Generated by Cython 3.0.2
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: sr_3D_radial_gradient_convergence.c
+001: # cython: infer_types=True, wraparound=False, nonecheck=False, boundscheck=False, cdivision=True, language_level=3, profile=False, autogen_pxd=True
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002:
003: from libc.math cimport sqrt, fabs, exp, isnan, floor
004:
005: from ..transform.interpolation_catmull_rom cimport _interpolate, Interpolator
+006: from ..transform.interpolation_fft_zoom import magnify as fft_zoom
__pyx_t_7 = PyList_New(1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 6, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); __Pyx_INCREF(__pyx_n_s_magnify); __Pyx_GIVEREF(__pyx_n_s_magnify); if (__Pyx_PyList_SET_ITEM(__pyx_t_7, 0, __pyx_n_s_magnify)) __PYX_ERR(0, 6, __pyx_L1_error); __pyx_t_4 = __Pyx_Import(__pyx_n_s_transform_interpolation_fft_zoom, __pyx_t_7, 2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 6, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_7 = __Pyx_ImportFrom(__pyx_t_4, __pyx_n_s_magnify); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 6, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); if (PyDict_SetItem(__pyx_d, __pyx_n_s_fft_zoom, __pyx_t_7) < 0) __PYX_ERR(0, 6, __pyx_L1_error) __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+007: from ..transform.image_magnify import cv2_zoom as zoom
__pyx_t_4 = PyList_New(1); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 7, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __Pyx_INCREF(__pyx_n_s_cv2_zoom); __Pyx_GIVEREF(__pyx_n_s_cv2_zoom); if (__Pyx_PyList_SET_ITEM(__pyx_t_4, 0, __pyx_n_s_cv2_zoom)) __PYX_ERR(0, 7, __pyx_L1_error); __pyx_t_7 = __Pyx_Import(__pyx_n_s_transform_image_magnify, __pyx_t_4, 2); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 7, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_4 = __Pyx_ImportFrom(__pyx_t_7, __pyx_n_s_cv2_zoom); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 7, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); if (PyDict_SetItem(__pyx_d, __pyx_n_s_zoom, __pyx_t_4) < 0) __PYX_ERR(0, 7, __pyx_L1_error) __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+008: from ..utils.timeit import timeit2
__pyx_t_7 = PyList_New(1); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 8, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); __Pyx_INCREF(__pyx_n_s_timeit2); __Pyx_GIVEREF(__pyx_n_s_timeit2); if (__Pyx_PyList_SET_ITEM(__pyx_t_7, 0, __pyx_n_s_timeit2)) __PYX_ERR(0, 8, __pyx_L1_error); __pyx_t_4 = __Pyx_Import(__pyx_n_s_utils_timeit, __pyx_t_7, 2); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 8, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_7 = __Pyx_ImportFrom(__pyx_t_4, __pyx_n_s_timeit2); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 8, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); if (PyDict_SetItem(__pyx_d, __pyx_n_s_timeit2, __pyx_t_7) < 0) __PYX_ERR(0, 8, __pyx_L1_error) __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
009:
010:
+011: import numpy as np
__pyx_t_4 = __Pyx_ImportDottedModule(__pyx_n_s_numpy, NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 11, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); if (PyDict_SetItem(__pyx_d, __pyx_n_s_np, __pyx_t_4) < 0) __PYX_ERR(0, 11, __pyx_L1_error) __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
012: cimport numpy as np
013:
014: from cython.parallel import prange
015:
+016: cdef float Gx_Gy_MAGNIFICATION = 2.0
__pyx_v_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_Gx_Gy_MAGNIFICATION = 2.0;
017:
018: cdef extern from "_c_gradients.h":
019: void _c_gradient_3d(float* image, float* imGx, float* imGy, float* imGz, int d, int h, int w) nogil
020:
+021: cdef class RadialGradientConvergence3D:
struct __pyx_obj_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D {
PyObject_HEAD
struct __pyx_vtabstruct_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *__pyx_vtab;
int magnification;
float fwhm;
float sensitivity;
float tSS;
float tSO;
int doIntensityWeighting;
};
/* … */
struct __pyx_vtabstruct_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D {
void (*_single_frame_RGC_map)(struct __pyx_obj_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice);
void (*_calculate_3d_gradient)(struct __pyx_obj_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice);
float (*_calculate_3d_RGC)(struct __pyx_obj_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *, int, int, int, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice);
float (*_calculateDW)(struct __pyx_obj_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *, float);
float (*_calculateDk)(struct __pyx_obj_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *, float, float, float, float, float, float, float);
};
static struct __pyx_vtabstruct_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *__pyx_vtabptr_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D;
022:
023: cdef int magnification
024: cdef float fwhm
025: cdef float sensitivity
026: cdef float tSS # two sigma squared
027: cdef float tSO # two sigma plus one
028: cdef bint doIntensityWeighting
029:
+030: def __init__(self, magnification: int = 5, radius: float = 1.5, sensitivity: float = 1 , doIntensityWeighting: bool = True):
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031: """
032: Calculate the Radial Gradient Convergence (RGC) of an image.
