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-rw-r--r--experiments/build/temp.macosx-10.6-x86_64-2.7/ml.obin294544 -> 299264 bytes
-rw-r--r--experiments/build/temp.macosx-10.6-x86_64-2.7/ml2.obin284628 -> 292772 bytes
-rw-r--r--experiments/build/temp.macosx-10.6-x86_64-2.7/ml3.obin264960 -> 271436 bytes
-rw-r--r--experiments/ml.c641
-rwxr-xr-xexperiments/ml.sobin104640 -> 108744 bytes
-rw-r--r--experiments/ml2.c816
-rw-r--r--experiments/ml2.pyx26
-rwxr-xr-xexperiments/ml2.sobin106060 -> 106020 bytes
-rw-r--r--experiments/ml3.c663
-rw-r--r--experiments/ml3.pyx21
-rwxr-xr-xexperiments/ml3.sobin101972 -> 106476 bytes
-rw-r--r--experiments/out.log500
-rw-r--r--experiments/process.py24
13 files changed, 1240 insertions, 1451 deletions
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
index 40511d4..5861fce 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
Binary files differ
diff --git a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml2.o b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml2.o
index a911bef..d3704b1 100644
--- a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml2.o
+++ b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml2.o
Binary files differ
diff --git a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml3.o b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml3.o
index 81dad16..b211a49 100644
--- a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml3.o
+++ b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml3.o
Binary files differ
diff --git a/experiments/ml.c b/experiments/ml.c
index 77f9840..eb67db6 100644
--- a/experiments/ml.c
+++ b/experiments/ml.c
@@ -695,7 +695,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
* DTYPE = np.float64
* ctypedef np.float_t DTYPE_t # <<<<<<<<<<<<<<
*
- * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta):
+ * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
*/
typedef __pyx_t_5numpy_float_t __pyx_t_2ml_DTYPE_t;
#if CYTHON_CCOMPLEX
@@ -759,7 +759,7 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
*/
typedef npy_cdouble __pyx_t_5numpy_complex_t;
-/* "ml.pyx":38
+/* "ml.pyx":35
* return result
*
* def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<<
@@ -773,7 +773,7 @@ struct __pyx_obj_2ml___pyx_scope_struct__ml {
};
-/* "ml.pyx":62
+/* "ml.pyx":59
* for (dist, dt, w1, w2, w3) in parents]
* # find parent that maximizes log(p) - log(\tilde{p})
* probs[i] = max(s - failures[l] for l, s in enumerate(successes)) # <<<<<<<<<<<<<<
@@ -1252,8 +1252,8 @@ int __pyx_module_is_main_ml = 0;
/* Implementation of 'ml' */
static PyObject *__pyx_builtin_enumerate;
-static PyObject *__pyx_builtin_max;
static PyObject *__pyx_builtin_sum;
+static PyObject *__pyx_builtin_max;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_RuntimeError;
@@ -1404,9 +1404,9 @@ static PyObject *__pyx_n_s_w1;
static PyObject *__pyx_n_s_w2;
static PyObject *__pyx_n_s_w3;
static PyObject *__pyx_n_s_zeros;
-static PyObject *__pyx_float_1_;
-static PyObject *__pyx_float__05;
-static PyObject *__pyx_float_0_09;
+static PyObject *__pyx_float__2;
+static PyObject *__pyx_float__002;
+static PyObject *__pyx_float_0_001;
static PyObject *__pyx_tuple_;
static PyObject *__pyx_tuple__2;
static PyObject *__pyx_tuple__3;
@@ -1420,43 +1420,6 @@ static PyObject *__pyx_codeobj__9;
/* "ml.pyx":9
* ctypedef np.float_t DTYPE_t
*
- * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): # <<<<<<<<<<<<<<
- * return 1./(1. + exp(-weight/delta))
- *
- */
-
-static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_plogis(__pyx_t_2ml_DTYPE_t __pyx_v_weight, __pyx_t_2ml_DTYPE_t __pyx_v_delta) {
- __pyx_t_2ml_DTYPE_t __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("plogis", 0);
-
- /* "ml.pyx":10
- *
- * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta):
- * return 1./(1. + exp(-weight/delta)) # <<<<<<<<<<<<<<
- *
- * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
- */
- __pyx_r = (1. / (1. + exp(((-__pyx_v_weight) / __pyx_v_delta))));
- goto __pyx_L0;
-
- /* "ml.pyx":9
- * ctypedef np.float_t DTYPE_t
- *
- * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): # <<<<<<<<<<<<<<
- * return 1./(1. + exp(-weight/delta))
- *
- */
-
- /* function exit code */
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "ml.pyx":12
- * return 1./(1. + exp(-weight/delta))
- *
* cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<<
* DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
* """weight for successful infection, exponential time model"""
@@ -1470,7 +1433,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("weight_success", 0);
- /* "ml.pyx":16
+ /* "ml.pyx":13
* """weight for successful infection, exponential time model"""
* cdef DTYPE_t structural, temporal, result
* structural = dist * log(delta) # <<<<<<<<<<<<<<
@@ -1479,7 +1442,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py
*/
__pyx_v_structural = (__pyx_v_dist * log(__pyx_v_delta));
- /* "ml.pyx":18
+ /* "ml.pyx":15
* structural = dist * log(delta)
* # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
* temporal = log(exp(alpha)-1.) - alpha*dt # <<<<<<<<<<<<<<
@@ -1488,7 +1451,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py
*/
__pyx_v_temporal = (log((exp(__pyx_v_alpha) - 1.)) - (__pyx_v_alpha * __pyx_v_dt));
- /* "ml.pyx":22
+ /* "ml.pyx":19
* # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
* # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
* result = structural + temporal # <<<<<<<<<<<<<<
@@ -1497,7 +1460,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py
*/
__pyx_v_result = (__pyx_v_structural + __pyx_v_temporal);
- /* "ml.pyx":24
+ /* "ml.pyx":21
* result = structural + temporal
* # print 'st', structural, temporal
* return result # <<<<<<<<<<<<<<
@@ -1507,8 +1470,8 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py
__pyx_r = __pyx_v_result;
goto __pyx_L0;
- /* "ml.pyx":12
- * return 1./(1. + exp(-weight/delta))
+ /* "ml.pyx":9
+ * ctypedef np.float_t DTYPE_t
*
* cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<<
* DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
@@ -1521,7 +1484,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py
return __pyx_r;
}
-/* "ml.pyx":26
+/* "ml.pyx":23
* return result
*
* cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<<
@@ -1537,7 +1500,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("weight_failure", 0);
- /* "ml.pyx":30
+ /* "ml.pyx":27
* """weight for failed infection, exponential time model"""
* cdef DTYPE_t structural, temporal, result
* structural = delta ** dist # <<<<<<<<<<<<<<
@@ -1546,7 +1509,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
*/
__pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist));
- /* "ml.pyx":32
+ /* "ml.pyx":29
* structural = delta ** dist
* # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
* temporal = exp(-alpha * dt) # <<<<<<<<<<<<<<
@@ -1555,7 +1518,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
*/
__pyx_v_temporal = exp(((-__pyx_v_alpha) * __pyx_v_dt));
- /* "ml.pyx":34
+ /* "ml.pyx":31
* temporal = exp(-alpha * dt)
* # temporal = 1. - 1. / (1. + dt/alpha)**0.01
* result = log(1. - structural + structural * temporal) # <<<<<<<<<<<<<<
@@ -1564,7 +1527,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
*/
__pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal)));
- /* "ml.pyx":36
+ /* "ml.pyx":33
* result = log(1. - structural + structural * temporal)
* # print 'stnv', structural, temporal
* return result # <<<<<<<<<<<<<<
@@ -1574,7 +1537,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
__pyx_r = __pyx_v_result;
goto __pyx_L0;
- /* "ml.pyx":26
+ /* "ml.pyx":23
* return result
*
* cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<<
@@ -1588,7 +1551,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
return __pyx_r;
}
-/* "ml.pyx":38
+/* "ml.pyx":35
* return result
*
* def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<<
@@ -1636,31 +1599,31 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py
case 1:
if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_victims)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_non_victims)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_age)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_alpha)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 5:
if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_delta)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 6) {
goto __pyx_L5_argtuple_error;
@@ -1675,21 +1638,21 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py
__pyx_v_root_victims = ((PyObject*)values[0]);
__pyx_v_victims = ((PyObject*)values[1]);
__pyx_v_non_victims = ((PyObject*)values[2]);
- __pyx_v_age = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_age == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_delta = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_age = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_age == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_delta = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("ml.ml", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_root_victims), (&PyDict_Type), 1, "root_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_victims), (&PyDict_Type), 1, "victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_non_victims), (&PyDict_Type), 1, "non_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_root_victims), (&PyDict_Type), 1, "root_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_victims), (&PyDict_Type), 1, "victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_non_victims), (&PyDict_Type), 1, "non_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = __pyx_pf_2ml_ml(__pyx_self, __pyx_v_root_victims, __pyx_v_victims, __pyx_v_non_victims, __pyx_v_age, __pyx_v_alpha, __pyx_v_delta);
/* function exit code */
@@ -1702,7 +1665,7 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py
}
static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
-/* "ml.pyx":62
+/* "ml.pyx":59
* for (dist, dt, w1, w2, w3) in parents]
* # find parent that maximizes log(p) - log(\tilde{p})
* probs[i] = max(s - failures[l] for l, s in enumerate(successes)) # <<<<<<<<<<<<<<
@@ -1728,7 +1691,7 @@ static PyObject *__pyx_pf_2ml_2ml_genexpr(PyObject *__pyx_self) {
__Pyx_INCREF(((PyObject *)__pyx_cur_scope->__pyx_outer_scope));
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_outer_scope);
{
