Generated by Cython 0.29.16
Yellow lines hint at Python interaction.
Click on a line that starts with a "+" to see the C code that Cython generated for it.
Raw output: analyse_sequence.c
+001: # distutils: extra_compile_args=-fopenmp
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002: # distutils: extra_link_args=-fopenmp
003: # cython: language_level=3, boundscheck=False
004:
+005: import numpy as np
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006: cimport cython
007: from cython.parallel import prange
008:
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010: """
011: Return a Matrix of correleation with q-1 state (the last correlation because of gauge chosen is eij(q,)= 0)
012: """
013: cdef :
+014: int site_i,site_j,index_spin_1,index_spin_2,n_states_gauge = int(n_states-1)
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015: ##PMI[site_i,site_j,spin_i,spin_j]
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017: double[::1,:,:,:] Fij
018: double[::1] weight
019: ##Cython
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031: cdef:
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__Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_np); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 32, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 32, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_1 = PyInt_FromSsize_t((__pyx_v_msa.shape[1])); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 32, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_states); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 32, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyInt_FromSsize_t((__pyx_v_msa.shape[1])); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 32, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_n_states); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 32, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __pyx_t_6 = PyTuple_New(4); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 32, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_6, 3, __pyx_t_5); __pyx_t_1 = 0; __pyx_t_3 = 0; __pyx_t_4 = 0; __pyx_t_5 = 0; __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 32, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_6); __pyx_t_6 = 0; __pyx_t_6 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 32, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_order, __pyx_n_u_F) < 0) __PYX_ERR(0, 32, __pyx_L1_error) __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 32, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_7 = __Pyx_PyObject_to_MemoryviewSlice_dcd_d_d__double(__pyx_t_4, PyBUF_WRITABLE); if (unlikely(!__pyx_t_7.memview)) __PYX_ERR(0, 32, __pyx_L1_error) __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_v_Fij = __pyx_t_7; __pyx_t_7.memview = NULL; __pyx_t_7.data = NULL;
033: int site_i,site_j,index_try,index_spin_1,index_spin_2
034: double z
035: double[::1] weight
+036: weight = weight_msa(msa, theta)
__pyx_t_8 = __pyx_f_11cython_code_16analyse_sequence_weight_msa(__pyx_v_msa, __pyx_v_theta, 0); if (unlikely(!__pyx_t_8.memview)) __PYX_ERR(0, 36, __pyx_L1_error)
__pyx_v_weight = __pyx_t_8;
__pyx_t_8.memview = NULL;
__pyx_t_8.data = NULL;
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__Pyx_GetModuleGlobalName(__pyx_t_6, __pyx_n_s_np); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 37, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_sum); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 37, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_6 = __pyx_memoryview_fromslice(__pyx_v_weight, 1, (PyObject *(*)(char *)) __pyx_memview_get_double, (int (*)(char *, PyObject *)) __pyx_memview_set_double, 0);; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 37, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __pyx_t_2 = NULL; if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_5))) { __pyx_t_2 = PyMethod_GET_SELF(__pyx_t_5); if (likely(__pyx_t_2)) { PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5); __Pyx_INCREF(__pyx_t_2); __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_5, function); } } __pyx_t_4 = (__pyx_t_2) ? __Pyx_PyObject_Call2Args(__pyx_t_5, __pyx_t_2, __pyx_t_6) : __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_6); __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 37, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_9 = __pyx_PyFloat_AsDouble(__pyx_t_4); if (unlikely((__pyx_t_9 == (double)-1) && PyErr_Occurred())) __PYX_ERR(0, 37, __pyx_L1_error) __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_v_z = __pyx_t_9;