033: :param magnification: magnification of the image
034: :param radius: radius of the RGC (the PSF Full-Width-Half-Maximum)
035: :param sensitivity: sensitivity of the RGC (sharpening factor)
036: :param doIntensityWeighting: whether to do intensity weighting
037: """
+038: self.magnification = magnification
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+039: self.fwhm = radius
__pyx_v_self->fwhm = __pyx_v_radius;
+040: self.sensitivity = sensitivity
__pyx_v_self->sensitivity = __pyx_v_sensitivity;
+041: self.doIntensityWeighting = doIntensityWeighting
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042:
+043: cdef float sigma = radius / 2.355
__pyx_v_sigma = (__pyx_v_radius / 2.355);
+044: self.tSS = 2 * sigma * sigma
__pyx_v_self->tSS = ((2.0 * __pyx_v_sigma) * __pyx_v_sigma);
+045: self.tSO = 2 * sigma + 1
__pyx_v_self->tSO = ((2.0 * __pyx_v_sigma) + 1.0);
046:
+047: @timeit2
/* Python wrapper */ static PyObject *__pyx_pw_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_27RadialGradientConvergence3D_3calculate(PyObject *__pyx_v_self, #if CYTHON_METH_FASTCALL PyObject *const *__pyx_args, Py_ssize_t __pyx_nargs, PyObject *__pyx_kwds #else PyObject *__pyx_args, PyObject *__pyx_kwds #endif ); /*proto*/ PyDoc_STRVAR(__pyx_doc_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_27RadialGradientConvergence3D_2calculate, "\n Calculate the RGC of an image-stack.\n :param im: the image to calculate the RGC of\n :return: the RGC of the image\n "); static PyMethodDef __pyx_mdef_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_27RadialGradientConvergence3D_3calculate = {"calculate", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_27RadialGradientConvergence3D_3calculate, __Pyx_METH_FASTCALL|METH_KEYWORDS, __pyx_doc_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_27RadialGradientConvergence3D_2calculate}; 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048: def calculate(self, im: np.ndarray):
049: """
050: Calculate the RGC of an image-stack.
051: :param im: the image to calculate the RGC of
052: :return: the RGC of the image
053: """
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055:
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064:
065: cdef int n
066:
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{
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PyThreadState *_save;
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Py_UNBLOCK_THREADS
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__Pyx_FastGIL_Forget();
Py_BLOCK_THREADS
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{
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#undef likely
#undef unlikely
#define likely(x) (x)
#define unlikely(x) (x)
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if (__pyx_t_13 > 0)
{
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{
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for (__pyx_t_12 = 0; __pyx_t_12 < __pyx_t_13; __pyx_t_12++){
{
__pyx_v_n = (int)(0 + 1 * __pyx_t_12);
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__pyx_t_14 = __pyx_v_n;
__pyx_t_15 = 0;
__pyx_t_16 = 0;
__pyx_t_17 = 0;
__pyx_t_18 = __pyx_v_n;
__pyx_t_19 = 0;
__pyx_t_20 = 0;
__pyx_t_21 = 0;
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__pyx_t_24 = 0;
__pyx_t_25 = 0;
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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
}
070:
071: cdef int p
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__pyx_t_12 = __pyx_t_13;
for (__pyx_t_1 = 0; __pyx_t_1 < __pyx_t_12; __pyx_t_1+=1) {
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+073: self._single_frame_RGC_map(imRaw[p,:,:,:], imRad[p,:,:,:], imInt[p,:,:,:], imGx[p,:,:,:], imGy[p,:,:,:], imGz[p,:,:,:])
__pyx_t_30.data = __pyx_v_imRaw.data;
__pyx_t_30.memview = __pyx_v_imRaw.memview;
__PYX_INC_MEMVIEW(&__pyx_t_30, 1);
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__pyx_t_30.shape[0] = __pyx_v_imRaw.shape[1];
__pyx_t_30.strides[0] = __pyx_v_imRaw.strides[1];
__pyx_t_30.suboffsets[0] = -1;
__pyx_t_30.shape[1] = __pyx_v_imRaw.shape[2];
__pyx_t_30.strides[1] = __pyx_v_imRaw.strides[2];
__pyx_t_30.suboffsets[1] = -1;
__pyx_t_30.shape[2] = __pyx_v_imRaw.shape[3];
__pyx_t_30.strides[2] = __pyx_v_imRaw.strides[3];
__pyx_t_30.suboffsets[2] = -1;
__pyx_t_31.data = __pyx_v_imRad.data;
__pyx_t_31.memview = __pyx_v_imRad.memview;
__PYX_INC_MEMVIEW(&__pyx_t_31, 1);
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Py_ssize_t __pyx_tmp_idx = __pyx_v_p;
Py_ssize_t __pyx_tmp_stride = __pyx_v_imRad.strides[0];
__pyx_t_31.data += __pyx_tmp_idx * __pyx_tmp_stride;
}
__pyx_t_31.shape[0] = __pyx_v_imRad.shape[1];
__pyx_t_31.strides[0] = __pyx_v_imRad.strides[1];
__pyx_t_31.suboffsets[0] = -1;
__pyx_t_31.shape[1] = __pyx_v_imRad.shape[2];
__pyx_t_31.strides[1] = __pyx_v_imRad.strides[2];
__pyx_t_31.suboffsets[1] = -1;
__pyx_t_31.shape[2] = __pyx_v_imRad.shape[3];
__pyx_t_31.strides[2] = __pyx_v_imRad.strides[3];
__pyx_t_31.suboffsets[2] = -1;
__pyx_t_32.data = __pyx_v_imInt.data;
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__PYX_INC_MEMVIEW(&__pyx_t_32, 1);
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__pyx_t_32.data += __pyx_tmp_idx * __pyx_tmp_stride;
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__pyx_t_32.shape[0] = __pyx_v_imInt.shape[1];
__pyx_t_32.strides[0] = __pyx_v_imInt.strides[1];
__pyx_t_32.suboffsets[0] = -1;
__pyx_t_32.shape[1] = __pyx_v_imInt.shape[2];
__pyx_t_32.strides[1] = __pyx_v_imInt.strides[2];
__pyx_t_32.suboffsets[1] = -1;
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__pyx_t_32.strides[2] = __pyx_v_imInt.strides[3];
