Old engine for Continuous Time Bayesian Networks. Superseded by reCTBN. 🐍
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903 lines
31 KiB
903 lines
31 KiB
# NumPy static imports for Cython < 3.0
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#
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# If any of the PyArray_* functions are called, import_array must be
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# called first.
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#
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# Author: Dag Sverre Seljebotn
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#
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DEF _buffer_format_string_len = 255
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cimport cpython.buffer as pybuf
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from cpython.ref cimport Py_INCREF
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from cpython.mem cimport PyObject_Malloc, PyObject_Free
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from cpython.object cimport PyObject, PyTypeObject
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from cpython.buffer cimport PyObject_GetBuffer
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from cpython.type cimport type
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cimport libc.stdio as stdio
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cdef extern from "Python.h":
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ctypedef int Py_intptr_t
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cdef extern from "numpy/arrayobject.h":
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ctypedef Py_intptr_t npy_intp
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ctypedef size_t npy_uintp
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cdef enum NPY_TYPES:
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NPY_BOOL
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NPY_BYTE
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NPY_UBYTE
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NPY_SHORT
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NPY_USHORT
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NPY_INT
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NPY_UINT
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NPY_LONG
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NPY_ULONG
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NPY_LONGLONG
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NPY_ULONGLONG
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NPY_FLOAT
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NPY_DOUBLE
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NPY_LONGDOUBLE
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NPY_CFLOAT
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NPY_CDOUBLE
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NPY_CLONGDOUBLE
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NPY_OBJECT
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NPY_STRING
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NPY_UNICODE
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NPY_VOID
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NPY_DATETIME
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NPY_TIMEDELTA
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NPY_NTYPES
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NPY_NOTYPE
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NPY_INT8
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NPY_INT16
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NPY_INT32
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NPY_INT64
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NPY_INT128
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NPY_INT256
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NPY_UINT8
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NPY_UINT16
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NPY_UINT32
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NPY_UINT64
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NPY_UINT128
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NPY_UINT256
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NPY_FLOAT16
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NPY_FLOAT32
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NPY_FLOAT64
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NPY_FLOAT80
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NPY_FLOAT96
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NPY_FLOAT128
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NPY_FLOAT256
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NPY_COMPLEX32
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NPY_COMPLEX64
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NPY_COMPLEX128
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NPY_COMPLEX160
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NPY_COMPLEX192
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NPY_COMPLEX256
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NPY_COMPLEX512
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NPY_INTP
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ctypedef enum NPY_ORDER:
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NPY_ANYORDER
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NPY_CORDER
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NPY_FORTRANORDER
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NPY_KEEPORDER
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ctypedef enum NPY_CASTING:
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NPY_NO_CASTING
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NPY_EQUIV_CASTING
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NPY_SAFE_CASTING
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NPY_SAME_KIND_CASTING
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NPY_UNSAFE_CASTING
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ctypedef enum NPY_CLIPMODE:
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NPY_CLIP
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NPY_WRAP
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NPY_RAISE
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ctypedef enum NPY_SCALARKIND:
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NPY_NOSCALAR,
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NPY_BOOL_SCALAR,
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NPY_INTPOS_SCALAR,
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NPY_INTNEG_SCALAR,
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NPY_FLOAT_SCALAR,
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NPY_COMPLEX_SCALAR,
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NPY_OBJECT_SCALAR
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ctypedef enum NPY_SORTKIND:
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NPY_QUICKSORT
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NPY_HEAPSORT
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NPY_MERGESORT
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ctypedef enum NPY_SEARCHSIDE:
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NPY_SEARCHLEFT
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NPY_SEARCHRIGHT
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enum:
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# DEPRECATED since NumPy 1.7 ! Do not use in new code!