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{
#ifdef WITH_THREAD
PyThreadState *_save;
Py_UNBLOCK_THREADS
__Pyx_FastGIL_Remember();
#endif
/*try:*/ {
/* … */
/*finally:*/ {
/*normal exit:*/{
#ifdef WITH_THREAD
__Pyx_FastGIL_Forget();
Py_BLOCK_THREADS
#endif
goto __pyx_L5;
}
__pyx_L4_error: {
#ifdef WITH_THREAD
__Pyx_FastGIL_Forget();
Py_BLOCK_THREADS
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goto __pyx_L1_error;
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__pyx_L5:;
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}
+039: for site_i in prange(msa.shape[1]):
if (unlikely(!__pyx_v_msa.memview)) { __Pyx_RaiseUnboundMemoryviewSliceNogil("msa"); __PYX_ERR(0, 39, __pyx_L4_error) }
__pyx_t_10 = (__pyx_v_msa.shape[1]);
if ((1 == 0)) abort();
{
#if ((defined(__APPLE__) || defined(__OSX__)) && (defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))))
#undef likely
#undef unlikely
#define likely(x) (x)
#define unlikely(x) (x)
#endif
__pyx_t_12 = (__pyx_t_10 - 0 + 1 - 1/abs(1)) / 1;
if (__pyx_t_12 > 0)
{
#ifdef _OPENMP
#pragma omp parallel
#endif /* _OPENMP */
{
#ifdef _OPENMP
#pragma omp for lastprivate(__pyx_v_index_spin_1) lastprivate(__pyx_v_index_spin_2) lastprivate(__pyx_v_index_try) firstprivate(__pyx_v_site_i) lastprivate(__pyx_v_site_i) lastprivate(__pyx_v_site_j)
#endif /* _OPENMP */
for (__pyx_t_11 = 0; __pyx_t_11 < __pyx_t_12; __pyx_t_11++){
{
__pyx_v_site_i = (int)(0 + 1 * __pyx_t_11);
/* Initialize private variables to invalid values */
__pyx_v_index_spin_1 = ((int)0xbad0bad0);
__pyx_v_index_spin_2 = ((int)0xbad0bad0);
__pyx_v_index_try = ((int)0xbad0bad0);
__pyx_v_site_j = ((int)0xbad0bad0);
+040: for site_j in range(msa.shape[1]):
__pyx_t_13 = (__pyx_v_msa.shape[1]);
__pyx_t_14 = __pyx_t_13;
for (__pyx_t_15 = 0; __pyx_t_15 < __pyx_t_14; __pyx_t_15+=1) {
__pyx_v_site_j = __pyx_t_15;
+041: for index_try in range(msa.shape[0]):
__pyx_t_16 = (__pyx_v_msa.shape[0]);
__pyx_t_17 = __pyx_t_16;
for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18+=1) {
__pyx_v_index_try = __pyx_t_18;
+042: Fij[site_i, msa[index_try,site_i], site_j, msa[index_try,site_j]] += weight[index_try]/z
__pyx_t_19 = __pyx_v_index_try;
if (__pyx_t_19 < 0) __pyx_t_19 += __pyx_v_weight.shape[0];
__pyx_t_9 = (*((double *) ( /* dim=0 */ ((char *) (((double *) __pyx_v_weight.data) + __pyx_t_19)) )));
if (unlikely(__pyx_v_z == 0)) {
#ifdef WITH_THREAD
PyGILState_STATE __pyx_gilstate_save = __Pyx_PyGILState_Ensure();
#endif
PyErr_SetString(PyExc_ZeroDivisionError, "float division");
#ifdef WITH_THREAD
__Pyx_PyGILState_Release(__pyx_gilstate_save);
#endif
__PYX_ERR(0, 42, __pyx_L8_error)
}
__pyx_t_20 = __pyx_v_index_try;
__pyx_t_21 = __pyx_v_site_i;
if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_v_msa.shape[0];
if (__pyx_t_21 < 0) __pyx_t_21 += __pyx_v_msa.shape[1];
__pyx_t_22 = __pyx_v_index_try;
__pyx_t_23 = __pyx_v_site_j;
if (__pyx_t_22 < 0) __pyx_t_22 += __pyx_v_msa.shape[0];
if (__pyx_t_23 < 0) __pyx_t_23 += __pyx_v_msa.shape[1];
__pyx_t_24 = __pyx_v_site_i;
__pyx_t_25 = (*((char *) ( /* dim=1 */ ((char *) (((char *) ( /* dim=0 */ (__pyx_v_msa.data + __pyx_t_20 * __pyx_v_msa.strides[0]) )) + __pyx_t_21)) )));
__pyx_t_26 = __pyx_v_site_j;
__pyx_t_27 = (*((char *) ( /* dim=1 */ ((char *) (((char *) ( /* dim=0 */ (__pyx_v_msa.data + __pyx_t_22 * __pyx_v_msa.strides[0]) )) + __pyx_t_23)) )));
if (__pyx_t_24 < 0) __pyx_t_24 += __pyx_v_Fij.shape[0];
if (__pyx_t_25 < 0) __pyx_t_25 += __pyx_v_Fij.shape[1];
if (__pyx_t_26 < 0) __pyx_t_26 += __pyx_v_Fij.shape[2];
if (__pyx_t_27 < 0) __pyx_t_27 += __pyx_v_Fij.shape[3];
*((double *) ( /* dim=3 */ (( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ ((char *) (((double *) __pyx_v_Fij.data) + __pyx_t_24)) ) + __pyx_t_25 * __pyx_v_Fij.strides[1]) ) + __pyx_t_26 * __pyx_v_Fij.strides[2]) ) + __pyx_t_27 * __pyx_v_Fij.strides[3]) )) += (__pyx_t_9 / __pyx_v_z);
}
+043: for index_spin_1 in range(n_states):
__pyx_t_18 = __pyx_v_n_states;
__pyx_t_28 = __pyx_t_18;
for (__pyx_t_29 = 0; __pyx_t_29 < __pyx_t_28; __pyx_t_29+=1) {
__pyx_v_index_spin_1 = __pyx_t_29;
+044: for index_spin_2 in range(n_states):
__pyx_t_30 = __pyx_v_n_states;
__pyx_t_31 = __pyx_t_30;
for (__pyx_t_32 = 0; __pyx_t_32 < __pyx_t_31; __pyx_t_32+=1) {
__pyx_v_index_spin_2 = __pyx_t_32;
+045: if site_i != site_j:
__pyx_t_33 = ((__pyx_v_site_i != __pyx_v_site_j) != 0);
if (__pyx_t_33) {
/* … */
goto __pyx_L18;
}
+046: Fij[site_i,index_spin_1,site_j,index_spin_2] = pseudocount/(n_states**2) + (1-pseudocount)*Fij[site_i,index_spin_1,site_j,index_spin_2]
