Generated by Cython 3.0.10
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: ecc.c
+001: cimport cython
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002: from libc.stdlib cimport malloc, free
003: from libc.math cimport ceil
+004: import gudhi as gd
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+005: import numpy as np
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006: cimport numpy as cnp
+007: cnp.import_array()
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008:
009:
+010: dtype_float = np.float32
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011:
012:
+013: cdef class RipsEccBackbone:
struct __pyx_obj_3ecc_RipsEccBackbone {
PyObject_HEAD
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float resolution;
float impulse;
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Py_ssize_t max_dim;
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014: cdef float max_edge_length, resolution, impulse
015: cdef Py_ssize_t steps, max_dim
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if (__Pyx_IternextUnpackEndCheck(__pyx_t_6(__pyx_t_3), 2) < 0) __PYX_ERR(0, 56, __pyx_L1_error) __pyx_t_6 = NULL; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; goto __pyx_L10_unpacking_done; __pyx_L9_unpacking_failed:; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_6 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); __PYX_ERR(0, 56, __pyx_L1_error) __pyx_L10_unpacking_done:; } __pyx_t_16 = __pyx_PyFloat_AsFloat(__pyx_t_4); if (unlikely((__pyx_t_16 == (float)-1) && PyErr_Occurred())) __PYX_ERR(0, 56, __pyx_L1_error) __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_XDECREF_SET(__pyx_v_vtx_idx, __pyx_t_2); __pyx_t_2 = 0; __pyx_v_filt = __pyx_t_16; /* … */ __pyx_L7_continue:; } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L18_for_end; __pyx_L8_break:; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L18_for_end; __pyx_L18_for_end:;
+057: if filt > self.max_edge_length:
__pyx_t_17 = (__pyx_v_filt > __pyx_v_self->max_edge_length);
if (__pyx_t_17) {
/* … */
}
+058: break
goto __pyx_L8_break;
+059: dim = len(vtx_idx) - 1 # dimension of simplex
__pyx_t_18 = PyObject_Length(__pyx_v_vtx_idx); if (unlikely(__pyx_t_18 == ((Py_ssize_t)-1))) __PYX_ERR(0, 59, __pyx_L1_error) __pyx_v_dim = (__pyx_t_18 - 1);
+060: t = max(<Py_ssize_t>ceil(filt / self.resolution), 0)
__pyx_t_19 = 0;
__pyx_t_18 = ((Py_ssize_t)ceil((__pyx_v_filt / __pyx_v_self->resolution)));
__pyx_t_17 = (__pyx_t_19 > __pyx_t_18);
if (__pyx_t_17) {
__pyx_t_20 = __pyx_t_19;
} else {
__pyx_t_20 = __pyx_t_18;
}
__pyx_v_t = __pyx_t_20;
+061: ecc_view[b, t] += (-1.)**dim
__pyx_t_21 = __pyx_v_b;
__pyx_t_22 = __pyx_v_t;
*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ecc_view.data + __pyx_t_21 * __pyx_v_ecc_view.strides[0]) ) + __pyx_t_22 * __pyx_v_ecc_view.strides[1]) )) += pow(-1., ((double)__pyx_v_dim));
062:
063: # calculation of gradient only for inputs that require gradient
+064: if backprop:
if (__pyx_v_backprop) {
/* … */
}
065: # vertex
+066: if dim == 0:
switch (__pyx_v_dim) {
case 0:
/* … */
break;
case 1:
+067: continue
goto __pyx_L7_continue;
068: # edge
+069: elif dim == 1:
break;
default:
+070: if grad_1 != NULL:
__pyx_t_17 = (__pyx_v_grad_1 != NULL);
if (__pyx_t_17) {
/* … */
}
+071: free(grad_1)
free(__pyx_v_grad_1);
+072: free(grad_2)
free(__pyx_v_grad_2);
073:
+074: vtx_idx_1 = vtx_idx[0]
__pyx_t_5 = __Pyx_GetItemInt(__pyx_v_vtx_idx, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 74, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __pyx_t_20 = __Pyx_PyIndex_AsSsize_t(__pyx_t_5); if (unlikely((__pyx_t_20 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 74, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_v_vtx_idx_1 = __pyx_t_20;
+075: vtx_idx_2 = vtx_idx[1]
__pyx_t_5 = __Pyx_GetItemInt(__pyx_v_vtx_idx, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 75, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __pyx_t_20 = __Pyx_PyIndex_AsSsize_t(__pyx_t_5); if (unlikely((__pyx_t_20 == (Py_ssize_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 75, __pyx_L1_error) __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_v_vtx_idx_2 = __pyx_t_20;
+076: vtx_1 = x_view[b, vtx_idx_1] # shape: (d, )
__pyx_t_23.data = __pyx_v_x_view.data;
__pyx_t_23.memview = __pyx_v_x_view.memview;
__PYX_INC_MEMVIEW(&__pyx_t_23, 1);
{
Py_ssize_t __pyx_tmp_idx = __pyx_v_b;
Py_ssize_t __pyx_tmp_stride = __pyx_v_x_view.strides[0];
__pyx_t_23.data += __pyx_tmp_idx * __pyx_tmp_stride;
}
{
Py_ssize_t __pyx_tmp_idx = __pyx_v_vtx_idx_1;
Py_ssize_t __pyx_tmp_stride = __pyx_v_x_view.strides[1];
__pyx_t_23.data += __pyx_tmp_idx * __pyx_tmp_stride;
}
__pyx_t_23.shape[0] = __pyx_v_x_view.shape[2];
__pyx_t_23.strides[0] = __pyx_v_x_view.strides[2];
__pyx_t_23.suboffsets[0] = -1;
__PYX_XCLEAR_MEMVIEW(&__pyx_v_vtx_1, 1);
__pyx_v_vtx_1 = __pyx_t_23;
__pyx_t_23.memview = NULL;
__pyx_t_23.data = NULL;
+077: vtx_2 = x_view[b, vtx_idx_2] # shape: (d, )
__pyx_t_23.data = __pyx_v_x_view.data;
__pyx_t_23.memview = __pyx_v_x_view.memview;
__PYX_INC_MEMVIEW(&__pyx_t_23, 1);
{
Py_ssize_t __pyx_tmp_idx = __pyx_v_b;
Py_ssize_t __pyx_tmp_stride = __pyx_v_x_view.strides[0];
__pyx_t_23.data += __pyx_tmp_idx * __pyx_tmp_stride;
}
{
Py_ssize_t __pyx_tmp_idx = __pyx_v_vtx_idx_2;
Py_ssize_t __pyx_tmp_stride = __pyx_v_x_view.strides[1];
__pyx_t_23.data += __pyx_tmp_idx * __pyx_tmp_stride;
}
__pyx_t_23.shape[0] = __pyx_v_x_view.shape[2];
__pyx_t_23.strides[0] = __pyx_v_x_view.strides[2];
__pyx_t_23.suboffsets[0] = -1;
__PYX_XCLEAR_MEMVIEW(&__pyx_v_vtx_2, 1);
__pyx_v_vtx_2 = __pyx_t_23;
__pyx_t_23.memview = NULL;
__pyx_t_23.data = NULL;
078:
+079: grad_1, grad_2 = RipsEccBackbone._cal_edge_grad(vtx_1, vtx_2, filt, d)
__pyx_t_24 = __pyx_f_3ecc_15RipsEccBackbone__cal_edge_grad(__pyx_v_vtx_1, __pyx_v_vtx_2, __pyx_v_filt, __pyx_v_d); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 79, __pyx_L1_error)
__pyx_t_25 = __pyx_t_24.f0;
__pyx_t_26 = __pyx_t_24.f1;
__pyx_v_grad_1 = __pyx_t_25;
__pyx_v_grad_2 = __pyx_t_26;
080:
+081: for i in range(d):
