diff options
Diffstat (limited to 'experiments/ml.c')
| -rw-r--r-- | experiments/ml.c | 676 |
1 files changed, 325 insertions, 351 deletions
diff --git a/experiments/ml.c b/experiments/ml.c index f0a7125..25c10ac 100644 --- a/experiments/ml.c +++ b/experiments/ml.c @@ -1018,8 +1018,6 @@ 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 CYTHON_INLINE long __Pyx_pow_long(long, long); /* proto */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); @@ -1380,7 +1378,7 @@ static PyObject *__pyx_codeobj__9; * """weight for successful infection, exponential time model""" */ -static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_lmbda, __pyx_t_2ml_DTYPE_t __pyx_v_t_scale, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w3) { +static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta, __pyx_t_2ml_DTYPE_t __pyx_v_lmbda, __pyx_t_2ml_DTYPE_t __pyx_v_t_scale, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w3) { __pyx_t_2ml_DTYPE_t __pyx_v_structural; __pyx_t_2ml_DTYPE_t __pyx_v_temporal; __pyx_t_2ml_DTYPE_t __pyx_v_result; @@ -1388,18 +1386,18 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("weight_success", 0); - /* "ml.pyx":13 - * """weight for successful infection, exponential time model""" + /* "ml.pyx":14 * cdef DTYPE_t structural, temporal, result - * structural = delta ** (dist**1) # <<<<<<<<<<<<<< - * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) + * # structural = delta ** (dist**1) + * structural = delta * lmbda**(dist-1) # <<<<<<<<<<<<<< * temporal = log(exp(alpha/t_scale)-1.) - alpha*dt/t_scale + * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 */ - __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__Pyx_pow_long(((long)__pyx_v_dist), 1))); + __pyx_v_structural = (__pyx_v_delta * pow(__pyx_v_lmbda, ((__pyx_t_2ml_DTYPE_t)(__pyx_v_dist - 1)))); /* "ml.pyx":15 - * structural = delta ** (dist**1) - * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) + * # structural = delta ** (dist**1) + * structural = delta * lmbda**(dist-1) * temporal = log(exp(alpha/t_scale)-1.) - alpha*dt/t_scale # <<<<<<<<<<<<<< * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 * result = log(structural) + temporal @@ -1447,7 +1445,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py * """weight for failed infection, exponential time model""" */ -static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_lmbda, __pyx_t_2ml_DTYPE_t __pyx_v_t_scale, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w3) { +static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta, __pyx_t_2ml_DTYPE_t __pyx_v_lmbda, __pyx_t_2ml_DTYPE_t __pyx_v_t_scale, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w3) { __pyx_t_2ml_DTYPE_t __pyx_v_structural; __pyx_t_2ml_DTYPE_t __pyx_v_temporal; __pyx_t_2ml_DTYPE_t __pyx_v_result; @@ -1455,18 +1453,18 @@ 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":24 - * """weight for failed infection, exponential time model""" + /* "ml.pyx":25 * cdef DTYPE_t structural, temporal, result - * structural = delta ** (dist**1) # <<<<<<<<<<<<<< - * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) + * # structural = delta ** (dist**1) + * structural = delta * lmbda**(dist-1) # <<<<<<<<<<<<<< * temporal = exp(-alpha * dt/t_scale) + * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 */ - __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__Pyx_pow_long(((long)__pyx_v_dist), 1))); + __pyx_v_structural = (__pyx_v_delta * pow(__pyx_v_lmbda, ((__pyx_t_2ml_DTYPE_t)(__pyx_v_dist - 1)))); /* "ml.pyx":26 - * structural = delta ** (dist**1) - * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) + * # structural = delta ** (dist**1) + * structural = delta * lmbda**(dist-1) * temporal = exp(-alpha * dt/t_scale) # <<<<<<<<<<<<<< * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 * result = log(1. - structural + structural * temporal) @@ -1477,14 +1475,14 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py * temporal = exp(-alpha * dt/t_scale) * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 * result = log(1. - structural + structural * temporal) # <<<<<<<<<<<<<< - * # if dt>100: result=0 * return result + * */ __pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal))); - /* "ml.pyx":30 + /* "ml.pyx":29 + * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 * result = log(1. - structural + structural * temporal) - * # if dt>100: result=0 * return result # <<<<<<<<<<<<<< * * def ml(dict root_victims, dict victims, dict non_victims, @@ -1506,7 +1504,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py return __pyx_r; } -/* "ml.pyx":32 +/* "ml.pyx":31 * return result * * def ml(dict root_victims, dict victims, dict non_victims, # <<<<<<<<<<<<<< @@ -1554,31 +1552,31 @@ 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 = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __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 = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_alpha)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_delta)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_lmbda)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __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 = 32; __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 = 31; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 6) { goto __pyx_L5_argtuple_error; @@ -1593,21 +1591,21 @@ 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_alpha = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_delta = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_lmbda = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_lmbda == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_delta = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_lmbda = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_lmbda == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __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 = 32; __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 = 31; __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 = 