__pyx_t_34 = __Pyx_pow_long(((long)__pyx_v_n_states), 2);
if (unlikely(__pyx_t_34 == 0)) {
#ifdef WITH_THREAD
PyGILState_STATE __pyx_gilstate_save = __Pyx_PyGILState_Ensure();
#endif
PyErr_SetString(PyExc_ZeroDivisionError, "float division");
#ifdef WITH_THREAD
__Pyx_PyGILState_Release(__pyx_gilstate_save);
#endif
__PYX_ERR(0, 46, __pyx_L8_error)
}
__pyx_t_35 = __pyx_v_site_i;
__pyx_t_36 = __pyx_v_index_spin_1;
__pyx_t_37 = __pyx_v_site_j;
__pyx_t_38 = __pyx_v_index_spin_2;
if (__pyx_t_35 < 0) __pyx_t_35 += __pyx_v_Fij.shape[0];
if (__pyx_t_36 < 0) __pyx_t_36 += __pyx_v_Fij.shape[1];
if (__pyx_t_37 < 0) __pyx_t_37 += __pyx_v_Fij.shape[2];
if (__pyx_t_38 < 0) __pyx_t_38 += __pyx_v_Fij.shape[3];
__pyx_t_39 = __pyx_v_site_i;
__pyx_t_40 = __pyx_v_index_spin_1;
__pyx_t_41 = __pyx_v_site_j;
__pyx_t_42 = __pyx_v_index_spin_2;
if (__pyx_t_39 < 0) __pyx_t_39 += __pyx_v_Fij.shape[0];
if (__pyx_t_40 < 0) __pyx_t_40 += __pyx_v_Fij.shape[1];
if (__pyx_t_41 < 0) __pyx_t_41 += __pyx_v_Fij.shape[2];
if (__pyx_t_42 < 0) __pyx_t_42 += __pyx_v_Fij.shape[3];
*((double *) ( /* dim=3 */ (( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ ((char *) (((double *) __pyx_v_Fij.data) + __pyx_t_39)) ) + __pyx_t_40 * __pyx_v_Fij.strides[1]) ) + __pyx_t_41 * __pyx_v_Fij.strides[2]) ) + __pyx_t_42 * __pyx_v_Fij.strides[3]) )) = ((__pyx_v_pseudocount / ((double)__pyx_t_34)) + ((1.0 - __pyx_v_pseudocount) * (*((double *) ( /* dim=3 */ (( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ ((char *) (((double *) __pyx_v_Fij.data) + __pyx_t_35)) ) + __pyx_t_36 * __pyx_v_Fij.strides[1]) ) + __pyx_t_37 * __pyx_v_Fij.strides[2]) ) + __pyx_t_38 * __pyx_v_Fij.strides[3]) )))));
047: else:
+048: Fij[site_i,index_spin_1,site_j,index_spin_2] = (index_spin_1 == index_spin_2)*1*(pseudocount/n_states) + (1-pseudocount)*Fij[site_i,index_spin_1,site_j,index_spin_2]
/*else*/ {
if (unlikely(__pyx_v_n_states == 0)) {
#ifdef WITH_THREAD
PyGILState_STATE __pyx_gilstate_save = __Pyx_PyGILState_Ensure();
#endif
PyErr_SetString(PyExc_ZeroDivisionError, "float division");
#ifdef WITH_THREAD
__Pyx_PyGILState_Release(__pyx_gilstate_save);
#endif
__PYX_ERR(0, 48, __pyx_L8_error)
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__pyx_t_43 = __pyx_v_site_i;
__pyx_t_44 = __pyx_v_index_spin_1;
__pyx_t_45 = __pyx_v_site_j;
__pyx_t_46 = __pyx_v_index_spin_2;
if (__pyx_t_43 < 0) __pyx_t_43 += __pyx_v_Fij.shape[0];
if (__pyx_t_44 < 0) __pyx_t_44 += __pyx_v_Fij.shape[1];
if (__pyx_t_45 < 0) __pyx_t_45 += __pyx_v_Fij.shape[2];
if (__pyx_t_46 < 0) __pyx_t_46 += __pyx_v_Fij.shape[3];
__pyx_t_47 = __pyx_v_site_i;
__pyx_t_48 = __pyx_v_index_spin_1;
__pyx_t_49 = __pyx_v_site_j;
__pyx_t_50 = __pyx_v_index_spin_2;
if (__pyx_t_47 < 0) __pyx_t_47 += __pyx_v_Fij.shape[0];
if (__pyx_t_48 < 0) __pyx_t_48 += __pyx_v_Fij.shape[1];
if (__pyx_t_49 < 0) __pyx_t_49 += __pyx_v_Fij.shape[2];
if (__pyx_t_50 < 0) __pyx_t_50 += __pyx_v_Fij.shape[3];
*((double *) ( /* dim=3 */ (( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ ((char *) (((double *) __pyx_v_Fij.data) + __pyx_t_47)) ) + __pyx_t_48 * __pyx_v_Fij.strides[1]) ) + __pyx_t_49 * __pyx_v_Fij.strides[2]) ) + __pyx_t_50 * __pyx_v_Fij.strides[3]) )) = ((((__pyx_v_index_spin_1 == __pyx_v_index_spin_2) * 1) * (__pyx_v_pseudocount / ((double)__pyx_v_n_states))) + ((1.0 - __pyx_v_pseudocount) * (*((double *) ( /* dim=3 */ (( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ ((char *) (((double *) __pyx_v_Fij.data) + __pyx_t_43)) ) + __pyx_t_44 * __pyx_v_Fij.strides[1]) ) + __pyx_t_45 * __pyx_v_Fij.strides[2]) ) + __pyx_t_46 * __pyx_v_Fij.strides[3]) )))));
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__pyx_L18:;
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}
}
goto __pyx_L20;
__pyx_L8_error:;
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__pyx_parallel_filename = __pyx_filename; __pyx_parallel_lineno = __pyx_lineno; __pyx_parallel_clineno = __pyx_clineno;
__Pyx_GOTREF(__pyx_parallel_exc_type);
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__Pyx_PyGILState_Release(__pyx_gilstate_save);
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__pyx_parallel_why = 4;
goto __pyx_L19;
__pyx_L19:;
#ifdef _OPENMP
#pragma omp critical(__pyx_parallel_lastprivates0)
#endif /* _OPENMP */
{
__pyx_parallel_temp0 = __pyx_v_index_spin_1;
__pyx_parallel_temp1 = __pyx_v_index_spin_2;
__pyx_parallel_temp2 = __pyx_v_index_try;
__pyx_parallel_temp3 = __pyx_v_site_i;
__pyx_parallel_temp4 = __pyx_v_site_j;
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__pyx_L20:;
#ifdef _OPENMP