__pyx_t_32.suboffsets[2] = -1;
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__pyx_t_33.strides[1] = __pyx_v_imGx.strides[2];
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__pyx_t_34.strides[0] = __pyx_v_imGy.strides[1];
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__pyx_t_34.strides[1] = __pyx_v_imGy.strides[2];
__pyx_t_34.suboffsets[1] = -1;
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__pyx_t_34.strides[2] = __pyx_v_imGy.strides[3];
__pyx_t_34.suboffsets[2] = -1;
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__pyx_t_35.memview = __pyx_v_imGz.memview;
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__pyx_t_35.shape[0] = __pyx_v_imGz.shape[1];
__pyx_t_35.strides[0] = __pyx_v_imGz.strides[1];
__pyx_t_35.suboffsets[0] = -1;
__pyx_t_35.shape[1] = __pyx_v_imGz.shape[2];
__pyx_t_35.strides[1] = __pyx_v_imGz.strides[2];
__pyx_t_35.suboffsets[1] = -1;
__pyx_t_35.shape[2] = __pyx_v_imGz.shape[3];
__pyx_t_35.strides[2] = __pyx_v_imGz.strides[3];
__pyx_t_35.suboffsets[2] = -1;
((struct __pyx_vtabstruct_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *)__pyx_v_self->__pyx_vtab)->_single_frame_RGC_map(__pyx_v_self, __pyx_t_30, __pyx_t_31, __pyx_t_32, __pyx_t_33, __pyx_t_34, __pyx_t_35); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 73, __pyx_L1_error)
__PYX_XCLEAR_MEMVIEW(&__pyx_t_30, 1);
__pyx_t_30.memview = NULL; __pyx_t_30.data = NULL;
__PYX_XCLEAR_MEMVIEW(&__pyx_t_31, 1);
__pyx_t_31.memview = NULL; __pyx_t_31.data = NULL;
__PYX_XCLEAR_MEMVIEW(&__pyx_t_32, 1);
__pyx_t_32.memview = NULL; __pyx_t_32.data = NULL;
__PYX_XCLEAR_MEMVIEW(&__pyx_t_33, 1);
__pyx_t_33.memview = NULL; __pyx_t_33.data = NULL;
__PYX_XCLEAR_MEMVIEW(&__pyx_t_34, 1);
__pyx_t_34.memview = NULL; __pyx_t_34.data = NULL;
__PYX_XCLEAR_MEMVIEW(&__pyx_t_35, 1);
__pyx_t_35.memview = NULL; __pyx_t_35.data = NULL;
}
074:
+075: return imRad, imInt, imGx, imGy, imGz
__Pyx_XDECREF(__pyx_r); __pyx_t_9 = __pyx_memoryview_fromslice(__pyx_v_imRad, 4, (PyObject *(*)(char *)) __pyx_memview_get_float, (int (*)(char *, PyObject *)) __pyx_memview_set_float, 0);; if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 75, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_9); __pyx_t_4 = __pyx_memoryview_fromslice(__pyx_v_imInt, 4, (PyObject *(*)(char *)) __pyx_memview_get_float, (int (*)(char *, PyObject *)) __pyx_memview_set_float, 0);; if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 75, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __pyx_t_7 = __pyx_memoryview_fromslice(__pyx_v_imGx, 4, (PyObject *(*)(char *)) __pyx_memview_get_float, (int (*)(char *, PyObject *)) __pyx_memview_set_float, 0);; if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 75, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); __pyx_t_10 = __pyx_memoryview_fromslice(__pyx_v_imGy, 4, (PyObject *(*)(char *)) __pyx_memview_get_float, (int (*)(char *, PyObject *)) __pyx_memview_set_float, 0);; if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 75, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_10); __pyx_t_6 = __pyx_memoryview_fromslice(__pyx_v_imGz, 4, (PyObject *(*)(char *)) __pyx_memview_get_float, (int (*)(char *, PyObject *)) __pyx_memview_set_float, 0);; if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 75, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __pyx_t_5 = PyTuple_New(5); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 75, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_9); if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_9)) __PYX_ERR(0, 75, __pyx_L1_error); __Pyx_GIVEREF(__pyx_t_4); if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_4)) __PYX_ERR(0, 75, __pyx_L1_error); __Pyx_GIVEREF(__pyx_t_7); if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 2, __pyx_t_7)) __PYX_ERR(0, 75, __pyx_L1_error); __Pyx_GIVEREF(__pyx_t_10); if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 3, __pyx_t_10)) __PYX_ERR(0, 75, __pyx_L1_error); __Pyx_GIVEREF(__pyx_t_6); if (__Pyx_PyTuple_SET_ITEM(__pyx_t_5, 4, __pyx_t_6)) __PYX_ERR(0, 75, __pyx_L1_error); __pyx_t_9 = 0; __pyx_t_4 = 0; __pyx_t_7 = 0; __pyx_t_10 = 0; __pyx_t_6 = 0; __pyx_r = __pyx_t_5; __pyx_t_5 = 0; goto __pyx_L0;
076:
+077: cdef void _single_frame_RGC_map(self, float[:,:,:] imRaw, float[:,:,:] imRad, float[:,:,:] imInt, float[:,:,:] imGx, float[:,:,:] imGy, float[:,:,:] imGz):
static void __pyx_f_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_27RadialGradientConvergence3D__single_frame_RGC_map(struct __pyx_obj_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *__pyx_v_self, __Pyx_memviewslice __pyx_v_imRaw, __Pyx_memviewslice __pyx_v_imRad, __Pyx_memviewslice __pyx_v_imInt, __Pyx_memviewslice __pyx_v_imGx, __Pyx_memviewslice __pyx_v_imGy, __Pyx_memviewslice __pyx_v_imGz) {
int __pyx_v_w;
int __pyx_v_h;
int __pyx_v_d;
int __pyx_v_magnification;
int __pyx_v_yM;
int __pyx_v_xM;
int __pyx_v_zM;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("_single_frame_RGC_map", 0);
/* … */
/* function exit code */
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_AddTraceback("nanopyx.core.transform.sr_3D_radial_gradient_convergence.RadialGradientConvergence3D._single_frame_RGC_map", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_L0:;
__Pyx_RefNannyFinishContext();
}
078: """
079: Calculate the RGC map of an image frame.