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NPY_C_CONTIGUOUS
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NPY_F_CONTIGUOUS
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NPY_CONTIGUOUS
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NPY_FORTRAN
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NPY_OWNDATA
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NPY_FORCECAST
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NPY_ENSURECOPY
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NPY_ENSUREARRAY
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NPY_ELEMENTSTRIDES
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NPY_ALIGNED
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NPY_NOTSWAPPED
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NPY_WRITEABLE
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NPY_UPDATEIFCOPY
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NPY_ARR_HAS_DESCR
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NPY_BEHAVED
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NPY_BEHAVED_NS
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NPY_CARRAY
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NPY_CARRAY_RO
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NPY_FARRAY
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NPY_FARRAY_RO
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NPY_DEFAULT
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NPY_IN_ARRAY
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NPY_OUT_ARRAY
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NPY_INOUT_ARRAY
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NPY_IN_FARRAY
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NPY_OUT_FARRAY
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NPY_INOUT_FARRAY
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NPY_UPDATE_ALL
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enum:
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# Added in NumPy 1.7 to replace the deprecated enums above.
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NPY_ARRAY_C_CONTIGUOUS
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NPY_ARRAY_F_CONTIGUOUS
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NPY_ARRAY_OWNDATA
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NPY_ARRAY_FORCECAST
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NPY_ARRAY_ENSURECOPY
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NPY_ARRAY_ENSUREARRAY
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NPY_ARRAY_ELEMENTSTRIDES
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NPY_ARRAY_ALIGNED
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NPY_ARRAY_NOTSWAPPED
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NPY_ARRAY_WRITEABLE
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NPY_ARRAY_UPDATEIFCOPY
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NPY_ARRAY_BEHAVED
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NPY_ARRAY_BEHAVED_NS
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NPY_ARRAY_CARRAY
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NPY_ARRAY_CARRAY_RO
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NPY_ARRAY_FARRAY
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NPY_ARRAY_FARRAY_RO
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NPY_ARRAY_DEFAULT
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NPY_ARRAY_IN_ARRAY
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NPY_ARRAY_OUT_ARRAY
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NPY_ARRAY_INOUT_ARRAY
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NPY_ARRAY_IN_FARRAY
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NPY_ARRAY_OUT_FARRAY
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NPY_ARRAY_INOUT_FARRAY
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NPY_ARRAY_UPDATE_ALL
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cdef enum:
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NPY_MAXDIMS
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npy_intp NPY_MAX_ELSIZE
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ctypedef void (*PyArray_VectorUnaryFunc)(void *, void *, npy_intp, void *, void *)
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ctypedef struct PyArray_ArrayDescr:
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# shape is a tuple, but Cython doesn't support "tuple shape"
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# inside a non-PyObject declaration, so we have to declare it
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# as just a PyObject*.
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PyObject* shape
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ctypedef struct PyArray_Descr:
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pass
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ctypedef class numpy.dtype [object PyArray_Descr, check_size ignore]:
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# Use PyDataType_* macros when possible, however there are no macros
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# for accessing some of the fields, so some are defined.
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cdef PyTypeObject* typeobj
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cdef char kind
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cdef char type
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# Numpy sometimes mutates this without warning (e.g. it'll
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# sometimes change "|" to "<" in shared dtype objects on
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# little-endian machines). If this matters to you, use
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# PyArray_IsNativeByteOrder(dtype.byteorder) instead of
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# directly accessing this field.
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cdef char byteorder
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cdef char flags
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cdef int type_num
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cdef int itemsize "elsize"
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cdef int alignment
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cdef dict fields
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cdef tuple names
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# Use PyDataType_HASSUBARRAY to test whether this field is
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# valid (the pointer can be NULL). Most users should access
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# this field via the inline helper method PyDataType_SHAPE.
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cdef PyArray_ArrayDescr* subarray
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ctypedef class numpy.flatiter [object PyArrayIterObject, check_size ignore]:
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# Use through macros
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pass
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ctypedef class numpy.broadcast [object PyArrayMultiIterObject, check_size ignore]:
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cdef int numiter
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cdef npy_intp size, index
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cdef int nd
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cdef npy_intp *dimensions
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cdef void **iters
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ctypedef struct PyArrayObject:
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# For use in situations where ndarray can't replace PyArrayObject*,
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# like PyArrayObject**.
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pass
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ctypedef class numpy.ndarray [object PyArrayObject, check_size ignore]:
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cdef __cythonbufferdefaults__ = {"mode": "strided"}
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cdef:
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# Only taking a few of the most commonly used and stable fields.
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# One should use PyArray_* macros instead to access the C fields.
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char *data
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int ndim "nd"
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npy_intp *shape "dimensions"
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npy_intp *strides
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dtype descr # deprecated since NumPy 1.7 !