32; __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 = 32; __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 = 32; __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 = 31; __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 = 31; __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 = 31; __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_alpha, __pyx_v_delta, __pyx_v_lmbda); /* function exit code */ @@ -1730,7 +1728,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_pybuffernd_probs_nv.data = NULL; __pyx_pybuffernd_probs_nv.rcbuffer = &__pyx_pybuffer_probs_nv; - /* "ml.pyx":38 + /* "ml.pyx":37 * DTYPE_t beta, ll, beta_add, max_beta, max_beta_add * list parents, failures, successes * n_roots, n_victims = len(root_victims), len(victims) # <<<<<<<<<<<<<< @@ -1739,18 +1737,18 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ */ if (unlikely(__pyx_v_root_victims == Py_None)) { PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (unlikely(__pyx_v_victims == Py_None)) { PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_n_roots = __pyx_t_1; __pyx_v_n_victims = __pyx_t_2; - /* "ml.pyx":39 + /* "ml.pyx":38 * list parents, failures, successes * n_roots, n_victims = len(root_victims), len(victims) * n_nodes = 148152 # <<<<<<<<<<<<<< @@ -1760,7 +1758,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_INCREF(__pyx_int_148152); __pyx_v_n_nodes = __pyx_int_148152; - /* "ml.pyx":40 + /* "ml.pyx":39 * n_roots, n_victims = len(root_victims), len(victims) * n_nodes = 148152 * n_days = 3012 # <<<<<<<<<<<<<< @@ -1769,7 +1767,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ */ __pyx_v_n_days = 3012; - /* "ml.pyx":41 + /* "ml.pyx":40 * n_nodes = 148152 * n_days = 3012 * t_scale = 1. # <<<<<<<<<<<<<< @@ -1778,43 +1776,43 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ */ __pyx_v_t_scale = 1.; - /* "ml.pyx":43 + /* "ml.pyx":42 * t_scale = 1. * 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] parent_dists = np.zeros(n_victims, dtype=DTYPE) */ - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __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_2ml_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) { __pyx_v_probs = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __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]; } } @@ -1822,43 +1820,43 @@ 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":44 + /* "ml.pyx":43 * 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] parent_dists = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] parent_dts = np.zeros(n_victims, dtype=DTYPE) */ - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_zeros); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_zeros); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; 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__pyx_t_6 = 0; - if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __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 = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; 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if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_zeros); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_zeros); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_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_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_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 = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __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 = 44; __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 = 45; __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 = 44; __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 = 45; __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 = 44; __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 = 45; __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 = 44; __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_parent_dists.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_parent_dists = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_parent_dists.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_parent_dists.diminfo[0].strides = __pyx_pybuffernd_parent_dists.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_parent_dists.diminfo[0].shape = __pyx_pybuffernd_parent_dists.rcbuffer->pybuffer.shape[0]; } } @@ -1910,43 +1908,43 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_v_parent_dists = ((PyArrayObject *)__pyx_t_3); __pyx_t_3 = 0; - /* "ml.pyx":46 + /* "ml.pyx":45 * np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] parent_dts = np.zeros(n_victims, dtype=DTYPE) # <<<<<<<<<<<<<< * np.ndarray[DTYPE_t] probs_nv = np.zeros(len(non_victims), dtype=DTYPE) * */ - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_10 = ((PyArrayObject *)__pyx_t_6); { __Pyx_BufFmt_StackElem __pyx_stack[1]; if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_parent_dts.rcbuffer->pybuffer, (PyObject*)__pyx_t_10, &__Pyx_TypeInfo_nn___pyx_t_2ml_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) { __pyx_v_parent_dts = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_parent_dts.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __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_parent_dts.diminfo[0].strides = __pyx_pybuffernd_parent_dts.