diff options
| -rw-r--r-- | R Scripts/find-cascades.R | 1 | ||||
| -rw-r--r-- | experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o | bin | 306268 -> 326236 bytes | |||
| -rw-r--r-- | experiments/ml.c | 1090 | ||||
| -rw-r--r-- | experiments/ml.pyx | 45 | ||||
| -rwxr-xr-x | experiments/ml.so | bin | 119276 -> 125128 bytes | |||
| -rw-r--r-- | experiments/ml2.pyx | 2 | ||||
| -rw-r--r-- | experiments/out.log | 136 | ||||
| -rw-r--r-- | experiments/process.py | 13 |
8 files changed, 750 insertions, 537 deletions
diff --git a/R Scripts/find-cascades.R b/R Scripts/find-cascades.R index 7673909..ded9b9c 100644 --- a/R Scripts/find-cascades.R +++ b/R Scripts/find-cascades.R @@ -3,7 +3,6 @@ setwd("~/Documents/Cascade Project/") load('Results/hyper-lcc.RData') load('Results/dag_dat_vics.RData') source('criminal_cascades/R Scripts/temporal.R') -# source('Scripts/homophily.R') source('criminal_cascades/R Scripts/structural.R') vic_ids = which(V(hyp_lcc)$vic==TRUE) diff --git a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o Binary files differindex 8cabba1..80ba2ba 100644 --- a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o +++ b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o diff --git a/experiments/ml.c b/experiments/ml.c index 4b9c2ef..0dfbb02 100644 --- a/experiments/ml.c +++ b/experiments/ml.c @@ -695,7 +695,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; * DTYPE = np.float64 * ctypedef np.float_t DTYPE_t # <<<<<<<<<<<<<< * - * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, + * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, */ typedef __pyx_t_5numpy_float_t __pyx_t_2ml_DTYPE_t; #if CYTHON_CCOMPLEX @@ -947,6 +947,8 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, int wraparound, int boundscheck); +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); + static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); @@ -1020,6 +1022,12 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); +static int __Pyx_Print(PyObject*, PyObject *, int); +#if CYTHON_COMPILING_IN_PYPY || PY_MAJOR_VERSION >= 3 +static PyObject* __pyx_print = 0; +static PyObject* __pyx_print_kwargs = 0; +#endif + #if CYTHON_CCOMPLEX #ifdef __cplusplus #define __Pyx_CREAL(z) ((z).real()) @@ -1169,8 +1177,8 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, cha /* Module declarations from 'libc.math' */ /* Module declarations from 'ml' */ -static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int, int, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t); /*proto*/ -static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int, int, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t); /*proto*/ +static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int, int, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t); /*proto*/ +static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int, int, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t); /*proto*/ static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_2ml_DTYPE_t = { "DTYPE_t", NULL, sizeof(__pyx_t_2ml_DTYPE_t), { 0 }, 0, 'R', 0, 0 }; #define __Pyx_MODULE_NAME "ml" int __pyx_module_is_main_ml = 0; @@ -1181,7 +1189,7 @@ static PyObject *__pyx_builtin_sum; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_RuntimeError; -static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_age, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta); /* proto */ +static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta, __pyx_t_2ml_DTYPE_t __pyx_v_lmbda); /* proto */ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ static char __pyx_k_B[] = "B"; @@ -1203,20 +1211,24 @@ static char __pyx_k_t[] = "t"; static char __pyx_k_Zd[] = "Zd"; static char __pyx_k_Zf[] = "Zf"; static char __pyx_k_Zg[] = "Zg"; -static char __pyx_k_dt[] = "dt"; +static char __pyx_k_dt[] = "dt:"; static char __pyx_k_ll[] = "ll"; static char __pyx_k_ml[] = "ml"; static char __pyx_k_np[] = "np"; static char __pyx_k_w1[] = "w1"; static char __pyx_k_w2[] = "w2"; static char __pyx_k_w3[] = "w3"; -static char __pyx_k_age[] = "age"; static char __pyx_k_dts[] = "dts"; +static char __pyx_k_end[] = "end"; static char __pyx_k_inf[] = "-inf"; static char __pyx_k_sum[] = "sum"; static char __pyx_k_beta[] = "beta"; -static char __pyx_k_dist[] = "dist"; +static char __pyx_k_dist[] = "dist:"; +static char __pyx_k_dt_2[] = "dt"; +static char __pyx_k_file[] = "file"; static char __pyx_k_main[] = "__main__"; +static char __pyx_k_mean[] = "mean"; +static char __pyx_k_pdts[] = "pdts"; static char __pyx_k_prnt[] = "prnt"; static char __pyx_k_prob[] = "prob"; static char __pyx_k_test[] = "__test__"; @@ -1225,19 +1237,25 @@ static char __pyx_k_alpha[] = "alpha"; static char __pyx_k_delta[] = "delta"; static char __pyx_k_dists[] = "dists"; static char __pyx_k_dtype[] = "dtype"; +static char __pyx_k_lmbda[] = "lmbda"; 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_seeds[] = "seeds"; static char __pyx_k_zeros[] = "zeros"; static char __pyx_k_arange[] = "arange"; +static char __pyx_k_dist_2[] = "dist"; static char __pyx_k_import[] = "__import__"; +static char __pyx_k_n_days[] = "n_days"; +static char __pyx_k_pdists[] = "pdists"; static char __pyx_k_thresh[] = "thresh"; static char __pyx_k_float64[] = "float64"; 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_t_scale[] = "t_scale"; static char __pyx_k_victims[] = "victims"; static char __pyx_k_beta_add[] = "beta_add"; static char __pyx_k_failures[] = "failures"; @@ -1271,19 +1289,22 @@ static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; static PyObject *__pyx_n_s_RuntimeError; static PyObject *__pyx_kp_s_Users_ben_Documents_Cascade_Pro; static PyObject *__pyx_n_s_ValueError; -static PyObject *__pyx_n_s_age; static PyObject *__pyx_n_s_alpha; static PyObject *__pyx_n_s_arange; static PyObject *__pyx_n_s_beta; static PyObject *__pyx_n_s_beta_add; static PyObject *__pyx_n_s_delta; -static PyObject *__pyx_n_s_dist; +static PyObject *__pyx_kp_s_dist; +static PyObject *__pyx_n_s_dist_2; static PyObject *__pyx_n_s_dists; -static PyObject *__pyx_n_s_dt; +static PyObject *__pyx_kp_s_dt; +static PyObject *__pyx_n_s_dt_2; static PyObject *__pyx_n_s_dts; static PyObject *__pyx_n_s_dtype; +static PyObject *__pyx_n_s_end; static PyObject *__pyx_n_s_enumerate; static PyObject *__pyx_n_s_failures; +static PyObject *__pyx_n_s_file; static PyObject *__pyx_n_s_float64; static PyObject *__pyx_n_s_i; static PyObject *__pyx_n_s_import; @@ -1291,11 +1312,14 @@ static PyObject *__pyx_kp_s_inf; static PyObject *__pyx_n_s_itervalues; static PyObject *__pyx_n_s_l; static PyObject *__pyx_n_s_ll; +static PyObject *__pyx_n_s_lmbda; static PyObject *__pyx_n_s_main; static PyObject *__pyx_n_s_max_beta; static PyObject *__pyx_n_s_max_beta_add; static PyObject *__pyx_n_s_max_roots; +static PyObject *__pyx_n_s_mean; static PyObject *__pyx_n_s_ml; +static PyObject *__pyx_n_s_n_days; static PyObject *__pyx_n_s_n_nodes; static PyObject *__pyx_n_s_n_roots; static PyObject *__pyx_n_s_n_victims; @@ -1308,6 +1332,9 @@ static PyObject *__pyx_n_s_numpy; static PyObject *__pyx_n_s_parent_dists; static PyObject *__pyx_n_s_parent_dts; static PyObject *__pyx_n_s_parents; +static PyObject *__pyx_n_s_pdists; +static PyObject *__pyx_n_s_pdts; +static PyObject *__pyx_n_s_print; static PyObject *__pyx_n_s_prnt; static PyObject *__pyx_n_s_prob; static PyObject *__pyx_n_s_probs; @@ -1321,6 +1348,7 @@ static PyObject *__pyx_n_s_seeds; static PyObject *__pyx_n_s_successes; static PyObject *__pyx_n_s_sum; static PyObject *__pyx_n_s_t; +static PyObject *__pyx_n_s_t_scale; static PyObject *__pyx_n_s_test; static PyObject *__pyx_n_s_thresh; static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; @@ -1330,9 +1358,8 @@ static PyObject *__pyx_n_s_w2; static PyObject *__pyx_n_s_w3; static PyObject *__pyx_n_s_zeros; static PyObject *__pyx_float_1_; -static PyObject *__pyx_float__01; static PyObject *__pyx_float_0_01; -static PyObject *__pyx_int_5000; +static PyObject *__pyx_int_148152; static PyObject *__pyx_tuple_; static PyObject *__pyx_tuple__2; static PyObject *__pyx_tuple__3; @@ -1346,12 +1373,12 @@ static PyObject *__pyx_codeobj__9; /* "ml.pyx":9 * ctypedef np.float_t DTYPE_t * - * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< - * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): + * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, # <<<<<<<<<<<<<< + * DTYPE_t t_scale, DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): * """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_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, 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) { __pyx_t_2ml_DTYPE_t __pyx_v_structural; __pyx_t_2ml_DTYPE_t __pyx_v_temporal; __pyx_t_2ml_DTYPE_t __pyx_v_result; @@ -1363,35 +1390,35 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py * """weight for successful infection, exponential time model""" * cdef DTYPE_t structural, temporal, result * structural = delta ** dist # <<<<<<<<<<<<<< - * temporal = log(exp(alpha)-1.) - alpha*dt/1. - * result = log(structural) + temporal + * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) + * temporal = log(exp(alpha/t_scale)-1.) - alpha*dt/t_scale */ __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist)); - /* "ml.pyx":14 - * cdef DTYPE_t structural, temporal, result + /* "ml.pyx":15 * structural = delta ** dist - * temporal = log(exp(alpha)-1.) - alpha*dt/1. # <<<<<<<<<<<<<< + * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) + * 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 - * return result */ - __pyx_v_temporal = (log((exp(__pyx_v_alpha) - 1.)) - ((__pyx_v_alpha * __pyx_v_dt) / 1.)); + __pyx_v_temporal = (log((exp((__pyx_v_alpha / __pyx_v_t_scale)) - 1.)) - ((__pyx_v_alpha * __pyx_v_dt) / __pyx_v_t_scale)); - /* "ml.pyx":15 - * structural = delta ** dist - * temporal = log(exp(alpha)-1.) - alpha*dt/1. + /* "ml.pyx":17 + * 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 # <<<<<<<<<<<<<< * return result * */ __pyx_v_result = (log(__pyx_v_structural) + __pyx_v_temporal); - /* "ml.pyx":16 - * temporal = log(exp(alpha)-1.) - alpha*dt/1. + /* "ml.pyx":18 + * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 * result = log(structural) + temporal * return result # <<<<<<<<<<<<<< * - * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, + * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, */ __pyx_r = __pyx_v_result; goto __pyx_L0; @@ -1399,8 +1426,8 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py /* "ml.pyx":9 * ctypedef np.float_t DTYPE_t * - * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< - * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): + * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, # <<<<<<<<<<<<<< + * DTYPE_t t_scale, DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): * """weight for successful infection, exponential time model""" */ @@ -1410,15 +1437,15 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py return __pyx_r; } -/* "ml.pyx":18 +/* "ml.pyx":20 * return result * - * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< - * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): + * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, # <<<<<<<<<<<<<< + * DTYPE_t t_scale, DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): * """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_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, 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) { __pyx_t_2ml_DTYPE_t __pyx_v_structural; __pyx_t_2ml_DTYPE_t __pyx_v_temporal; __pyx_t_2ml_DTYPE_t __pyx_v_result; @@ -1426,48 +1453,48 @@ 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":22 + /* "ml.pyx":24 * """weight for failed infection, exponential time model""" * cdef DTYPE_t structural, temporal, result * structural = delta ** dist # <<<<<<<<<<<<<< - * temporal = exp(-alpha * dt/1.) - * result = log(1. - structural + structural * temporal) + * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) + * temporal = exp(-alpha * dt/t_scale) */ __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist)); - /* "ml.pyx":23 - * cdef DTYPE_t structural, temporal, result + /* "ml.pyx":26 * structural = delta ** dist - * temporal = exp(-alpha * dt/1.) # <<<<<<<<<<<<<< + * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) + * temporal = exp(-alpha * dt/t_scale) # <<<<<<<<<<<<<< + * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 * result = log(1. - structural + structural * temporal) - * return result */ - __pyx_v_temporal = exp((((-__pyx_v_alpha) * __pyx_v_dt) / 1.)); + __pyx_v_temporal = exp((((-__pyx_v_alpha) * __pyx_v_dt) / __pyx_v_t_scale)); - /* "ml.pyx":24 - * structural = delta ** dist - * temporal = exp(-alpha * dt/1.) + /* "ml.pyx":28 + * temporal = exp(-alpha * dt/t_scale) + * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 * result = log(1. - structural + structural * temporal) # <<<<<<<<<<<<<< * return result * */ __pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal))); - /* "ml.pyx":25 - * temporal = exp(-alpha * dt/1.) + /* "ml.pyx":29 + * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 * result = log(1. - structural + structural * temporal) * return result # <<<<<<<<<<<<<< * - * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, + * def ml(dict root_victims, dict victims, dict non_victims, */ __pyx_r = __pyx_v_result; goto __pyx_L0; - /* "ml.pyx":18 + /* "ml.pyx":20 * return result * - * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< - * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): + * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, # <<<<<<<<<<<<<< + * DTYPE_t