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: fragments_helpers.c
+001: #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
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002: #cython: language_level=3
003: cimport cython
+004: import numpy as np
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005: cimport numpy as np
+006: np.import_array()
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007:
+008: INT64 = np.int64
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+009: ctypedef np.int64_t INT64_t
typedef __pyx_t_5numpy_int64_t __pyx_t_11chromatinhd_7loaders_17fragments_helpers_INT64_t;
+010: FLOAT64 = np.float64
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011: ctypedef np.float64_t FLOAT64_t
012:
+013: @cython.boundscheck(False) # turn off bounds-checking for entire function
/* Python wrapper */ static PyObject *__pyx_pw_11chromatinhd_7loaders_17fragments_helpers_1extract_fragments(PyObject *__pyx_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*/ static PyMethodDef __pyx_mdef_11chromatinhd_7loaders_17fragments_helpers_1extract_fragments = {"extract_fragments", (PyCFunction)(void*)(__Pyx_PyCFunction_FastCallWithKeywords)__pyx_pw_11chromatinhd_7loaders_17fragments_helpers_1extract_fragments, __Pyx_METH_FASTCALL|METH_KEYWORDS, 0}; static PyObject *__pyx_pw_11chromatinhd_7loaders_17fragments_helpers_1extract_fragments(PyObject *__pyx_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 ) { __Pyx_memviewslice __pyx_v_cellxgene_oi = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_memviewslice __pyx_v_cellxgene_indptr = { 0, 0, { 0 }, { 0 }, { 0 } }; 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__pyx_t_11chromatinhd_7loaders_17fragments_helpers_INT64_t __pyx_v_local_cellxgene_ix; __pyx_t_11chromatinhd_7loaders_17fragments_helpers_INT64_t __pyx_v_cellxgene_ix; __pyx_t_11chromatinhd_7loaders_17fragments_helpers_INT64_t __pyx_v_position; PyObject *__pyx_r = NULL; /* … */ /* function exit code */ __pyx_L1_error:; __PYX_XCLEAR_MEMVIEW(&__pyx_t_8, 1); __PYX_XCLEAR_MEMVIEW(&__pyx_t_9, 1); __Pyx_XDECREF(__pyx_t_12); __Pyx_AddTraceback("chromatinhd.loaders.fragments_helpers.extract_fragments", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* … */ __pyx_tuple__22 = PyTuple_Pack(11, __pyx_n_s_cellxgene_oi, __pyx_n_s_cellxgene_indptr, __pyx_n_s_coordinates, __pyx_n_s_genemapping, __pyx_n_s_out_coordinates, __pyx_n_s_out_genemapping, __pyx_n_s_out_local_cellxgene_ix, __pyx_n_s_out_ix, __pyx_n_s_local_cellxgene_ix, __pyx_n_s_cellxgene_ix, __pyx_n_s_position); if (unlikely(!__pyx_tuple__22)) __PYX_ERR(0, 13, __pyx_L1_error) __Pyx_GOTREF(__pyx_tuple__22); __Pyx_GIVEREF(__pyx_tuple__22); /* … */ __pyx_t_7 = __Pyx_CyFunction_New(&__pyx_mdef_11chromatinhd_7loaders_17fragments_helpers_1extract_fragments, 0, __pyx_n_s_extract_fragments, NULL, __pyx_n_s_chromatinhd_loaders_fragments_he, __pyx_d, ((PyObject *)__pyx_codeobj__23)); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 13, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_7); if (PyDict_SetItem(__pyx_d, __pyx_n_s_extract_fragments, __pyx_t_7) < 0) __PYX_ERR(0, 13, __pyx_L1_error) __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_codeobj__23 = (PyObject*)__Pyx_PyCode_New(7, 0, 0, 11, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__22, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_src_chromatinhd_loaders_fragment, __pyx_n_s_extract_fragments, 13, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__23)) __PYX_ERR(0, 13, __pyx_L1_error)