080: :param imRaw: the frame to calculate the RGC map of
081: :param imRad: the RGC map of the frame (previously initialised as a 2D array the size of imRaw x magnification)
082: :param imInt: the interpolated image (previously initialised as a 2D array the size of imRaw x magnification)
083: :param imGx: the intensity gradients of the interpolated image in the horizontal direction (same size as imInt)
084: :param imGy: the intensity gradients of the interpolated image in the vertical direction (same size as imInt)
085: :return: the RGC of the image frame.
086: """
087:
+088: cdef int w = imRaw.shape[2]
__pyx_v_w = (__pyx_v_imRaw.shape[2]);
+089: cdef int h = imRaw.shape[1]
__pyx_v_h = (__pyx_v_imRaw.shape[1]);
+090: cdef int d = imRaw.shape[0]
__pyx_v_d = (__pyx_v_imRaw.shape[0]);
+091: cdef int magnification = self.magnification
__pyx_t_1 = __pyx_v_self->magnification; __pyx_v_magnification = __pyx_t_1;
092: cdef int yM, xM
093:
094: #TODO: interpolate 3D image
095: # cdef Interpolator interpolator = Interpolator(imRaw)
096: # imInt[:,:] = interpolator._magnify(self.magnification)
097:
098: # self._calculate_3d_gradient(imRaw, imGx, imGy, imGz) # calculate gradients of the interpolated image
099:
100: # with nogil:
+101: for zM in range(magnification, d * magnification):
__pyx_t_1 = (__pyx_v_d * __pyx_v_magnification);
__pyx_t_2 = __pyx_t_1;
for (__pyx_t_3 = __pyx_v_magnification; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
__pyx_v_zM = __pyx_t_3;
+102: for yM in range(magnification, h * magnification):
__pyx_t_4 = (__pyx_v_h * __pyx_v_magnification);
__pyx_t_5 = __pyx_t_4;
for (__pyx_t_6 = __pyx_v_magnification; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
__pyx_v_yM = __pyx_t_6;
+103: for xM in range(magnification, w * magnification):
__pyx_t_7 = (__pyx_v_w * __pyx_v_magnification);
__pyx_t_8 = __pyx_t_7;
for (__pyx_t_9 = __pyx_v_magnification; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
__pyx_v_xM = __pyx_t_9;
+104: if self.doIntensityWeighting:
if (__pyx_v_self->doIntensityWeighting) {
/* … */
goto __pyx_L9;
}
+105: imRad[zM, yM, xM] = self._calculate_3d_RGC(xM, yM, zM, imGx, imGy, imGz) * imInt[zM, yM, xM]
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__pyx_t_11 = __pyx_v_zM;
__pyx_t_12 = __pyx_v_yM;
__pyx_t_13 = __pyx_v_xM;
__pyx_t_14 = __pyx_v_zM;
__pyx_t_15 = __pyx_v_yM;
__pyx_t_16 = __pyx_v_xM;
*((float *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_imRad.data + __pyx_t_14 * __pyx_v_imRad.strides[0]) ) + __pyx_t_15 * __pyx_v_imRad.strides[1]) ) + __pyx_t_16 * __pyx_v_imRad.strides[2]) )) = (__pyx_t_10 * (*((float *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_imInt.data + __pyx_t_11 * __pyx_v_imInt.strides[0]) ) + __pyx_t_12 * __pyx_v_imInt.strides[1]) ) + __pyx_t_13 * __pyx_v_imInt.strides[2]) ))));
106: else:
+107: imRad[zM, yM, xM] = self._calculate_3d_RGC(xM, yM, zM, imGx, imGy, imGz)
/*else*/ {
__pyx_t_10 = ((struct __pyx_vtabstruct_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *)__pyx_v_self->__pyx_vtab)->_calculate_3d_RGC(__pyx_v_self, __pyx_v_xM, __pyx_v_yM, __pyx_v_zM, __pyx_v_imGx, __pyx_v_imGy, __pyx_v_imGz); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 107, __pyx_L1_error)
__pyx_t_13 = __pyx_v_zM;
__pyx_t_12 = __pyx_v_yM;
__pyx_t_11 = __pyx_v_xM;
*((float *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_imRad.data + __pyx_t_13 * __pyx_v_imRad.strides[0]) ) + __pyx_t_12 * __pyx_v_imRad.strides[1]) ) + __pyx_t_11 * __pyx_v_imRad.strides[2]) )) = __pyx_t_10;
}
__pyx_L9:;
}
}
}
108:
109:
+110: cdef void _calculate_3d_gradient(self, float[:,:,:] image, float[:,:,:] imGx, float[:,:,:] imGy, float[:,:,:] imGz):