t_scale, DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): * """weight for failed infection, exponential time model""" */ @@ -1477,11 +1504,11 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py return __pyx_r; } -/* "ml.pyx":27 +/* "ml.pyx":31 * return result * - * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< - * DTYPE_t alpha, DTYPE_t delta): + * def ml(dict root_victims, dict victims, dict non_victims, # <<<<<<<<<<<<<< + * DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda): * cdef: */ @@ -1492,9 +1519,9 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py PyObject *__pyx_v_root_victims = 0; PyObject *__pyx_v_victims = 0; PyObject *__pyx_v_non_victims = 0; - CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_age; __pyx_t_2ml_DTYPE_t __pyx_v_alpha; __pyx_t_2ml_DTYPE_t __pyx_v_delta; + __pyx_t_2ml_DTYPE_t __pyx_v_lmbda; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -1502,7 +1529,7 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ml (wrapper)", 0); { - static PyObject **__pyx_pyargnames[] = {&__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,0}; + static PyObject **__pyx_pyargnames[] = {&__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,0}; PyObject* values[6] = {0,0,0,0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -1525,31 +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 = 27; __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 = 27; __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_age)) != 0)) kw_args--; + 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 = 27; __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_alpha)) != 0)) kw_args--; + 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 = 27; __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_delta)) != 0)) kw_args--; + 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 = 27; __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 = 27; __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; @@ -1564,22 +1591,22 @@ 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 = 27; __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 = 28; __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 = 28; __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 = 27; __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 = 27; __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 = 27; __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 = 27; __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); + 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 */ goto __pyx_L0; @@ -1590,7 +1617,7 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py return __pyx_r; } -static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_age, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta) { +static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta, __pyx_t_2ml_DTYPE_t __pyx_v_lmbda) { int __pyx_v_n_roots; int __pyx_v_n_victims; int __pyx_v_roots; @@ -1598,6 +1625,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ int __pyx_v_dist; int __pyx_v_dt; int __pyx_v_l; + int __pyx_v_n_days; __pyx_t_2ml_DTYPE_t __pyx_v_beta; __pyx_t_2ml_DTYPE_t __pyx_v_ll; __pyx_t_2ml_DTYPE_t __pyx_v_beta_add; @@ 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __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 = 36; __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 = 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__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 = 37; __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 = 37; __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__; 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 = 37; __pyx_clineno = 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__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 = 37; __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 = 43; __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 = 37; __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 = 43; __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, 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__Pyx_GetModuleGlobalName(__pyx_n_s_np); 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 = 38; __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 = 38; __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;} 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__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 = 38; __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 = 38; __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 = 38; __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 = 38; 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__pyx_lineno = 39; __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 = 39; __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 = 39; __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 = 39; __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 = 39; __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 = 39; __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 = 39; __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 = 39; __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 = 39; __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 = 39; __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]; } } @@ -1903,48 +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":40 + /* "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 = 40; __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 = 40; __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 = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; 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40; __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 = 40; __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 = 40; __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 = 40; __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]; } } @@ -1952,7 +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":43 + /* "ml.pyx":49 * * # loop through victims * for i, parents in enumerate(victims.itervalues()): # <<<<<<<<<<<<<< @@ -1963,9 +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 = 43; __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 = 43; __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; @@ -1973,42 +2022,42 @@ 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 = 43; __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 = 43; __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":47 + /* "ml.pyx":53 * # fail to infect it, also computes the probability that its most * # likely parent infects it - * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< + * 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 = 47; __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":48 + /* "ml.pyx":54 * # likely parent infects it - * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) + * 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, w1, w2, w3) + * successes = [weight_success(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) */ if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __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 = 48; __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 = 48; __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; @@ -2020,7 +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 = 48; __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))) { @@ -2049,7 +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 = 48; __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; } @@ -2059,7 +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 = 48; __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; @@ -2068,7 +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 = 48; __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; @@ -2076,12 +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 = 48; __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 = 48; __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 = 48; __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; @@ -2094,82 +2143,82 @@ 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":47 + /* "ml.pyx":53 * # fail to infect it, also computes the probability that its most * # likely parent infects it - * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< + * 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 = 47; __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 = 47; __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 = 47; __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_t_25, __pyx_t_26, __pyx_t_27)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __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 = 47; __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":48 + /* "ml.pyx":54 * # likely parent infects it - * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) + * 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, w1, w2, w3) + * successes = [weight_success(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) */ } __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_XDECREF_SET(__pyx_v_failures, ((PyObject*)__pyx_t_6)); __pyx_t_6 = 0; - /* "ml.pyx":49 - * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) + /* "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, w1, w2, w3) + * 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 = 49; __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 = 49; __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 = 49; __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":50 + /* "ml.pyx":56 * for (prnt, dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) - * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< + * 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 = 50; __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":51 + /* "ml.pyx":57 * probs_fail[i] = sum(failures) - * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) + * 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] */ if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __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 = 51; __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 = 51; __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; @@ -2181,7 +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 = 51; __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))) { @@ -2210,7 +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 = 51; __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; } @@ -2220,7 +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 = 51; __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; @@ -2229,7 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__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 = 51; __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 = 51; __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; @@ -2255,24 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__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 = 50; __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_t_27, __pyx_t_26, __pyx_t_25)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __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 = 56; __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 = 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 = 50; __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":51 + /* "ml.pyx":57 * probs_fail[i] = sum(failures) - * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) + * 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] @@ -2282,26 +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":52 - * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) + /* "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 = 52; __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 = 52; __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 = 52; __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 = 52; __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; @@ -2313,7 +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 = 52; __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))) { @@ -2342,7 +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 = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(item); *(temps[i]) = item; } @@ -2352,7 +2401,7 @@ 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 = 52; __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 = 58; __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; @@ -2361,7 +2410,7 @@ 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 = 52; __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; @@ -2369,12 +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 = 52; __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 = 52; __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 = 52; __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; @@ -2386,35 +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 = 52; __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 = 52; __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":53 + /* "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] = max(s - failures[l] for l, s in enumerate(successes)) + * probs[i] = float("-inf") */ - __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __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 = 53; __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 = 53; __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 = 53; __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; @@ -2426,7 +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 = 53; __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))) { @@ -2455,7 +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 = 53; __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; } @@ -2465,7 +2514,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } else { Py_ssize_t index = -1; PyObject** temps[6] = 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__pyx_t_23 = NULL; __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; goto __pyx_L20_unpacking_done; @@ -2482,12 +2531,12 @@ 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 = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L20_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 = 53; __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 = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0; 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __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; *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_28, __pyx_pybuffernd_probs.diminfo[0].strides) = __pyx_t_29; - /* "ml.pyx":57 - * # probs[i] = max(s - failures[l] for l, s in enumerate(successes)) + /* "ml.pyx":62 + * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = float("-inf") * for l, s in enumerate(successes): # <<<<<<<<<<<<<< * prob = s - failures[l] @@ -2532,31 +2581,31 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ for (;;) { if (__pyx_t_15 >= 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__pyx_t_6 = 0; if (__pyx_t_31) { - /* "ml.pyx":60 + /* "ml.pyx":65 * prob = s - failures[l] * if prob > probs[i]: * probs[i] = prob # <<<<<<<<<<<<<< * parent_dists[i] = dists[l] * parent_dts[i] = dts[l] */ - __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_prob); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_prob); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_32 = __pyx_v_i; if (__pyx_t_32 < 0) __pyx_t_32 += __pyx_pybuffernd_probs.diminfo[0].shape; *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_32, __pyx_pybuffernd_probs.diminfo[0].strides) = __pyx_t_25; - /* "ml.pyx":61 + /* "ml.pyx":66 * if prob > probs[i]: * probs[i] = prob * parent_dists[i] = 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__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":62 + /* "ml.pyx":67 * probs[i] = prob * parent_dists[i] = dists[l] * parent_dts[i] = dts[l] # <<<<<<<<<<<<<< - * # probs_fail[i] = failures[l] * + * # loop through non-victims */ - __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 = 62; __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 = 62; __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; @@ -2618,8 +2667,8 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } __pyx_L23:; - /* "ml.pyx":57 - * # probs[i] = max(s - failures[l] for l, s in enumerate(successes)) + /* "ml.pyx":62 + * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = float("-inf") * for l, s in enumerate(successes): # <<<<<<<<<<<<<< * prob = s - failures[l] @@ -2630,7 +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":66 + /* "ml.pyx":70 * * # loop through non-victims * for i, parents in enumerate(non_victims.itervalues()): # <<<<<<<<<<<<<< @@ -2641,9 +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 = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __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 = 66; __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 = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = __pyx_t_5; @@ -2651,42 +2700,42 @@ 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 = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __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 = 66; __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 = 70; __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":69 + /* "ml.pyx":73 * # 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) # <<<<<<<<<<<<<< + * 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 = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - /* "ml.pyx":70 + /* "ml.pyx":74 * # parents fail to infect it - * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) + * 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) * */ if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __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 = 70; __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 = 74; __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 = 70; __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 = 74; __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; @@ 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/* "ml.pyx":69 + /* "ml.pyx":73 * # 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) # <<<<<<<<<<<<<< + * 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 = 69; __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 = 69; __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 = 69; __pyx_clineno 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__pyx_pybuffernd_probs_nv.diminfo[0].shape; @@ -2822,14 +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":74 + /* "ml.pyx":78 * * # 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 = 74; __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 = 78; __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))) { @@ -2842,27 +2891,27 @@ 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PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_27 = __pyx_PyFloat_AsDouble(__pyx_t_20); if (unlikely((__pyx_t_27 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0; __pyx_v_beta_add = __pyx_t_27; - /* "ml.pyx":91 - * beta_add += roots * log(beta/1000.) + (n_nodes-roots) * log(1. - beta) + /* "ml.pyx":95 + * beta_add += roots * log(beta/n_days) + (n_nodes-roots) * log(1. - beta) * * if beta_add > max_beta_add: # <<<<<<<<<<<<<< * max_beta = beta @@ -3112,7 +3161,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_t_31 = ((__pyx_v_beta_add > __pyx_v_max_beta_add) != 0); if (__pyx_t_31) { - /* "ml.pyx":92 + /* "ml.pyx":96 * * if beta_add > max_beta_add: * max_beta = beta # <<<<<<<<<<<<<< @@ -3121,38 +3170,104 @@ static PyObject 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__pyx_f[0]; __pyx_lineno = 108; __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 = 101; __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 = 108; __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 = 101; __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 = 108; __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); @@ -3206,11 +3358,11 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_t_21 = 0; goto __pyx_L0; - /* "ml.pyx":27 + /* "ml.pyx":31 * return result * - * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< - * DTYPE_t alpha, DTYPE_t delta): + * def ml(dict root_victims, dict victims, dict non_victims, # <<<<<<<<<<<<<< + * DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda): * cdef: */ @@ -3260,6 +3412,8 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF(__pyx_v_prob); __Pyx_XDECREF(__pyx_v_seeds); __Pyx_XDECREF(__pyx_v_non_seeds); + __Pyx_XDECREF(__pyx_v_pdists); + __Pyx_XDECREF(__pyx_v_pdts); __Pyx_XDECREF(__pyx_v_prnt); __Pyx_XDECREF(__pyx_v_w1); __Pyx_XDECREF(__pyx_v_w2); @@ -5301,19 +5455,22 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_RuntimeError, __pyx_k_RuntimeError, sizeof(__pyx_k_RuntimeError), 0, 0, 1, 1}, {&__pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_k_Users_ben_Documents_Cascade_Pro, sizeof(__pyx_k_Users_ben_Documents_Cascade_Pro), 0, 0, 1, 0}, {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1}, - {&__pyx_n_s_age, __pyx_k_age, sizeof(__pyx_k_age), 0, 0, 1, 1}, {&__pyx_n_s_alpha, __pyx_k_alpha, sizeof(__pyx_k_alpha), 0, 0, 1, 1}, {&__pyx_n_s_arange, __pyx_k_arange, sizeof(__pyx_k_arange), 0, 0, 1, 1}, {&__pyx_n_s_beta, __pyx_k_beta, sizeof(__pyx_k_beta), 0, 0, 1, 1}, {&__pyx_n_s_beta_add, __pyx_k_beta_add, sizeof(__pyx_k_beta_add), 0, 0, 1, 1}, {&__pyx_n_s_delta, __pyx_k_delta, sizeof(__pyx_k_delta), 0, 0, 1, 1}, - {&__pyx_n_s_dist, __pyx_k_dist, sizeof(__pyx_k_dist), 0, 0, 1, 1}, + {&__pyx_kp_s_dist, __pyx_k_dist, sizeof(__pyx_k_dist), 0, 0, 1, 0}, + {&__pyx_n_s_dist_2, __pyx_k_dist_2, sizeof(__pyx_k_dist_2), 0, 0, 1, 1}, {&__pyx_n_s_dists, __pyx_k_dists, sizeof(__pyx_k_dists), 0, 0, 1, 1}, - {&__pyx_n_s_dt, __pyx_k_dt, sizeof(__pyx_k_dt), 0, 0, 1, 1}, + {&__pyx_kp_s_dt, __pyx_k_dt, sizeof(__pyx_k_dt), 0, 0, 1, 0}, + {&__pyx_n_s_dt_2, __pyx_k_dt_2, sizeof(__pyx_k_dt_2), 0, 0, 1, 1}, {&__pyx_n_s_dts, __pyx_k_dts, sizeof(__pyx_k_dts), 0, 0, 1, 1}, {&__pyx_n_s_dtype, __pyx_k_dtype, sizeof(__pyx_k_dtype), 0, 0, 1, 1}, + {&__pyx_n_s_end, __pyx_k_end, sizeof(__pyx_k_end), 0, 0, 1, 1}, {&__pyx_n_s_enumerate, __pyx_k_enumerate, sizeof(__pyx_k_enumerate), 0, 0, 1, 1}, {&__pyx_n_s_failures, __pyx_k_failures, sizeof(__pyx_k_failures), 0, 0, 1, 1}, + {&__pyx_n_s_file, __pyx_k_file, sizeof(__pyx_k_file), 0, 0, 1, 1}, {&__pyx_n_s_float64, __pyx_k_float64, sizeof(__pyx_k_float64), 0, 0, 1, 1}, {&__pyx_n_s_i, __pyx_k_i, sizeof(__pyx_k_i), 0, 0, 1, 1}, {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1}, @@ -5321,11 +5478,14 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_itervalues, __pyx_k_itervalues, sizeof(__pyx_k_itervalues), 0, 0, 1, 1}, {&__pyx_n_s_l, __pyx_k_l, sizeof(__pyx_k_l), 0, 0, 1, 1}, {&__pyx_n_s_ll, __pyx_k_ll, sizeof(__pyx_k_ll), 0, 0, 1, 1}, + {&__pyx_n_s_lmbda, __pyx_k_lmbda, sizeof(__pyx_k_lmbda), 0, 0, 1, 1}, {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1}, {&__pyx_n_s_max_beta, __pyx_k_max_beta, sizeof(__pyx_k_max_beta), 0, 0, 1, 1}, {&__pyx_n_s_max_beta_add, __pyx_k_max_beta_add, sizeof(__pyx_k_max_beta_add), 0, 0, 1, 1}, {&__pyx_n_s_max_roots, __pyx_k_max_roots, sizeof(__pyx_k_max_roots), 0, 0, 1, 1}, + {&__pyx_n_s_mean, __pyx_k_mean, sizeof(__pyx_k_mean), 0, 0, 1, 1}, {&__pyx_n_s_ml, __pyx_k_ml, sizeof(__pyx_k_ml), 0, 0, 1, 1}, + {&__pyx_n_s_n_days, __pyx_k_n_days, sizeof(__pyx_k_n_days), 0, 0, 1, 1}, {&__pyx_n_s_n_nodes, __pyx_k_n_nodes, sizeof(__pyx_k_n_nodes), 0, 0, 1, 1}, {&__pyx_n_s_n_roots, __pyx_k_n_roots, sizeof(__pyx_k_n_roots), 0, 0, 1, 1}, {&__pyx_n_s_n_victims, __pyx_k_n_victims, sizeof(__pyx_k_n_victims), 0, 0, 1, 1}, @@ -5338,6 +5498,9 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_parent_dists, __pyx_k_parent_dists, sizeof(__pyx_k_parent_dists), 0, 0, 1, 1}, {&__pyx_n_s_parent_dts, __pyx_k_parent_dts, sizeof(__pyx_k_parent_dts), 0, 0, 1, 1}, {&__pyx_n_s_parents, __pyx_k_parents, sizeof(__pyx_k_parents), 0, 0, 1, 1}, + {&__pyx_n_s_pdists, __pyx_k_pdists, sizeof(__pyx_k_pdists), 0, 0, 1, 1}, + {&__pyx_n_s_pdts, __pyx_k_pdts, sizeof(__pyx_k_pdts), 0, 0, 1, 1}, + {&__pyx_n_s_print, __pyx_k_print, sizeof(__pyx_k_print), 0, 0, 1, 1}, {&__pyx_n_s_prnt, __pyx_k_prnt, sizeof(__pyx_k_prnt), 0, 0, 1, 1}, {&__pyx_n_s_prob, __pyx_k_prob, sizeof(__pyx_k_prob), 0, 0, 1, 1}, {&__pyx_n_s_probs, __pyx_k_probs, sizeof(__pyx_k_probs), 0, 0, 1, 1}, @@ -5351,6 +5514,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_successes, __pyx_k_successes, sizeof(__pyx_k_successes), 0, 0, 1, 1}, {&__pyx_n_s_sum, __pyx_k_sum, sizeof(__pyx_k_sum), 0, 0, 1, 1}, {&__pyx_n_s_t, __pyx_k_t, sizeof(__pyx_k_t), 0, 0, 1, 1}, + {&__pyx_n_s_t_scale, __pyx_k_t_scale, sizeof(__pyx_k_t_scale), 0, 0, 1, 1}, {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1}, {&__pyx_n_s_thresh, __pyx_k_thresh, sizeof(__pyx_k_thresh), 0, 0, 1, 1}, {&__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_k_unknown_dtype_code_in_numpy_pxd, sizeof(__pyx_k_unknown_dtype_code_in_numpy_pxd), 0, 1, 0, 0}, @@ -5362,8 +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 = 43; __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 = 49; __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;} @@ -5376,14 +5540,14 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); - /* "ml.pyx":79 + /* "ml.pyx":83 * max_beta_add = float('-inf') * # iterate over all victim nodes to find the optimal threshold - * for beta in np.arange(0.01, 1., .01): # <<<<<<<<<<<<<< - * thresh = log(beta/(1000.*(1.-beta))) + * 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__01); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __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 = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple_); __Pyx_GIVEREF(__pyx_tuple_); @@ -5453,17 +5617,17 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__7); __Pyx_GIVEREF(__pyx_tuple__7); - /* "ml.pyx":27 + /* "ml.pyx":31 * return result * - * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< - * DTYPE_t alpha, DTYPE_t delta): + * 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(40, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_age, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_roots, __pyx_n_s_i, __pyx_n_s_dist, __pyx_n_s_dt, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_beta, __pyx_n_s_ll, __pyx_n_s_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_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_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 = 27; __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, 40, 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, 27, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __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_Cascade_Pro, __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:; @@ -5474,9 +5638,8 @@ static int __Pyx_InitCachedConstants(void) { static int __Pyx_InitGlobals(void) { if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __pyx_float_1_ = PyFloat_FromDouble(1.); if (unlikely(!__pyx_float_1_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_float__01 = PyFloat_FromDouble(.01); if (unlikely(!