- __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_2ml_2ml_2generator, (PyObject *) __pyx_cur_scope, __pyx_n_s_genexpr, __pyx_n_s_ml_locals_genexpr); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_2ml_2ml_2generator, (PyObject *) __pyx_cur_scope, __pyx_n_s_genexpr, __pyx_n_s_ml_locals_genexpr); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_cur_scope);
__Pyx_RefNannyFinishContext();
return (PyObject *) gen;
@@ -1766,16 +1729,16 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera
return NULL;
}
__pyx_L3_first_run:;
- if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_1 = 0;
- if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_successes)) { __Pyx_RaiseClosureNameError("successes"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_successes)) { __Pyx_RaiseClosureNameError("successes"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
__pyx_t_2 = __pyx_cur_scope->__pyx_outer_scope->__pyx_v_successes; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
for (;;) {
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+ __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_4 = 0;
__pyx_cur_scope->__pyx_v_l = __pyx_t_1;
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_XGOTREF(__pyx_t_2);
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return NULL;
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+/* "ml.pyx":35
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struct __pyx_obj_2ml___pyx_scope_struct__ml *__pyx_cur_scope;
int __pyx_v_n_roots;
int __pyx_v_n_victims;
- CYTHON_UNUSED int __pyx_v_n_nodes;
+ int __pyx_v_n_nodes;
int __pyx_v_roots;
int __pyx_v_i;
int __pyx_v_dist;
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+ /* "ml.pyx":41
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(__pyx_v_victims == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_n_roots = __pyx_t_1;
__pyx_v_n_victims = __pyx_t_2;
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+ /* "ml.pyx":42
* list parents, failures, successes
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@@ -1950,43 +1913,43 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
*/
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+ /* "ml.pyx":44
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* np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE)
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+ __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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+ __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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+ if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_probs = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf = NULL;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_probs = ((PyArrayObject *)__pyx_t_6);
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__pyx_v_probs_fail = ((PyArrayObject *)__pyx_t_4);
__pyx_t_4 = 0;
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+ /* "ml.pyx":46
* np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE)
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*
* # loop through victims
*/
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PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_4);
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__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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+ if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_BufFmt_StackElem __pyx_stack[1];
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__pyx_v_probs_nv = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_probs_nv.rcbuffer->pybuffer.buf = NULL;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
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@@ -2087,7 +2050,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
__pyx_v_probs_nv = ((PyArrayObject *)__pyx_t_3);
__pyx_t_3 = 0;
- /* "ml.pyx":52
+ /* "ml.pyx":49
*
* # loop through victims
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@@ -2098,9 +2061,9 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
__pyx_t_2 = 0;
if (unlikely(__pyx_v_victims == Py_None)) {
PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "itervalues");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_4 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_11)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_11)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_3);
__pyx_t_3 = __pyx_t_4;
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__pyx_t_12 = __Pyx_dict_iter_next(__pyx_t_3, __pyx_t_1, &__pyx_t_2, NULL, &__pyx_t_4, NULL, __pyx_t_11);
if (unlikely(__pyx_t_12 == 0)) break;
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+ if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- if (!(likely(PyList_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_4)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyList_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_4)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_parents, ((PyObject*)__pyx_t_4));
__pyx_t_4 = 0;
__pyx_v_i = __pyx_t_10;
__pyx_t_10 = (__pyx_t_10 + 1);
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+ /* "ml.pyx":53
* # fail to infect it, also computes the probability that its most
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* failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<<
* for (dist, dt, w1, w2, w3) in parents]
- * probs_fail[i] = max(failures)
+ * probs_fail[i] = sum(failures)
*/
- __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- /* "ml.pyx":57
+ /* "ml.pyx":54
* # likely parent infects it
* failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
* for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<<
- * probs_fail[i] = max(failures)
+ * probs_fail[i] = sum(failures)
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if (unlikely(__pyx_v_parents == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_5 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_5); __pyx_t_13 = 0;
for (;;) {
if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_5)) break;
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+ __pyx_t_6 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __pyx_t_6 = PySequence_ITEM(__pyx_t_5, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PySequence_ITEM(__pyx_t_5, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyObject* sequence = __pyx_t_6;
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if (size > 5) __Pyx_RaiseTooManyValuesError(5);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2181,7 +2144,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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for (i=0; i < 5; i++) {
- PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2191,7 +2154,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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+ __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
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__Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_18);
__pyx_t_18 = 0;
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* for (dist, dt, w1, w2, w3) in parents]
- * probs_fail[i] = max(failures)
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+ if (unlikely(__Pyx_ListComp_Append(__pyx_t_4, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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* for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<<
- * probs_fail[i] = max(failures)
+ * probs_fail[i] = sum(failures)
* successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
*/
}
@@ -2253,39 +2216,39 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
__Pyx_GIVEREF(__pyx_t_4);
__pyx_t_4 = 0;
- /* "ml.pyx":58
+ /* "ml.pyx":55
* failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
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- * probs_fail[i] = max(failures) # <<<<<<<<<<<<<<
+ * probs_fail[i] = sum(failures) # <<<<<<<<<<<<<<
* successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
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+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_failures);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_cur_scope->__pyx_v_failures);
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_failures);
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+ __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
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+ /* "ml.pyx":56
* for (dist, dt, w1, w2, w3) in parents]
- * probs_fail[i] = max(failures)
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* for (dist, dt, w1, w2, w3) in parents]
* # find parent that maximizes log(p) - log(\tilde{p})
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- __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;}
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__Pyx_GOTREF(__pyx_t_5);
- /* "ml.pyx":60
- * probs_fail[i] = max(failures)
+ /* "ml.pyx":57
+ * probs_fail[i] = sum(failures)
* successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
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* # find parent that maximizes log(p) - log(\tilde{p})
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
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+ __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(item);
*(temps[i]) = item;
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@@ -2349,7 +2312,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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- __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_19);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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__Pyx_GOTREF(item);
*(temps[index]) = item;
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+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
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__Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_14);
__pyx_t_14 = 0;
- /* "ml.pyx":59
+ /* "ml.pyx":56
* for (dist, dt, w1, w2, w3) in parents]
- * probs_fail[i] = max(failures)
+ * probs_fail[i] = sum(failures)
* successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<<
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- __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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__Pyx_GIVEREF(__pyx_t_5);
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* for (dist, dt, w1, w2, w3) in parents]
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+ __pyx_t_5 = __pyx_pf_2ml_2ml_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