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PyObject* base # NOT PUBLIC, DO NOT USE !
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ctypedef unsigned char npy_bool
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ctypedef signed char npy_byte
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ctypedef signed short npy_short
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ctypedef signed int npy_int
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ctypedef signed long npy_long
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ctypedef signed long long npy_longlong
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ctypedef unsigned char npy_ubyte
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ctypedef unsigned short npy_ushort
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ctypedef unsigned int npy_uint
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ctypedef unsigned long npy_ulong
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ctypedef unsigned long long npy_ulonglong
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ctypedef float npy_float
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ctypedef double npy_double
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ctypedef long double npy_longdouble
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ctypedef signed char npy_int8
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ctypedef signed short npy_int16
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ctypedef signed int npy_int32
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ctypedef signed long long npy_int64
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ctypedef signed long long npy_int96
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ctypedef signed long long npy_int128
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ctypedef unsigned char npy_uint8
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ctypedef unsigned short npy_uint16
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ctypedef unsigned int npy_uint32
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ctypedef unsigned long long npy_uint64
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ctypedef unsigned long long npy_uint96
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ctypedef unsigned long long npy_uint128
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ctypedef float npy_float32
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ctypedef double npy_float64
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ctypedef long double npy_float80
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ctypedef long double npy_float96
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ctypedef long double npy_float128
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ctypedef struct npy_cfloat:
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double real
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double imag
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ctypedef struct npy_cdouble:
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double real
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double imag
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ctypedef struct npy_clongdouble:
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long double real
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long double imag
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ctypedef struct npy_complex64:
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float real
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float imag
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ctypedef struct npy_complex128:
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double real
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double imag
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ctypedef struct npy_complex160:
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long double real
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long double imag
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ctypedef struct npy_complex192:
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long double real
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long double imag
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ctypedef struct npy_complex256:
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long double real
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long double imag
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ctypedef struct PyArray_Dims:
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npy_intp *ptr
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int len
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int _import_array() except -1
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# A second definition so _import_array isn't marked as used when we use it here.
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# Do not use - subject to change any time.
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int __pyx_import_array "_import_array"() except -1
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#
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# Macros from ndarrayobject.h
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#
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bint PyArray_CHKFLAGS(ndarray m, int flags) nogil
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bint PyArray_IS_C_CONTIGUOUS(ndarray arr) nogil
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bint PyArray_IS_F_CONTIGUOUS(ndarray arr) nogil
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bint PyArray_ISCONTIGUOUS(ndarray m) nogil
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bint PyArray_ISWRITEABLE(ndarray m) nogil
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bint PyArray_ISALIGNED(ndarray m) nogil
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int PyArray_NDIM(ndarray) nogil
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bint PyArray_ISONESEGMENT(ndarray) nogil
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bint PyArray_ISFORTRAN(ndarray) nogil
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int PyArray_FORTRANIF(ndarray) nogil
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void* PyArray_DATA(ndarray) nogil
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char* PyArray_BYTES(ndarray) nogil
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npy_intp* PyArray_DIMS(ndarray) nogil
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npy_intp* PyArray_STRIDES(ndarray) nogil
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npy_intp PyArray_DIM(ndarray, size_t) nogil
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npy_intp PyArray_STRIDE(ndarray, size_t) nogil
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PyObject *PyArray_BASE(ndarray) nogil # returns borrowed reference!
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PyArray_Descr *PyArray_DESCR(ndarray) nogil # returns borrowed reference to dtype!