#pragma omp flush(__pyx_parallel_why)
#endif /* _OPENMP */
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#ifdef _OPENMP
Py_END_ALLOW_THREADS
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{
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PyGILState_STATE __pyx_gilstate_save = __Pyx_PyGILState_Ensure();
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/* Clean up any temporaries */
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__Pyx_PyGILState_Release(__pyx_gilstate_save);
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#ifndef _OPENMP
}
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if (__pyx_parallel_exc_type) {
/* This may have been overridden by a continue, break or return in another thread. Prefer the error. */
__pyx_parallel_why = 4;
}
if (__pyx_parallel_why) {
__pyx_v_index_spin_1 = __pyx_parallel_temp0;
__pyx_v_index_spin_2 = __pyx_parallel_temp1;
__pyx_v_index_try = __pyx_parallel_temp2;
__pyx_v_site_i = __pyx_parallel_temp3;
__pyx_v_site_j = __pyx_parallel_temp4;
switch (__pyx_parallel_why) {
case 4:
{
#ifdef WITH_THREAD
PyGILState_STATE __pyx_gilstate_save = __Pyx_PyGILState_Ensure();
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__Pyx_GIVEREF(__pyx_parallel_exc_type);
__Pyx_ErrRestoreWithState(__pyx_parallel_exc_type, __pyx_parallel_exc_value, __pyx_parallel_exc_tb);
__pyx_filename = __pyx_parallel_filename; __pyx_lineno = __pyx_parallel_lineno; __pyx_clineno = __pyx_parallel_clineno;
#ifdef WITH_THREAD
__Pyx_PyGILState_Release(__pyx_gilstate_save);
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}
goto __pyx_L4_error;
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}
#if ((defined(__APPLE__) || defined(__OSX__)) && (defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))))
#undef likely
#undef unlikely
#define likely(x) __builtin_expect(!!(x), 1)
#define unlikely(x) __builtin_expect(!!(x), 0)
#endif
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__pyx_v_i = __pyx_t_3;
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074:
+075: def Energy_Partner(char[:,::1] MSA_Testing, double[:,:,:,::1] Jij, int middle_index):
/* Python wrapper */
static PyObject *__pyx_pw_11cython_code_16analyse_sequence_7Energy_Partner(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static char __pyx_doc_11cython_code_16analyse_sequence_6Energy_Partner[] = "\n Input :\n MSA_Testing\n Jij = Coupling inferred on MSA_training\n Output \n Eij = Energy protein in MSA_L1 with protein in MSA_L2\n ";
static PyMethodDef __pyx_mdef_11cython_code_16analyse_sequence_7Energy_Partner = {"Energy_Partner", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_11cython_code_16analyse_sequence_7Energy_Partner, METH_VARARGS|METH_KEYWORDS, __pyx_doc_11cython_code_16analyse_sequence_6Energy_Partner};
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Py_ssize_t kw_args;
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CYTHON_FALLTHROUGH;
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int __pyx_v_protein1;
int __pyx_v_protein2;
int __pyx_v_index_site_i;
int __pyx_v_index_site_j;
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/* … */
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076: """
077: Input :
078: MSA_Testing
079: Jij = Coupling inferred on MSA_training
080: Output
081: Eij = Energy protein in MSA_L1 with protein in MSA_L2
082: """
083: cdef:
084: int protein1, protein2, index_site_i,index_site_j
+085: double[:,::1] Eij = np.zeros((MSA_Testing.shape[0],MSA_Testing.shape[0]))
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+086: with nogil:
{
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PyThreadState *_save;
Py_UNBLOCK_THREADS
__Pyx_FastGIL_Remember();
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/*try:*/ {
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+087: for protein1 in prange(MSA_Testing.shape[0]):
if (unlikely(!__pyx_v_MSA_Testing.memview)) { __Pyx_RaiseUnboundMemoryviewSliceNogil("MSA_Testing"); __PYX_ERR(0, 87, __pyx_L4_error) }
__pyx_t_7 = (__pyx_v_MSA_Testing.shape[0]);
if ((1 == 0)) abort();
{
#if ((defined(__APPLE__) || defined(__OSX__)) && (defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))))
#undef likely
#undef unlikely
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#define unlikely(x) (x)
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__pyx_t_9 = (__pyx_t_7 - 0 + 1 - 1/abs(1)) / 1;
if (__pyx_t_9 > 0)
{
#ifdef _OPENMP
#pragma omp parallel
#endif /* _OPENMP */
{
#ifdef _OPENMP