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__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_25 = __pyx_v_i;
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "itervalues");
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}
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__Pyx_GOTREF(__pyx_t_5);
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+ /* "ml.pyx":66
* # parents fail to infect it
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2530,7 +2493,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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for (i=0; i < 5; i++) {
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__Pyx_GOTREF(item);
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- __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_19);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GIVEREF(__pyx_t_5);
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__Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_failures);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_cur_scope->__pyx_v_failures);
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_failures);
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__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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+ __pyx_v_beta_add = (__pyx_v_beta_add + ((__pyx_v_roots * log((__pyx_v_beta / 3012.))) + ((__pyx_v_n_nodes - __pyx_v_roots) * log((1. - __pyx_v_beta)))));
- /* "ml.pyx":97
- * beta_add += roots * log(beta) + len(probs[probs>=thresh]) * log(1. - beta)
+ /* "ml.pyx":94
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__pyx_t_29 = ((__pyx_v_beta_add > __pyx_v_max_beta_add) != 0);
if (__pyx_t_29) {
- /* "ml.pyx":98
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*/
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- /* "ml.pyx":99
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__pyx_v_ll = (__pyx_v_ll + __pyx_v_max_beta_add);
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- /* "ml.pyx":105
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__pyx_v_beta = __pyx_v_max_beta;
- /* "ml.pyx":107
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__Pyx_GIVEREF(__pyx_t_4);
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__pyx_t_4 = 0;
__pyx_t_18 = 0;
- __pyx_t_5 = 0;
- __pyx_r = __pyx_t_3;
__pyx_t_3 = 0;
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goto __pyx_L0;
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- __pyx_builtin_max = __Pyx_GetBuiltinName(__pyx_n_s_max); if (!__pyx_builtin_max) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __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 = 70; __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_max = __Pyx_GetBuiltinName(__pyx_n_s_max); if (!__pyx_builtin_max) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __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;}
@@ -5306,14 +5297,14 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
- /* "ml.pyx":86
+ /* "ml.pyx":83
* max_beta_add = float('-inf')
* # iterate over all victim nodes to find the optimal threshold
- * for beta in np.arange(0.09, 1., .05): # <<<<<<<<<<<<<<
+ * for beta in np.arange(0.001, .2, .002): # <<<<<<<<<<<<<<
* thresh = log(beta/(3012.*(1.-beta)))
* # print 'beta:', beta, 'thresh:', thresh, 'infected:', len(probs[probs>=thresh])
*/
- __pyx_tuple_ = PyTuple_Pack(3, __pyx_float_0_09, __pyx_float_1_, __pyx_float__05); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple_ = PyTuple_Pack(3, __pyx_float_0_001, __pyx_float__2, __pyx_float__002); 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_);
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__Pyx_GOTREF(__pyx_tuple__7);
__Pyx_GIVEREF(__pyx_tuple__7);
- /* "ml.pyx":38
+ /* "ml.pyx":35
* return result
*
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* DTYPE_t alpha, DTYPE_t delta):
* cdef:
*/
- __pyx_tuple__8 = PyTuple_Pack(33, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_age, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_n_nodes, __pyx_n_s_roots, __pyx_n_s_i, __pyx_n_s_dist, __pyx_n_s_dt, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_beta, __pyx_n_s_ll, __pyx_n_s_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_probs, __pyx_n_s_probs_fail, __pyx_n_s_probs_nv, __pyx_n_s_thresh, __pyx_n_s_max_roots, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3, __pyx_n_s_genexpr, __pyx_n_s_genexpr); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__8 = PyTuple_Pack(33, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_age, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_n_nodes, __pyx_n_s_roots, __pyx_n_s_i, __pyx_n_s_dist, __pyx_n_s_dt, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_beta, __pyx_n_s_ll, __pyx_n_s_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_probs, __pyx_n_s_probs_fail, __pyx_n_s_probs_nv, __pyx_n_s_thresh, __pyx_n_s_max_roots, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3, __pyx_n_s_genexpr, __pyx_n_s_genexpr); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__8);
__Pyx_GIVEREF(__pyx_tuple__8);
- __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(6, 0, 33, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__8, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml, 38, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(6, 0, 33, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__8, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml, 35, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
@@ -5403,9 +5394,9 @@ static int __Pyx_InitCachedConstants(void) {
static int __Pyx_InitGlobals(void) {
if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_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__05 = PyFloat_FromDouble(.05); if (unlikely(!__pyx_float__05)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_float_0_09 = PyFloat_FromDouble(0.09); if (unlikely(!__pyx_float_0_09)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_float__2 = PyFloat_FromDouble(.2); if (unlikely(!__pyx_float__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_float__002 = PyFloat_FromDouble(.002); if (unlikely(!__pyx_float__002)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_float_0_001 = PyFloat_FromDouble(0.001); if (unlikely(!__pyx_float_0_001)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
__pyx_L1_error:;
return -1;
@@ -5492,10 +5483,10 @@ PyMODINIT_FUNC PyInit_ml(void)
/*--- Variable export code ---*/
/*--- Function export code ---*/
/*--- Type init code ---*/
- if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct__ml) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct__ml) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_2ml___pyx_scope_struct__ml.tp_print = 0;
__pyx_ptype_2ml___pyx_scope_struct__ml = &__pyx_type_2ml___pyx_scope_struct__ml;
- if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_2ml___pyx_scope_struct_1_genexpr.tp_print = 0;
__pyx_ptype_2ml___pyx_scope_struct_1_genexpr = &__pyx_type_2ml___pyx_scope_struct_1_genexpr;
/*--- Type import code ---*/
@@ -5541,16 +5532,16 @@ PyMODINIT_FUNC PyInit_ml(void)
if (PyDict_SetItem(__pyx_d, __pyx_n_s_DTYPE, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "ml.pyx":38
+ /* "ml.pyx":35
* return result
*
* def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<<
* DTYPE_t alpha, DTYPE_t delta):
* cdef:
*/
- __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_2ml_1ml, NULL, __pyx_n_s_ml); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_2ml_1ml, NULL, __pyx_n_s_ml); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "ml.pyx":1
diff --git a/experiments/ml.so b/experiments/ml.so
index b548b9c..7832e67 100755
--- a/experiments/ml.so
+++ b/experiments/ml.so
Binary files differ
diff --git a/experiments/ml2.c b/experiments/ml2.c
index 9deccbc..572a8c5 100644
--- a/experiments/ml2.c
+++ b/experiments/ml2.c
@@ -695,7 +695,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
* DTYPE = np.float64
* ctypedef np.float_t DTYPE_t # <<<<<<<<<<<<<<
*
- * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta):
+ * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda,
*/
typedef __pyx_t_5numpy_float_t __pyx_t_3ml2_DTYPE_t;
#if CYTHON_CCOMPLEX
@@ -1182,8 +1182,8 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, cha
/* Module declarations from 'libc.math' */
/* Module declarations from 'ml2' */
-static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(int, int, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t); /*proto*/
-static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(int, int, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t); /*proto*/
+static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(int, int, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t); /*proto*/
+static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(int, int, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t, __pyx_t_3ml2_DTYPE_t); /*proto*/
static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_3ml2_DTYPE_t = { "DTYPE_t", NULL, sizeof(__pyx_t_3ml2_DTYPE_t), { 0 }, 0, 'R', 0, 0 };
#define __Pyx_MODULE_NAME "ml2"
int __pyx_module_is_main_ml2 = 0;
@@ -1194,7 +1194,7 @@ static PyObject *__pyx_builtin_sum;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_RuntimeError;
-static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_age, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta); /* proto */
+static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, __pyx_t_3ml2_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";
@@ -1222,16 +1222,15 @@ 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_ml2[] = "ml2";
static char __pyx_k_sum[] = "sum";
-static char __pyx_k_beta[] = "beta";
static char __pyx_k_dist[] = "dist";
static char __pyx_k_file[] = "file";
static char __pyx_k_main[] = "__main__";
+static char __pyx_k_mean[] = "mean";
static char __pyx_k_prob[] = "prob";
static char __pyx_k_test[] = "__test__";
static char __pyx_k_DTYPE[] = "DTYPE";
@@ -1239,6 +1238,7 @@ 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";
@@ -1277,9 +1277,7 @@ 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_beta;
static PyObject *__pyx_n_s_delta;
static PyObject *__pyx_n_s_dist;
static PyObject *__pyx_n_s_dists;
@@ -1297,7 +1295,9 @@ 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_mean;
static PyObject *__pyx_n_s_ml2;
static PyObject *__pyx_n_s_n_roots;
static PyObject *__pyx_n_s_n_victims;
@@ -1344,49 +1344,12 @@ static PyObject *__pyx_codeobj__10;
