diff options
Diffstat (limited to 'experiments/ml.c')
| -rw-r--r-- | experiments/ml.c | 1295 |
1 files changed, 479 insertions, 816 deletions
diff --git a/experiments/ml.c b/experiments/ml.c index 976accb..cdf4064 100644 --- a/experiments/ml.c +++ b/experiments/ml.c @@ -759,7 +759,7 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; */ typedef npy_cdouble __pyx_t_5numpy_complex_t; -/* "ml.pyx":37 +/* "ml.pyx":38 * return result * * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< @@ -773,7 +773,7 @@ struct __pyx_obj_2ml___pyx_scope_struct__ml { }; -/* "ml.pyx":61 +/* "ml.pyx":62 * for (dist, dt, w1, w2, w3) in parents] * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) # <<<<<<<<<<<<<< @@ -990,6 +990,8 @@ static double __Pyx__PyObject_AsDouble(PyObject* obj); PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj)) #endif +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); + static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); #if PY_MAJOR_VERSION >= 3 @@ -1070,8 +1072,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); - #if CYTHON_CCOMPLEX #ifdef __cplusplus #define __Pyx_CREAL(z) ((z).real()) @@ -1170,6 +1170,8 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do #endif #endif +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); + static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type); @@ -1266,7 +1268,6 @@ int __pyx_module_is_main_ml = 0; static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_sum; static PyObject *__pyx_builtin_max; -static PyObject *__pyx_builtin_xrange; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_RuntimeError; @@ -1287,7 +1288,7 @@ static char __pyx_k_d[] = "d"; static char __pyx_k_f[] = "f"; static char __pyx_k_g[] = "g"; static char __pyx_k_h[] = "h"; -static char __pyx_k_i[] = "i:"; +static char __pyx_k_i[] = "i"; static char __pyx_k_l[] = "l"; static char __pyx_k_q[] = "q"; static char __pyx_k_t[] = "t"; @@ -1298,14 +1299,11 @@ static char __pyx_k_dt[] = "dt"; static char __pyx_k_ll[] = "ll"; static char __pyx_k_ml[] = "ml"; static char __pyx_k_np[] = "np"; -static char __pyx_k_st[] = "st"; static char __pyx_k_w1[] = "w1"; static char __pyx_k_w2[] = "w2"; static char __pyx_k_w3[] = "w3"; -static char __pyx_k_add[] = "add:"; static char __pyx_k_age[] = "age"; static char __pyx_k_end[] = "end"; -static char __pyx_k_i_2[] = "i"; static char __pyx_k_inf[] = "-inf"; static char __pyx_k_max[] = "max"; static char __pyx_k_sum[] = "sum"; @@ -1315,37 +1313,34 @@ static char __pyx_k_dist[] = "dist"; static char __pyx_k_file[] = "file"; static char __pyx_k_main[] = "__main__"; static char __pyx_k_send[] = "send"; -static char __pyx_k_stnv[] = "stnv"; static char __pyx_k_test[] = "__test__"; static char __pyx_k_DTYPE[] = "DTYPE"; static char __pyx_k_alpha[] = "alpha"; -static char __pyx_k_beta2[] = "beta2"; static char __pyx_k_close[] = "close"; static char __pyx_k_delta[] = "delta"; static char __pyx_k_dtype[] = "dtype"; -static char __pyx_k_max_i[] = "max_i"; static char __pyx_k_numpy[] = "numpy"; static char __pyx_k_print[] = "print"; static char __pyx_k_probs[] = "probs"; static char __pyx_k_range[] = "range"; -static char __pyx_k_roots[] = "roots:"; +static char __pyx_k_roots[] = "roots"; static char __pyx_k_throw[] = "throw"; static char __pyx_k_zeros[] = "zeros"; +static char __pyx_k_arange[] = "arange"; static char __pyx_k_import[] = "__import__"; -static char __pyx_k_thresh[] = "thresh:"; -static char __pyx_k_xrange[] = "xrange"; +static char __pyx_k_thresh[] = "thresh"; static char __pyx_k_float64[] = "float64"; static char __pyx_k_genexpr[] = "genexpr"; static char __pyx_k_n_nodes[] = "n_nodes"; static char __pyx_k_n_roots[] = "n_roots"; static char __pyx_k_parents[] = "parents"; -static char __pyx_k_roots_2[] = "roots"; static char __pyx_k_victims[] = "victims"; static char __pyx_k_beta_add[] = "beta_add"; static char __pyx_k_failures[] = "failures"; +static char __pyx_k_max_beta[] = "max_beta"; static char __pyx_k_probs_nv[] = "probs_nv"; -static char __pyx_k_thresh_2[] = "thresh"; static char __pyx_k_enumerate[] = "enumerate"; +static char __pyx_k_max_roots[] = "max_roots"; static char __pyx_k_n_victims[] = "n_victims"; static char __pyx_k_successes[] = "successes"; static char __pyx_k_ValueError[] = "ValueError"; @@ -1357,7 +1352,6 @@ static char __pyx_k_max_beta_add[] = "max_beta_add"; static char __pyx_k_root_victims[] = "root_victims"; static char __pyx_k_UNDERFLOW_ERROR[] = "UNDERFLOW ERROR"; static char __pyx_k_ml_locals_genexpr[] = "ml.