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int PyArray_FLAGS(ndarray) nogil
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npy_intp PyArray_ITEMSIZE(ndarray) nogil
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int PyArray_TYPE(ndarray arr) nogil
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object PyArray_GETITEM(ndarray arr, void *itemptr)
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int PyArray_SETITEM(ndarray arr, void *itemptr, object obj)
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bint PyTypeNum_ISBOOL(int) nogil
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bint PyTypeNum_ISUNSIGNED(int) nogil
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bint PyTypeNum_ISSIGNED(int) nogil
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bint PyTypeNum_ISINTEGER(int) nogil
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bint PyTypeNum_ISFLOAT(int) nogil
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bint PyTypeNum_ISNUMBER(int) nogil
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bint PyTypeNum_ISSTRING(int) nogil
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bint PyTypeNum_ISCOMPLEX(int) nogil
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bint PyTypeNum_ISPYTHON(int) nogil
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bint PyTypeNum_ISFLEXIBLE(int) nogil
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bint PyTypeNum_ISUSERDEF(int) nogil
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bint PyTypeNum_ISEXTENDED(int) nogil
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bint PyTypeNum_ISOBJECT(int) nogil
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bint PyDataType_ISBOOL(dtype) nogil
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bint PyDataType_ISUNSIGNED(dtype) nogil
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bint PyDataType_ISSIGNED(dtype) nogil
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bint PyDataType_ISINTEGER(dtype) nogil
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bint PyDataType_ISFLOAT(dtype) nogil
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bint PyDataType_ISNUMBER(dtype) nogil
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bint PyDataType_ISSTRING(dtype) nogil
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bint PyDataType_ISCOMPLEX(dtype) nogil
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bint PyDataType_ISPYTHON(dtype) nogil
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bint PyDataType_ISFLEXIBLE(dtype) nogil
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bint PyDataType_ISUSERDEF(dtype) nogil
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bint PyDataType_ISEXTENDED(dtype) nogil
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bint PyDataType_ISOBJECT(dtype) nogil
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bint PyDataType_HASFIELDS(dtype) nogil
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bint PyDataType_HASSUBARRAY(dtype) nogil
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bint PyArray_ISBOOL(ndarray) nogil
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bint PyArray_ISUNSIGNED(ndarray) nogil
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bint PyArray_ISSIGNED(ndarray) nogil
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bint PyArray_ISINTEGER(ndarray) nogil
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bint PyArray_ISFLOAT(ndarray) nogil
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bint PyArray_ISNUMBER(ndarray) nogil
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bint PyArray_ISSTRING(ndarray) nogil
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bint PyArray_ISCOMPLEX(ndarray) nogil
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bint PyArray_ISPYTHON(ndarray) nogil
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bint PyArray_ISFLEXIBLE(ndarray) nogil
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bint PyArray_ISUSERDEF(ndarray) nogil
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bint PyArray_ISEXTENDED(ndarray) nogil
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bint PyArray_ISOBJECT(ndarray) nogil
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bint PyArray_HASFIELDS(ndarray) nogil
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bint PyArray_ISVARIABLE(ndarray) nogil
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bint PyArray_SAFEALIGNEDCOPY(ndarray) nogil
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bint PyArray_ISNBO(char) nogil # works on ndarray.byteorder
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bint PyArray_IsNativeByteOrder(char) nogil # works on ndarray.byteorder
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bint PyArray_ISNOTSWAPPED(ndarray) nogil
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bint PyArray_ISBYTESWAPPED(ndarray) nogil
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bint PyArray_FLAGSWAP(ndarray, int) nogil
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bint PyArray_ISCARRAY(ndarray) nogil
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bint PyArray_ISCARRAY_RO(ndarray) nogil
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bint PyArray_ISFARRAY(ndarray) nogil
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bint PyArray_ISFARRAY_RO(ndarray) nogil