__pyx_t_20 = __pyx_v_d;
__pyx_t_18 = __pyx_t_20;
for (__pyx_t_27 = 0; __pyx_t_27 < __pyx_t_18; __pyx_t_27+=1) {
__pyx_v_i = __pyx_t_27;
+082: grad_local_view[b, vtx_idx_1, i, t] += grad_1[i] * self.impulse
__pyx_t_22 = __pyx_v_b;
__pyx_t_21 = __pyx_v_vtx_idx_1;
__pyx_t_28 = __pyx_v_i;
__pyx_t_29 = __pyx_v_t;
*((float *) ( /* dim=3 */ (( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_grad_local_view.data + __pyx_t_22 * __pyx_v_grad_local_view.strides[0]) ) + __pyx_t_21 * __pyx_v_grad_local_view.strides[1]) ) + __pyx_t_28 * __pyx_v_grad_local_view.strides[2]) ) + __pyx_t_29 * __pyx_v_grad_local_view.strides[3]) )) += ((__pyx_v_grad_1[__pyx_v_i]) * __pyx_v_self->impulse);
+083: grad_local_view[b, vtx_idx_2, i, t] += grad_2[i] * self.impulse
__pyx_t_29 = __pyx_v_b;
__pyx_t_28 = __pyx_v_vtx_idx_2;
__pyx_t_21 = __pyx_v_i;
__pyx_t_22 = __pyx_v_t;
*((float *) ( /* dim=3 */ (( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_grad_local_view.data + __pyx_t_29 * __pyx_v_grad_local_view.strides[0]) ) + __pyx_t_28 * __pyx_v_grad_local_view.strides[1]) ) + __pyx_t_21 * __pyx_v_grad_local_view.strides[2]) ) + __pyx_t_22 * __pyx_v_grad_local_view.strides[3]) )) += ((__pyx_v_grad_2[__pyx_v_i]) * __pyx_v_self->impulse);
}
084: # triangle or higher dimensional simplex
085: else:
+086: for i in range(d):
__pyx_t_20 = __pyx_v_d;
__pyx_t_18 = __pyx_t_20;
for (__pyx_t_27 = 0; __pyx_t_27 < __pyx_t_18; __pyx_t_27+=1) {
__pyx_v_i = __pyx_t_27;
+087: grad_local_view[b, vtx_idx_1, i, t] += (-1)**(dim+1) * grad_1[i] * self.impulse
__pyx_t_22 = __pyx_v_b;
__pyx_t_21 = __pyx_v_vtx_idx_1;
__pyx_t_28 = __pyx_v_i;
__pyx_t_29 = __pyx_v_t;
*((float *) ( /* dim=3 */ (( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_grad_local_view.data + __pyx_t_22 * __pyx_v_grad_local_view.strides[0]) ) + __pyx_t_21 * __pyx_v_grad_local_view.strides[1]) ) + __pyx_t_28 * __pyx_v_grad_local_view.strides[2]) ) + __pyx_t_29 * __pyx_v_grad_local_view.strides[3]) )) += ((pow(-1.0, ((double)(__pyx_v_dim + 1))) * (__pyx_v_grad_1[__pyx_v_i])) * __pyx_v_self->impulse);
+088: grad_local_view[b, vtx_idx_2, i, t] += (-1)**(dim+1) * grad_2[i] * self.impulse
__pyx_t_29 = __pyx_v_b;
__pyx_t_28 = __pyx_v_vtx_idx_2;
__pyx_t_21 = __pyx_v_i;
__pyx_t_22 = __pyx_v_t;
*((float *) ( /* dim=3 */ (( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_grad_local_view.data + __pyx_t_29 * __pyx_v_grad_local_view.strides[0]) ) + __pyx_t_28 * __pyx_v_grad_local_view.strides[1]) ) + __pyx_t_21 * __pyx_v_grad_local_view.strides[2]) ) + __pyx_t_22 * __pyx_v_grad_local_view.strides[3]) )) += ((pow(-1.0, ((double)(__pyx_v_dim + 1))) * (__pyx_v_grad_2[__pyx_v_i])) * __pyx_v_self->impulse);
}
break;
}
089: # free memory after each data
+090: free(grad_1)
free(__pyx_v_grad_1);
+091: free(grad_2)
free(__pyx_v_grad_2);
092: # cumsum
+093: for i in range(self.steps - 1):
__pyx_t_14 = (__pyx_v_self->steps - 1);
__pyx_t_20 = __pyx_t_14;
for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_20; __pyx_t_18+=1) {
__pyx_v_i = __pyx_t_18;
+094: ecc_view[b, i+1] += ecc_view[b, i]