static void __pyx_f_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_27RadialGradientConvergence3D__calculate_3d_gradient(CYTHON_UNUSED struct __pyx_obj_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *__pyx_v_self, __Pyx_memviewslice __pyx_v_image, __Pyx_memviewslice __pyx_v_imGx, __Pyx_memviewslice __pyx_v_imGy, __Pyx_memviewslice __pyx_v_imGz) {
int __pyx_v_w;
int __pyx_v_h;
int __pyx_v_d;
float __pyx_v_ip0;
float __pyx_v_ip1;
float __pyx_v_ip2;
float __pyx_v_ip3;
float __pyx_v_ip4;
float __pyx_v_ip5;
float __pyx_v_ip6;
float __pyx_v_ip7;
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int __pyx_v_y_i;
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+111: cdef int w = image.shape[2]
__pyx_v_w = (__pyx_v_image.shape[2]);
+112: cdef int h = image.shape[1]
__pyx_v_h = (__pyx_v_image.shape[1]);
+113: cdef int d = image.shape[0]
__pyx_v_d = (__pyx_v_image.shape[0]);
114:
115: cdef float ip0, ip1, ip2, ip3, ip4, ip5, ip6, ip7
116:
117: cdef int z_i, y_i, x_i
118:
+119: for z_i in range(d-1):
__pyx_t_1 = (__pyx_v_d - 1);
__pyx_t_2 = __pyx_t_1;
for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
__pyx_v_z_i = __pyx_t_3;
+120: for y_i in range(h-1):
__pyx_t_4 = (__pyx_v_h - 1);
__pyx_t_5 = __pyx_t_4;
for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
__pyx_v_y_i = __pyx_t_6;
+121: for x_i in range(w-1):
__pyx_t_7 = (__pyx_v_w - 1);
__pyx_t_8 = __pyx_t_7;
for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
__pyx_v_x_i = __pyx_t_9;
+122: ip0 = image[z_i, y_i, x_i]
__pyx_t_10 = __pyx_v_z_i;
__pyx_t_11 = __pyx_v_y_i;
__pyx_t_12 = __pyx_v_x_i;
__pyx_v_ip0 = (*((float *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_image.data + __pyx_t_10 * __pyx_v_image.strides[0]) ) + __pyx_t_11 * __pyx_v_image.strides[1]) ) + __pyx_t_12 * __pyx_v_image.strides[2]) )));
+123: ip1 = image[z_i, y_i, x_i + 1]
__pyx_t_12 = __pyx_v_z_i;
__pyx_t_11 = __pyx_v_y_i;
__pyx_t_10 = (__pyx_v_x_i + 1);
__pyx_v_ip1 = (*((float *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_image.data + __pyx_t_12 * __pyx_v_image.strides[0]) ) + __pyx_t_11 * __pyx_v_image.strides[1]) ) + __pyx_t_10 * __pyx_v_image.strides[2]) )));
+124: ip2 = image[z_i, y_i + 1, x_i]
__pyx_t_10 = __pyx_v_z_i;
__pyx_t_11 = (__pyx_v_y_i + 1);
__pyx_t_12 = __pyx_v_x_i;
__pyx_v_ip2 = (*((float *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_image.data + __pyx_t_10 * __pyx_v_image.strides[0]) ) + __pyx_t_11 * __pyx_v_image.strides[1]) ) + __pyx_t_12 * __pyx_v_image.strides[2]) )));
+125: ip3 = image[z_i, y_i + 1, x_i + 1]
__pyx_t_12 = __pyx_v_z_i;
__pyx_t_11 = (__pyx_v_y_i + 1);
__pyx_t_10 = (__pyx_v_x_i + 1);
__pyx_v_ip3 = (*((float *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_image.data + __pyx_t_12 * __pyx_v_image.strides[0]) ) + __pyx_t_11 * __pyx_v_image.strides[1]) ) + __pyx_t_10 * __pyx_v_image.strides[2]) )));
+126: ip4 = image[z_i + 1, y_i, x_i]
__pyx_t_10 = (__pyx_v_z_i + 1);
__pyx_t_11 = __pyx_v_y_i;
__pyx_t_12 = __pyx_v_x_i;
__pyx_v_ip4 = (*((float *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_image.data + __pyx_t_10 * __pyx_v_image.strides[0]) ) + __pyx_t_11 * __pyx_v_image.strides[1]) ) + __pyx_t_12 * __pyx_v_image.strides[2]) )));
+127: ip5 = image[z_i + 1, y_i, x_i + 1]
__pyx_t_12 = (__pyx_v_z_i + 1);
__pyx_t_11 = __pyx_v_y_i;
__pyx_t_10 = (__pyx_v_x_i + 1);
__pyx_v_ip5 = (*((float *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_image.data + __pyx_t_12 * __pyx_v_image.strides[0]) ) + __pyx_t_11 * __pyx_v_image.strides[1]) ) + __pyx_t_10 * __pyx_v_image.strides[2]) )));
+128: ip6 = image[z_i + 1, y_i + 1, x_i]