#pragma omp for lastprivate(__pyx_v_index_site_i) lastprivate(__pyx_v_index_site_j) firstprivate(__pyx_v_protein1) lastprivate(__pyx_v_protein1) lastprivate(__pyx_v_protein2)
#endif /* _OPENMP */
for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_9; __pyx_t_8++){
{
__pyx_v_protein1 = (int)(0 + 1 * __pyx_t_8);
/* Initialize private variables to invalid values */
__pyx_v_index_site_i = ((int)0xbad0bad0);
__pyx_v_index_site_j = ((int)0xbad0bad0);
__pyx_v_protein2 = ((int)0xbad0bad0);
+088: for protein2 in range(MSA_Testing.shape[0]):
__pyx_t_10 = (__pyx_v_MSA_Testing.shape[0]);
__pyx_t_11 = __pyx_t_10;
for (__pyx_t_12 = 0; __pyx_t_12 < __pyx_t_11; __pyx_t_12+=1) {
__pyx_v_protein2 = __pyx_t_12;
+089: for index_site_i in range(middle_index):
__pyx_t_13 = __pyx_v_middle_index;
__pyx_t_14 = __pyx_t_13;
for (__pyx_t_15 = 0; __pyx_t_15 < __pyx_t_14; __pyx_t_15+=1) {
__pyx_v_index_site_i = __pyx_t_15;
+090: for index_site_j in range(middle_index,MSA_Testing.shape[1]):
__pyx_t_16 = (__pyx_v_MSA_Testing.shape[1]);
__pyx_t_17 = __pyx_t_16;
for (__pyx_t_18 = __pyx_v_middle_index; __pyx_t_18 < __pyx_t_17; __pyx_t_18+=1) {
__pyx_v_index_site_j = __pyx_t_18;
+091: Eij[protein1,protein2] -= Jij[index_site_i,MSA_Testing[protein1,index_site_i],index_site_j,MSA_Testing[protein2,index_site_j]]
__pyx_t_19 = __pyx_v_protein1;
__pyx_t_20 = __pyx_v_index_site_i;
if (__pyx_t_19 < 0) __pyx_t_19 += __pyx_v_MSA_Testing.shape[0];
if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_v_MSA_Testing.shape[1];
__pyx_t_21 = __pyx_v_protein2;
__pyx_t_22 = __pyx_v_index_site_j;
if (__pyx_t_21 < 0) __pyx_t_21 += __pyx_v_MSA_Testing.shape[0];
if (__pyx_t_22 < 0) __pyx_t_22 += __pyx_v_MSA_Testing.shape[1];
__pyx_t_23 = __pyx_v_index_site_i;
__pyx_t_24 = (*((char *) ( /* dim=1 */ ((char *) (((char *) ( /* dim=0 */ (__pyx_v_MSA_Testing.data + __pyx_t_19 * __pyx_v_MSA_Testing.strides[0]) )) + __pyx_t_20)) )));
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if (__pyx_t_23 < 0) __pyx_t_23 += __pyx_v_Jij.shape[0];
if (__pyx_t_24 < 0) __pyx_t_24 += __pyx_v_Jij.shape[1];
if (__pyx_t_25 < 0) __pyx_t_25 += __pyx_v_Jij.shape[2];
if (__pyx_t_26 < 0) __pyx_t_26 += __pyx_v_Jij.shape[3];
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__pyx_t_28 = __pyx_v_protein2;
if (__pyx_t_27 < 0) __pyx_t_27 += __pyx_v_Eij.shape[0];
if (__pyx_t_28 < 0) __pyx_t_28 += __pyx_v_Eij.shape[1];
*((double *) ( /* dim=1 */ ((char *) (((double *) ( /* dim=0 */ (__pyx_v_Eij.data + __pyx_t_27 * __pyx_v_Eij.strides[0]) )) + __pyx_t_28)) )) -= (*((double *) ( /* dim=3 */ ((char *) (((double *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_Jij.data + __pyx_t_23 * __pyx_v_Jij.strides[0]) ) + __pyx_t_24 * __pyx_v_Jij.strides[1]) ) + __pyx_t_25 * __pyx_v_Jij.strides[2]) )) + __pyx_t_26)) )));
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#if ((defined(__APPLE__) || defined(__OSX__)) && (defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))))
#undef likely
#undef unlikely
#define likely(x) __builtin_expect(!!(x), 1)
#define unlikely(x) __builtin_expect(!!(x), 0)
#endif
}
+092: return np.asarray(Eij)
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093:
+094: def Ising_gauge_Jij(double[::1,:,:,:] Jij):
/* Python wrapper */
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static char __pyx_doc_11cython_code_16analyse_sequence_8Ising_gauge_Jij[] = "\n In : Jij L*(q-1) gauge Jij[:,q] = 0\n Out : Jij L*q gauge Ising\n ";
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static PyObject *__pyx_pf_11cython_code_16analyse_sequence_8Ising_gauge_Jij(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_Jij) {
int __pyx_v_index_i;
int __pyx_v_index_j;
int __pyx_v_state_1;
int __pyx_v_state_2;
int __pyx_v_n_states_gauge;
double __pyx_v_mean_second_site;
double __pyx_v_mean_first_site;
double __pyx_v_mean_two_sites;
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/* … */
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095: """
096: In : Jij L*(q-1) gauge Jij[:,q] = 0
097: Out : Jij L*q gauge Ising
098: """
099: cdef:
+100: int index_i, index_j, state_1, state_2, n_states_gauge = Jij.shape[1]
__pyx_v_n_states_gauge = (__pyx_v_Jij.shape[1]);
101: double mean_second_site, mean_first_site, mean_two_sites
+102: double[:,:,:,::1] Jij_out = np.zeros((Jij.shape[0],Jij.shape[1]+1,Jij.shape[2],Jij.shape[3]+1))
__Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_np); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 102, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_zeros); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 102, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = PyInt_FromSsize_t((__pyx_v_Jij.shape[0])); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 102, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __pyx_t_4 = PyInt_FromSsize_t(((__pyx_v_Jij.shape[1]) + 1)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 102, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __pyx_t_5 = PyInt_FromSsize_t((__pyx_v_Jij.shape[2])); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 102, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __pyx_t_6 = PyInt_FromSsize_t(((__pyx_v_Jij.shape[3]) + 1)); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 102, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __pyx_t_7 = PyTuple_New(4); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 102, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_t_6); __pyx_t_2 = 0; __pyx_t_4 = 0; __pyx_t_5 = 0; __pyx_t_6 = 0; __pyx_t_6 = NULL; if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_3))) { __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_3); if (likely(__pyx_t_6)) { PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); __Pyx_INCREF(__pyx_t_6); __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_3, function); } } __pyx_t_1 = (__pyx_t_6) ? __Pyx_PyObject_Call2Args(__pyx_t_3, __pyx_t_6, __pyx_t_7) : __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_t_7); __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 102, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_8 = __Pyx_PyObject_to_MemoryviewSlice_d_d_d_dc_double(__pyx_t_1, PyBUF_WRITABLE); if (unlikely(!__pyx_t_8.memview)) __PYX_ERR(0, 102, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_v_Jij_out = __pyx_t_8; __pyx_t_8.memview = NULL; __pyx_t_8.data = NULL;
+103: with nogil:
{
#ifdef WITH_THREAD
PyThreadState *_save;
Py_UNBLOCK_THREADS
__Pyx_FastGIL_Remember();
#endif
/*try:*/ {
/* … */
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Py_BLOCK_THREADS
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goto __pyx_L5;
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if (unlikely(!__pyx_v_Jij.memview)) { __Pyx_RaiseUnboundMemoryviewSliceNogil("Jij"); __PYX_ERR(0, 104, __pyx_L4_error) }
__pyx_t_9 = (__pyx_v_Jij.shape[0]);
if ((1 == 0)) abort();
{
#if ((defined(__APPLE__) || defined(__OSX__)) && (defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))))
#undef likely
#undef unlikely
#define likely(x) (x)
#define unlikely(x) (x)
#endif
__pyx_t_11 = (__pyx_t_9 - 0 + 1 - 1/abs(1)) / 1;
if (__pyx_t_11 > 0)
{
#ifdef _OPENMP
#pragma omp parallel
#endif /* _OPENMP */
{
#ifdef _OPENMP
#pragma omp for firstprivate(__pyx_v_index_i) lastprivate(__pyx_v_index_i) lastprivate(__pyx_v_index_j) lastprivate(__pyx_v_mean_first_site) lastprivate(__pyx_v_mean_second_site) lastprivate(__pyx_v_mean_two_sites) lastprivate(__pyx_v_state_1) lastprivate(__pyx_v_state_2)
#endif /* _OPENMP */
for (__pyx_t_10 = 0; __pyx_t_10 < __pyx_t_11; __pyx_t_10++){
{
__pyx_v_index_i = (int)(0 + 1 * __pyx_t_10);
/* Initialize private variables to invalid values */
__pyx_v_index_j = ((int)0xbad0bad0);
__pyx_v_mean_first_site = ((double)__PYX_NAN());
__pyx_v_mean_second_site = ((double)__PYX_NAN());
__pyx_v_mean_two_sites = ((double)__PYX_NAN());
__pyx_v_state_1 = ((int)0xbad0bad0);
__pyx_v_state_2 = ((int)0xbad0bad0);
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__pyx_t_12 = (__pyx_v_Jij.shape[2]);
__pyx_t_13 = __pyx_t_12;
for (__pyx_t_14 = 0; __pyx_t_14 < __pyx_t_13; __pyx_t_14+=1) {
__pyx_v_index_j = __pyx_t_14;
+106: mean_two_sites = mean_list_2(Jij,index_i,index_j)
__pyx_v_mean_two_sites = __pyx_f_11cython_code_16analyse_sequence_mean_list_2(__pyx_v_Jij, __pyx_v_index_i, __pyx_v_index_j);
+107: for state_1 in range(n_states_gauge):
__pyx_t_15 = __pyx_v_n_states_gauge;
__pyx_t_16 = __pyx_t_15;
for (__pyx_t_17 = 0; __pyx_t_17 < __pyx_t_16; __pyx_t_17+=1) {
__pyx_v_state_1 = __pyx_t_17;
+108: mean_second_site = mean_list(Jij,index_i,state_1,index_j)
__pyx_v_mean_second_site = __pyx_f_11cython_code_16analyse_sequence_mean_list(__pyx_v_Jij, __pyx_v_index_i, __pyx_v_state_1, __pyx_v_index_j);
+109: for state_2 in range(n_states_gauge):
__pyx_t_18 = __pyx_v_n_states_gauge;
__pyx_t_19 = __pyx_t_18;
for (__pyx_t_20 = 0; __pyx_t_20 < __pyx_t_19; __pyx_t_20+=1) {
__pyx_v_state_2 = __pyx_t_20;
+110: mean_first_site = mean_list_1(Jij,index_i,index_j,state_2)
__pyx_v_mean_first_site = __pyx_f_11cython_code_16analyse_sequence_mean_list_1(__pyx_v_Jij, __pyx_v_index_i, __pyx_v_index_j, __pyx_v_state_2);
+111: Jij_out[index_i,state_1,index_j,state_2] = Jij[index_i,state_1,index_j,state_2] - mean_first_site - mean_second_site + mean_two_sites