<locals>.genexpr"; -static char __pyx_k_len_probs_probs_thresh[] = "len(probs[probs>=thresh]):"; static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; static char __pyx_k_Users_ben_Documents_Cascade_Pro[] = "/Users/ben/Documents/Cascade Project/criminal_cascades/experiments/ml.pyx"; static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; @@ -1373,12 +1367,11 @@ static PyObject *__pyx_n_s_RuntimeError; static PyObject *__pyx_kp_s_UNDERFLOW_ERROR; static PyObject *__pyx_kp_s_Users_ben_Documents_Cascade_Pro; static PyObject *__pyx_n_s_ValueError; -static PyObject *__pyx_kp_s_add; static PyObject *__pyx_n_s_age; static PyObject *__pyx_n_s_alpha; +static PyObject *__pyx_n_s_arange; static PyObject *__pyx_n_s_args; static PyObject *__pyx_n_s_beta; -static PyObject *__pyx_n_s_beta2; static PyObject *__pyx_n_s_beta_add; static PyObject *__pyx_n_s_close; static PyObject *__pyx_n_s_delta; @@ -1391,18 +1384,17 @@ static PyObject *__pyx_n_s_failures; static PyObject *__pyx_n_s_file; static PyObject *__pyx_n_s_float64; static PyObject *__pyx_n_s_genexpr; -static PyObject *__pyx_kp_s_i; -static PyObject *__pyx_n_s_i_2; +static PyObject *__pyx_n_s_i; static PyObject *__pyx_n_s_import; static PyObject *__pyx_kp_s_inf; static PyObject *__pyx_n_s_itervalues; static PyObject *__pyx_n_s_l; -static PyObject *__pyx_kp_s_len_probs_probs_thresh; static PyObject *__pyx_n_s_ll; static PyObject *__pyx_n_s_main; static PyObject *__pyx_n_s_max; +static PyObject *__pyx_n_s_max_beta; static PyObject *__pyx_n_s_max_beta_add; -static PyObject *__pyx_n_s_max_i; +static PyObject *__pyx_n_s_max_roots; static PyObject *__pyx_n_s_ml; static PyObject *__pyx_n_s_ml_locals_genexpr; static PyObject *__pyx_n_s_n_nodes; @@ -1420,26 +1412,23 @@ static PyObject *__pyx_n_s_probs_fail; static PyObject *__pyx_n_s_probs_nv; static PyObject *__pyx_n_s_range; static PyObject *__pyx_n_s_root_victims; -static PyObject *__pyx_kp_s_roots; -static PyObject *__pyx_n_s_roots_2; +static PyObject *__pyx_n_s_roots; static PyObject *__pyx_n_s_send; -static PyObject *__pyx_n_s_st; -static PyObject *__pyx_n_s_stnv; static PyObject *__pyx_n_s_successes; static PyObject *__pyx_n_s_sum; static PyObject *__pyx_n_s_t; static PyObject *__pyx_n_s_test; -static PyObject *__pyx_kp_s_thresh; -static PyObject *__pyx_n_s_thresh_2; +static PyObject *__pyx_n_s_thresh; static PyObject *__pyx_n_s_throw; static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; static PyObject *__pyx_n_s_victims; static PyObject *__pyx_n_s_w1; static PyObject *__pyx_n_s_w2; static PyObject *__pyx_n_s_w3; -static PyObject *__pyx_n_s_xrange; static PyObject *__pyx_n_s_zeros; -static PyObject *__pyx_int_neg_1; +static PyObject *__pyx_float__1; +static PyObject *__pyx_float__001; +static PyObject *__pyx_float_0_001; static PyObject *__pyx_tuple_; static PyObject *__pyx_tuple__2; static PyObject *__pyx_tuple__3; @@ -1447,7 +1436,8 @@ static PyObject *__pyx_tuple__4; static PyObject *__pyx_tuple__5; static PyObject *__pyx_tuple__6; static PyObject *__pyx_tuple__7; -static PyObject *__pyx_codeobj__8; +static PyObject *__pyx_tuple__8; +static PyObject *__pyx_codeobj__9; /* "ml.pyx":9 * ctypedef np.float_t DTYPE_t @@ -1501,9 +1491,6 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py __pyx_t_2ml_DTYPE_t __pyx_r; __Pyx_RefNannyDeclarations int __pyx_t_1; - PyObject *__pyx_t_2 = NULL; - PyObject *__pyx_t_3 = NULL; - PyObject *__pyx_t_4 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -1514,70 +1501,45 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py * cdef DTYPE_t structural, temporal, result * structural = delta ** dist # <<<<<<<<<<<<<< * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) - * temporal = exp(-alpha*dt) * (exp(alpha)-1) + * # temporal = exp(-alpha*dt) * (exp(alpha)-1) */ __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist)); - /* "ml.pyx":18 - * structural = delta ** dist + /* "ml.pyx":19 * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) - * temporal = exp(-alpha*dt) * (exp(alpha)-1) # <<<<<<<<<<<<<< + * # temporal = exp(-alpha*dt) * (exp(alpha)-1) + * temporal = 1 - exp(-alpha*dt) # <<<<<<<<<<<<<< * if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 */ - __pyx_v_temporal = (exp(((-__pyx_v_alpha) * __pyx_v_dt)) * (exp(__pyx_v_alpha) - 1.0)); + __pyx_v_temporal = (1.0 - exp(((-__pyx_v_alpha) * __pyx_v_dt))); - /* "ml.pyx":19 - * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) - * temporal = exp(-alpha*dt) * (exp(alpha)-1) + /* "ml.pyx":20 + * # temporal = exp(-alpha*dt) * (exp(alpha)-1) + * temporal = 1 - exp(-alpha*dt) * if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' # <<<<<<<<<<<<<< * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 * result = log(structural * temporal) */ __pyx_t_1 = ((exp(((-__pyx_v_alpha) * __pyx_v_dt)) == 0.) != 0); if (__pyx_t_1) { - if (__Pyx_PrintOne(0, __pyx_kp_s_UNDERFLOW_ERROR) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 19; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_PrintOne(0, __pyx_kp_s_UNDERFLOW_ERROR) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L3; } __pyx_L3:; - /* "ml.pyx":21 + /* "ml.pyx":22 * if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 * result = log(structural * temporal) # <<<<<<<<<<<<<< - * print 'st', structural, temporal + * # print 'st', structural, temporal * return result */ __pyx_v_result = log((__pyx_v_structural * __pyx_v_temporal)); - /* "ml.pyx":22 - * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 + /* "ml.pyx":24 * result = log(structural * temporal) - * print 'st', structural, temporal # <<<<<<<<<<<<<< - * return result - * - */ - __pyx_t_2 = PyFloat_FromDouble(__pyx_v_structural); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyFloat_FromDouble(__pyx_v_temporal); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_4); - __Pyx_INCREF(__pyx_n_s_st); - PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_n_s_st); - __Pyx_GIVEREF(__pyx_n_s_st); - PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_2); - __Pyx_GIVEREF(__pyx_t_2); - PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_t_3); - __Pyx_GIVEREF(__pyx_t_3); - __pyx_t_2 = 0; - __pyx_t_3 = 0; - if (__Pyx_Print(0, __pyx_t_4, 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - - /* "ml.pyx":23 - * result = log(structural * temporal) - * print 'st', structural, temporal + * # print 'st', structural, temporal * return result # <<<<<<<<<<<<<< * * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, @@ -1595,9 +1557,6 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py /* function exit code */ __pyx_L1_error:; - __Pyx_XDECREF(__pyx_t_2); - __Pyx_XDECREF(__pyx_t_3); - __Pyx_XDECREF(__pyx_t_4); __Pyx_WriteUnraisable("ml.weight_success", __pyx_clineno, __pyx_lineno, __pyx_filename, 0); __pyx_r = 0; __pyx_L0:; @@ -1605,7 +1564,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py return __pyx_r; } -/* "ml.pyx":25 +/* "ml.pyx":26 * return result * * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< @@ -1619,15 +1578,9 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py __pyx_t_2ml_DTYPE_t __pyx_v_result; __pyx_t_2ml_DTYPE_t __pyx_r; __Pyx_RefNannyDeclarations - PyObject *__pyx_t_1 = NULL; - PyObject *__pyx_t_2 = NULL; - PyObject *__pyx_t_3 = NULL; - int __pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; __Pyx_RefNannySetupContext("weight_failure", 0); - /* "ml.pyx":29 + /* "ml.pyx":30 * """weight for failed infection, exponential time model""" * cdef DTYPE_t structural, temporal, result * structural = delta ** dist # <<<<<<<<<<<<<< @@ -1636,7 +1589,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py */ __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist)); - /* "ml.pyx":31 + /* "ml.pyx":32 * structural = delta ** dist * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = exp(-alpha * dt) # <<<<<<<<<<<<<< @@ -1645,43 +1598,18 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py */ __pyx_v_temporal = exp(((-__pyx_v_alpha) * __pyx_v_dt)); - /* "ml.pyx":33 + /* "ml.pyx":34 * temporal = exp(-alpha * dt) * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 * result = log(1. - structural + structural * temporal) # <<<<<<<<<<<<<< - * print 'stnv', structural, temporal + * # print 'stnv', structural, temporal * return result */ __pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal))); - /* "ml.pyx":34 - * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 - * result = log(1. - structural + structural * temporal) - * print 'stnv', structural, temporal # <<<<<<<<<<<<<< - * return result - * - */ - __pyx_t_1 = PyFloat_FromDouble(__pyx_v_structural); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PyFloat_FromDouble(__pyx_v_temporal); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyTuple_New(3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); - __Pyx_INCREF(__pyx_n_s_stnv); - PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_n_s_stnv); - __Pyx_GIVEREF(__pyx_n_s_stnv); - PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1); - __Pyx_GIVEREF(__pyx_t_1); - PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_t_2); - __Pyx_GIVEREF(__pyx_t_2); - __pyx_t_1 = 0; - __pyx_t_2 = 0; - if (__Pyx_Print(0, __pyx_t_3, 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - - /* "ml.pyx":35 + /* "ml.pyx":36 * result = log(1. - structural + structural * temporal) - * print 'stnv', structural, temporal + * # print 'stnv', structural, temporal * return result # <<<<<<<<<<<<<< * * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, @@ -1689,7 +1617,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py __pyx_r = __pyx_v_result; goto __pyx_L0; - /* "ml.pyx":25 + /* "ml.pyx":26 * return result * * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< @@ -1698,18 +1626,12 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py */ /* function exit code */ - __pyx_L1_error:; - __Pyx_XDECREF(__pyx_t_1); - __Pyx_XDECREF(__pyx_t_2); - __Pyx_XDECREF(__pyx_t_3); - __Pyx_WriteUnraisable("ml.weight_failure", __pyx_clineno, __pyx_lineno, __pyx_filename, 0); - __pyx_r = 0; __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ml.pyx":37 +/* "ml.pyx":38 * return result * * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< @@ -1757,31 +1679,31 @@ 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 = 37; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __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 = 37; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_age)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_alpha)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_delta)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __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 = 37; __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 = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 6) { goto __pyx_L5_argtuple_error; @@ -1796,21 +1718,21 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py __pyx_v_root_victims = ((PyObject*)values[0]); __pyx_v_victims = ((PyObject*)values[1]); __pyx_v_non_victims = ((PyObject*)values[2]); - __pyx_v_age = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_age == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_delta = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_age = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_age == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_delta = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - 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1, "non_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __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 = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_victims), (&PyDict_Type), 1, "victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_non_victims), (&PyDict_Type), 1, "non_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_2ml_ml(__pyx_self, __pyx_v_root_victims, __pyx_v_victims, __pyx_v_non_victims, __pyx_v_age, __pyx_v_alpha, __pyx_v_delta); /* function exit code */ @@ -1823,7 +1745,7 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py } static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */ -/* "ml.pyx":61 +/* "ml.pyx":62 * for (dist, dt, w1, w2, w3) in parents] * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) # <<<<<<<<<<<<<< @@ -1849,7 +1771,7 @@ static PyObject *__pyx_pf_2ml_2ml_genexpr(PyObject *__pyx_self) { __Pyx_INCREF(((PyObject *)__pyx_cur_scope->__pyx_outer_scope)); __Pyx_GIVEREF(__pyx_cur_scope->__pyx_outer_scope); { - __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_2ml_2ml_2generator, (PyObject *) __pyx_cur_scope, __pyx_n_s_genexpr, __pyx_n_s_ml_locals_genexpr); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_2ml_2ml_2generator, (PyObject *) __pyx_cur_scope, __pyx_n_s_genexpr, __pyx_n_s_ml_locals_genexpr); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_cur_scope); __Pyx_RefNannyFinishContext(); return (PyObject *) gen; @@ -1887,16 +1809,16 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera return NULL; } __pyx_L3_first_run:; - if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_1 = 0; - if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_successes)) { __Pyx_RaiseClosureNameError("successes"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } + if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_successes)) { __Pyx_RaiseClosureNameError("successes"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_2 = __pyx_cur_scope->__pyx_outer_scope->__pyx_v_successes; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0; for (;;) { if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_4); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_4); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif __Pyx_XGOTREF(__pyx_cur_scope->__pyx_v_s); __Pyx_XDECREF_SET(__pyx_cur_scope->__pyx_v_s, __pyx_t_4); @@ -1904,14 +1826,14 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera __pyx_t_4 = 0; __pyx_cur_scope->__pyx_v_l = __pyx_t_1; __pyx_t_1 = (__pyx_t_1 + 1); - if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures)) { __Pyx_RaiseClosureNameError("failures"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } + if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures)) { __Pyx_RaiseClosureNameError("failures"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } if (unlikely(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_4 = __Pyx_GetItemInt_List(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures, __pyx_cur_scope->__pyx_v_l, Py_ssize_t, 1, PyInt_FromSsize_t, 1, 1, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_4 = __Pyx_GetItemInt_List(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures, __pyx_cur_scope->__pyx_v_l, Py_ssize_t, 1, PyInt_FromSsize_t, 1, 1, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = PyNumber_Subtract(__pyx_cur_scope->__pyx_v_s, __pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyNumber_Subtract(__pyx_cur_scope->__pyx_v_s, __pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_r = __pyx_t_5; @@ -1931,7 +1853,7 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera __pyx_cur_scope->__pyx_t_1 = 0; __Pyx_XGOTREF(__pyx_t_2); __pyx_t_3 = __pyx_cur_scope->__pyx_t_2; - if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -1951,7 +1873,7 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera return NULL; } -/* "ml.pyx":37 +/* "ml.pyx":38 * return result * * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< @@ -1974,10 +1896,11 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ PyArrayObject *__pyx_v_probs = 0; PyArrayObject *__pyx_v_probs_fail = 0; PyArrayObject *__pyx_v_probs_nv = 0; - PyObject *__pyx_v_max_i = NULL; PyObject *__pyx_v_max_beta_add = NULL; double __pyx_v_thresh; PyObject *__pyx_v_beta_add = NULL; + PyObject *__pyx_v_max_beta = NULL; + int __pyx_v_max_roots; PyObject *__pyx_v_w1 = NULL; PyObject *__pyx_v_w2 = NULL; PyObject *__pyx_v_w3 = NULL; @@ -2014,10 +1937,9 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_t_2ml_DTYPE_t __pyx_t_23; __pyx_t_2ml_DTYPE_t __pyx_t_24; int __pyx_t_25; - int __pyx_t_26; - double __pyx_t_27; - long __pyx_t_28; - int __pyx_t_29; + double __pyx_t_26; + PyObject *(*__pyx_t_27)(PyObject *); + int __pyx_t_28; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -2041,72 +1963,72 @@ 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":43 - * DTYPE_t beta, ll, beta2 + /* "ml.pyx":44 + * DTYPE_t beta, ll * list parents, failures, successes * n_roots, n_victims = len(root_victims), len(victims) # <<<<<<<<<<<<<< - * n_nodes = 4#148152 + * n_nodes = 11270 * cdef: */ 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 = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 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 = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_n_roots = __pyx_t_1; __pyx_v_n_victims = __pyx_t_2; - /* "ml.pyx":44 + /* "ml.pyx":45 * list parents, failures, successes * n_roots, n_victims = len(root_victims), len(victims) - * n_nodes = 4#148152 # <<<<<<<<<<<<<< + * n_nodes = 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__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 = 47; __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 = 47; __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 = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); 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__pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __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 = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_probs.diminfo[0].strides = __pyx_pybuffernd_probs.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_probs.diminfo[0].shape = __pyx_pybuffernd_probs.rcbuffer->pybuffer.shape[0]; } } @@ -2114,43 +2036,43 @@ static PyObject 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__Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_zeros); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (unlikely(__pyx_v_non_victims == Py_None)) { PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_2 = PyDict_Size(__pyx_v_non_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_4 = PyInt_FromSsize_t(__pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyDict_Size(__pyx_v_non_victims); if (unlikely(__pyx_t_2 == -1)) 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__Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_9 = ((PyArrayObject *)__pyx_t_3); { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_probs_nv.rcbuffer->pybuffer, (PyObject*)__pyx_t_9, &__Pyx_TypeInfo_nn___pyx_t_2ml_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) { + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_probs_nv.rcbuffer->pybuffer, (PyObject*)__pyx_t_9, &__Pyx_TypeInfo_nn___pyx_t_2ml_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 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 = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __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]; } } @@ -2207,7 +2129,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_v_probs_nv = ((PyArrayObject *)__pyx_t_3); __pyx_t_3 = 0; - /* "ml.pyx":51 + /* "ml.pyx":52 * * # loop through victims * for i, parents in enumerate(victims.itervalues()): # <<<<<<<<<<<<<< @@ -2218,9 +2140,9 @@ 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 = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_4 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_11)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_11)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = __pyx_t_4; @@ -2228,25 +2150,25 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ while (1) { __pyx_t_12 = __Pyx_dict_iter_next(__pyx_t_3, __pyx_t_1, &__pyx_t_2, NULL, &__pyx_t_4, NULL, __pyx_t_11); if (unlikely(__pyx_t_12 == 0)) break; - if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - if (!(likely(PyList_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_4)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(PyList_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_4)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_XDECREF_SET(__pyx_v_parents, ((PyObject*)__pyx_t_4)); __pyx_t_4 = 0; __pyx_v_i = __pyx_t_10; __pyx_t_10 = (__pyx_t_10 + 1); - /* "ml.pyx":55 + /* "ml.pyx":56 * # fail to infect it, also computes the probability that its most * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) */ - __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - /* "ml.pyx":56 + /* "ml.pyx":57 * # 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__pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_6 = PySequence_ITEM(__pyx_t_5, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PySequence_ITEM(__pyx_t_5, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) { PyObject* sequence = __pyx_t_6; @@ -2275,7 +2197,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ if (unlikely(size != 5)) { if (size > 5) __Pyx_RaiseTooManyValuesError(5); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __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))) { @@ -2301,7 +2223,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ Py_ssize_t i; PyObject** temps[5] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_16,&__pyx_t_17,&__pyx_t_18}; for (i=0; i < 5; i++) { - PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __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; } @@ -2311,7 +2233,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } else { Py_ssize_t index = -1; PyObject** temps[5] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_16,&__pyx_t_17,&__pyx_t_18}; - __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_19); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_20 = Py_TYPE(__pyx_t_19)->tp_iternext; @@ -2320,7 +2242,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GOTREF(item); *(temps[index]) = item; } - if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_20 = NULL; __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; goto __pyx_L8_unpacking_done; @@ -2328,12 +2250,12 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; __pyx_t_20 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L8_unpacking_done:; } - __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; - __pyx_t_21 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_21 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_21 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_21 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0; __pyx_v_dist = __pyx_t_12; __pyx_v_dt = __pyx_t_21; @@ -2344,22 +2266,22 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_18); __pyx_t_18 = 0; - /* "ml.pyx":55 + /* "ml.pyx":56 * # fail to infect it, also computes the probability that its most * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) */ - __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if 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__pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_22, __pyx_t_23, __pyx_t_24)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_4, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if 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= PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_INCREF(__pyx_cur_scope->__pyx_v_failures); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_cur_scope->__pyx_v_failures); __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_failures); - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_21 = __pyx_v_i; if (__pyx_t_21 < 0) __pyx_t_21 += __pyx_pybuffernd_probs_fail.diminfo[0].shape; *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_probs_fail.diminfo[0].strides) = __pyx_t_24; - /* "ml.pyx":58 + /* "ml.pyx":59 * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * # find parent that maximizes log(p) - log(\tilde{p}) */ - __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __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); - /* "ml.pyx":59 + /* "ml.pyx":60 * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2413,15 +2335,15 @@ 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 = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_4 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_4); __pyx_t_13 = 0; for (;;) { if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_4)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_6 = PySequence_ITEM(__pyx_t_4, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PySequence_ITEM(__pyx_t_4, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) { PyObject* sequence = __pyx_t_6; @@ -2433,7 +2355,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ if (unlikely(size != 5)) { if (size > 5) __Pyx_RaiseTooManyValuesError(5); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -2459,7 +2381,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ Py_ssize_t i; PyObject** temps[5] = {&__pyx_t_18,&__pyx_t_17,&__pyx_t_16,&__pyx_t_15,&__pyx_t_14}; for (i=0; i < 5; i++) { - PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(item); *(temps[i]) = item; } @@ -2469,7 +2391,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } else { Py_ssize_t index = -1; PyObject** temps[5] = {&__pyx_t_18,&__pyx_t_17,&__pyx_t_16,&__pyx_t_15,&__pyx_t_14}; - __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_19); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_20 = Py_TYPE(__pyx_t_19)->tp_iternext; @@ -2478,7 +2400,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GOTREF(item); *(temps[index]) = item; } - if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_20 = NULL; __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; goto __pyx_L12_unpacking_done; @@ -2486,12 +2408,12 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; __pyx_t_20 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L12_unpacking_done:; } - __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_18); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_18); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0; - __pyx_t_25 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_25 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_25 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_25 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0; __pyx_v_dist = __pyx_t_12; __pyx_v_dt = __pyx_t_25; @@ -2502,22 +2424,22 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_14); __pyx_t_14 = 0; - /* "ml.pyx":58 + /* "ml.pyx":59 * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * # find parent that maximizes log(p) - log(\tilde{p}) */ - __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_success(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_24, __pyx_t_23, __pyx_t_22)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_success(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_24, __pyx_t_23, __pyx_t_22)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "ml.pyx":59 + /* "ml.pyx":60 * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< @@ -2531,24 +2453,24 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = 0; - /* "ml.pyx":61 + /* "ml.pyx":62 * for (dist, dt, w1, w2, w3) in parents] * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) # <<<<<<<<<<<<<< * * # loop through non-victims */ - __pyx_t_5 = __pyx_pf_2ml_2ml_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __pyx_pf_2ml_2ml_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_max, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_max, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_25 = __pyx_v_i; if (__pyx_t_25 < 0) __pyx_t_25 += __pyx_pybuffernd_probs.diminfo[0].shape; @@ -2556,608 +2478,344 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* 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break; - if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); - if (!