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bint PyArray_ISBEHAVED(ndarray) nogil
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bint PyArray_ISBEHAVED_RO(ndarray) nogil
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bint PyDataType_ISNOTSWAPPED(dtype) nogil
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bint PyDataType_ISBYTESWAPPED(dtype) nogil
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bint PyArray_DescrCheck(object)
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bint PyArray_Check(object)
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bint PyArray_CheckExact(object)
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# Cannot be supported due to out arg:
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# bint PyArray_HasArrayInterfaceType(object, dtype, object, object&)
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# bint PyArray_HasArrayInterface(op, out)
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bint PyArray_IsZeroDim(object)
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# Cannot be supported due to ## ## in macro:
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# bint PyArray_IsScalar(object, verbatim work)
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bint PyArray_CheckScalar(object)
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bint PyArray_IsPythonNumber(object)
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bint PyArray_IsPythonScalar(object)
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bint PyArray_IsAnyScalar(object)
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bint PyArray_CheckAnyScalar(object)
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ndarray PyArray_GETCONTIGUOUS(ndarray)
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bint PyArray_SAMESHAPE(ndarray, ndarray) nogil
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npy_intp PyArray_SIZE(ndarray) nogil
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npy_intp PyArray_NBYTES(ndarray) nogil
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object PyArray_FROM_O(object)
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object PyArray_FROM_OF(object m, int flags)
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object PyArray_FROM_OT(object m, int type)
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object PyArray_FROM_OTF(object m, int type, int flags)
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object PyArray_FROMANY(object m, int type, int min, int max, int flags)
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object PyArray_ZEROS(int nd, npy_intp* dims, int type, int fortran)
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object PyArray_EMPTY(int nd, npy_intp* dims, int type, int fortran)
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void PyArray_FILLWBYTE(object, int val)
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npy_intp PyArray_REFCOUNT(object)
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object PyArray_ContiguousFromAny(op, int, int min_depth, int max_depth)
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unsigned char PyArray_EquivArrTypes(ndarray a1, ndarray a2)
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bint PyArray_EquivByteorders(int b1, int b2) nogil
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object PyArray_SimpleNew(int nd, npy_intp* dims, int typenum)
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object PyArray_SimpleNewFromData(int nd, npy_intp* dims, int typenum, void* data)
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#object PyArray_SimpleNewFromDescr(int nd, npy_intp* dims, dtype descr)
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object PyArray_ToScalar(void* data, ndarray arr)
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void* PyArray_GETPTR1(ndarray m, npy_intp i) nogil
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void* PyArray_GETPTR2(ndarray m, npy_intp i, npy_intp j) nogil
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void* PyArray_GETPTR3(ndarray m, npy_intp i, npy_intp j, npy_intp k) nogil
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void* PyArray_GETPTR4(ndarray m, npy_intp i, npy_intp j, npy_intp k, npy_intp l) nogil
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void PyArray_XDECREF_ERR(ndarray)
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# Cannot be supported due to out arg
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# void PyArray_DESCR_REPLACE(descr)
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object PyArray_Copy(ndarray)
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object PyArray_FromObject(object op, int type, int min_depth, int max_depth)
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object PyArray_ContiguousFromObject(object op, int type, int min_depth, int max_depth)
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object PyArray_CopyFromObject(object op, int type, int min_depth, int max_depth)
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object PyArray_Cast(ndarray mp, int type_num)
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object PyArray_Take(ndarray ap, object items, int axis)
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object PyArray_Put(ndarray ap, object items, object values)