/* "ml2.pyx":9
* ctypedef np.float_t DTYPE_t
*
- * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): # <<<<<<<<<<<<<<
- * return 1./(1. + exp(-weight/delta))
- *
- */
-
-static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_plogis(__pyx_t_3ml2_DTYPE_t __pyx_v_weight, __pyx_t_3ml2_DTYPE_t __pyx_v_delta) {
- __pyx_t_3ml2_DTYPE_t __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("plogis", 0);
-
- /* "ml2.pyx":10
- *
- * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta):
- * return 1./(1. + exp(-weight/delta)) # <<<<<<<<<<<<<<
- *
- * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
- */
- __pyx_r = (1. / (1. + exp(((-__pyx_v_weight) / __pyx_v_delta))));
- goto __pyx_L0;
-
- /* "ml2.pyx":9
- * ctypedef np.float_t DTYPE_t
- *
- * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): # <<<<<<<<<<<<<<
- * return 1./(1. + exp(-weight/delta))
- *
- */
-
- /* function exit code */
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "ml2.pyx":12
- * return 1./(1. + exp(-weight/delta))
- *
- * 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, # <<<<<<<<<<<<<<
* DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
* """weight for successful infection, exponential time model"""
*/
-static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w3) {
+static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(CYTHON_UNUSED int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, __pyx_t_3ml2_DTYPE_t __pyx_v_lmbda, __pyx_t_3ml2_DTYPE_t __pyx_v_w1, __pyx_t_3ml2_DTYPE_t __pyx_v_w2, __pyx_t_3ml2_DTYPE_t __pyx_v_w3) {
__pyx_t_3ml2_DTYPE_t __pyx_v_structural;
__pyx_t_3ml2_DTYPE_t __pyx_v_temporal;
__pyx_t_3ml2_DTYPE_t __pyx_v_result;
@@ -1394,47 +1357,47 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(int __pyx_v_dist, int __
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("weight_success", 0);
- /* "ml2.pyx":16
- * """weight for successful infection, exponential time model"""
+ /* "ml2.pyx":14
* cdef DTYPE_t structural, temporal, result
- * structural = dist * log(delta) # <<<<<<<<<<<<<<
- * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
+ * # structural = delta ** dist
+ * structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) # <<<<<<<<<<<<<<
* temporal = log(exp(alpha)-1.) - alpha*dt
+ * # temporal = 1 - exp(-alpha*dt)
*/
- __pyx_v_structural = (__pyx_v_dist * log(__pyx_v_delta));
+ __pyx_v_structural = (__pyx_v_delta / (((1. + (1. / (__pyx_v_w1 * __pyx_v_lmbda))) + (1. / (__pyx_v_w2 * __pyx_v_lmbda))) + (1. / (__pyx_v_w3 * __pyx_v_lmbda))));
- /* "ml2.pyx":18
- * structural = dist * log(delta)
- * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
+ /* "ml2.pyx":15
+ * # structural = delta ** dist
+ * structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
* temporal = log(exp(alpha)-1.) - alpha*dt # <<<<<<<<<<<<<<
* # temporal = 1 - exp(-alpha*dt)
* # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
*/
__pyx_v_temporal = (log((exp(__pyx_v_alpha) - 1.)) - (__pyx_v_alpha * __pyx_v_dt));
- /* "ml2.pyx":22
+ /* "ml2.pyx":19
* # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
* # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
- * result = structural + temporal # <<<<<<<<<<<<<<
+ * result = log(structural) + temporal # <<<<<<<<<<<<<<
* # print 'st', structural, temporal
* return result
*/
- __pyx_v_result = (__pyx_v_structural + __pyx_v_temporal);
+ __pyx_v_result = (log(__pyx_v_structural) + __pyx_v_temporal);
- /* "ml2.pyx":24
- * result = structural + temporal
+ /* "ml2.pyx":21
+ * 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,
+ * 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;
- /* "ml2.pyx":12
- * return 1./(1. + exp(-weight/delta))
+ /* "ml2.pyx":9
+ * 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, # <<<<<<<<<<<<<<
* DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
* """weight for successful infection, exponential time model"""
*/
@@ -1445,15 +1408,15 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(int __pyx_v_dist, int __
return __pyx_r;
}
-/* "ml2.pyx":26
+/* "ml2.pyx":23
* 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, # <<<<<<<<<<<<<<
* DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
* """weight for failed infection, exponential time model"""
*/
-static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w3) {
+static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(CYTHON_UNUSED int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, __pyx_t_3ml2_DTYPE_t __pyx_v_lmbda, __pyx_t_3ml2_DTYPE_t __pyx_v_w1, __pyx_t_3ml2_DTYPE_t __pyx_v_w2, __pyx_t_3ml2_DTYPE_t __pyx_v_w3) {
__pyx_t_3ml2_DTYPE_t __pyx_v_structural;
__pyx_t_3ml2_DTYPE_t __pyx_v_temporal;
__pyx_t_3ml2_DTYPE_t __pyx_v_result;
@@ -1461,25 +1424,25 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(int __pyx_v_dist, int __
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("weight_failure", 0);
- /* "ml2.pyx":30
- * """weight for failed infection, exponential time model"""
+ /* "ml2.pyx":28
* cdef DTYPE_t structural, temporal, result
- * structural = delta ** dist # <<<<<<<<<<<<<<
- * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
+ * # structural = delta ** dist
+ * structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)) # <<<<<<<<<<<<<<
* temporal = exp(-alpha * dt)
+ * # temporal = 1. - 1. / (1. + dt/alpha)**0.01
*/
- __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_3ml2_DTYPE_t)__pyx_v_dist));
+ __pyx_v_structural = (__pyx_v_delta / (((1. + (1. / (__pyx_v_w1 * __pyx_v_lmbda))) + (1. / (__pyx_v_w2 * __pyx_v_lmbda))) + (1. / (__pyx_v_w3 * __pyx_v_lmbda))));
- /* "ml2.pyx":32
- * structural = delta ** dist
- * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
+ /* "ml2.pyx":29
+ * # structural = delta ** dist
+ * structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
* temporal = exp(-alpha * dt) # <<<<<<<<<<<<<<
* # temporal = 1. - 1. / (1. + dt/alpha)**0.01
* result = log(1. - structural + structural * temporal)
*/
__pyx_v_temporal = exp(((-__pyx_v_alpha) * __pyx_v_dt));
- /* "ml2.pyx":34
+ /* "ml2.pyx":31
* temporal = exp(-alpha * dt)
* # temporal = 1. - 1. / (1. + dt/alpha)**0.01
* result = log(1. - structural + structural * temporal) # <<<<<<<<<<<<<<
@@ -1488,20 +1451,20 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(int __pyx_v_dist, int __
*/
__pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal)));
- /* "ml2.pyx":36
+ /* "ml2.pyx":33
* result = log(1. - structural + structural * temporal)
* # print 'stnv', structural, temporal
* return result # <<<<<<<<<<<<<<
*
- * def ml2(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
+ * def ml2(dict root_victims, dict victims, dict non_victims,
*/
__pyx_r = __pyx_v_result;
goto __pyx_L0;
- /* "ml2.pyx":26
+ /* "ml2.pyx":23
* 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, # <<<<<<<<<<<<<<
* DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
* """weight for failed infection, exponential time model"""
*/
@@ -1512,11 +1475,11 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(int __pyx_v_dist, int __
return __pyx_r;
}
-/* "ml2.pyx":38
+/* "ml2.pyx":35
* return result
*
- * def ml2(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<<
- * DTYPE_t alpha, DTYPE_t delta):
+ * def ml2(dict root_victims, dict victims, dict non_victims, # <<<<<<<<<<<<<<
+ * DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda):
* cdef:
*/
@@ -1527,9 +1490,9 @@ static PyObject *__pyx_pw_3ml2_1ml2(PyObject *__pyx_self, PyObject *__pyx_args,
PyObject *__pyx_v_root_victims = 0;
PyObject *__pyx_v_victims = 0;
PyObject *__pyx_v_non_victims = 0;
- CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_age;
__pyx_t_3ml2_DTYPE_t __pyx_v_alpha;
__pyx_t_3ml2_DTYPE_t __pyx_v_delta;
+ __pyx_t_3ml2_DTYPE_t __pyx_v_lmbda;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
@@ -1537,7 +1500,7 @@ static PyObject *__pyx_pw_3ml2_1ml2(PyObject *__pyx_self, PyObject *__pyx_args,
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("ml2 (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;
@@ -1560,31 +1523,31 @@ static PyObject *__pyx_pw_3ml2_1ml2(PyObject *__pyx_self, PyObject *__pyx_args,
case 1:
if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_victims)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_non_victims)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_age)) != 0)) kw_args--;
+ if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_alpha)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
- if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_alpha)) != 0)) kw_args--;
+ if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_delta)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 5:
- if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_delta)) != 0)) kw_args--;
+ if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_lmbda)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml2") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml2") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 6) {
goto __pyx_L5_argtuple_error;
@@ -1599,22 +1562,22 @@ static PyObject *__pyx_pw_3ml2_1ml2(PyObject *__pyx_self, PyObject *__pyx_args,
__pyx_v_root_victims = ((PyObject*)values[0]);
__pyx_v_victims = ((PyObject*)values[1]);
__pyx_v_non_victims = ((PyObject*)values[2]);
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- __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_delta = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_delta = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("ml2.ml2", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
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+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_root_victims), (&PyDict_Type), 1, "root_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_victims), (&PyDict_Type), 1, "victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_non_victims), (&PyDict_Type), 1, "non_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_3ml2_ml2(__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;
@@ -1625,7 +1588,7 @@ static PyObject *__pyx_pw_3ml2_1ml2(PyObject *__pyx_self, PyObject *__pyx_args,
return __pyx_r;
}
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+static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, __pyx_t_3ml2_DTYPE_t __pyx_v_lmbda) {
int __pyx_v_n_roots;
int __pyx_v_n_victims;
int __pyx_v_roots;
@@ -1633,7 +1596,6 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject
int __pyx_v_dist;
int __pyx_v_dt;
int __pyx_v_l;
- __pyx_t_3ml2_DTYPE_t __pyx_v_beta;