(likely(PyList_CheckExact(__pyx_t_5))||((__pyx_t_5) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_5)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_XDECREF_SET(__pyx_v_parents, ((PyObject*)__pyx_t_5)); - __pyx_t_5 = 0; - __pyx_v_i = __pyx_t_10; - __pyx_t_10 = (__pyx_t_10 + 1); - - /* "ml.pyx":67 - * # for each non victim node, compute the probability that all its - * # parents fail to infect it - * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< - * for (dist, dt, w1, w2, w3) in parents] - * probs_nv[i] = sum(failures) - */ - __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto 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__Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - #else - __pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_xrange); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - #endif + __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_sum = __Pyx_GetBuiltinName(__pyx_n_s_sum); if (!__pyx_builtin_sum) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_max = __Pyx_GetBuiltinName(__pyx_n_s_max); if (!__pyx_builtin_max) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_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;} @@ -5556,6 +5202,17 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); + /* "ml.pyx":82 + * max_beta_add = float('-inf') + * # iterate over all victim nodes to find the optimal threshold + * for beta in np.arange(0.001, .1, .001): # <<<<<<<<<<<<<< + * thresh = log(beta/(1.-beta)) + * # print 'beta:', beta, 'thresh:', thresh, 'infected:', len(probs[probs>=thresh]) + */ + __pyx_tuple_ = PyTuple_Pack(3, __pyx_float_0_001, __pyx_float__1, __pyx_float__001); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple_); + __Pyx_GIVEREF(__pyx_tuple_); + /* "../../../../Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): @@ -5563,9 +5220,9 @@ static int __Pyx_InitCachedConstants(void) { * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) */ - __pyx_tuple_ = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple_); - __Pyx_GIVEREF(__pyx_tuple_); + __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__2); + __Pyx_GIVEREF(__pyx_tuple__2); /* "../../../../Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) @@ -5574,9 +5231,9 @@ static int __Pyx_InitCachedConstants(void) { * * info.buf = PyArray_DATA(self) */ - __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__2); - __Pyx_GIVEREF(__pyx_tuple__2); + __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__3); + __Pyx_GIVEREF(__pyx_tuple__3); /* "../../../../Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260 * if ((descr.byteorder == c'>' and little_endian) or @@ -5585,9 +5242,9 @@ static int __Pyx_InitCachedConstants(void) { * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" */ - __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__3); - __Pyx_GIVEREF(__pyx_tuple__3); + __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__4); + __Pyx_GIVEREF(__pyx_tuple__4); /* "../../../../Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 * @@ -5596,9 +5253,9 @@ static int __Pyx_InitCachedConstants(void) { * * if ((child.byteorder == c'>' and little_endian) or */ - __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__4); - __Pyx_GIVEREF(__pyx_tuple__4); + __pyx_tuple__5 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__5); + __Pyx_GIVEREF(__pyx_tuple__5); /* "../../../../Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":806 * if ((child.byteorder == c'>' and little_endian) or @@ -5607,9 +5264,9 @@ static int __Pyx_InitCachedConstants(void) { * # One could encode it in the format string and have Cython * # complain instead, BUT: < and > in format strings also imply */ - __pyx_tuple__5 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__5); - __Pyx_GIVEREF(__pyx_tuple__5); + __pyx_tuple__6 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__6); + __Pyx_GIVEREF(__pyx_tuple__6); /* "../../../../Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":826 * t = child.type_num @@ -5618,21 +5275,21 @@ static int __Pyx_InitCachedConstants(void) { * * # Until ticket #99 is fixed, use integers to avoid warnings */ - __pyx_tuple__6 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__6); - __Pyx_GIVEREF(__pyx_tuple__6); + __pyx_tuple__7 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__7)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__7); + __Pyx_GIVEREF(__pyx_tuple__7); - /* "ml.pyx":37 + /* "ml.pyx":38 * return result * * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< * DTYPE_t alpha, DTYPE_t delta): * cdef: */ - __pyx_tuple__7 = PyTuple_Pack(33, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_age, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_n_nodes, __pyx_n_s_roots_2, __pyx_n_s_i_2, __pyx_n_s_dist, __pyx_n_s_dt, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_beta, __pyx_n_s_ll, __pyx_n_s_beta2, __pyx_n_s_parents, __pyx_n_s_failures, __pyx_n_s_successes, __pyx_n_s_probs, __pyx_n_s_probs_fail, __pyx_n_s_probs_nv, __pyx_n_s_max_i, __pyx_n_s_max_beta_add, __pyx_n_s_thresh_2, __pyx_n_s_beta_add, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3, __pyx_n_s_genexpr, __pyx_n_s_genexpr); if (unlikely(!