__pyx_t_22 = __pyx_v_b;
__pyx_t_21 = __pyx_v_i;
__pyx_t_28 = __pyx_v_b;
__pyx_t_29 = (__pyx_v_i + 1);
*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ecc_view.data + __pyx_t_28 * __pyx_v_ecc_view.strides[0]) ) + __pyx_t_29 * __pyx_v_ecc_view.strides[1]) )) += (*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_ecc_view.data + __pyx_t_22 * __pyx_v_ecc_view.strides[0]) ) + __pyx_t_21 * __pyx_v_ecc_view.strides[1]) )));
}
}
+095: return ecc, grad_local
__Pyx_XDECREF(__pyx_r); __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 95, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(__pyx_v_ecc); __Pyx_GIVEREF(__pyx_v_ecc); if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_ecc)) __PYX_ERR(0, 95, __pyx_L1_error); __Pyx_INCREF(__pyx_v_grad_local); __Pyx_GIVEREF(__pyx_v_grad_local); if (__Pyx_PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_grad_local)) __PYX_ERR(0, 95, __pyx_L1_error); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0;
096:
097:
098: @staticmethod
099: @cython.boundscheck(False) # turn off bounds-checking for entire function
100: @cython.wraparound(False) # turn off negative index wrapping for entire function
101: @cython.cdivision(True) # turn off checking for division by zero
+102: cdef inline (float*, float*) _cal_edge_grad(float[:] vtx_1, float[:] vtx_2, float filt, int d):
static CYTHON_INLINE __pyx_ctuple_float__ptr__and_float__ptr __pyx_f_3ecc_15RipsEccBackbone__cal_edge_grad(__Pyx_memviewslice __pyx_v_vtx_1, __Pyx_memviewslice __pyx_v_vtx_2, float __pyx_v_filt, int __pyx_v_d) {
float *__pyx_v_grad_1;
float *__pyx_v_grad_2;
int __pyx_v_i;
__pyx_ctuple_float__ptr__and_float__ptr __pyx_r;
/* … */
/* function exit code */
__pyx_L0:;
return __pyx_r;
}
/* … */
struct __pyx_ctuple_float__ptr__and_float__ptr {
float *f0;
float *f1;
};
+103: cdef float *grad_1 = <float *> malloc(d * sizeof(float))
__pyx_v_grad_1 = ((float *)malloc((__pyx_v_d * (sizeof(float)))));
+104: cdef float *grad_2 = <float *> malloc(d * sizeof(float))
__pyx_v_grad_2 = ((float *)malloc((__pyx_v_d * (sizeof(float)))));
105:
+106: for i in range(d):
__pyx_t_1 = __pyx_v_d;
__pyx_t_2 = __pyx_t_1;
for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
__pyx_v_i = __pyx_t_3;
+107: grad_1[i] = (vtx_1[i] - vtx_2[i]) / filt
__pyx_t_4 = __pyx_v_i;
__pyx_t_5 = __pyx_v_i;
(__pyx_v_grad_1[__pyx_v_i]) = (((*((float *) ( /* dim=0 */ (__pyx_v_vtx_1.data + __pyx_t_4 * __pyx_v_vtx_1.strides[0]) ))) - (*((float *) ( /* dim=0 */ (__pyx_v_vtx_2.data + __pyx_t_5 * __pyx_v_vtx_2.strides[0]) )))) / __pyx_v_filt);
+108: grad_2[i] = (vtx_2[i] - vtx_1[i]) / filt
__pyx_t_5 = __pyx_v_i;
__pyx_t_4 = __pyx_v_i;
(__pyx_v_grad_2[__pyx_v_i]) = (((*((float *) ( /* dim=0 */ (__pyx_v_vtx_2.data + __pyx_t_5 * __pyx_v_vtx_2.strides[0]) ))) - (*((float *) ( /* dim=0 */ (__pyx_v_vtx_1.data + __pyx_t_4 * __pyx_v_vtx_1.strides[0]) )))) / __pyx_v_filt);
}
109:
+110: return grad_1, grad_2
__pyx_t_6.f0 = __pyx_v_grad_1; __pyx_t_6.f1 = __pyx_v_grad_2; __pyx_r = __pyx_t_6; goto __pyx_L0;