__pyx_t_3ml2_DTYPE_t __pyx_v_ll;
PyObject *__pyx_v_parents = 0;
PyObject *__pyx_v_failures = 0;
@@ -1721,8 +1683,8 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject
__pyx_pybuffernd_parent_dts.data = NULL;
__pyx_pybuffernd_parent_dts.rcbuffer = &__pyx_pybuffer_parent_dts;
- /* "ml2.pyx":44
- * DTYPE_t beta, ll
+ /* "ml2.pyx":41
+ * DTYPE_t ll
* list parents, failures, successes
* n_roots, n_victims = len(root_victims), len(victims) # <<<<<<<<<<<<<<
* cdef:
@@ -1730,54 +1692,54 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject
*/
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PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(__pyx_v_victims == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_n_roots = __pyx_t_1;
__pyx_v_n_victims = __pyx_t_2;
- /* "ml2.pyx":46
+ /* "ml2.pyx":43
* n_roots, n_victims = len(root_victims), len(victims)
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+ __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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+ __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
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+ __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
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__pyx_v_probs = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf = NULL;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_probs = ((PyArrayObject *)__pyx_t_6);
__pyx_t_6 = 0;
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if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_parent_dts.rcbuffer->pybuffer, (PyObject*)__pyx_t_11, &__Pyx_TypeInfo_nn___pyx_t_3ml2_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 = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
} else {__pyx_pybuffernd_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];
}
}
@@ -1966,7 +1928,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject
__pyx_v_parent_dts = ((PyArrayObject *)__pyx_t_4);
__pyx_t_4 = 0;
- /* "ml2.pyx":53
+ /* "ml2.pyx":50
*
* # loop through victims
* for i, parents in enumerate(victims.itervalues()): # <<<<<<<<<<<<<<
@@ -1977,9 +1939,9 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject
__pyx_t_2 = 0;
if (unlikely(__pyx_v_victims == Py_None)) {
PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "itervalues");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_6 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_13)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_13)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_4);
__pyx_t_4 = __pyx_t_6;
@@ -1987,42 +1949,42 @@ static PyObject *__pyx_pf_3ml2_ml2(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;
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__Pyx_GOTREF(__pyx_t_6);
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+ if (!(likely(PyList_CheckExact(__pyx_t_6))||((__pyx_t_6) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_6)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__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);
- /* "ml2.pyx":57
+ /* "ml2.pyx":54
* # 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, w1, w2, w3) # <<<<<<<<<<<<<<
* for (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 = 57; __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 = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- /* "ml2.pyx":58
+ /* "ml2.pyx":55
* # likely parent infects it
- * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
+ * failures = [weight_failure(dist, dt, alpha, delta, lmbda, w1, w2, w3)
* for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<<
* probs_fail[i] = sum(failures)
- * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
+ * successes = [weight_success(dist, dt, alpha, delta, lmbda, 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 = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __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;
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- __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 = 58; __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 = 55; __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 = 58; __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 = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) {
PyObject* sequence = __pyx_t_3;
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if (size > 5) __Pyx_RaiseTooManyValuesError(5);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
@@ -2060,7 +2022,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject
Py_ssize_t i;
PyObject** temps[5] = {&__pyx_t_16,&__pyx_t_17,&__pyx_t_18,&__pyx_t_19,&__pyx_t_20};
for (i=0; i < 5; i++) {
- PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(item);
*(temps[i]) = item;
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@@ -2070,7 +2032,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject
} else {
Py_ssize_t index = -1;
PyObject** temps[5] = {&__pyx_t_16,&__pyx_t_17,&__pyx_t_18,&__pyx_t_19,&__pyx_t_20};
- __pyx_t_21 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_21 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_21);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_22 = Py_TYPE(__pyx_t_21)->tp_iternext;
@@ -2079,7 +2041,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject
__Pyx_GOTREF(item);
*(temps[index]) = item;
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- if (__Pyx_IternextUnpackEndCheck(__pyx_t_22(__pyx_t_21), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_22(__pyx_t_21), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_22 = NULL;
__Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
goto __pyx_L8_unpacking_done;
@@ -2087,12 +2049,12 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_L8_unpacking_done:;
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+ __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_16); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
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__Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_20);
__pyx_t_20 = 0;
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+ /* "ml2.pyx":54
* # fail to infect it, also computes the probability that its most
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- * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<<
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+ __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;}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(item);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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;}
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
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+ __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;}
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+ __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;}
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PyObject* sequence = __pyx_t_3;
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@@ -2343,7 +2305,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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__Pyx_XDECREF_SET(__pyx_v_dists, ((PyObject*)__pyx_t_5));
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* for (dist, dt, w1, w2, w3) in parents]
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+ if (!(likely(PyList_CheckExact(__pyx_t_5))||((__pyx_t_5) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_5)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_5);
- /* "ml2.pyx":79
+ /* "ml2.pyx":76
* # parents fail to infect it
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __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 = 79; __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 = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2718,7 +2680,7 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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for (i=0; i < 5; i++) {
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__Pyx_GOTREF(item);
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__Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
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__Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_20);
__pyx_t_20 = 0;
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* # for each non victim node, compute the probability that all its
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- * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<<
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{&__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_beta, __pyx_k_beta, sizeof(__pyx_k_beta), 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_n_s_dists, __pyx_k_dists, sizeof(__pyx_k_dists), 0, 0, 1, 1},
@@ -5094,7 +5125,9 @@ 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_mean, __pyx_k_mean, sizeof(__pyx_k_mean), 0, 0, 1, 1},
{&__pyx_n_s_ml2, __pyx_k_ml2, sizeof(__pyx_k_ml2), 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},
@@ -5128,8 +5161,8 @@ 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 = 53; __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 = 59; __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 = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_sum = __Pyx_GetBuiltinName(__pyx_n_s_sum); if (!__pyx_builtin_sum) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_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;}
@@ -5142,24 +5175,25 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
- /* "ml2.pyx":97
- * beta = 0
+ /* "ml2.pyx":86
+ * roots = n_roots
* # print n_nodes, n_roots, n_victims, max_i, roots
* print parent_dists[1:100] # <<<<<<<<<<<<<<
* print parent_dts[1:100]
- * return (beta, roots, ll)
+ * print np.mean(parent_dists)
*/
- __pyx_slice_ = PySlice_New(__pyx_int_1, __pyx_int_100, Py_None); if (unlikely(!__pyx_slice_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 97; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_slice_ = PySlice_New(__pyx_int_1, __pyx_int_100, Py_None); if (unlikely(!__pyx_slice_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_slice_);
__Pyx_GIVEREF(__pyx_slice_);
- /* "ml2.pyx":98
+ /* "ml2.pyx":87
* # print n_nodes, n_roots, n_victims, max_i, roots
* print parent_dists[1:100]
* print parent_dts[1:100] # <<<<<<<<<<<<<<
- * return (beta, roots, ll)
+ * print np.mean(parent_dists)
+ * print np.mean(parent_dts)
*/