__pyx_t_21 = __pyx_v_index_i;
__pyx_t_22 = __pyx_v_state_1;
__pyx_t_23 = __pyx_v_index_j;
__pyx_t_24 = __pyx_v_state_2;
if (__pyx_t_21 < 0) __pyx_t_21 += __pyx_v_Jij.shape[0];
if (__pyx_t_22 < 0) __pyx_t_22 += __pyx_v_Jij.shape[1];
if (__pyx_t_23 < 0) __pyx_t_23 += __pyx_v_Jij.shape[2];
if (__pyx_t_24 < 0) __pyx_t_24 += __pyx_v_Jij.shape[3];
__pyx_t_25 = __pyx_v_index_i;
__pyx_t_26 = __pyx_v_state_1;
__pyx_t_27 = __pyx_v_index_j;
__pyx_t_28 = __pyx_v_state_2;
if (__pyx_t_25 < 0) __pyx_t_25 += __pyx_v_Jij_out.shape[0];
if (__pyx_t_26 < 0) __pyx_t_26 += __pyx_v_Jij_out.shape[1];
if (__pyx_t_27 < 0) __pyx_t_27 += __pyx_v_Jij_out.shape[2];
if (__pyx_t_28 < 0) __pyx_t_28 += __pyx_v_Jij_out.shape[3];
*((double *) ( /* dim=3 */ ((char *) (((double *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_Jij_out.data + __pyx_t_25 * __pyx_v_Jij_out.strides[0]) ) + __pyx_t_26 * __pyx_v_Jij_out.strides[1]) ) + __pyx_t_27 * __pyx_v_Jij_out.strides[2]) )) + __pyx_t_28)) )) = ((((*((double *) ( /* dim=3 */ (( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ ((char *) (((double *) __pyx_v_Jij.data) + __pyx_t_21)) ) + __pyx_t_22 * __pyx_v_Jij.strides[1]) ) + __pyx_t_23 * __pyx_v_Jij.strides[2]) ) + __pyx_t_24 * __pyx_v_Jij.strides[3]) ))) - __pyx_v_mean_first_site) - __pyx_v_mean_second_site) + __pyx_v_mean_two_sites);
}
}
}
}
}
}
}
}
#if ((defined(__APPLE__) || defined(__OSX__)) && (defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))))
#undef likely
#undef unlikely
#define likely(x) __builtin_expect(!!(x), 1)
#define unlikely(x) __builtin_expect(!!(x), 0)
#endif
}
+112: return np.asarray(Jij_out)
__Pyx_XDECREF(__pyx_r); __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_np); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 112, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_asarray); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 112, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_Jij_out, 4, (PyObject *(*)(char *)) __pyx_memview_get_double, (int (*)(char *, PyObject *)) __pyx_memview_set_double, 0);; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 112, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __pyx_t_6 = NULL; if (CYTHON_UNPACK_METHODS && unlikely(PyMethod_Check(__pyx_t_7))) { __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_7); if (likely(__pyx_t_6)) { PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7); __Pyx_INCREF(__pyx_t_6); __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_7, function); } } __pyx_t_1 = (__pyx_t_6) ? __Pyx_PyObject_Call2Args(__pyx_t_7, __pyx_t_6, __pyx_t_3) : __Pyx_PyObject_CallOneArg(__pyx_t_7, __pyx_t_3); __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 112, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0;
113:
+114: cdef double mean_list(double[::1,:,:,:] List, int index_fix, int index_fix_2,int index_fix_3 ) nogil:
static double __pyx_f_11cython_code_16analyse_sequence_mean_list(__Pyx_memviewslice __pyx_v_List, int __pyx_v_index_fix, int __pyx_v_index_fix_2, int __pyx_v_index_fix_3) {
double __pyx_v_mean;
int __pyx_v_index_list;
double __pyx_r;
/* … */
/* function exit code */
__pyx_L1_error:;
__Pyx_WriteUnraisable("cython_code.analyse_sequence.mean_list", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 1);
__pyx_r = 0;
__pyx_L0:;
return __pyx_r;
}
115: cdef:
+116: double mean = 0.0
__pyx_v_mean = 0.0;
117: int index_list
+118: for index_list in range(List.shape[3]):
__pyx_t_1 = (__pyx_v_List.shape[3]);
__pyx_t_2 = __pyx_t_1;
for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
__pyx_v_index_list = __pyx_t_3;
+119: mean += List[index_fix,index_fix_2,index_fix_3,index_list]
__pyx_t_4 = __pyx_v_index_fix;
__pyx_t_5 = __pyx_v_index_fix_2;
__pyx_t_6 = __pyx_v_index_fix_3;
__pyx_t_7 = __pyx_v_index_list;
if (__pyx_t_4 < 0) __pyx_t_4 += __pyx_v_List.shape[0];
if (__pyx_t_5 < 0) __pyx_t_5 += __pyx_v_List.shape[1];
if (__pyx_t_6 < 0) __pyx_t_6 += __pyx_v_List.shape[2];
if (__pyx_t_7 < 0) __pyx_t_7 += __pyx_v_List.shape[3];
__pyx_v_mean = (__pyx_v_mean + (*((double *) ( /* dim=3 */ (( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ ((char *) (((double *) __pyx_v_List.data) + __pyx_t_4)) ) + __pyx_t_5 * __pyx_v_List.strides[1]) ) + __pyx_t_6 * __pyx_v_List.strides[2]) ) + __pyx_t_7 * __pyx_v_List.strides[3]) ))));
}
+120: return mean/(List.shape[3]+1) #zero of gauge excluded in list
__pyx_t_1 = ((__pyx_v_List.shape[3]) + 1);
if (unlikely(__pyx_t_1 == 0)) {
#ifdef WITH_THREAD
PyGILState_STATE __pyx_gilstate_save = __Pyx_PyGILState_Ensure();