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_parent_dts.diminfo[0].shape = __pyx_pybuffernd_parent_dts.rcbuffer->pybuffer.shape[0]; } } @@ -1954,48 +1952,48 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_v_parent_dts = ((PyArrayObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "ml.pyx":47 + /* "ml.pyx":46 * np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] parent_dts = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] probs_nv = np.zeros(len(non_victims), dtype=DTYPE) # <<<<<<<<<<<<<< * * # loop through victims */ - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __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 = 46; __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 = 47; __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 = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 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 = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __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 = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_6 = PyInt_FromSsize_t(__pyx_t_2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __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 = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyInt_FromSsize_t(__pyx_t_2); 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_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_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 = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyDict_New(); 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_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); 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); - if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __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 = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_11 = ((PyArrayObject *)__pyx_t_4); { __Pyx_BufFmt_StackElem __pyx_stack[1]; if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_probs_nv.rcbuffer->pybuffer, (PyObject*)__pyx_t_11, &__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 = 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_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]; } } @@ -2003,7 +2001,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_v_probs_nv = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "ml.pyx":50 + /* "ml.pyx":49 * * # loop through victims * for i, parents in enumerate(victims.itervalues()): # <<<<<<<<<<<<<< @@ -2014,9 +2012,9 @@ 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 = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_6 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_13)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_13)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = __pyx_t_6; @@ -2024,25 +2022,25 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ while (1) { __pyx_t_14 = __Pyx_dict_iter_next(__pyx_t_4, __pyx_t_1, &__pyx_t_2, NULL, &__pyx_t_6, NULL, __pyx_t_13); if (unlikely(__pyx_t_14 == 0)) break; - if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (!(likely(PyList_CheckExact(__pyx_t_6))||((__pyx_t_6) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_6)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(PyList_CheckExact(__pyx_t_6))||((__pyx_t_6) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_6)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_XDECREF_SET(__pyx_v_parents, ((PyObject*)__pyx_t_6)); __pyx_t_6 = 0; __pyx_v_i = __pyx_t_12; __pyx_t_12 = (__pyx_t_12 + 1); - /* "ml.pyx":54 + /* "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, lmbda, t_scale, w1, w2, w3) # <<<<<<<<<<<<<< * for (prnt, dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) */ - __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - /* "ml.pyx":55 + /* "ml.pyx":54 * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) * for (prnt, dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2051,15 +2049,15 @@ 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 = 55; __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_15 = 0; for (;;) { if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_5)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_3 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_3 = PySequence_ITEM(__pyx_t_5, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PySequence_ITEM(__pyx_t_5, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) { PyObject* sequence = __pyx_t_3; @@ -2071,7 +2069,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ if (unlikely(size != 6)) { if (size > 6) __Pyx_RaiseTooManyValuesError(6); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __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))) { @@ -2100,7 +2098,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ Py_ssize_t i; PyObject** temps[6] = {&__pyx_t_16,&__pyx_t_17,&__pyx_t_18,&__pyx_t_19,&__pyx_t_20,&__pyx_t_21}; for (i=0; i < 6; i++) { - PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __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; } @@ -2110,7 +2108,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } else { Py_ssize_t index = -1; PyObject** temps[6] = {&__pyx_t_16,&__pyx_t_17,&__pyx_t_18,&__pyx_t_19,&__pyx_t_20,&__pyx_t_21}; - __pyx_t_22 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_23 = Py_TYPE(__pyx_t_22)->tp_iternext; @@ -2119,7 +2117,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GOTREF(item); *(temps[index]) = item; } - if (__Pyx_IternextUnpackEndCheck(__pyx_t_23(__pyx_t_22), 6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_23(__pyx_t_22), 6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_23 = NULL; __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; goto __pyx_L8_unpacking_done; @@ -2127,12 +2125,12 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; __pyx_t_23 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __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_14 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0; - __pyx_t_24 = __Pyx_PyInt_As_int(__pyx_t_18); if (unlikely((__pyx_t_24 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __Pyx_PyInt_As_int(__pyx_t_18); if (unlikely((__pyx_t_24 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0; __Pyx_XDECREF_SET(__pyx_v_prnt, __pyx_t_16); __pyx_t_16 = 0; @@ -2145,22 +2143,22 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_21); __pyx_t_21 = 0; - /* "ml.pyx":54 + /* "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, lmbda, t_scale, w1, w2, w3) # <<<<<<<<<<<<<< * for (prnt, dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) */ - __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_26 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_27 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_27 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_3 = PyFloat_FromDouble(__pyx_f_2ml_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_lmbda, __pyx_v_t_scale, __pyx_t_25, __pyx_t_26, __pyx_t_27)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_26 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_27 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_27 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyFloat_FromDouble(__pyx_f_2ml_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_lmbda, __pyx_v_t_scale, __pyx_t_25, __pyx_t_26, __pyx_t_27)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_6, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_6, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "ml.pyx":55 + /* "ml.pyx":54 * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) * for (prnt, dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2172,38 +2170,38 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF_SET(__pyx_v_failures, ((PyObject*)__pyx_t_6)); __pyx_t_6 = 0; - /* "ml.pyx":56 + /* "ml.pyx":55 * failures = [weight_failure(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) * for (prnt, dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) # <<<<<<<<<<<<<< * successes = [weight_success(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) * for (prnt, dist, dt, w1, w2, w3) in parents] */ - __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(1); 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); __Pyx_INCREF(__pyx_v_failures); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_failures); __Pyx_GIVEREF(__pyx_v_failures); - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_6, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_6, 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_6); __pyx_t_6 = 0; - __pyx_t_27 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_27 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_27 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_27 == (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_24 = __pyx_v_i; if (__pyx_t_24 < 0) __pyx_t_24 += __pyx_pybuffernd_probs_fail.diminfo[0].shape; *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.buf, __pyx_t_24, __pyx_pybuffernd_probs_fail.diminfo[0].strides) = __pyx_t_27; - /* "ml.pyx":57 + /* "ml.pyx":56 * for (prnt, dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) # <<<<<<<<<<<<<< * for (prnt, dist, dt, w1, w2, w3) in parents] * dists = [dist for (prnt, dist, dt, w1, w2, w3) in parents] */ - __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __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":58 + /* "ml.pyx":57 * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) * for (prnt, dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2212,15 +2210,15 @@ 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 = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_6 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_6); __pyx_t_15 = 0; for (;;) { if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_6)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) { PyObject* sequence = __pyx_t_3; @@ -2232,7 +2230,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ if (unlikely(size != 6)) { if (size > 6) __Pyx_RaiseTooManyValuesError(6); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -2261,7 +2259,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ Py_ssize_t i; PyObject** temps[6] = {&__pyx_t_21,&__pyx_t_20,&__pyx_t_19,&__pyx_t_18,&__pyx_t_17,&__pyx_t_16}; for (i=0; i < 6; i++) { - PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(item); *(temps[i]) = item; } @@ -2271,7 +2269,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } else { Py_ssize_t index = -1; PyObject** temps[6] = {&__pyx_t_21,&__pyx_t_20,&__pyx_t_19,&__pyx_t_18,&__pyx_t_17,&__pyx_t_16}; - __pyx_t_22 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_23 = Py_TYPE(__pyx_t_22)->tp_iternext; @@ -2280,7 +2278,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GOTREF(item); *(temps[index]) = item; } - if (__Pyx_IternextUnpackEndCheck(__pyx_t_23(__pyx_t_22), 6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_23(__pyx_t_22), 6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_23 = NULL; __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; goto __pyx_L12_unpacking_done; @@ -2288,12 +2286,12 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; __pyx_t_23 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L12_unpacking_done:; } - __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_20); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_20); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0; - __pyx_t_28 = __Pyx_PyInt_As_int(__pyx_t_19); if (unlikely((__pyx_t_28 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_28 = __Pyx_PyInt_As_int(__pyx_t_19); if (unlikely((__pyx_t_28 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; __Pyx_XDECREF_SET(__pyx_v_prnt, __pyx_t_21); __pyx_t_21 = 0; @@ -2306,22 +2304,22 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_16); __pyx_t_16 = 0; - /* "ml.pyx":57 + /* "ml.pyx":56 * for (prnt, dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) # <<<<<<<<<<<<<< * for (prnt, dist, dt, w1, w2, w3) in parents] * dists = [dist for (prnt, dist, dt, w1, w2, w3) in parents] */ - __pyx_t_27 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_27 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_v_w2); 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__pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyFloat_FromDouble(__pyx_f_2ml_weight_success(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_lmbda, __pyx_v_t_scale, __pyx_t_27, __pyx_t_26, __pyx_t_25)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "ml.pyx":58 + /* "ml.pyx":57 * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) * for (prnt, dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2333,26 +2331,26 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF_SET(__pyx_v_successes, ((PyObject*)__pyx_t_5)); __pyx_t_5 = 0; - /* "ml.pyx":59 + /* "ml.pyx":58 * successes = [weight_success(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) * for (prnt, dist, dt, w1, w2, w3) in parents] * dists = [dist for (prnt, dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< * dts = [dt for (prnt, 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); if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_6 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_6); __pyx_t_15 = 0; for (;;) { if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_6)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) { PyObject* sequence = __pyx_t_3; @@ -2364,7 +2362,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ if (unlikely(size != 6)) { if (size > 6) __Pyx_RaiseTooManyValuesError(6); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -2393,7 +2391,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ Py_ssize_t i; PyObject** temps[6] = {&__pyx_t_16,&__pyx_t_17,&__pyx_t_18,&__pyx_t_19,&__pyx_t_20,&__pyx_t_21}; for (i=0; i < 6; i++) { - PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; 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__pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_23(__pyx_t_22), 6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_23 = NULL; __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; goto __pyx_L16_unpacking_done; @@ -2420,12 +2418,12 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; __pyx_t_23 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L16_unpacking_done:; } - __pyx_t_28 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_28 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_28 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_28 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0; - __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_18); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_18); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0; __Pyx_XDECREF_SET(__pyx_v_prnt, __pyx_t_16); __pyx_t_16 = 0; @@ -2437,35 +2435,35 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_t_20 = 0; __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_21); __pyx_t_21 = 0; - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_dist); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_dist); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; } __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_XDECREF_SET(__pyx_v_dists, ((PyObject*)__pyx_t_5)); __pyx_t_5 = 0; - /* "ml.pyx":60 + /* "ml.pyx":59 * for (prnt, dist, dt, w1, w2, w3) in parents] * dists = [dist for (prnt, dist, dt, w1, w2, w3) in parents] * dts = [dt for (prnt, dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = float("-inf") */ - __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 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_6 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_6); __pyx_t_15 = 0; for (;;) { if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_6)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) { PyObject* sequence = __pyx_t_3; @@ -2477,7 +2475,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ if (unlikely(size != 6)) { if (size > 6) __Pyx_RaiseTooManyValuesError(6); 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))) { @@ -2506,7 +2504,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ Py_ssize_t i; PyObject** temps[6] = {&__pyx_t_21,&__pyx_t_20,&__pyx_t_19,&__pyx_t_18,&__pyx_t_17,&__pyx_t_16}; for (i=0; i < 6; 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; } @@ -2516,7 +2514,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } else { Py_ssize_t index = -1; PyObject** temps[6] = {&__pyx_t_21,&__pyx_t_20,&__pyx_t_19,&__pyx_t_18,&__pyx_t_17,&__pyx_t_16}; - __pyx_t_22 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_23 = Py_TYPE(__pyx_t_22)->tp_iternext; @@ -2525,7 +2523,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GOTREF(item); *(temps[index]) = item; } - if (__Pyx_IternextUnpackEndCheck(__pyx_t_23(__pyx_t_22), 6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_23(__pyx_t_22), 6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_23 = NULL; __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; goto __pyx_L20_unpacking_done; @@ -2533,12 +2531,12 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_DECREF(__pyx_t_22); 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if (unlikely((__pyx_t_28 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; __Pyx_XDECREF_SET(__pyx_v_prnt, __pyx_t_21); __pyx_t_21 = 0; @@ -2550,28 +2548,28 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_t_17 = 0; __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_16); __pyx_t_16 = 0; - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_dt); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_dt); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; } __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_XDECREF_SET(__pyx_v_dts, ((PyObject*)__pyx_t_5)); __pyx_t_5 = 0; - /* "ml.pyx":62 + /* "ml.pyx":61 * dts = [dt for (prnt, dist, dt, w1, w2, w3) in parents] * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = float("-inf") # <<<<<<<<<<<<<< * for l, s in enumerate(successes): * prob = s - failures[l] */ - __pyx_t_29 = __Pyx_PyObject_AsDouble(__pyx_kp_s_inf); if (unlikely(__pyx_t_29 == ((double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_29 = __Pyx_PyObject_AsDouble(__pyx_kp_s_inf); if (unlikely(__pyx_t_29 == ((double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_28 = __pyx_v_i; if (__pyx_t_28 < 0) __pyx_t_28 += __pyx_pybuffernd_probs.diminfo[0].shape; 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if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyFloat_FromDouble((*__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_30, __pyx_pybuffernd_probs.diminfo[0].strides))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_6 = PyObject_RichCompare(__pyx_v_prob, __pyx_t_3, Py_GT); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyObject_RichCompare(__pyx_v_prob, __pyx_t_3, Py_GT); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_31 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_31 < 0)) {__pyx_filename = __pyx_f[0]; 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goto __pyx_L1_error;} + __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_t_6); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_33 = __pyx_v_i; if (__pyx_t_33 < 0) __pyx_t_33 += __pyx_pybuffernd_parent_dists.diminfo[0].shape; *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_parent_dists.rcbuffer->pybuffer.buf, __pyx_t_33, __pyx_pybuffernd_parent_dists.diminfo[0].strides) = __pyx_t_25; - /* "ml.pyx":68 + /* "ml.pyx":67 * probs[i] = prob * parent_dists[i] = dists[l] * parent_dts[i] = dts[l] # <<<<<<<<<<<<<< * # probs_fail[i] = failures[l] * */ - __pyx_t_6 = __Pyx_GetItemInt_List(__pyx_v_dts, __pyx_v_l, int, 1, __Pyx_PyInt_From_int, 1, 1, 0); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_6 = __Pyx_GetItemInt_List(__pyx_v_dts, __pyx_v_l, int, 1, __Pyx_PyInt_From_int, 1, 1, 0); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_6); - __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_t_6); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_t_6); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_34 = __pyx_v_i; if (__pyx_t_34 < 0) __pyx_t_34 += __pyx_pybuffernd_parent_dts.diminfo[0].shape; @@ -2669,7 +2667,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } __pyx_L23:; - /* "ml.pyx":63 + /* "ml.pyx":62 * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = float("-inf") * for l, s in enumerate(successes): # <<<<<<<<<<<<<< @@ -2681,7 +2679,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - /* "ml.pyx":72 + /* "ml.pyx":71 * * # loop through non-victims * for i, parents in enumerate(non_victims.itervalues()): # <<<<<<<<<<<<<< @@ -2692,9 +2690,9 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_t_1 = 0; if (unlikely(__pyx_v_non_victims == Py_None)) { PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "itervalues"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_5 = __Pyx_dict_iterator(__pyx_v_non_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_2), (&__pyx_t_13)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_dict_iterator(__pyx_v_non_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_2), (&__pyx_t_13)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = __pyx_t_5; @@ -2702,25 +2700,25 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ while (1) { __pyx_t_14 = __Pyx_dict_iter_next(__pyx_t_4, __pyx_t_2, &__pyx_t_1, NULL, &__pyx_t_5, NULL, __pyx_t_13); if (unlikely(__pyx_t_14 == 0)) break; - if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __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 = 72; __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 = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_XDECREF_SET(__pyx_v_parents, ((PyObject*)__pyx_t_5)); __pyx_t_5 = 0; __pyx_v_i = __pyx_t_12; __pyx_t_12 = (__pyx_t_12 + 1); - /* "ml.pyx":75 + /* "ml.pyx":74 * # for each non victim node, compute the probability that all its * # parents fail to infect it * failures = [weight_failure(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) # <<<<<<<<<<<<<< * for (prnt, 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 = 75; __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 = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - /* "ml.pyx":76 + /* "ml.pyx":75 * # parents fail to infect it * failures = [weight_failure(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) * for (prnt, dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2729,15 +2727,15 @@ 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 = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_6 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_6); __pyx_t_15 = 0; for (;;) { if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_6)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) { PyObject* sequence = __pyx_t_3; @@ -2749,7 +2747,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ if (unlikely(size != 6)) { if (size > 6) __Pyx_RaiseTooManyValuesError(6); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -2778,7 +2776,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ Py_ssize_t i; PyObject** temps[6] = {&__pyx_t_16,&__pyx_t_17,&__pyx_t_18,&__pyx_t_19,&__pyx_t_20,&__pyx_t_21}; for (i=0; i < 6; i++) { - PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(item); *(temps[i]) = item; } @@ -2788,7 +2786,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } else { Py_ssize_t index = -1; PyObject** temps[6] = {&__pyx_t_16,&__pyx_t_17,&__pyx_t_18,&__pyx_t_19,&__pyx_t_20,&__pyx_t_21}; - __pyx_t_22 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_23 = Py_TYPE(__pyx_t_22)->tp_iternext; @@ -2797,7 +2795,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GOTREF(item); *(temps[index]) = item; } - if (__Pyx_IternextUnpackEndCheck(__pyx_t_23(__pyx_t_22), 6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_23(__pyx_t_22), 6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_23 = NULL; __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; goto __pyx_L29_unpacking_done; @@ -2805,12 +2803,12 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; __pyx_t_23 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L29_unpacking_done:; } - __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0; - __pyx_t_35 = __Pyx_PyInt_As_int(__pyx_t_18); if (unlikely((__pyx_t_35 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_35 = __Pyx_PyInt_As_int(__pyx_t_18); if (unlikely((__pyx_t_35 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0; __Pyx_XDECREF_SET(__pyx_v_prnt, __pyx_t_16); __pyx_t_16 = 0; @@ -2823,22 +2821,22 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_21); __pyx_t_21 = 0; - /* "ml.pyx":75 + /* "ml.pyx":74 * # for each non victim node, compute the probability that all its * # parents fail to infect it * failures = [weight_failure(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) # <<<<<<<<<<<<<< * for (prnt, dist, dt, w1, w2, w3) in parents] * probs_nv[i] = sum(failures) */ - __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_26 