__pyx_float__01)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_float_0_01 = PyFloat_FromDouble(0.01); if (unlikely(!__pyx_float_0_01)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_int_5000 = PyInt_FromLong(5000); if (unlikely(!__pyx_int_5000)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_int_148152 = PyInt_FromLong(148152L); if (unlikely(!__pyx_int_148152)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} return 0; __pyx_L1_error:; return -1; @@ -5606,16 +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":27 + /* "ml.pyx":31 * return result * - * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< - * DTYPE_t alpha, DTYPE_t delta): + * 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 = 27; __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 = 27; __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 @@ -6863,6 +7026,10 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); } +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { + PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); +} + static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; @@ -7446,6 +7613,111 @@ raise_neg_overflow: return (int) -1; } +#if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3 +static PyObject *__Pyx_GetStdout(void) { + PyObject *f = PySys_GetObject((char *)"stdout"); + if (!f) { + PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout"); + } + return f; +} +static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) { + int i; + if (!f) { + if (!(f = __Pyx_GetStdout())) + return -1; + } + Py_INCREF(f); + for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) { + PyObject* v; + if (PyFile_SoftSpace(f, 1)) { + if (PyFile_WriteString(" ", f) < 0) + goto error; + } + v = PyTuple_GET_ITEM(arg_tuple, i); + if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0) + goto error; + if (PyString_Check(v)) { + char *s = PyString_AsString(v); + Py_ssize_t len = PyString_Size(v); + if (len > 0) { + switch (s[len-1]) { + case ' ': break; + case '\f': case '\r': case '\n': case '\t': case '\v': + PyFile_SoftSpace(f, 0); + break; + default: break; + } + } + } + } + if (newline) { + if (PyFile_WriteString("\n", f) < 0) + goto error; + PyFile_SoftSpace(f, 0); + } + Py_DECREF(f); + return 0; +error: + Py_DECREF(f); + return -1; +} +#else +static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) { + PyObject* kwargs = 0; + PyObject* result = 0; + PyObject* end_string; + if (unlikely(!__pyx_print)) { + __pyx_print = PyObject_GetAttr(__pyx_b, __pyx_n_s_print); + if (!__pyx_print) + return -1; + } + if (stream) { + kwargs = PyDict_New(); + if (unlikely(!kwargs)) + return -1; + if (unlikely(PyDict_SetItem(kwargs, __pyx_n_s_file, stream) < 0)) + goto bad; + if (!newline) { + end_string = PyUnicode_FromStringAndSize(" ", 1); + if (unlikely(!end_string)) + goto bad; + if (PyDict_SetItem(kwargs, __pyx_n_s_end, end_string) < 0) { + Py_DECREF(end_string); + goto bad; + } + Py_DECREF(end_string); + } + } else if (!newline) { + if (unlikely(!__pyx_print_kwargs)) { + __pyx_print_kwargs = PyDict_New(); + if (unlikely(!__pyx_print_kwargs)) + return -1; + end_string = PyUnicode_FromStringAndSize(" ", 1); + if (unlikely(!end_string)) + return -1; + if (PyDict_SetItem(__pyx_print_kwargs, __pyx_n_s_end, end_string) < 0) { + Py_DECREF(end_string); + return -1; + } + Py_DECREF(end_string); + } + kwargs = __pyx_print_kwargs; + } + result = PyObject_Call(__pyx_print, arg_tuple, kwargs); + if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs)) + Py_DECREF(kwargs); + if (!result) + return -1; + Py_DECREF(result); + return 0; +bad: + if (kwargs != __pyx_print_kwargs) + Py_XDECREF(kwargs); + return -1; +} +#endif + #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { diff --git a/experiments/ml.pyx b/experiments/ml.pyx index 0d72c44..7eca30a 100644 --- a/experiments/ml.pyx +++ b/experiments/ml.pyx @@ -6,32 +6,38 @@ from libc.math cimport log, exp DTYPE = np.float64 ctypedef np.float_t DTYPE_t -cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, - DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): +cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, + DTYPE_t t_scale, DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): """weight for successful infection, exponential time model""" cdef DTYPE_t structural, temporal, result structural = delta ** dist - temporal = log(exp(alpha)-1.) - alpha*dt/1. + # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) + 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 return result -cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, - DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): +cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, + DTYPE_t t_scale, DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): """weight for failed infection, exponential time model""" cdef DTYPE_t structural, temporal, result structural = delta ** dist - temporal = exp(-alpha * dt/1.) + # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) + temporal = exp(-alpha * dt/t_scale) + # temporal = 1. - 1. / (1. + dt/alpha)**0.01 result = log(1. - structural + structural * temporal) return result -def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, - DTYPE_t alpha, DTYPE_t delta): +def ml(dict root_victims, dict victims, dict non_victims, + DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda): cdef: - int n_roots, n_victims, roots, i, dist, dt, t, l + int n_roots, n_victims, roots, i, dist, dt, t, l, n_days DTYPE_t beta, ll, beta_add, max_beta, max_beta_add list parents, failures, successes n_roots, n_victims = len(root_victims), len(victims) - n_nodes = 5000 + n_nodes = 148152 + n_days = 3012 + 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) @@ -44,15 +50,14 @@ def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # for each victim node i, compute the probability that all its parents # 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) + 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, w1, w2, w3) + 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}) - # probs[i] = max(s - failures[l] for l, s in enumerate(successes)) probs[i] = float("-inf") for l, s in enumerate(successes): prob = s - failures[l] @@ -60,13 +65,12 @@ def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, probs[i] = prob parent_dists[i] = dists[l] parent_dts[i] = dts[l] - # probs_fail[i] = failures[l] # loop through non-victims for i, parents in enumerate(non_victims.itervalues()): # for each non victim node, compute the probability that all its # parents fail to infect it - failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) + 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) @@ -76,8 +80,8 @@ def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, max_beta_add = float('-inf') # iterate over all victim nodes to find the optimal threshold - for beta in np.arange(0.01, 1., .01): - thresh = log(beta/(1000.