__pyx_t_10 = (__pyx_v_z_i + 1);
__pyx_t_11 = (__pyx_v_y_i + 1);
__pyx_t_12 = __pyx_v_x_i;
__pyx_v_ip6 = (*((float *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_image.data + __pyx_t_10 * __pyx_v_image.strides[0]) ) + __pyx_t_11 * __pyx_v_image.strides[1]) ) + __pyx_t_12 * __pyx_v_image.strides[2]) )));
+129: ip7 = image[z_i + 1, y_i + 1, x_i + 1]
__pyx_t_12 = (__pyx_v_z_i + 1);
__pyx_t_11 = (__pyx_v_y_i + 1);
__pyx_t_10 = (__pyx_v_x_i + 1);
__pyx_v_ip7 = (*((float *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_image.data + __pyx_t_12 * __pyx_v_image.strides[0]) ) + __pyx_t_11 * __pyx_v_image.strides[1]) ) + __pyx_t_10 * __pyx_v_image.strides[2]) )));
+130: imGx[z_i, y_i, x_i] = (ip1 + ip3 + ip5 + ip7 - ip0 - ip2 - ip4 - ip6) / 4
__pyx_t_10 = __pyx_v_z_i;
__pyx_t_11 = __pyx_v_y_i;
__pyx_t_12 = __pyx_v_x_i;
*((float *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_imGx.data + __pyx_t_10 * __pyx_v_imGx.strides[0]) ) + __pyx_t_11 * __pyx_v_imGx.strides[1]) ) + __pyx_t_12 * __pyx_v_imGx.strides[2]) )) = ((((((((__pyx_v_ip1 + __pyx_v_ip3) + __pyx_v_ip5) + __pyx_v_ip7) - __pyx_v_ip0) - __pyx_v_ip2) - __pyx_v_ip4) - __pyx_v_ip6) / 4.0);
+131: imGy[z_i, y_i, x_i] = (ip2 + ip3 + ip6 + ip7 - ip0 - ip1 - ip4 - ip5) / 4
__pyx_t_12 = __pyx_v_z_i;
__pyx_t_11 = __pyx_v_y_i;
__pyx_t_10 = __pyx_v_x_i;
*((float *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_imGy.data + __pyx_t_12 * __pyx_v_imGy.strides[0]) ) + __pyx_t_11 * __pyx_v_imGy.strides[1]) ) + __pyx_t_10 * __pyx_v_imGy.strides[2]) )) = ((((((((__pyx_v_ip2 + __pyx_v_ip3) + __pyx_v_ip6) + __pyx_v_ip7) - __pyx_v_ip0) - __pyx_v_ip1) - __pyx_v_ip4) - __pyx_v_ip5) / 4.0);
+132: imGz[z_i, y_i, x_i] = (ip4 + ip5 + ip6 + ip7 - ip0 - ip1 - ip2 - ip3) / 4
__pyx_t_10 = __pyx_v_z_i;
__pyx_t_11 = __pyx_v_y_i;
__pyx_t_12 = __pyx_v_x_i;
*((float *) ( /* dim=2 */ (( /* dim=1 */ (( /* dim=0 */ (__pyx_v_imGz.data + __pyx_t_10 * __pyx_v_imGz.strides[0]) ) + __pyx_t_11 * __pyx_v_imGz.strides[1]) ) + __pyx_t_12 * __pyx_v_imGz.strides[2]) )) = ((((((((__pyx_v_ip4 + __pyx_v_ip5) + __pyx_v_ip6) + __pyx_v_ip7) - __pyx_v_ip0) - __pyx_v_ip1) - __pyx_v_ip2) - __pyx_v_ip3) / 4.0);
}
}
}
133:
134:
+135: cdef float _calculate_3d_RGC(self, int xM, int yM, int zM, float[:,:,:] imGx, float[:,:,:] imGy, float[:,:,:] imGz):
static float __pyx_f_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_27RadialGradientConvergence3D__calculate_3d_RGC(struct __pyx_obj_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *__pyx_v_self, int __pyx_v_xM, int __pyx_v_yM, int __pyx_v_zM, __Pyx_memviewslice __pyx_v_imGx, CYTHON_UNUSED __Pyx_memviewslice __pyx_v_imGy, CYTHON_UNUSED __Pyx_memviewslice __pyx_v_imGz) {
int __pyx_v_w;
int __pyx_v_h;
int __pyx_v_d;
float __pyx_v_vx;
float __pyx_v_vy;
float __pyx_v_vz;
float __pyx_v_Gx;
float __pyx_v_Gy;
float __pyx_v_Gz;
float __pyx_v_dx;
float __pyx_v_dy;
float __pyx_v_dz;
float __pyx_v_distance;
float __pyx_v_distanceWeight;
float __pyx_v_GdotR;
float __pyx_v_Dk;
float __pyx_v_xc;
float __pyx_v_yc;
float __pyx_v_zc;
float __pyx_v_RGC;
float __pyx_v_distanceWeightSum;
int __pyx_v__start;
int __pyx_v__end;
int __pyx_v_i;
int __pyx_v_j;
int __pyx_v_k;
float __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("_calculate_3d_RGC", 0);
/* … */
/* function exit code */
__pyx_L1_error:;
__Pyx_AddTraceback("nanopyx.core.transform.sr_3D_radial_gradient_convergence.RadialGradientConvergence3D._calculate_3d_RGC", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
+136: cdef int w = imGx.shape[2]
__pyx_v_w = (__pyx_v_imGx.shape[2]);
+137: cdef int h = imGx.shape[1]
__pyx_v_h = (__pyx_v_imGx.shape[1]);
+138: cdef int d = imGx.shape[0]
__pyx_v_d = (__pyx_v_imGx.shape[0]);
139:
140: cdef float vx, vy, vz, Gx, Gy, Gz
141:
142: cdef float dx, dy, dz
143: cdef float distance, distanceWeight, GdotR, Dk