- __pyx_slice__2 = PySlice_New(__pyx_int_1, __pyx_int_100, Py_None); if (unlikely(!__pyx_slice__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_slice__2 = PySlice_New(__pyx_int_1, __pyx_int_100, Py_None); if (unlikely(!__pyx_slice__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_slice__2);
__Pyx_GIVEREF(__pyx_slice__2);
@@ -5229,17 +5263,17 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GOTREF(__pyx_tuple__8);
__Pyx_GIVEREF(__pyx_tuple__8);
- /* "ml2.pyx":38
+ /* "ml2.pyx":35
* return result
*
- * def ml2(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<<
- * DTYPE_t alpha, DTYPE_t delta):
+ * def ml2(dict root_victims, dict victims, dict non_victims, # <<<<<<<<<<<<<<
+ * DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda):
* cdef:
*/
- __pyx_tuple__9 = PyTuple_Pack(31, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_age, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_roots, __pyx_n_s_i, __pyx_n_s_dist, __pyx_n_s_dt, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_beta, __pyx_n_s_ll, __pyx_n_s_parents, __pyx_n_s_failures, __pyx_n_s_successes, __pyx_n_s_probs, __pyx_n_s_probs_fail, __pyx_n_s_probs_nv, __pyx_n_s_parent_dists, __pyx_n_s_parent_dts, __pyx_n_s_dists, __pyx_n_s_dts, __pyx_n_s_s, __pyx_n_s_prob, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3); if (unlikely(!__pyx_tuple__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__9 = PyTuple_Pack(30, __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, __pyx_n_s_dt, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_ll, __pyx_n_s_parents, __pyx_n_s_failures, __pyx_n_s_successes, __pyx_n_s_probs, __pyx_n_s_probs_fail, __pyx_n_s_probs_nv, __pyx_n_s_parent_dists, __pyx_n_s_parent_dts, __pyx_n_s_dists, __pyx_n_s_dts, __pyx_n_s_s, __pyx_n_s_prob, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3); if (unlikely(!__pyx_tuple__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__9);
__Pyx_GIVEREF(__pyx_tuple__9);
- __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(6, 0, 31, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml2, 38, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(6, 0, 30, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml2, 35, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
@@ -5380,16 +5414,16 @@ PyMODINIT_FUNC PyInit_ml2(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;
- /* "ml2.pyx":38
+ /* "ml2.pyx":35
* return result
*
- * def ml2(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<<
- * DTYPE_t alpha, DTYPE_t delta):
+ * def ml2(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_3ml2_1ml2, NULL, __pyx_n_s_ml2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_3ml2_1ml2, NULL, __pyx_n_s_ml2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml2, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml2, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "ml2.pyx":1
diff --git a/experiments/ml2.pyx b/experiments/ml2.pyx
index fb2ec0d..99c9784 100644
--- a/experiments/ml2.pyx
+++ b/experiments/ml2.pyx
@@ -6,35 +6,32 @@ 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,
+cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda,
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
- structural = delta/(1. + exp(-w1*lmbda) + exp(-w2*lmbda) + exp(-w3*lmbda))
+ structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
temporal = log(exp(alpha)-1.) - alpha*dt
- # temporal = 1 - exp(-alpha*dt)
- # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
# temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
result = log(structural) + temporal
# print 'st', 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,
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
- structural = delta/(1. + exp(-w1/lmbda) + exp(-w2/lmbda) + exp(-w3/lmbda))
+ structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
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, DTYPE_t age,
- DTYPE_t alpha, DTYPE_t delta):
- print 'ML2'
+def ml2(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
DTYPE_t ll
@@ -52,10 +49,10 @@ def ml2(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, w1, w2, w3)
for (dist, dt, w1, w2, w3) in parents]
probs_fail[i] = sum(failures)
- successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
+ successes = [weight_success(dist, dt, alpha, delta, lmbda, w1, w2, w3)
for (dist, dt, w1, w2, w3) in parents]
dists = [dist for (dist, dt, w1, w2, w3) in parents]
dts = [dt for (dist, dt, w1, w2, w3) in parents]
@@ -73,7 +70,7 @@ def ml2(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
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, w1, w2, w3)
for (dist, dt, w1, w2, w3) in parents]
probs_nv[i] = sum(failures)
@@ -83,8 +80,9 @@ def ml2(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
ll += probs.sum() # add probability for realized edges and subtract probability these edges fail
roots = n_roots
- beta = float('nan')
# print n_nodes, n_roots, n_victims, max_i, roots
print parent_dists[1:100]
print parent_dts[1:100]
- return (beta, roots, ll)
+ print np.mean(parent_dists)
+ print np.mean(parent_dts)
+ return (lmbda, roots, ll)
diff --git a/experiments/ml2.so b/experiments/ml2.so
index 99d57db..b8c850b 100755
--- a/experiments/ml2.so
+++ b/experiments/ml2.so
Binary files differ
diff --git a/experiments/ml3.c b/experiments/ml3.c
index 1f271a8..08730d3 100644
--- a/experiments/ml3.c
+++ b/experiments/ml3.c
@@ -1228,6 +1228,7 @@ static char __pyx_k_numpy[] = "numpy";
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_import[] = "__import__";
@@ -1242,6 +1243,7 @@ static char __pyx_k_max_beta[] = "max_beta";
static char __pyx_k_enumerate[] = "enumerate";
static char __pyx_k_max_roots[] = "max_roots";
static char __pyx_k_n_victims[] = "n_victims";
+static char __pyx_k_non_seeds[] = "non_seeds";
static char __pyx_k_successes[] = "successes";
static char __pyx_k_ValueError[] = "ValueError";
static char __pyx_k_itervalues[] = "itervalues";
@@ -1295,6 +1297,7 @@ static PyObject *__pyx_n_s_n_roots;
static PyObject *__pyx_n_s_n_victims;
static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous;
static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou;
+static PyObject *__pyx_n_s_non_seeds;
static PyObject *__pyx_n_s_non_victims;
static PyObject *__pyx_n_s_np;
static PyObject *__pyx_n_s_numpy;
@@ -1308,6 +1311,7 @@ static PyObject *__pyx_n_s_range;
static PyObject *__pyx_n_s_root_victims;
static PyObject *__pyx_n_s_roots;
static PyObject *__pyx_n_s_s;
+static PyObject *__pyx_n_s_seeds;
static PyObject *__pyx_n_s_successes;
static PyObject *__pyx_n_s_sum;
static PyObject *__pyx_n_s_t;
@@ -1319,6 +1323,7 @@ static PyObject *__pyx_n_s_w1;
static PyObject *__pyx_n_s_w2;
static PyObject *__pyx_n_s_w3;
static PyObject *__pyx_n_s_zeros;
+static PyObject *__pyx_float__1;
static PyObject *__pyx_float_1_;
static PyObject *__pyx_float_0_2;
static PyObject *__pyx_tuple_;
@@ -1351,32 +1356,32 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __
* """weight for successful infection, exponential time model"""
* cdef DTYPE_t structural, temporal, result
* structural = delta ** dist # <<<<<<<<<<<<<<
- * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
* temporal = log(exp(alpha)-1.) - alpha*dt
+ * result = log(structural) + temporal
*/
__pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_3ml3_DTYPE_t)__pyx_v_dist));
- /* "ml3.pyx":15
+ /* "ml3.pyx":14
+ * cdef DTYPE_t structural, temporal, result
* structural = delta ** dist
- * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
* temporal = log(exp(alpha)-1.) - alpha*dt # <<<<<<<<<<<<<<
- * # temporal = 1 - exp(-alpha*dt)
- * # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
+ * result = log(structural) + temporal
+ * return result
*/
__pyx_v_temporal = (log((exp(__pyx_v_alpha) - 1.)) - (__pyx_v_alpha * __pyx_v_dt));
- /* "ml3.pyx":19
- * # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
- * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
+ /* "ml3.pyx":15
+ * structural = delta ** dist
+ * temporal = log(exp(alpha)-1.) - alpha*dt
* result = log(structural) + temporal # <<<<<<<<<<<<<<
- * # print 'st', structural, temporal
* return result
+ *
*/
__pyx_v_result = (log(__pyx_v_structural) + __pyx_v_temporal);
- /* "ml3.pyx":21
+ /* "ml3.pyx":16
+ * temporal = log(exp(alpha)-1.) - alpha*dt
* 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,
@@ -1398,7 +1403,7 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __
return __pyx_r;
}
-/* "ml3.pyx":23
+/* "ml3.pyx":18
* return result
*
* cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<<
@@ -1414,36 +1419,36 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("weight_failure", 0);
- /* "ml3.pyx":27
+ /* "ml3.pyx":22
* """weight for failed infection, exponential time model"""
* cdef DTYPE_t structural, temporal, result
* structural = delta ** dist # <<<<<<<<<<<<<<
- * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
* temporal = exp(-alpha * dt)
+ * result = log(1. - structural + structural * temporal)
*/
__pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_3ml3_DTYPE_t)__pyx_v_dist));
- /* "ml3.pyx":29
+ /* "ml3.pyx":23
+ * cdef DTYPE_t structural, temporal, result
* structural = delta ** dist
- * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
* temporal = exp(-alpha * dt) # <<<<<<<<<<<<<<
- * # temporal = 1. - 1. / (1. + dt/alpha)**0.01
- * result = log(1. - structural + structural*temporal)
+ * result = log(1. - structural + structural * temporal)
+ * return result
*/
__pyx_v_temporal = exp(((-__pyx_v_alpha) * __pyx_v_dt));
- /* "ml3.pyx":31
+ /* "ml3.pyx":24
+ * structural = delta ** dist
* temporal = exp(-alpha * dt)
- * # temporal = 1. - 1. / (1. + dt/alpha)**0.01
- * result = log(1. - structural + structural*temporal) # <<<<<<<<<<<<<<
- * # print 'stnv', structural, temporal
+ * result = log(1. - structural + structural * temporal) # <<<<<<<<<<<<<<
* return result
+ *
*/
__pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal)));
- /* "ml3.pyx":33
- * result = log(1. - structural + structural*temporal)
- * # print 'stnv', structural, temporal
+ /* "ml3.pyx":25
+ * temporal = exp(-alpha * dt)
+ * result = log(1. - structural + structural * temporal)
* return result # <<<<<<<<<<<<<<
*
* def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
@@ -1451,7 +1456,7 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __
__pyx_r = __pyx_v_result;
goto __pyx_L0;
- /* "ml3.pyx":23
+ /* "ml3.pyx":18
* return result
*
* cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<<
@@ -1465,7 +1470,7 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __
return __pyx_r;
}