*(1.-beta))) + for beta in np.arange(0.01, 1., 0.01): + thresh = log(beta/(n_days*(1.-beta))) seeds = probs<thresh non_seeds = probs>=thresh roots = n_roots + sum(seeds) @@ -86,16 +90,19 @@ def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # add probability for realized edges and subtract probability these edges fail beta_add += (probs[non_seeds]).sum() # add probability for the seeds and non-seeds - beta_add += roots * log(beta/1000.) + (n_nodes-roots) * log(1. - beta) + beta_add += roots * log(beta/n_days) + (n_nodes-roots) * log(1. - beta) if beta_add > max_beta_add: max_beta = beta max_roots = roots max_beta_add = beta_add + pdists = (parent_dists[non_seeds]).mean() + pdts = (parent_dts[non_seeds]).mean() # print 'beta:', max_beta, 'add:', max_beta_add, 'roots:', max_roots ll += max_beta_add roots = max_roots beta = max_beta - # print n_nodes, n_roots, n_victims, max_i, roots + print 'dist:', pdists + print 'dt:', pdts return (beta, roots, ll) diff --git a/experiments/ml.so b/experiments/ml.so Binary files differindex d4cd7b4..87d16ae 100755 --- a/experiments/ml.so +++ b/experiments/ml.so diff --git a/experiments/ml2.pyx b/experiments/ml2.pyx index dd0e7a8..1458683 100644 --- a/experiments/ml2.pyx +++ b/experiments/ml2.pyx @@ -15,7 +15,6 @@ cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYP temporal = log(exp(alpha)-1.) - alpha*dt # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 result = log(structural) + temporal - # print 'st', structural, temporal return result cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda, @@ -27,7 +26,6 @@ cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYP temporal = exp(-alpha * dt) # temporal = 1. - 1. / (1. + dt/alpha)**0.01 result = log(1. - structural + structural * temporal) - # print 'stnv', structural, temporal return result def ml2(dict root_victims, dict victims, dict non_victims, diff --git a/experiments/out.log b/experiments/out.log index 895f69f..b83b746 100644 --- a/experiments/out.log +++ b/experiments/out.log @@ -1,100 +1,36 @@ -0.1 0.01 0.32 1587 -16246.2835303 -0.1 0.0129154966501 0.3 1522 -16193.1560593 -0.1 0.016681005372 0.3 1482 -16136.7007139 -0.1 0.0215443469003 0.29 1445 -16083.927662 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-16306.1951749 -0.244843674682 0.1 0.24 1195 -16688.1452238 -0.278255940221 0.01 0.33 1637 -16116.7453334 -0.278255940221 0.0129154966501 0.32 1613 -16080.0365035 -0.278255940221 0.016681005372 0.32 1587 -16046.9682889 -0.278255940221 0.0215443469003 0.31 1560 -16021.5867637 -0.278255940221 0.0278255940221 0.31 1537 -16011.7866661 -0.278255940221 0.035938136638 0.3 1522 -16030.8034204 -0.278255940221 0.0464158883361 0.27 1367 -16078.1951393 -0.278255940221 0.0599484250319 0.26 1298 -16144.7176332 -0.278255940221 0.0774263682681 0.25 1249 -16315.5245594 -0.278255940221 0.1 0.24 1207 -16702.3027221 -0.316227766017 0.01 0.33 1637 -16109.5865483 -0.316227766017 0.0129154966501 0.32 1613 -16075.7276647 -0.316227766017 0.016681005372 0.32 1587 -16046.7383729 -0.316227766017 0.0215443469003 0.31 1560 -16026.6264576 -0.316227766017 0.0278255940221 0.31 1537 -16022.2115914 -0.316227766017 0.035938136638 0.31 1537 -16044.7445633 -0.316227766017 0.0464158883361 0.27 1374 -16084.9299944 -0.316227766017 0.0599484250319 0.26 1308 -16152.3121983 -0.316227766017 0.0774263682681 0.25 1260 -16327.1609197 -0.316227766017 0.1 0.25 1235 -16718.4366844 +0.00316227766017 0.001 0.08 11270 -130258.659536 +0.00316227766017 0.00158489319246 0.08 11270 -130320.098111 +0.00316227766017 0.00251188643151 0.08 11270 -130418.855032 +0.00316227766017 0.00398107170553 0.08 11270 -130578.916829 +0.00316227766017 0.0063095734448 0.08 11270 -130841.766453 +0.00316227766017 0.01 0.07 10355 -131193.273467 +0.0063095734448 0.001 0.08 11270 -130266.723239 +0.0063095734448 0.00158489319246 0.08 11270 -130332.947659 +0.0063095734448 0.00251188643151 0.08 11270 -130439.396324 +0.0063095734448 0.00398107170553 0.08 11270 -130611.92178 +0.0063095734448 0.0063095734448 0.07 10368 -130696.780278 +0.0063095734448 0.01 0.07 9770 -130607.951576 +0.0125892541179 0.001 0.08 11270 -130270.55116 +0.0125892541179 0.00158489319246 0.08 11270 -130339.046219 +0.0125892541179 0.00251188643151 0.07 10997 -130440.900987 +0.0125892541179 0.00398107170553 0.07 10575 -130395.334056 +0.0125892541179 0.0063095734448 0.07 10192 -130275.394388 +0.0125892541179 0.01 0.07 9903 -130197.753003 +0.0251188643151 0.001 0.08 11270 -130272.219781 +0.0251188643151 0.00158489319246 0.07 10997 -130301.46282 +0.0251188643151 0.00251188643151 0.07 10780 -130242.15389 +0.0251188643151 0.00398107170553 0.07 10575 -130147.586922 +0.0251188643151 0.0063095734448 0.07 10368 -130074.110407 +0.0251188643151 0.01 0.07 10192 -130116.088601 +0.0501187233627 0.001 0.07 11059 -130224.789544 +0.0501187233627 0.00158489319246 0.07 10959 -130171.655291 +0.0501187233627 0.00251188643151 0.07 10852 -130113.879207 +0.0501187233627 0.00398107170553 0.07 10721 -130073.026485 +0.0501187233627 0.0063095734448 0.07 10607 -130094.992533 +0.0501187233627 0.01 0.07 10515 -130269.846455 +0.1 0.001 0.07 11059 -130152.650459 +0.1 0.00158489319246 0.07 11007 -130110.306047 +0.1 0.00251188643151 0.07 10959 -130089.374712 +0.1 0.00398107170553 0.07 10900 -130113.925035 +0.1 0.0063095734448 0.07 10852 -130230.792293 +0.1 0.01 0.07 10780 -130522.660012 diff --git a/experiments/process.py b/experiments/process.py index 6c71934..33c83b6 100644 --- a/experiments/process.py +++ b/experiments/process.py @@ -16,12 +16,13 @@ if __name__ == "__main__": root_victims, victims, non_victims, age = load(open(sys.argv[1])) # alphas = np.arange(.02, .1, .01) # parameter of the time component - alphas = np.logspace(-1,-.5,num=10) + alphas = np.logspace(-2.5,-1,num=6) # deltas = np.arange(.02, .1, .01) # parameter of the structural component - deltas = np.logspace(-2,-1,num=10) + deltas = np.logspace(-3,-2,num=6) + lmbda = 1. with open("out.log", "w") as fh: for alpha, delta in product(alphas, deltas): - beta, roots, ll = ml(root_victims, victims, non_victims, age, alpha, delta) + beta, roots, ll = ml(root_victims, victims, non_victims, alpha, delta, lmbda) print "\t".join(map(str, [alpha, delta, beta, roots, ll])) fh.write("\t".join(map(str, [alpha, delta, beta, roots, ll])) + "\n") fh.flush() @@ -38,7 +39,7 @@ if __name__ == "__main__": # fh.write("\t".join(map(str, [alpha, delta, lmbda, roots, ll])) + "\n") # fh.flush() - # alpha = .016 - # delta = 0.077 - # beta, roots, ll = ml2(root_victims, victims, non_victims, alpha, delta, 1.) + # alpha = 0.0373 + # delta = 0.00518 + # beta, roots, ll = ml(root_victims, victims, non_victims, alpha, delta, 1.) # print "\t".join(map(str, [alpha, delta, beta, roots, ll]))
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