144:
+145: cdef float xc = (xM + 0.5) / self.magnification # subpixel in the centre
__pyx_v_xc = ((__pyx_v_xM + 0.5) / ((double)__pyx_v_self->magnification));
+146: cdef float yc = (yM + 0.5) / self.magnification # subpixel in the centre
__pyx_v_yc = ((__pyx_v_yM + 0.5) / ((double)__pyx_v_self->magnification));
+147: cdef float zc = (zM + 0.5) / self.magnification
__pyx_v_zc = ((__pyx_v_zM + 0.5) / ((double)__pyx_v_self->magnification));
148:
+149: cdef float RGC = 0 # Radial Gradient Convergence
__pyx_v_RGC = 0.0;
+150: cdef float distanceWeightSum = 0
__pyx_v_distanceWeightSum = 0.0;
151:
+152: cdef int _start = -(<int>(Gx_Gy_MAGNIFICATION * self.fwhm))
__pyx_v__start = (-((int)(__pyx_v_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_Gx_Gy_MAGNIFICATION * __pyx_v_self->fwhm)));
+153: cdef int _end = <int>(Gx_Gy_MAGNIFICATION * self.fwhm + 1)
__pyx_v__end = ((int)((__pyx_v_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_Gx_Gy_MAGNIFICATION * __pyx_v_self->fwhm) + 1.0));
154:
155: cdef int i, j, k
156:
+157: for k in range(_start, _end):
__pyx_t_1 = __pyx_v__end;
__pyx_t_2 = __pyx_t_1;
for (__pyx_t_3 = __pyx_v__start; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
__pyx_v_k = __pyx_t_3;
+158: vz = (<int>(Gx_Gy_MAGNIFICATION * zc) + k) / Gx_Gy_MAGNIFICATION
__pyx_v_vz = (((float)(((int)(__pyx_v_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_Gx_Gy_MAGNIFICATION * __pyx_v_zc)) + __pyx_v_k)) / __pyx_v_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_Gx_Gy_MAGNIFICATION);
159:
+160: if 0 < vz <= d - 1:
__pyx_t_4 = (0.0 < __pyx_v_vz);
if (__pyx_t_4) {
__pyx_t_4 = (__pyx_v_vz <= (__pyx_v_d - 1));
}
if (__pyx_t_4) {
/* … */
}
}
+161: for j in range(_start, _end):
__pyx_t_5 = __pyx_v__end;
__pyx_t_6 = __pyx_t_5;
for (__pyx_t_7 = __pyx_v__start; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) {
__pyx_v_j = __pyx_t_7;
+162: vy = (<int>(Gx_Gy_MAGNIFICATION * yc) + j) / Gx_Gy_MAGNIFICATION # position in continuous space
__pyx_v_vy = (((float)(((int)(__pyx_v_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_Gx_Gy_MAGNIFICATION * __pyx_v_yc)) + __pyx_v_j)) / __pyx_v_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_Gx_Gy_MAGNIFICATION);
163:
+164: if 0 < vy <= h - 1:
__pyx_t_4 = (0.0 < __pyx_v_vy);
if (__pyx_t_4) {
__pyx_t_4 = (__pyx_v_vy <= (__pyx_v_h - 1));
}
if (__pyx_t_4) {
/* … */
}
}
165:
+166: for i in range(_start, _end):
__pyx_t_8 = __pyx_v__end;
__pyx_t_9 = __pyx_t_8;
for (__pyx_t_10 = __pyx_v__start; __pyx_t_10 < __pyx_t_9; __pyx_t_10+=1) {
__pyx_v_i = __pyx_t_10;
+167: vx = (<int>(Gx_Gy_MAGNIFICATION * xc) + i) / Gx_Gy_MAGNIFICATION # position in continuous space
__pyx_v_vx = (((float)(((int)(__pyx_v_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_Gx_Gy_MAGNIFICATION * __pyx_v_xc)) + __pyx_v_i)) / __pyx_v_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_Gx_Gy_MAGNIFICATION);
168:
+169: if 0 < vx <= w - 1:
__pyx_t_4 = (0.0 < __pyx_v_vx);
if (__pyx_t_4) {
__pyx_t_4 = (__pyx_v_vx <= (__pyx_v_w - 1));
}
if (__pyx_t_4) {
/* … */
}
}
170:
+171: dx = vx - xc
__pyx_v_dx = (__pyx_v_vx - __pyx_v_xc);
+172: dy = vy - yc
__pyx_v_dy = (__pyx_v_vy - __pyx_v_yc);
+173: dz = vz - zc
__pyx_v_dz = (__pyx_v_vz - __pyx_v_zc);
+174: distance = sqrt(dx * dx + dy * dy + dz * dz)
__pyx_v_distance = sqrt((((__pyx_v_dx * __pyx_v_dx) + (__pyx_v_dy * __pyx_v_dy)) + (__pyx_v_dz * __pyx_v_dz)));
175:
+176: if distance != 0 and distance <= self.tSO:
__pyx_t_11 = (__pyx_v_distance != 0.0);
if (__pyx_t_11) {
} else {
__pyx_t_4 = __pyx_t_11;
goto __pyx_L13_bool_binop_done;
}
__pyx_t_11 = (__pyx_v_distance <= __pyx_v_self->tSO);
__pyx_t_4 = __pyx_t_11;
__pyx_L13_bool_binop_done:;
if (__pyx_t_4) {