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_27 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_27 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_3 = PyFloat_FromDouble(__pyx_f_2ml_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_lmbda, __pyx_v_t_scale, __pyx_t_25, __pyx_t_26, __pyx_t_27)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_26 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_27 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_27 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyFloat_FromDouble(__pyx_f_2ml_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_lmbda, __pyx_v_t_scale, __pyx_t_25, __pyx_t_26, __pyx_t_27)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "ml.pyx":76 + /* "ml.pyx":75 * # parents fail to infect it * failures = [weight_failure(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) * for (prnt, dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2850,22 +2848,22 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF_SET(__pyx_v_failures, ((PyObject*)__pyx_t_5)); __pyx_t_5 = 0; - /* "ml.pyx":77 + /* "ml.pyx":76 * failures = [weight_failure(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) * for (prnt, dist, dt, w1, w2, w3) in parents] * probs_nv[i] = sum(failures) # <<<<<<<<<<<<<< * * # calculate log likelihood */ - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_INCREF(__pyx_v_failures); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_failures); __Pyx_GIVEREF(__pyx_v_failures); - __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_5, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_5, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_27 = __pyx_PyFloat_AsDouble(__pyx_t_6); if (unlikely((__pyx_t_27 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_27 = __pyx_PyFloat_AsDouble(__pyx_t_6); if (unlikely((__pyx_t_27 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_35 = __pyx_v_i; if (__pyx_t_35 < 0) __pyx_t_35 += __pyx_pybuffernd_probs_nv.diminfo[0].shape; @@ -2873,14 +2871,14 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - /* "ml.pyx":80 + /* "ml.pyx":79 * * # calculate log likelihood * ll = probs_fail.sum() # add probability that all edges to all victims fail # <<<<<<<<<<<<<< * ll += probs_nv.sum() # add probability that all edges to non_victims fail * */ - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs_fail), __pyx_n_s_sum); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs_fail), __pyx_n_s_sum); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __pyx_t_5 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_6))) { @@ -2893,27 +2891,27 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } } if (__pyx_t_5) { - __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } else { - __pyx_t_4 = __Pyx_PyObject_CallNoArg(__pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_CallNoArg(__pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_27 = __pyx_PyFloat_AsDouble(__pyx_t_4); if (unlikely((__pyx_t_27 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_27 = __pyx_PyFloat_AsDouble(__pyx_t_4); if (unlikely((__pyx_t_27 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_v_ll = __pyx_t_27; - /* "ml.pyx":81 + /* "ml.pyx":80 * # calculate log likelihood * ll = probs_fail.sum() # add probability that all edges to all victims fail * ll += probs_nv.sum() # add probability that all edges to non_victims fail # <<<<<<<<<<<<<< * * max_beta_add = float('-inf') */ - __pyx_t_4 = PyFloat_FromDouble(__pyx_v_ll); 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__pyx_lineno = 102; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_21, __pyx_n_s_mean); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 101; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0; __pyx_t_21 = NULL; @@ -3246,10 +3244,10 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } } if (__pyx_t_21) { - __pyx_t_20 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_21); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 102; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_20 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_21); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 101; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0; } else { - __pyx_t_20 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 102; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_20 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 101; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_GOTREF(__pyx_t_20); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -3259,7 +3257,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } __pyx_L32:; - /* "ml.pyx":85 + /* "ml.pyx":84 * max_beta_add = float('-inf') * # iterate over all victim nodes to find the optimal threshold * for beta in np.arange(0.01, 1., 0.01): # <<<<<<<<<<<<<< @@ -3269,7 +3267,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "ml.pyx":105 + /* "ml.pyx":104 * # print 'beta:', max_beta, 'add:', max_beta_add, 'roots:', max_roots * * ll += max_beta_add # <<<<<<<<<<<<<< @@ -3278,7 +3276,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ */ __pyx_v_ll = (__pyx_v_ll + __pyx_v_max_beta_add); 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } + __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_INCREF(__pyx_kp_s_dist); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_kp_s_dist); @@ -3312,17 +3310,17 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_INCREF(__pyx_v_pdists); PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_v_pdists); __Pyx_GIVEREF(__pyx_v_pdists); - if (__Pyx_Print(0, __pyx_t_6, 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_Print(0, __pyx_t_6, 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "ml.pyx":109 + /* "ml.pyx":108 * beta = max_beta * print 'dist:', pdists * print 'dt:', pdts # <<<<<<<<<<<<<< * return (beta, roots, ll) */ - if (unlikely(!