#endif
PyErr_SetString(PyExc_ZeroDivisionError, "float division");
#ifdef WITH_THREAD
__Pyx_PyGILState_Release(__pyx_gilstate_save);
#endif
__PYX_ERR(0, 120, __pyx_L1_error)
}
__pyx_r = (__pyx_v_mean / ((double)__pyx_t_1));
goto __pyx_L0;
121:
+122: cdef double mean_list_1(double[::1,:,:,:] List, int index_fix, int index_fix_2, int index_fix_3 ) nogil:
static double __pyx_f_11cython_code_16analyse_sequence_mean_list_1(__Pyx_memviewslice __pyx_v_List, int __pyx_v_index_fix, int __pyx_v_index_fix_2, int __pyx_v_index_fix_3) {
double __pyx_v_mean;
int __pyx_v_index_list;
double __pyx_r;
/* … */
/* function exit code */
__pyx_L1_error:;
__Pyx_WriteUnraisable("cython_code.analyse_sequence.mean_list_1", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 1);
__pyx_r = 0;
__pyx_L0:;
return __pyx_r;
}
123: cdef:
+124: double mean = 0.0
__pyx_v_mean = 0.0;
125: int index_list
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__pyx_t_1 = (__pyx_v_List.shape[1]);
__pyx_t_2 = __pyx_t_1;
for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
__pyx_v_index_list = __pyx_t_3;
+127: mean += List[index_fix,index_list,index_fix_2,index_fix_3]
__pyx_t_4 = __pyx_v_index_fix;
__pyx_t_5 = __pyx_v_index_list;
__pyx_t_6 = __pyx_v_index_fix_2;
__pyx_t_7 = __pyx_v_index_fix_3;
if (__pyx_t_4 < 0) __pyx_t_4 += __pyx_v_List.shape[0];
if (__pyx_t_5 < 0) __pyx_t_5 += __pyx_v_List.shape[1];
if (__pyx_t_6 < 0) __pyx_t_6 += __pyx_v_List.shape[2];
if (__pyx_t_7 < 0) __pyx_t_7 += __pyx_v_List.shape[3];
__pyx_v_mean = (__pyx_v_mean + (*((double *) ( /* dim=3 */ (( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ ((char *) (((double *) __pyx_v_List.data) + __pyx_t_4)) ) + __pyx_t_5 * __pyx_v_List.strides[1]) ) + __pyx_t_6 * __pyx_v_List.strides[2]) ) + __pyx_t_7 * __pyx_v_List.strides[3]) ))));
}
+128: return mean/(List.shape[1]+1)#zero of gauge excluded in list
__pyx_t_1 = ((__pyx_v_List.shape[1]) + 1);
if (unlikely(__pyx_t_1 == 0)) {
#ifdef WITH_THREAD
PyGILState_STATE __pyx_gilstate_save = __Pyx_PyGILState_Ensure();
#endif
PyErr_SetString(PyExc_ZeroDivisionError, "float division");
#ifdef WITH_THREAD
__Pyx_PyGILState_Release(__pyx_gilstate_save);
#endif
__PYX_ERR(0, 128, __pyx_L1_error)
}
__pyx_r = (__pyx_v_mean / ((double)__pyx_t_1));
goto __pyx_L0;
129:
+130: cdef double mean_list_2(double[::1,:,:,:] List, int index_fix_0,int index_fix_2) nogil:
static double __pyx_f_11cython_code_16analyse_sequence_mean_list_2(__Pyx_memviewslice __pyx_v_List, int __pyx_v_index_fix_0, int __pyx_v_index_fix_2) {
double __pyx_v_mean;
int __pyx_v_index_list;
int __pyx_v_index_list_2;
double __pyx_r;
/* … */
/* function exit code */
__pyx_L1_error:;
__Pyx_WriteUnraisable("cython_code.analyse_sequence.mean_list_2", __pyx_clineno, __pyx_lineno, __pyx_filename, 1, 1);
__pyx_r = 0;
__pyx_L0:;
return __pyx_r;
}
131: cdef:
+132: double mean = 0.0
__pyx_v_mean = 0.0;
133: int index_list, index_list_2
+134: for index_list in range(List.shape[1]):
__pyx_t_1 = (__pyx_v_List.shape[1]);
__pyx_t_2 = __pyx_t_1;
for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
__pyx_v_index_list = __pyx_t_3;
+135: for index_list_2 in range(List.shape[3]):
__pyx_t_4 = (__pyx_v_List.shape[3]);
__pyx_t_5 = __pyx_t_4;
for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
__pyx_v_index_list_2 = __pyx_t_6;
+136: mean += List[index_fix_0,index_list,index_fix_2,index_list_2]
__pyx_t_7 = __pyx_v_index_fix_0;
__pyx_t_8 = __pyx_v_index_list;
__pyx_t_9 = __pyx_v_index_fix_2;
__pyx_t_10 = __pyx_v_index_list_2;
if (__pyx_t_7 < 0) __pyx_t_7 += __pyx_v_List.shape[0];
if (__pyx_t_8 < 0) __pyx_t_8 += __pyx_v_List.shape[1];
if (__pyx_t_9 < 0) __pyx_t_9 += __pyx_v_List.shape[2];
if (__pyx_t_10 < 0) __pyx_t_10 += __pyx_v_List.shape[3];
__pyx_v_mean = (__pyx_v_mean + (*((double *) ( /* dim=3 */ (( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ ((char *) (((double *) __pyx_v_List.data) + __pyx_t_7)) ) + __pyx_t_8 * __pyx_v_List.strides[1]) ) + __pyx_t_9 * __pyx_v_List.strides[2]) ) + __pyx_t_10 * __pyx_v_List.strides[3]) ))));
}
}
+137: return mean/((List.shape[1]+1)*(List.shape[3]+1))#zero of gauge excluded in list
__pyx_t_1 = (((__pyx_v_List.shape[1]) + 1) * ((__pyx_v_List.shape[3]) + 1));
if (unlikely(__pyx_t_1 == 0)) {
#ifdef WITH_THREAD
PyGILState_STATE __pyx_gilstate_save = __Pyx_PyGILState_Ensure();
#endif
PyErr_SetString(PyExc_ZeroDivisionError, "float division");
#ifdef WITH_THREAD
__Pyx_PyGILState_Release(__pyx_gilstate_save);
#endif
__PYX_ERR(0, 137, __pyx_L1_error)
}
__pyx_r = (__pyx_v_mean / ((double)__pyx_t_1));
goto __pyx_L0;