/* … */
}
177: #TODO: interpolate gradients in 3D
+178: Gx = 1
__pyx_v_Gx = 1.0;
+179: Gy = 1
__pyx_v_Gy = 1.0;
+180: Gz = 1
__pyx_v_Gz = 1.0;
181:
+182: distanceWeight = self._calculateDW(distance)
__pyx_t_12 = ((struct __pyx_vtabstruct_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *)__pyx_v_self->__pyx_vtab)->_calculateDW(__pyx_v_self, __pyx_v_distance); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 182, __pyx_L1_error)
__pyx_v_distanceWeight = __pyx_t_12;
+183: distanceWeightSum += distanceWeight
__pyx_v_distanceWeightSum = (__pyx_v_distanceWeightSum + __pyx_v_distanceWeight);
+184: GdotR = Gx*dx + Gy*dy + Gz*dz
__pyx_v_GdotR = (((__pyx_v_Gx * __pyx_v_dx) + (__pyx_v_Gy * __pyx_v_dy)) + (__pyx_v_Gz * __pyx_v_dz));
185:
+186: if GdotR < 0:
__pyx_t_4 = (__pyx_v_GdotR < 0.0);
if (__pyx_t_4) {
/* … */
}
+187: Dk = self._calculateDk(Gx, Gy, Gz, dx, dy, dz, distance)
__pyx_t_12 = ((struct __pyx_vtabstruct_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *)__pyx_v_self->__pyx_vtab)->_calculateDk(__pyx_v_self, __pyx_v_Gx, __pyx_v_Gy, __pyx_v_Gz, __pyx_v_dx, __pyx_v_dy, __pyx_v_dz, __pyx_v_distance); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 187, __pyx_L1_error)
__pyx_v_Dk = __pyx_t_12;
+188: RGC += Dk * distanceWeight
__pyx_v_RGC = (__pyx_v_RGC + (__pyx_v_Dk * __pyx_v_distanceWeight));
+189: RGC /= distanceWeightSum
__pyx_v_RGC = (__pyx_v_RGC / __pyx_v_distanceWeightSum);
+190: if RGC >= 0:
__pyx_t_4 = (__pyx_v_RGC >= 0.0);
if (__pyx_t_4) {
/* … */
goto __pyx_L16;
}
+191: RGC = RGC ** self.sensitivity
__pyx_v_RGC = powf(__pyx_v_RGC, __pyx_v_self->sensitivity);
192: else:
+193: RGC = 0
/*else*/ {
__pyx_v_RGC = 0.0;
}
__pyx_L16:;
194:
+195: return RGC
__pyx_r = __pyx_v_RGC; goto __pyx_L0;
196:
197:
+198: cdef float _calculateDW(self, float distance) nogil: # distance weight
static float __pyx_f_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_27RadialGradientConvergence3D__calculateDW(struct __pyx_obj_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *__pyx_v_self, float __pyx_v_distance) {
float __pyx_r;
/* … */
/* function exit code */
__pyx_L0:;
return __pyx_r;
}
+199: return (distance * exp((-distance * distance) / self.tSS)) ** 4
__pyx_r = pow((__pyx_v_distance * exp((((-__pyx_v_distance) * __pyx_v_distance) / __pyx_v_self->tSS))), 4.0); goto __pyx_L0;
200:
201:
+202: cdef float _calculateDk(self, float Gx, float Gy, float Gz, float dx, float dy, float dz, float distance) nogil:
static float __pyx_f_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_27RadialGradientConvergence3D__calculateDk(CYTHON_UNUSED struct __pyx_obj_7nanopyx_4core_9transform_33sr_3D_radial_gradient_convergence_RadialGradientConvergence3D *__pyx_v_self, float __pyx_v_Gx, float __pyx_v_Gy, float __pyx_v_Gz, float __pyx_v_dx, float __pyx_v_dy, float __pyx_v_dz, float __pyx_v_distance) {
double __pyx_v_Dk;
float __pyx_r;
/* … */
/* function exit code */
__pyx_L0:;
return __pyx_r;
}
+203: Dk = fabs(Gy * dz - Gz * dy - Gx * dz + Gz * dx + Gx * dy - Gy * dx) / sqrt(Gx * Gx + Gy * Gy + Gz * Gz)
__pyx_v_Dk = (fabs(((((((__pyx_v_Gy * __pyx_v_dz) - (__pyx_v_Gz * __pyx_v_dy)) - (__pyx_v_Gx * __pyx_v_dz)) + (__pyx_v_Gz * __pyx_v_dx)) + (__pyx_v_Gx * __pyx_v_dy)) - (__pyx_v_Gy * __pyx_v_dx))) / sqrt((((__pyx_v_Gx * __pyx_v_Gx) + (__pyx_v_Gy * __pyx_v_Gy)) + (__pyx_v_Gz * __pyx_v_Gz))));
+204: if isnan(Dk):
__pyx_t_1 = isnan(__pyx_v_Dk);
if (__pyx_t_1) {
/* … */
}
+205: Dk = distance
__pyx_v_Dk = __pyx_v_distance;
+206: Dk = 1 - Dk / distance # if 1: vector pointing exactly to the centre
__pyx_v_Dk = (1.0 - (__pyx_v_Dk / ((double)__pyx_v_distance)));
+207: return Dk
__pyx_r = __pyx_v_Dk; goto __pyx_L0;