__pyx_tuple__7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__7); - __Pyx_GIVEREF(__pyx_tuple__7); - __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(6, 0, 33, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml, 37, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__8 = PyTuple_Pack(33, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_age, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_n_nodes, __pyx_n_s_roots, __pyx_n_s_i, __pyx_n_s_dist, __pyx_n_s_dt, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_beta, __pyx_n_s_ll, __pyx_n_s_parents, __pyx_n_s_failures, __pyx_n_s_successes, __pyx_n_s_probs, __pyx_n_s_probs_fail, __pyx_n_s_probs_nv, __pyx_n_s_max_beta_add, __pyx_n_s_thresh, __pyx_n_s_beta_add, __pyx_n_s_max_beta, __pyx_n_s_max_roots, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3, __pyx_n_s_genexpr, __pyx_n_s_genexpr); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __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, 33, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__8, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml, 38, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -5642,7 +5299,9 @@ static int __Pyx_InitCachedConstants(void) { static int __Pyx_InitGlobals(void) { if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; - __pyx_int_neg_1 = PyInt_FromLong(-1); if (unlikely(!__pyx_int_neg_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_float__1 = PyFloat_FromDouble(.1); if (unlikely(!__pyx_float__1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_float__001 = PyFloat_FromDouble(.001); if (unlikely(!__pyx_float__001)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_float_0_001 = PyFloat_FromDouble(0.001); if (unlikely(!__pyx_float_0_001)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} return 0; __pyx_L1_error:; return -1; @@ -5729,10 +5388,10 @@ PyMODINIT_FUNC PyInit_ml(void) /*--- Variable export code ---*/ /*--- Function export code ---*/ /*--- Type init code ---*/ - if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct__ml) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct__ml) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type_2ml___pyx_scope_struct__ml.tp_print = 0; __pyx_ptype_2ml___pyx_scope_struct__ml = &__pyx_type_2ml___pyx_scope_struct__ml; - if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type_2ml___pyx_scope_struct_1_genexpr.tp_print = 0; __pyx_ptype_2ml___pyx_scope_struct_1_genexpr = &__pyx_type_2ml___pyx_scope_struct_1_genexpr; /*--- Type import code ---*/ @@ -5778,16 +5437,16 @@ 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":37 + /* "ml.pyx":38 * return result * * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< * DTYPE_t alpha, DTYPE_t delta): * cdef: */ - __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_2ml_1ml, NULL, __pyx_n_s_ml); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __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 = 38; __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 = 37; __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 = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; /* "ml.pyx":1 @@ -7097,6 +6756,10 @@ bad: return (double)-1; } +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { + PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); +} + #if PY_MAJOR_VERSION < 3 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, CYTHON_UNUSED PyObject *cause) { @@ -7790,32 +7453,6 @@ raise_neg_overflow: return (int) -1; } -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { - const long neg_one = (long) -1, const_zero = 0; - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); - } else if (sizeof(long) <= sizeof(unsigned long long)) { - return PyLong_FromUnsignedLongLong((unsigned long long) value); - } - } else { - if (sizeof(long) <= sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(long long)) { - return PyLong_FromLongLong((long long) value); - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), - little, !is_unsigned); - } -} - #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { @@ -8056,6 +7693,32 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { #endif #endif +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(long) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(long) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); + } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); + } +} + static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { const long neg_one = (long) -1, const_zero = 0; const int is_unsigned = neg_one > const_zero; |