-/* "ml3.pyx":35
+/* "ml3.pyx":27
* return result
*
* def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<<
@@ -1513,31 +1518,31 @@ static PyObject *__pyx_pw_3ml3_1ml3(PyObject *__pyx_self, PyObject *__pyx_args,
case 1:
if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_victims)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __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("ml3", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_age)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_alpha)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 5:
if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_delta)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml3") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml3") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 6) {
goto __pyx_L5_argtuple_error;
@@ -1552,21 +1557,21 @@ static PyObject *__pyx_pw_3ml3_1ml3(PyObject *__pyx_self, PyObject *__pyx_args,
__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 = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_delta = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __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;}
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("ml3.ml3", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
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- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_victims), (&PyDict_Type), 1, "victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_non_victims), (&PyDict_Type), 1, "non_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ 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_3ml3_ml3(__pyx_self, __pyx_v_root_victims, __pyx_v_victims, __pyx_v_non_victims, __pyx_v_age, __pyx_v_alpha, __pyx_v_delta);
/* function exit code */
@@ -1603,6 +1608,8 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
PyObject *__pyx_v_s = NULL;
PyObject *__pyx_v_prob = NULL;
double __pyx_v_thresh;
+ PyObject *__pyx_v_seeds = NULL;
+ PyObject *__pyx_v_non_seeds = NULL;
int __pyx_v_max_roots;
PyObject *__pyx_v_w1 = NULL;
PyObject *__pyx_v_w2 = NULL;
@@ -1671,7 +1678,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
__pyx_pybuffernd_parent_dts.data = NULL;
__pyx_pybuffernd_parent_dts.rcbuffer = &__pyx_pybuffer_parent_dts;
- /* "ml3.pyx":41
+ /* "ml3.pyx":33
* DTYPE_t beta, ll, beta_add, max_beta, max_beta_add
* list parents, failures, successes
* n_roots, n_victims = len(root_victims), len(victims) # <<<<<<<<<<<<<<
@@ -1680,54 +1687,54 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
*/
if (unlikely(__pyx_v_root_victims == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(__pyx_v_victims == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_n_roots = __pyx_t_1;
__pyx_v_n_victims = __pyx_t_2;
- /* "ml3.pyx":43
+ /* "ml3.pyx":35
* n_roots, n_victims = len(root_victims), len(victims)
* cdef:
* np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE) # <<<<<<<<<<<<<<
* np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE)
* np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE)
*/
- __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __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_3ml3_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {
__pyx_v_probs = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf = NULL;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -1735,43 +1742,43 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
__pyx_v_probs = ((PyArrayObject *)__pyx_t_6);
__pyx_t_6 = 0;
- /* "ml3.pyx":44
+ /* "ml3.pyx":36
* cdef:
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* np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE) # <<<<<<<<<<<<<<
* np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE)
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+ __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_6);
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__pyx_v_parent_dists = ((PyArrayObject *)__pyx_t_3);
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__Pyx_GOTREF(__pyx_t_3);
- /* "ml3.pyx":54
+ /* "ml3.pyx":46
* # likely parent infects it
* failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
* for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<<
@@ -1915,15 +1922,15 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
*/
if (unlikely(__pyx_v_parents == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_5 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_5); __pyx_t_14 = 0;
for (;;) {
if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_5)) break;
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- __pyx_t_4 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_4); __pyx_t_14++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_4); __pyx_t_14++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
- __pyx_t_4 = PySequence_ITEM(__pyx_t_5, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_5, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
PyObject* sequence = __pyx_t_4;
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if (unlikely(size != 5)) {
if (size > 5) __Pyx_RaiseTooManyValuesError(5);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
@@ -1961,7 +1968,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
Py_ssize_t i;
PyObject** temps[5] = {&__pyx_t_15,&__pyx_t_16,&__pyx_t_17,&__pyx_t_18,&__pyx_t_19};
for (i=0; i < 5; i++) {
- PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(item);
*(temps[i]) = item;
}
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} else {
Py_ssize_t index = -1;
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- __pyx_t_20 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_20 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_20);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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__Pyx_GOTREF(item);
*(temps[index]) = item;
}
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_21(__pyx_t_20), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_21(__pyx_t_20), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_21 = NULL;
__Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
goto __pyx_L8_unpacking_done;
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L8_unpacking_done:;
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+ __pyx_t_13 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
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+ __pyx_t_22 = __Pyx_PyInt_As_int(__pyx_t_16); if (unlikely((__pyx_t_22 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
__pyx_v_dist = __pyx_t_13;
__pyx_v_dt = __pyx_t_22;
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__Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_19);
__pyx_t_19 = 0;
- /* "ml3.pyx":53
+ /* "ml3.pyx":45
* # fail to infect it, also computes the probability that its most
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* failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<<
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*/
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+ __pyx_t_4 = PyFloat_FromDouble(__pyx_f_3ml3_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_23, __pyx_t_24, __pyx_t_25)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (unlikely(__Pyx_ListComp_Append(__pyx_t_3, (PyObject*)__pyx_t_4))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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+ /* "ml3.pyx":46
* # likely parent infects it
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@@ -2031,38 +2038,38 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
__Pyx_XDECREF_SET(__pyx_v_failures, ((PyObject*)__pyx_t_3));
__pyx_t_3 = 0;
- /* "ml3.pyx":55
+ /* "ml3.pyx":47
* failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
* for (dist, dt, w1, w2, w3) in parents]
* probs_fail[i] = sum(failures) # <<<<<<<<<<<<<<
* successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
* for (dist, dt, w1, w2, w3) in parents]
*/
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_failures);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_failures);
__Pyx_GIVEREF(__pyx_v_failures);
- __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_3, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_3, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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+ __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_t_5); 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_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_22 = __pyx_v_i;
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* for (dist, dt, w1, w2, w3) in parents]
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* successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<<
* for (dist, dt, w1, w2, w3) in parents]
* dists = [dist for (dist, dt, w1, w2, w3) in parents]
*/
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+ __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- /* "ml3.pyx":57
+ /* "ml3.pyx":49
* probs_fail[i] = sum(failures)
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_3 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_3); __pyx_t_14 = 0;
for (;;) {
if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_3)) break;
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+ __pyx_t_4 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_14); __Pyx_INCREF(__pyx_t_4); __pyx_t_14++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
- __pyx_t_4 = PySequence_ITEM(__pyx_t_3, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_3, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyObject* sequence = __pyx_t_4;
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (likely(PyTuple_CheckExact(sequence))) {
@@ -2117,7 +2124,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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for (i=0; i < 5; i++) {
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+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(item);
*(temps[i]) = item;
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+ __pyx_t_20 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_20);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_21 = Py_TYPE(__pyx_t_20)->tp_iternext;
@@ -2136,7 +2143,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_21(__pyx_t_20), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_L12_unpacking_done:;
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+ /* "ml3.pyx":70
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- * beta_add = 0.
