diff options
Diffstat (limited to 'experiments/ml.c')
| -rw-r--r-- | experiments/ml.c | 1205 |
1 files changed, 564 insertions, 641 deletions
diff --git a/experiments/ml.c b/experiments/ml.c index cdf4064..eb67db6 100644 --- a/experiments/ml.c +++ b/experiments/ml.c @@ -695,7 +695,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; * DTYPE = np.float64 * ctypedef np.float_t DTYPE_t # <<<<<<<<<<<<<< * - * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): + * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, */ typedef __pyx_t_5numpy_float_t __pyx_t_2ml_DTYPE_t; #if CYTHON_CCOMPLEX @@ -759,7 +759,7 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; */ typedef npy_cdouble __pyx_t_5numpy_complex_t; -/* "ml.pyx":38 +/* "ml.pyx":35 * return result * * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< @@ -773,7 +773,7 @@ struct __pyx_obj_2ml___pyx_scope_struct__ml { }; -/* "ml.pyx":62 +/* "ml.pyx":59 * 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); @@ -990,7 +983,8 @@ static double __Pyx__PyObject_AsDouble(PyObject* obj); PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj)) #endif -static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); +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); @@ -1060,14 +1054,6 @@ 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 *); @@ -1303,14 +1289,12 @@ 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_inf[] = "-inf"; static char __pyx_k_max[] = "max"; 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__"; @@ -1320,7 +1304,6 @@ 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"; @@ -1350,7 +1333,6 @@ static char __pyx_k_non_victims[] = "non_victims"; static char __pyx_k_RuntimeError[] = "RuntimeError"; static char __pyx_k_max_beta_add[] = "max_beta_add"; static char __pyx_k_root_victims[] = "root_victims"; -static char __pyx_k_UNDERFLOW_ERROR[] = "UNDERFLOW ERROR"; static char __pyx_k_ml_locals_genexpr[] = "ml.<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/ml.pyx"; @@ -1364,7 +1346,6 @@ 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; @@ -1378,10 +1359,8 @@ 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; @@ -1406,7 +1385,6 @@ 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; @@ -1426,8 +1404,8 @@ static PyObject *__pyx_n_s_w1; static PyObject *__pyx_n_s_w2; static PyObject *__pyx_n_s_w3; static PyObject *__pyx_n_s_zeros; -static PyObject *__pyx_float__1; -static PyObject *__pyx_float__001; +static PyObject *__pyx_float__2; +static PyObject *__pyx_float__002; static PyObject *__pyx_float_0_001; static PyObject *__pyx_tuple_; static PyObject *__pyx_tuple__2; @@ -1442,43 +1420,6 @@ static PyObject *__pyx_codeobj__9; /* "ml.pyx":9 * ctypedef np.float_t DTYPE_t * - * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): # <<<<<<<<<<<<<< - * return 1./(1. + exp(-weight/delta)) - * - */ - -static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_plogis(__pyx_t_2ml_DTYPE_t __pyx_v_weight, __pyx_t_2ml_DTYPE_t __pyx_v_delta) { - __pyx_t_2ml_DTYPE_t __pyx_r; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("plogis", 0); - - /* "ml.pyx":10 - * - * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): - * return 1./(1. + exp(-weight/delta)) # <<<<<<<<<<<<<< - * - * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, - */ - __pyx_r = (1. / (1. + exp(((-__pyx_v_weight) / __pyx_v_delta)))); - goto __pyx_L0; - - /* "ml.pyx":9 - * ctypedef np.float_t DTYPE_t - * - * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): # <<<<<<<<<<<<<< - * return 1./(1. + exp(-weight/delta)) - * - */ - - /* function exit code */ - __pyx_L0:; - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - -/* "ml.pyx":12 - * return 1./(1. + exp(-weight/delta)) - * * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): * """weight for successful infection, exponential time model""" @@ -1490,55 +1431,37 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py __pyx_t_2ml_DTYPE_t __pyx_v_result; __pyx_t_2ml_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); - /* "ml.pyx":16 + /* "ml.pyx":13 * """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_2ml_DTYPE_t)__pyx_v_dist)); + __pyx_v_structural = (__pyx_v_dist * log(__pyx_v_delta)); - /* "ml.pyx":19 + /* "ml.pyx":15 + * structural = dist * log(delta) * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) - * # 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 + * temporal = log(exp(alpha)-1.) - alpha*dt # <<<<<<<<<<<<<< + * # temporal = 1 - exp(-alpha*dt) + * # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' */ - __pyx_v_temporal = (1.0 - exp(((-__pyx_v_alpha) * __pyx_v_dt))); + __pyx_v_temporal = (log((exp(__pyx_v_alpha) - 1.)) - (__pyx_v_alpha * __pyx_v_dt)); - /* "ml.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:; - - /* "ml.pyx":22 - * if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' + /* "ml.pyx":19 + * # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 - * result = 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); - /* "ml.pyx":24 - * result = log(structural * temporal) + /* "ml.pyx":21 + * result = structural + temporal * # print 'st', structural, temporal * return result # <<<<<<<<<<<<<< * @@ -1547,8 +1470,8 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py __pyx_r = __pyx_v_result; goto __pyx_L0; - /* "ml.pyx":12 - * return 1./(1. + exp(-weight/delta)) + /* "ml.pyx":9 + * ctypedef np.float_t DTYPE_t * * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): @@ -1556,15 +1479,12 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py */ /* function exit code */ - __pyx_L1_error:; - __Pyx_WriteUnraisable("ml.weight_success", __pyx_clineno, __pyx_lineno, __pyx_filename, 0); - __pyx_r = 0; __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ml.pyx":26 +/* "ml.pyx":23 * return result * * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< @@ -1580,7 +1500,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("weight_failure", 0); - /* "ml.pyx":30 + /* "ml.pyx":27 * """weight for failed infection, exponential time model""" * cdef DTYPE_t structural, temporal, result * structural = delta ** dist # <<<<<<<<<<<<<< @@ -1589,7 +1509,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py */ __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist)); - /* "ml.pyx":32 + /* "ml.pyx":29 * structural = delta ** dist * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = exp(-alpha * dt) # <<<<<<<<<<<<<< @@ -1598,7 +1518,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py */ __pyx_v_temporal = exp(((-__pyx_v_alpha) * __pyx_v_dt)); - /* "ml.pyx":34 + /* "ml.pyx":31 * temporal = exp(-alpha * dt) * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 * result = log(1. - structural + structural * temporal) # <<<<<<<<<<<<<< @@ -1607,7 +1527,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py */ __pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal))); - /* "ml.pyx":36 + /* "ml.pyx":33 * result = log(1. - structural + structural * temporal) * # print 'stnv', structural, temporal * return result # <<<<<<<<<<<<<< @@ -1617,7 +1537,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py __pyx_r = __pyx_v_result; goto __pyx_L0; - /* "ml.pyx":26 + /* "ml.pyx":23 * return result * * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< @@ -1631,7 +1551,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py return __pyx_r; } -/* "ml.pyx":38 +/* "ml.pyx":35 * return result * * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< @@ -1679,31 +1599,31 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_victims)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_non_victims)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_age)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_alpha)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_delta)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 6) { goto __pyx_L5_argtuple_error; @@ -1718,21 +1638,21 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py __pyx_v_root_victims = ((PyObject*)values[0]); __pyx_v_victims = ((PyObject*)values[1]); __pyx_v_non_victims = ((PyObject*)values[2]); - __pyx_v_age = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_age == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_delta = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_age = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_age == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_delta = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("ml.ml", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_root_victims), (&PyDict_Type), 1, "root_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_victims), (&PyDict_Type), 1, "victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_non_victims), (&PyDict_Type), 1, "non_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_root_victims), (&PyDict_Type), 1, "root_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_victims), (&PyDict_Type), 1, "victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_non_victims), (&PyDict_Type), 1, "non_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_2ml_ml(__pyx_self, __pyx_v_root_victims, __pyx_v_victims, __pyx_v_non_victims, __pyx_v_age, __pyx_v_alpha, __pyx_v_delta); /* function exit code */ @@ -1745,7 +1665,7 @@ 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":62 +/* "ml.pyx":59 * 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)) # <<<<<<<<<<<<<< @@ -1771,7 +1691,7 @@ 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 = 62; __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 = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_cur_scope); __Pyx_RefNannyFinishContext(); return (PyObject *) gen; @@ -1809,16 +1729,16 @@ 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 = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __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 = 59; __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 = 59; __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 = 59; __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); @@ -1826,14 +1746,14 @@ 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 = 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 = 59; __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 = 59; __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 = 59; __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 = 59; __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; @@ -1853,7 +1773,7 @@ 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 = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -1873,7 +1793,7 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera return NULL; 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__pyx_pybuffernd_probs.diminfo[0].shape = __pyx_pybuffernd_probs.rcbuffer->pybuffer.shape[0]; } } @@ -2036,43 +1957,43 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_v_probs = ((PyArrayObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "ml.pyx":48 + /* "ml.pyx":45 * 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 = 45; __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 = 45; __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 = 45; __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 = 45; __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 = 45; __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]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 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 = 45; __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_2ml_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 = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_probs_fail.diminfo[0].strides = __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_probs_fail.diminfo[0].shape = __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.shape[0]; } } @@ -2080,48 +2001,48 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_v_probs_fail = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "ml.pyx":49 + /* "ml.pyx":46 * 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) # <<<<<<<<<<<<<< * * # loop through victims */ - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_zeros); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 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 = 46; 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__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 = 46; __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 = 46; __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 = 46; __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 = 46; __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_2ml_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_probs_nv.rcbuffer->pybuffer, (PyObject*)__pyx_t_9, &__Pyx_TypeInfo_nn___pyx_t_2ml_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 = 46; __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]; } } @@ -2129,7 +2050,7 @@ 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":52 + /* "ml.pyx":49 * * # loop through victims * for i, parents in enumerate(victims.itervalues()): # <<<<<<<<<<<<<< @@ -2140,9 +2061,9 @@ 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 = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __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 = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = __pyx_t_4; @@ -2150,25 +2071,25 @@ 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 = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __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 = 49; __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":56 + /* "ml.pyx":53 * # 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 = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - /* "ml.pyx":57 + /* "ml.pyx":54 * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2177,15 +2098,15 @@ static PyObject *__pyx_pf_2ml_ml(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 = 54; __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 = 54; __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 = 54; __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; @@ -2197,7 +2118,7 @@ static PyObject *__pyx_pf_2ml_ml(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 = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -2223,7 +2144,7 @@ static PyObject *__pyx_pf_2ml_ml(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 = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(item); *(temps[i]) = item; } @@ -2233,7 +2154,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } else { Py_ssize_t index = -1; 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 = 57; __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 = 54; __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; @@ -2242,7 +2163,7 @@ static PyObject *__pyx_pf_2ml_ml(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 = 57; __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 = 54; __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; @@ -2250,12 +2171,12 @@ static PyObject *__pyx_pf_2ml_ml(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 = 54; __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 = 54; __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 = 54; __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; @@ -2266,22 +2187,22 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_18); __pyx_t_18 = 0; - /* "ml.pyx":56 + /* "ml.pyx":53 * # 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_2ml_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 = 53; __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 = 53; __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 = 53; __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_t_22, __pyx_t_23, __pyx_t_24)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __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 = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "ml.pyx":57 + /* "ml.pyx":54 * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2295,38 +2216,38 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GIVEREF(__pyx_t_4); __pyx_t_4 = 0; - /* "ml.pyx":58 + /* "ml.pyx":55 * 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 = 55; __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 = 55; __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 = 55; __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_2ml_DTYPE_t *, __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_probs_fail.diminfo[0].strides) = __pyx_t_24; - /* "ml.pyx":59 + /* "ml.pyx":56 * 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 = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - /* "ml.pyx":60 + /* "ml.pyx":57 * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2335,15 +2256,15 @@ static PyObject *__pyx_pf_2ml_ml(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 = 57; __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 = 57; __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 = 57; __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; @@ -2355,7 +2276,7 @@ static PyObject *__pyx_pf_2ml_ml(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 = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -2381,7 +2302,7 @@ static PyObject *__pyx_pf_2ml_ml(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 = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(item); *(temps[i]) = item; } @@ -2391,7 +2312,7 @@ static PyObject *__pyx_pf_2ml_ml(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 = 57; __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; @@ -2400,7 +2321,7 @@ static PyObject *__pyx_pf_2ml_ml(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 = 57; __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; @@ -2408,12 +2329,12 @@ static PyObject *__pyx_pf_2ml_ml(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 = 57; __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 = 57; __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 = 57; __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; @@ -2424,22 +2345,22 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_14); __pyx_t_14 = 0; - /* "ml.pyx":59 + /* "ml.pyx":56 * 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_2ml_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 = 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_22 = __pyx_PyFloat_AsDouble(__pyx_v_w3); 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_6 = PyFloat_FromDouble(__pyx_f_2ml_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 = 56; __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 = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "ml.pyx":60 + /* "ml.pyx":57 * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2453,24 +2374,24 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = 0; - /* "ml.pyx":62 + /* "ml.pyx":59 * 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_2ml_2ml_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_2ml_2ml_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __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 = 59; __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 = 59; __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 = 59; __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; @@ -2478,249 +2399,440 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "ml.pyx":76 + /* "ml.pyx":62 + * + * # 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 + */ + __pyx_t_10 = 0; + __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 = 62; __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 = 62; __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_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 = 62; __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 = 62; __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":65 + * # 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 = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + + /* "ml.pyx":66 + * # 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) + * + */ + if (unlikely(__pyx_v_parents == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __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 = 66; __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 = 66; __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; + #if CYTHON_COMPILING_IN_CPYTHON + Py_ssize_t size = Py_SIZE(sequence); + #else + Py_ssize_t size = PySequence_Size(sequence); + #endif + if (unlikely(size != 5)) { + if (size > 5) __Pyx_RaiseTooManyValuesError(5); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __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 + { + 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 = 66; __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; + 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 = 66; __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; + 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 = 66; __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; 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if (unlikely(!__pyx_codeobj__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(6, 0, 33, 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, 35, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -5299,8 +5394,8 @@ static int __Pyx_InitCachedConstants(void) { static int __Pyx_InitGlobals(void) { if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; - __pyx_float__1 = PyFloat_FromDouble(.1); if (unlikely(!__pyx_float__1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_float__001 = PyFloat_FromDouble(.001); if (unlikely(!__pyx_float__001)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_float__2 = PyFloat_FromDouble(.2); if (unlikely(!__pyx_float__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_float__002 = PyFloat_FromDouble(.002); if (unlikely(!__pyx_float__002)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_float_0_001 = PyFloat_FromDouble(0.001); if (unlikely(!__pyx_float_0_001)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} return 0; __pyx_L1_error:; @@ -5388,10 +5483,10 @@ PyMODINIT_FUNC PyInit_ml(void) /*--- Variable export code ---*/ /*--- Function export code ---*/ /*--- Type init code ---*/ - if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct__ml) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct__ml) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __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 = 62; __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 = 59; __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 ---*/ @@ -5437,16 +5532,16 @@ PyMODINIT_FUNC PyInit_ml(void) if (PyDict_SetItem(__pyx_d, __pyx_n_s_DTYPE, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "ml.pyx":38 + /* "ml.pyx":35 * return result * * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< * DTYPE_t alpha, DTYPE_t delta): * cdef: */ - __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_2ml_1ml, NULL, __pyx_n_s_ml); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_2ml_1ml, NULL, __pyx_n_s_ml); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; /* "ml.pyx":1 @@ -5520,64 +5615,6 @@ 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, @@ -6756,8 +6793,35 @@ bad: return (double)-1; } -static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { - PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); +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 @@ -7170,147 +7234,6 @@ 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; |