014: @cython.wraparound(False) # turn off negative index wrapping for entire function
015: @cython.cdivision
016: def extract_fragments(
017: INT64_t [::1] cellxgene_oi,
018: INT64_t [::1] cellxgene_indptr,
019: INT64_t [:,::1] coordinates,
020: INT64_t [::1] genemapping,
021: INT64_t [:,::1] out_coordinates,
022: INT64_t [::1] out_genemapping,
023: INT64_t [::1] out_local_cellxgene_ix,
024: ):
025: cdef INT64_t out_ix, local_cellxgene_ix, cellxgene_ix, position
+026: out_ix = 0 # will store where in the output array we are currently
__pyx_v_out_ix = 0;
+027: local_cellxgene_ix = 0 # will store the current fragment counting from 0
__pyx_v_local_cellxgene_ix = 0;
028:
+029: with nogil:
{ #ifdef WITH_THREAD PyThreadState *_save; _save = NULL; 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 #endif goto __pyx_L1_error; } __pyx_L5:; } }
+030: for local_cellxgene_ix in range(cellxgene_oi.shape[0]):
__pyx_t_1 = (__pyx_v_cellxgene_oi.shape[0]); __pyx_t_2 = __pyx_t_1; for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_local_cellxgene_ix = __pyx_t_3;
+031: cellxgene_ix = cellxgene_oi[local_cellxgene_ix]
__pyx_t_4 = __pyx_v_local_cellxgene_ix; __pyx_v_cellxgene_ix = (*((__pyx_t_11chromatinhd_7loaders_17fragments_helpers_INT64_t *) ( /* dim=0 */ ((char *) (((__pyx_t_11chromatinhd_7loaders_17fragments_helpers_INT64_t *) __pyx_v_cellxgene_oi.data) + __pyx_t_4)) )));
+032: for position in range(cellxgene_indptr[cellxgene_ix], cellxgene_indptr[cellxgene_ix+1]):
__pyx_t_4 = (__pyx_v_cellxgene_ix + 1); __pyx_t_5 = (*((__pyx_t_11chromatinhd_7loaders_17fragments_helpers_INT64_t *) ( /* dim=0 */ ((char *) (((__pyx_t_11chromatinhd_7loaders_17fragments_helpers_INT64_t *) __pyx_v_cellxgene_indptr.data) + __pyx_t_4)) ))); __pyx_t_4 = __pyx_v_cellxgene_ix; __pyx_t_6 = __pyx_t_5; for (__pyx_t_7 = (*((__pyx_t_11chromatinhd_7loaders_17fragments_helpers_INT64_t *) ( /* dim=0 */ ((char *) (((__pyx_t_11chromatinhd_7loaders_17fragments_helpers_INT64_t *) __pyx_v_cellxgene_indptr.data) + __pyx_t_4)) ))); __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { __pyx_v_position = __pyx_t_7;
+033: out_coordinates[out_ix] = coordinates[position]
__pyx_t_8.data = __pyx_v_coordinates.data;
__pyx_t_8.memview = __pyx_v_coordinates.memview;
__PYX_INC_MEMVIEW(&__pyx_t_8, 0);
{
Py_ssize_t __pyx_tmp_idx = __pyx_v_position;
Py_ssize_t __pyx_tmp_stride = __pyx_v_coordinates.strides[0];
__pyx_t_8.data += __pyx_tmp_idx * __pyx_tmp_stride;
}
__pyx_t_8.shape[0] = __pyx_v_coordinates.shape[1];
__pyx_t_8.strides[0] = __pyx_v_coordinates.strides[1];
__pyx_t_8.suboffsets[0] = -1;
__pyx_t_9.data = __pyx_v_out_coordinates.data;
__pyx_t_9.memview = __pyx_v_out_coordinates.memview;
__PYX_INC_MEMVIEW(&__pyx_t_9, 0);
{
Py_ssize_t __pyx_tmp_idx = __pyx_v_out_ix;
Py_ssize_t __pyx_tmp_stride = __pyx_v_out_coordinates.strides[0];
__pyx_t_9.data += __pyx_tmp_idx * __pyx_tmp_stride;
}
__pyx_t_9.shape[0] = __pyx_v_out_coordinates.shape[1];
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036:
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/*else*/ { __pyx_t_7 = __pyx_v_i; __pyx_t_8 = 4; *((__pyx_t_11chromatinhd_7loaders_17fragments_helpers_INT64_t *) ( /* dim=1 */ ((char *) (((__pyx_t_11chromatinhd_7loaders_17fragments_helpers_INT64_t *) ( /* dim=0 */ (__pyx_v_out_onehot.data + __pyx_t_7 * __pyx_v_out_onehot.strides[0]) )) + __pyx_t_8)) )) = 1; } __pyx_L5:; }
108:
+109: return out_onehot
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