48; __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_probs_fail.diminfo[0].strides = __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.strides[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_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_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 = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__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 = 49; __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 = 49; __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_GOTREF(__pyx_t_4); - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __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 = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); 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_DTYPE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_dtype, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __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 = 48; __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 = 49; __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 = 48; __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 = 49; __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 = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_9 = ((PyArrayObject *)__pyx_t_3); { __Pyx_BufFmt_StackElem __pyx_stack[1]; if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_probs_nv.rcbuffer->pybuffer, (PyObject*)__pyx_t_9, &__Pyx_TypeInfo_nn___pyx_t_3ml2_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) { __pyx_v_probs_nv = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_probs_nv.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 = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_probs_nv.diminfo[0].strides = __pyx_pybuffernd_probs_nv.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_probs_nv.diminfo[0].shape = __pyx_pybuffernd_probs_nv.rcbuffer->pybuffer.shape[0]; } } @@ -2090,7 +2037,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_v_probs_nv = ((PyArrayObject *)__pyx_t_3); __pyx_t_3 = 0; - /* "ml2.pyx":52 + /* "ml2.pyx":51 * * # loop through victims * for i, parents in enumerate(victims.itervalues()): # <<<<<<<<<<<<<< @@ -2101,9 +2048,9 @@ 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 = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __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 = 52; __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 = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = __pyx_t_4; @@ -2111,25 +2058,25 @@ static PyObject *__pyx_pf_3ml2_ml2(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 = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __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 = 52; __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 = 51; __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); - /* "ml2.pyx":56 + /* "ml2.pyx":55 * # 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) # <<<<<<<<<<<<<< * 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 = 56; __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 = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - /* "ml2.pyx":57 + /* "ml2.pyx":56 * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2138,15 +2085,15 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject */ if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __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 = 57; __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 = 56; __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 = 57; __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 = 56; __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; @@ -2158,7 +2105,7 @@ 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 = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -2184,7 +2131,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject 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 = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(item); *(temps[i]) = item; } @@ -2194,7 +2141,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject } else { Py_ssize_t index = -1; 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__Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; goto __pyx_L8_unpacking_done; @@ -2211,12 +2158,12 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __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 = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __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 = 57; __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 = 56; __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 = 57; __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 = 56; __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_21; @@ -2227,22 +2174,22 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_18); __pyx_t_18 = 0; - /* "ml2.pyx":56 + /* "ml2.pyx":55 * # 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) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) */ - __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __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 = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_6 = PyFloat_FromDouble(__pyx_f_3ml2_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_22, __pyx_t_23, __pyx_t_24)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __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 = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyFloat_FromDouble(__pyx_f_3ml2_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_22, __pyx_t_23, __pyx_t_24)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __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 = 56; __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 = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "ml2.pyx":57 + /* "ml2.pyx":56 * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2256,38 +2203,38 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_GIVEREF(__pyx_t_4); __pyx_t_4 = 0; - /* "ml2.pyx":58 + /* "ml2.pyx":57 * failures = [weight_failure(dist, dt, alpha, delta, 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) * 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 = 58; __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 = 57; __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 = 58; __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 = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_5); 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_DECREF(__pyx_t_5); __pyx_t_5 = 0; __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_3ml2_DTYPE_t *, __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_probs_fail.diminfo[0].strides) = __pyx_t_24; - /* "ml2.pyx":59 + /* "ml2.pyx":58 * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< * 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 = 59; __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 = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - /* "ml2.pyx":60 + /* "ml2.pyx":59 * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2296,15 +2243,15 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject */ if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __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 = 60; __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 = 59; __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 = 60; __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 = 59; __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; @@ -2316,7 +2263,7 @@ 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 = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -2342,7 +2289,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject 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 = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(item); *(temps[i]) = item; } @@ -2352,7 +2299,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject } else { Py_ssize_t index = -1; 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 = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_19); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_20 = Py_TYPE(__pyx_t_19)->tp_iternext; @@ -2361,7 +2308,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_GOTREF(item); *(temps[index]) = item; } - if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __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; @@ -2369,12 +2316,12 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __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 = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L12_unpacking_done:; } - __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 = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __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 = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0; - __pyx_t_25 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_25 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_25 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_25 == (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_12; __pyx_v_dt = __pyx_t_25; @@ -2385,22 +2332,22 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_14); __pyx_t_14 = 0; - /* "ml2.pyx":59 + /* "ml2.pyx":58 * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * # find parent that maximizes log(p) - log(\tilde{p}) */ - __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_6 = PyFloat_FromDouble(__pyx_f_3ml2_weight_success(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_24, __pyx_t_23, __pyx_t_22)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyFloat_FromDouble(__pyx_f_3ml2_weight_success(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_24, __pyx_t_23, __pyx_t_22)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __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 = 59; __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 = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "ml2.pyx":60 + /* "ml2.pyx":59 * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2414,24 +2361,24 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = 0; - /* "ml2.pyx":62 + /* "ml2.pyx":61 * for (dist, dt, w1, w2, w3) in parents] * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) # <<<<<<<<<<<<<< * * # loop through non-victims */ - __pyx_t_5 = __pyx_pf_3ml2_3ml2_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __pyx_pf_3ml2_3ml2_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __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 = 62; __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 = 61; __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 = 62; __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 = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __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 = 62; __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 = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_25 = __pyx_v_i; if (__pyx_t_25 < 0) __pyx_t_25 += __pyx_pybuffernd_probs.diminfo[0].shape; @@ -2439,7 +2386,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "ml2.pyx":65 + /* "ml2.pyx":64 * * # loop through non-victims * for i, parents in enumerate(non_victims.itervalues()): # <<<<<<<<<<<<<< @@ -2450,9 +2397,9 @@ 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 = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __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 = 65; __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 = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = __pyx_t_5; @@ -2460,25 +2407,25 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject while (1) { __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 = 65; __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_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 = 65; __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 = 64; __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); - /* "ml2.pyx":68 + /* "ml2.pyx":67 * # 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) # <<<<<<<<<<<<<< * 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 = 68; __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 = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - /* "ml2.pyx":69 + /* "ml2.pyx":68 * # parents fail to infect it * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2487,15 +2434,15 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject */ if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __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 = 69; __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 = 68; __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 = 69; __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 = 68; __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; @@ -2507,7 +2454,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject if (unlikely(size != 5)) { if (size > 5) __Pyx_RaiseTooManyValuesError(5); 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@@ -2628,14 +2575,14 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "ml2.pyx":80 + /* "ml2.pyx":79 * # cdef: * # np.ndarray[DTYPE_t] cums = probs.cumsum() * 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 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs_fail), __pyx_n_s_sum); 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_fail), __pyx_n_s_sum); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __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))) { @@ -2648,27 +2595,27 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject } } if (__pyx_t_5) { - __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_5); 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if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __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 = 80; __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))) { @@ -2681,31 +2628,31 @@ static PyObject *__pyx_pf_3ml2_ml2(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 = 81; __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 = 80; __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 = 81; __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 = 80; __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 = 81; __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 = 80; __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_24 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_v_ll = __pyx_t_24; - /* "ml2.pyx":82 + /* "ml2.pyx":81 * 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); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyFloat_FromDouble(__pyx_v_ll); 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 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs), __pyx_n_s_sum); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs), __pyx_n_s_sum); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_6 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_3))) { @@ -2718,22 +2665,22 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject } } if (__pyx_t_6) { - __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __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_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_CallNoArg(__pyx_t_3); 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_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_t_5, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_t_5, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_3); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_3); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_v_ll = __pyx_t_24; - /* "ml2.pyx":84 + /* "ml2.pyx":83 * ll += probs.sum() # add probability for realized edges and subtract probability these edges fail * * roots = n_roots # <<<<<<<<<<<<<< @@ -2742,7 +2689,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject */ __pyx_v_roots = __pyx_v_n_roots; - /* "ml2.pyx":85 + /* "ml2.pyx":84 * * roots = n_roots * beta = 0 # <<<<<<<<<<<<<< @@ -2751,19 +2698,19 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject */ __pyx_v_beta = 0.0; - /* "ml2.pyx":87 + /* "ml2.pyx":86 * beta = 0 * # print n_nodes, n_roots, n_victims, max_i, roots * return (beta, roots, ll) # <<<<<<<<<<<<<< */ __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = PyFloat_FromDouble(__pyx_v_beta); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyFloat_FromDouble(__pyx_v_beta); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_roots); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __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 = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); @@ -5082,7 +5029,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_u_Format_string_allocated_too_shor_2, __pyx_k_Format_string_allocated_too_shor_2, sizeof(__pyx_k_Format_string_allocated_too_shor_2), 0, 1, 0, 0}, {&__pyx_kp_u_Non_native_byte_order_not_suppor, __pyx_k_Non_native_byte_order_not_suppor, sizeof(__pyx_k_Non_native_byte_order_not_suppor), 0, 1, 0, 0}, {&__pyx_n_s_RuntimeError, __pyx_k_RuntimeError, sizeof(__pyx_k_RuntimeError), 0, 0, 1, 1}, - {&__pyx_kp_s_UNDERFLOW_ERROR, __pyx_k_UNDERFLOW_ERROR, sizeof(__pyx_k_UNDERFLOW_ERROR), 0, 0, 1, 0}, {&__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}, @@ -5094,10 +5040,8 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_dist, __pyx_k_dist, sizeof(__pyx_k_dist), 0, 0, 1, 1}, {&__pyx_n_s_dt, __pyx_k_dt, sizeof(__pyx_k_dt), 0, 0, 1, 1}, {&__pyx_n_s_dtype, __pyx_k_dtype, sizeof(__pyx_k_dtype), 0, 0, 1, 1}, - {&__pyx_n_s_end, __pyx_k_end, sizeof(__pyx_k_end), 0, 0, 1, 1}, {&__pyx_n_s_enumerate, __pyx_k_enumerate, sizeof(__pyx_k_enumerate), 0, 0, 1, 1}, {&__pyx_n_s_failures, __pyx_k_failures, sizeof(__pyx_k_failures), 0, 0, 1, 1}, - {&__pyx_n_s_file, __pyx_k_file, sizeof(__pyx_k_file), 0, 0, 1, 1}, {&__pyx_n_s_float64, __pyx_k_float64, sizeof(__pyx_k_float64), 0, 0, 1, 1}, {&__pyx_n_s_genexpr, __pyx_k_genexpr, sizeof(__pyx_k_genexpr), 0, 0, 1, 1}, {&__pyx_n_s_i, __pyx_k_i, sizeof(__pyx_k_i), 0, 0, 1, 1}, @@ -5109,7 +5053,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_max, __pyx_k_max, sizeof(__pyx_k_max), 0, 0, 1, 1}, {&__pyx_n_s_ml2, __pyx_k_ml2, sizeof(__pyx_k_ml2), 0, 0, 1, 1}, {&__pyx_n_s_ml2_locals_genexpr, __pyx_k_ml2_locals_genexpr, sizeof(__pyx_k_ml2_locals_genexpr), 0, 0, 1, 1}, - {&__pyx_n_s_n_nodes, __pyx_k_n_nodes, sizeof(__pyx_k_n_nodes), 0, 0, 1, 1}, {&__pyx_n_s_n_roots, __pyx_k_n_roots, sizeof(__pyx_k_n_roots), 0, 0, 1, 1}, {&__pyx_n_s_n_victims, __pyx_k_n_victims, sizeof(__pyx_k_n_victims), 0, 0, 1, 1}, {&__pyx_kp_u_ndarray_is_not_C_contiguous, __pyx_k_ndarray_is_not_C_contiguous, sizeof(__pyx_k_ndarray_is_not_C_contiguous), 0, 1, 0, 0}, @@ -5118,7 +5061,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_np, __pyx_k_np, sizeof(__pyx_k_np), 0, 0, 1, 1}, {&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1}, {&__pyx_n_s_parents, __pyx_k_parents, sizeof(__pyx_k_parents), 0, 0, 1, 1}, - {&__pyx_n_s_print, __pyx_k_print, sizeof(__pyx_k_print), 0, 0, 1, 1}, {&__pyx_n_s_probs, __pyx_k_probs, sizeof(__pyx_k_probs), 0, 0, 1, 1}, {&__pyx_n_s_probs_fail, __pyx_k_probs_fail, sizeof(__pyx_k_probs_fail), 0, 0, 1, 1}, {&__pyx_n_s_probs_nv, __pyx_k_probs_nv, sizeof(__pyx_k_probs_nv), 0, 0, 1, 1}, @@ -5140,9 +5082,9 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {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 = 52; __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 = 58; __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 = 62; __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 = 51; __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 = 57; __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 = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -5228,10 +5170,10 @@ static int __Pyx_InitCachedConstants(void) { * DTYPE_t alpha, DTYPE_t delta): * cdef: */ - __pyx_tuple__7 = PyTuple_Pack(28, __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_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_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_w1, __pyx_n_s_w2, __pyx_n_s_w3, __pyx_n_s_genexpr, __pyx_n_s_genexpr); if (unlikely(!__pyx_tuple__7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__7 = PyTuple_Pack(27, __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_n_roots, __pyx_n_s_n_victims, __pyx_n_s_roots, __pyx_n_s_i, __pyx_n_s_dist, __pyx_n_s_dt, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_beta, __pyx_n_s_ll, __pyx_n_s_parents, __pyx_n_s_failures, __pyx_n_s_successes, __pyx_n_s_probs, __pyx_n_s_probs_fail, __pyx_n_s_probs_nv, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3, __pyx_n_s_genexpr, __pyx_n_s_genexpr); if (unlikely(!__pyx_tuple__7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__7); __Pyx_GIVEREF(__pyx_tuple__7); - __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(6, 0, 28, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml2, 38, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(6, 0, 27, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml2, 38, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -5330,7 +5272,7 @@ PyMODINIT_FUNC PyInit_ml2(void) if (PyType_Ready(&__pyx_type_3ml2___pyx_scope_struct__ml2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type_3ml2___pyx_scope_struct__ml2.tp_print = 0; __pyx_ptype_3ml2___pyx_scope_struct__ml2 = &__pyx_type_3ml2___pyx_scope_struct__ml2; - if (PyType_Ready(&__pyx_type_3ml2___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type_3ml2___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type_3ml2___pyx_scope_struct_1_genexpr.tp_print = 0; __pyx_ptype_3ml2___pyx_scope_struct_1_genexpr = &__pyx_type_3ml2___pyx_scope_struct_1_genexpr; /*--- Type import code ---*/ @@ -5459,64 +5401,6 @@ static PyObject *__Pyx_GetBuiltinName(PyObject *name) { return result; } -static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { -#if CYTHON_COMPILING_IN_CPYTHON - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyThreadState *tstate = PyThreadState_GET(); - tmp_type = tstate->curexc_type; - tmp_value = tstate->curexc_value; - tmp_tb = tstate->curexc_traceback; - tstate->curexc_type = type; - tstate->curexc_value = value; - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_Restore(type, value, tb); -#endif -} -static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { -#if CYTHON_COMPILING_IN_CPYTHON - PyThreadState *tstate = PyThreadState_GET(); - *type = tstate->curexc_type; - *value = tstate->curexc_value; - *tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(type, value, tb); -#endif -} - -static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, - CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename, - int full_traceback) { - PyObject *old_exc, *old_val, *old_tb; - PyObject *ctx; - __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); - if (full_traceback) { - Py_XINCREF(old_exc); - Py_XINCREF(old_val); - Py_XINCREF(old_tb); - __Pyx_ErrRestore(old_exc, old_val, old_tb); - PyErr_PrintEx(1); - } - #if PY_MAJOR_VERSION < 3 - ctx = PyString_FromString(name); - #else - ctx = PyUnicode_FromString(name); - #endif - __Pyx_ErrRestore(old_exc, old_val, old_tb); - if (!ctx) { - PyErr_WriteUnraisable(Py_None); - } else { - PyErr_WriteUnraisable(ctx); - Py_DECREF(ctx); - } -} - static void __Pyx_RaiseArgtupleInvalid( const char* func_name, int exact, @@ -6656,6 +6540,37 @@ static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* iter_obj, Py_ssize_t ori return 1; } +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_Restore(type, value, tb); +#endif +} +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->curexc_type; + *value = tstate->curexc_value; + *tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(type, value, tb); +#endif +} + #if PY_MAJOR_VERSION < 3 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, CYTHON_UNUSED PyObject *cause) { @@ -7066,147 +6981,6 @@ bad: return module; } -#if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3 -static PyObject *__Pyx_GetStdout(void) { - PyObject *f = PySys_GetObject((char *)"stdout"); - if (!f) { - PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout"); - } - return f; -} -static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) { - int i; - if (!f) { - if (!(f = __Pyx_GetStdout())) - return -1; - } - Py_INCREF(f); - for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) { - PyObject* v; - if (PyFile_SoftSpace(f, 1)) { - if (PyFile_WriteString(" ", f) < 0) - goto error; - } - v = PyTuple_GET_ITEM(arg_tuple, i); - if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0) - goto error; - if (PyString_Check(v)) { - char *s = PyString_AsString(v); - Py_ssize_t len = PyString_Size(v); - if (len > 0) { - switch (s[len-1]) { - case ' ': break; - case '\f': case '\r': case '\n': case '\t': case '\v': - PyFile_SoftSpace(f, 0); - break; - default: break; - } - } - } - } - if (newline) { - if (PyFile_WriteString("\n", f) < 0) - goto error; - PyFile_SoftSpace(f, 0); - } - Py_DECREF(f); - return 0; -error: - Py_DECREF(f); - return -1; -} -#else -static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) { - PyObject* kwargs = 0; - PyObject* result = 0; - PyObject* end_string; - if (unlikely(!__pyx_print)) { - __pyx_print = PyObject_GetAttr(__pyx_b, __pyx_n_s_print); - if (!__pyx_print) - return -1; - } - if (stream) { - kwargs = PyDict_New(); - if (unlikely(!kwargs)) - return -1; - if (unlikely(PyDict_SetItem(kwargs, __pyx_n_s_file, stream) < 0)) - goto bad; - if (!newline) { - end_string = PyUnicode_FromStringAndSize(" ", 1); - if (unlikely(!end_string)) - goto bad; - if (PyDict_SetItem(kwargs, __pyx_n_s_end, end_string) < 0) { - Py_DECREF(end_string); - goto bad; - } - Py_DECREF(end_string); - } - } else if (!newline) { - if (unlikely(!__pyx_print_kwargs)) { - __pyx_print_kwargs = PyDict_New(); - if (unlikely(!__pyx_print_kwargs)) - return -1; - end_string = PyUnicode_FromStringAndSize(" ", 1); - if (unlikely(!end_string)) - return -1; - if (PyDict_SetItem(__pyx_print_kwargs, __pyx_n_s_end, end_string) < 0) { - Py_DECREF(end_string); - return -1; - } - Py_DECREF(end_string); - } - kwargs = __pyx_print_kwargs; - } - result = PyObject_Call(__pyx_print, arg_tuple, kwargs); - if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs)) - Py_DECREF(kwargs); - if (!result) - return -1; - Py_DECREF(result); - return 0; -bad: - if (kwargs != __pyx_print_kwargs) - Py_XDECREF(kwargs); - return -1; -} -#endif - -#if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3 -static int __Pyx_PrintOne(PyObject* f, PyObject *o) { - if (!f) { - if (!(f = __Pyx_GetStdout())) - return -1; - } - Py_INCREF(f); - if (PyFile_SoftSpace(f, 0)) { - if (PyFile_WriteString(" ", f) < 0) - goto error; - } - if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0) - goto error; - if (PyFile_WriteString("\n", f) < 0) - goto error; - Py_DECREF(f); - return 0; -error: - Py_DECREF(f); - return -1; - /* the line below is just to avoid C compiler - * warnings about unused functions */ - return __Pyx_Print(f, NULL, 0); -} -#else -static int __Pyx_PrintOne(PyObject* stream, PyObject *o) { - int res; - PyObject* arg_tuple = PyTuple_Pack(1, o); - if (unlikely(!arg_tuple)) - return -1; - res = __Pyx_Print(stream, arg_tuple, 1); - Py_DECREF(arg_tuple); - return res; -} -#endif - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { const int neg_one = (int) -1, const_zero = 0; const int is_unsigned = neg_one > const_zero; |