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__Pyx_XDECREF(__pyx_v_s);
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__Pyx_XDECREF(__pyx_v_w3);
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{&__pyx_kp_u_ndarray_is_not_C_contiguous, __pyx_k_ndarray_is_not_C_contiguous, sizeof(__pyx_k_ndarray_is_not_C_contiguous), 0, 1, 0, 0},
{&__pyx_kp_u_ndarray_is_not_Fortran_contiguou, __pyx_k_ndarray_is_not_Fortran_contiguou, sizeof(__pyx_k_ndarray_is_not_Fortran_contiguou), 0, 1, 0, 0},
+ {&__pyx_n_s_non_seeds, __pyx_k_non_seeds, sizeof(__pyx_k_non_seeds), 0, 0, 1, 1},
{&__pyx_n_s_non_victims, __pyx_k_non_victims, sizeof(__pyx_k_non_victims), 0, 0, 1, 1},
{&__pyx_n_s_np, __pyx_k_np, sizeof(__pyx_k_np), 0, 0, 1, 1},
{&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1},
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{&__pyx_n_s_roots, __pyx_k_roots, sizeof(__pyx_k_roots), 0, 0, 1, 1},
{&__pyx_n_s_s, __pyx_k_s, sizeof(__pyx_k_s), 0, 0, 1, 1},
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{&__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},
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__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;}
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* max_beta_add = float('-inf')
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- * for beta in np.arange(0.2, 1., 1.): # <<<<<<<<<<<<<<
+ * for beta in np.arange(0.2, 1., .1): # <<<<<<<<<<<<<<
* thresh = log(beta/(3012.*(1.-beta)))
- * # print 'beta:', beta, 'thresh:', thresh, 'infected:', len(probs[probs>=thresh])
+ * seeds = probs<thresh
*/
- __pyx_tuple_ = PyTuple_Pack(3, __pyx_float_0_2, __pyx_float_1_, __pyx_float_1_); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple_ = PyTuple_Pack(3, __pyx_float_0_2, __pyx_float_1_, __pyx_float__1); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple_);
__Pyx_GIVEREF(__pyx_tuple_);
@@ -5060,17 +5120,17 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GOTREF(__pyx_tuple__7);
__Pyx_GIVEREF(__pyx_tuple__7);
- /* "ml3.pyx":35
+ /* "ml3.pyx":27
* return result
*
* def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<<
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* cdef:
*/
- __pyx_tuple__8 = PyTuple_Pack(35, __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_probs, __pyx_n_s_probs_fail, __pyx_n_s_parent_dists, __pyx_n_s_parent_dts, __pyx_n_s_dists, __pyx_n_s_dts, __pyx_n_s_s, __pyx_n_s_prob, __pyx_n_s_thresh, __pyx_n_s_max_roots, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(6, 0, 37, 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_ml3, 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_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
@@ -5080,6 +5140,7 @@ 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_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_0_2 = PyFloat_FromDouble(0.2); if (unlikely(!__pyx_float_0_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
@@ -5211,16 +5272,16 @@ PyMODINIT_FUNC PyInit_ml3(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;
- /* "ml3.pyx":35
+ /* "ml3.pyx":27
* return result
*
* def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<<
* DTYPE_t alpha, DTYPE_t delta):
* cdef:
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- __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_3ml3_1ml3, NULL, __pyx_n_s_ml3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_3ml3_1ml3, NULL, __pyx_n_s_ml3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
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+ if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml3, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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/* "ml3.pyx":1
diff --git a/experiments/ml3.pyx b/experiments/ml3.pyx
index 5cbe3ba..49b24cf 100644
--- a/experiments/ml3.pyx
+++ b/experiments/ml3.pyx
@@ -11,13 +11,8 @@ cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
"""weight for successful infection, exponential time model"""
cdef DTYPE_t structural, temporal, result
structural = delta ** dist
- # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
temporal = log(exp(alpha)-1.) - alpha*dt
- # temporal = 1 - exp(-alpha*dt)
- # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
- # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
result = log(structural) + temporal
- # print 'st', structural, temporal
return result
cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
@@ -25,11 +20,8 @@ cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
"""weight for failed infection, exponential time model"""
cdef DTYPE_t structural, temporal, result
structural = delta ** dist
- # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
temporal = exp(-alpha * dt)
- # temporal = 1. - 1. / (1. + dt/alpha)**0.01
- result = log(1. - structural + structural*temporal)
- # print 'stnv', structural, temporal
+ result = log(1. - structural + structural * temporal)
return result
def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
@@ -74,16 +66,17 @@ def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
# print 'probs', probs
max_beta_add = float('-inf')
# iterate over all victim nodes to find the optimal threshold
- for beta in np.arange(0.2, 1., 1.):
+ for beta in np.arange(0.2, 1., .1):
thresh = log(beta/(3012.*(1.-beta)))
- # print 'beta:', beta, 'thresh:', thresh, 'infected:', len(probs[probs>=thresh])
- roots = n_roots + len(probs[probs<thresh])
+ seeds = probs<thresh
+ non_seeds = probs>=thresh
+ roots = n_roots + sum(seeds)
beta_add = 0.
# add probability for realized edges and subtract probability these edges fail
- beta_add += (probs[probs>=thresh]).sum()
+ beta_add += (probs[non_seeds]).sum()
# add probability for the seeds and non-seeds
- beta_add += roots * log(beta/3012.) + len(probs[probs>=thresh]) * log(1. - beta)
+ beta_add += roots * log(beta/3012.) + sum(non_seeds) * log(1. - beta)
if beta_add > max_beta_add:
max_beta = beta
diff --git a/experiments/ml3.so b/experiments/ml3.so
index a1f5718..ff3bf05 100755
--- a/experiments/ml3.so
+++ b/experiments/ml3.so
Binary files differ
diff --git a/experiments/out.log b/experiments/out.log
index a9e77a5..eb2c025 100644
--- a/experiments/out.log
+++ b/experiments/out.log
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diff --git a/experiments/process.py b/experiments/process.py
index a9e0463..8201dea 100644
--- a/experiments/process.py
+++ b/experiments/process.py
@@ -14,9 +14,9 @@ if __name__ == "__main__":
root_victims, victims, non_victims, age = load(open(sys.argv[1]))
# alphas = np.arange(1e-3, 1e-2, 8e-4) # parameter of the time component
- alphas = np.logspace(-4,-.8,num=20)
+ alphas = np.logspace(-3,-.1,num=10)
# deltas = np.arange(0.001, 0.3, 0.008) # parameter of the structural component
- deltas = np.logspace(-2,-.0001,num=20)
+ deltas = np.logspace(-2,-.1,num=10)
with open("out.log", "w") as fh:
for alpha, delta in product(alphas, deltas):
beta, roots, ll = ml3(root_victims, victims, non_victims, age, alpha, delta)
@@ -24,7 +24,19 @@ if __name__ == "__main__":
fh.write("\t".join(map(str, [alpha, delta, beta, roots, ll])) + "\n")
fh.flush()
- # alpha = 0.0028
- # delta = 0.06
- # beta, roots, ll = ml2(root_victims, victims, non_victims, age, alpha, delta)
- # print "\t".join(map(str, [1./alpha, delta, beta, roots, ll])) \ No newline at end of file
+ # # alphas = np.arange(1e-3, 1e-2, 8e-4) # parameter of the time component
+ # alphas = np.logspace(-4,-1.5,num=20)
+ # # deltas = np.arange(0.001, 0.3, 0.008) # parameter of the structural component
+ # deltas = np.logspace(-4,-2,num=20)
+ # lmbda = 1.#np.logspace(-12,-3,num=10)
+ # with open("out.log", "w") as fh:
+ # for alpha, delta in product(alphas, deltas):
+ # lmbda, roots, ll = ml2(root_victims, victims, non_victims, alpha, delta, lmbda)
+ # print "\t".join(map(str, [alpha, delta, lmbda, roots, ll]))
+ # fh.write("\t".join(map(str, [alpha, delta, lmbda, roots, ll])) + "\n")
+ # fh.flush()
+
+ # alpha = 0.0094
+ # delta = 0.0048
+ # beta, roots, ll = ml2(root_victims, victims, non_victims, alpha, delta, 1.)
+ # print "\t".join(map(str, [alpha, delta, beta, roots, ll])) \ No newline at end of file
generated by cgit v1.2.3-70-g09d2 (git 2.52.0) at 2025-12-21 19:51:14 +0000