__pyx_v_pdts)) { __Pyx_RaiseUnboundLocalError("pdts"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_v_pdts)) { __Pyx_RaiseUnboundLocalError("pdts"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } + __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_INCREF(__pyx_kp_s_dt); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_kp_s_dt); @@ -3330,22 +3328,22 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_INCREF(__pyx_v_pdts); PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_v_pdts); __Pyx_GIVEREF(__pyx_v_pdts); - if (__Pyx_Print(0, __pyx_t_6, 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_Print(0, __pyx_t_6, 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "ml.pyx":110 + /* "ml.pyx":109 * print 'dist:', pdists * print 'dt:', pdts * return (beta, roots, ll) # <<<<<<<<<<<<<< */ __Pyx_XDECREF(__pyx_r); - __pyx_t_6 = PyFloat_FromDouble(__pyx_v_beta); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyFloat_FromDouble(__pyx_v_beta); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_20 = __Pyx_PyInt_From_int(__pyx_v_roots); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_20 = __Pyx_PyInt_From_int(__pyx_v_roots); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_20); - __pyx_t_4 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_21 = PyTuple_New(3); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_21 = PyTuple_New(3); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_21); PyTuple_SET_ITEM(__pyx_t_21, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); @@ -3360,7 +3358,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_t_21 = 0; goto __pyx_L0; - /* "ml.pyx":32 + /* "ml.pyx":31 * return result * * def ml(dict root_victims, dict victims, dict non_victims, # <<<<<<<<<<<<<< @@ -5528,8 +5526,8 @@ 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 = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_sum = __Pyx_GetBuiltinName(__pyx_n_s_sum); if (!__pyx_builtin_sum) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_sum = __Pyx_GetBuiltinName(__pyx_n_s_sum); if (!__pyx_builtin_sum) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_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;} @@ -5542,14 +5540,14 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); - /* "ml.pyx":85 + /* "ml.pyx":84 * max_beta_add = float('-inf') * # iterate over all victim nodes to find the optimal threshold * for beta in np.arange(0.01, 1., 0.01): # <<<<<<<<<<<<<< * thresh = log(beta/(n_days*(1.-beta))) * seeds = probs<thresh */ - __pyx_tuple_ = PyTuple_Pack(3, __pyx_float_0_01, __pyx_float_1_, __pyx_float_0_01); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple_ = PyTuple_Pack(3, __pyx_float_0_01, __pyx_float_1_, __pyx_float_0_01); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple_); __Pyx_GIVEREF(__pyx_tuple_); @@ -5619,17 +5617,17 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__7); __Pyx_GIVEREF(__pyx_tuple__7); - /* "ml.pyx":32 + /* "ml.pyx":31 * return result * * def ml(dict root_victims, dict victims, dict non_victims, # <<<<<<<<<<<<<< * DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda): * cdef: */ - __pyx_tuple__8 = PyTuple_Pack(44, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_lmbda, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_roots, __pyx_n_s_i, __pyx_n_s_dist_2, __pyx_n_s_dt_2, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_n_days, __pyx_n_s_beta, __pyx_n_s_ll, __pyx_n_s_beta_add, __pyx_n_s_max_beta, __pyx_n_s_max_beta_add, __pyx_n_s_parents, __pyx_n_s_failures, __pyx_n_s_successes, __pyx_n_s_n_nodes, __pyx_n_s_t_scale, __pyx_n_s_probs, __pyx_n_s_probs_fail, __pyx_n_s_parent_dists, __pyx_n_s_parent_dts, __pyx_n_s_probs_nv, __pyx_n_s_dists, __pyx_n_s_dts, __pyx_n_s_s, __pyx_n_s_prob, __pyx_n_s_thresh, __pyx_n_s_seeds, __pyx_n_s_non_seeds, __pyx_n_s_max_roots, __pyx_n_s_pdists, __pyx_n_s_pdts, __pyx_n_s_prnt, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__8 = PyTuple_Pack(44, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_lmbda, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_roots, __pyx_n_s_i, __pyx_n_s_dist_2, __pyx_n_s_dt_2, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_n_days, __pyx_n_s_beta, __pyx_n_s_ll, __pyx_n_s_beta_add, __pyx_n_s_max_beta, __pyx_n_s_max_beta_add, __pyx_n_s_parents, __pyx_n_s_failures, __pyx_n_s_successes, __pyx_n_s_n_nodes, __pyx_n_s_t_scale, __pyx_n_s_probs, __pyx_n_s_probs_fail, __pyx_n_s_parent_dists, __pyx_n_s_parent_dts, __pyx_n_s_probs_nv, __pyx_n_s_dists, __pyx_n_s_dts, __pyx_n_s_s, __pyx_n_s_prob, __pyx_n_s_thresh, __pyx_n_s_seeds, __pyx_n_s_non_seeds, __pyx_n_s_max_roots, __pyx_n_s_pdists, __pyx_n_s_pdts, __pyx_n_s_prnt, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__8); __Pyx_GIVEREF(__pyx_tuple__8); - __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(6, 0, 44, 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_Violence_Ca, __pyx_n_s_ml, 32, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(6, 0, 44, 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_Violence_Ca, __pyx_n_s_ml, 31, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -5771,16 +5769,16 @@ 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":32 + /* "ml.pyx":31 * return result * * def ml(dict root_victims, dict victims, dict non_victims, # <<<<<<<<<<<<<< * DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda): * cdef: */ - __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_2ml_1ml, NULL, __pyx_n_s_ml); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __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 = 31; __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 = 32; __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 = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; /* "ml.pyx":1 @@ -7473,30 +7471,6 @@ bad: return module; } -static CYTHON_INLINE long __Pyx_pow_long(long b, long e) { - long t = b; - switch (e) { - case 3: - t *= b; - case 2: - t *= b; - case 1: - return t; - case 0: - return 1; - } - #if 1 - if (unlikely(e<0)) return 0; - #endif - t = 1; - while (likely(e)) { - t *= (b * (e&1)) | ((~e)&1); /* 1 or b */ - b *= b; - e >>= 1; - } - return t; -} - 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; |