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|
|
void PyArray_ITER_RESET(flatiter it) nogil
|
|
void PyArray_ITER_NEXT(flatiter it) nogil
|
|
void PyArray_ITER_GOTO(flatiter it, npy_intp* destination) nogil
|
|
void PyArray_ITER_GOTO1D(flatiter it, npy_intp ind) nogil
|
|
void* PyArray_ITER_DATA(flatiter it) nogil
|
|
bint PyArray_ITER_NOTDONE(flatiter it) nogil
|
|
|
|
void PyArray_MultiIter_RESET(broadcast multi) nogil
|
|
void PyArray_MultiIter_NEXT(broadcast multi) nogil
|
|
void PyArray_MultiIter_GOTO(broadcast multi, npy_intp dest) nogil
|
|
void PyArray_MultiIter_GOTO1D(broadcast multi, npy_intp ind) nogil
|
|
void* PyArray_MultiIter_DATA(broadcast multi, npy_intp i) nogil
|
|
void PyArray_MultiIter_NEXTi(broadcast multi, npy_intp i) nogil
|
|
bint PyArray_MultiIter_NOTDONE(broadcast multi) nogil
|
|
|
|
# Functions from __multiarray_api.h
|
|
|
|
# Functions taking dtype and returning object/ndarray are disabled
|
|
# for now as they steal dtype references. I'm conservative and disable
|
|
# more than is probably needed until it can be checked further.
|
|
int PyArray_SetNumericOps (object)
|
|
object PyArray_GetNumericOps ()
|
|
int PyArray_INCREF (ndarray)
|
|
int PyArray_XDECREF (ndarray)
|
|
void PyArray_SetStringFunction (object, int)
|
|
dtype PyArray_DescrFromType (int)
|
|
object PyArray_TypeObjectFromType (int)
|
|
char * PyArray_Zero (ndarray)
|
|
char * PyArray_One (ndarray)
|
|
#object PyArray_CastToType (ndarray, dtype, int)
|
|
int PyArray_CastTo (ndarray, ndarray)
|
|
int PyArray_CastAnyTo (ndarray, ndarray)
|
|
int PyArray_CanCastSafely (int, int)
|
|
npy_bool PyArray_CanCastTo (dtype, dtype)
|
|
int PyArray_ObjectType (object, int)
|
|
dtype PyArray_DescrFromObject (object, dtype)
|
|
#ndarray* PyArray_ConvertToCommonType (object, int *)
|
|
dtype PyArray_DescrFromScalar (object)
|
|
dtype PyArray_DescrFromTypeObject (object)
|
|
npy_intp PyArray_Size (object)
|
|
#object PyArray_Scalar (void *, dtype, object)
|
|
#object PyArray_FromScalar (object, dtype)
|
|
void PyArray_ScalarAsCtype (object, void *)
|
|
#int PyArray_CastScalarToCtype (object, void *, dtype)
|
|
#int PyArray_CastScalarDirect (object, dtype, void *, int)
|
|
object PyArray_ScalarFromObject (object)
|
|
#PyArray_VectorUnaryFunc * PyArray_GetCastFunc (dtype, int)
|
|
object PyArray_FromDims (int, int *, int)
|
|
#object PyArray_FromDimsAndDataAndDescr (int, int *, dtype, char *)
|
|
#object PyArray_FromAny (object, dtype, int, int, int, object)
|
|
object PyArray_EnsureArray (object)
|
|
object PyArray_EnsureAnyArray (object)
|
|
#object PyArray_FromFile (stdio.FILE *, dtype, npy_intp, char *)
|
|
#object PyArray_FromString (char *, npy_intp, dtype, npy_intp, char *)
|
|
#object PyArray_FromBuffer (object, dtype, npy_intp, npy_intp)
|
|
#object PyArray_FromIter (object, dtype, npy_intp)
|
|
object PyArray_Return (ndarray)
|
|
#object PyArray_GetField (ndarray, dtype, int)
|
|
#int PyArray_SetField (ndarray, dtype, int, object)
|
|
object PyArray_Byteswap (ndarray, npy_bool)
|
|
object PyArray_Resize (ndarray, PyArray_Dims *, int, NPY_ORDER)
|
|
int PyArray_MoveInto (ndarray, ndarray)
|
|
int PyArray_CopyInto (ndarray, ndarray)
|
|
int PyArray_CopyAnyInto (ndarray, ndarray)
|
|
int PyArray_CopyObject (ndarray, object)
|
|
object PyArray_NewCopy (ndarray, NPY_ORDER)
|
|
object PyArray_ToList (ndarray)
|
|
object PyArray_ToString (ndarray, NPY_ORDER)
|
|
int PyArray_ToFile (ndarray, stdio.FILE *, char *, char *)
|
|
int PyArray_Dump (object, object, int)
|
|
object PyArray_Dumps (object, int)
|
|
int PyArray_ValidType (int)
|
|
void PyArray_UpdateFlags (ndarray, int)
|
|
object PyArray_New (type, int, npy_intp *, int, npy_intp *, void *, int, int, object)
|
|
#object PyArray_NewFromDescr (type, dtype, int, npy_intp *, npy_intp *, void *, int, object)
|
|
#dtype PyArray_DescrNew (dtype)
|
|
dtype PyArray_DescrNewFromType (int)
|
|
double PyArray_GetPriority (object, double)
|
|
object PyArray_IterNew (object)
|
|
object PyArray_MultiIterNew (int, ...)
|
|
|
|
int PyArray_PyIntAsInt (object)
|
|
npy_intp PyArray_PyIntAsIntp (object)
|
|
int PyArray_Broadcast (broadcast)
|
|
void PyArray_FillObjectArray (ndarray, object)
|
|
int PyArray_FillWithScalar (ndarray, object)
|
|
npy_bool PyArray_CheckStrides (int, int, npy_intp, npy_intp, npy_intp *, npy_intp *)
|
|
dtype PyArray_DescrNewByteorder (dtype, char)
|
|
object PyArray_IterAllButAxis (object, int *)
|
|
#object PyArray_CheckFromAny (object, dtype, int, int, int, object)
|
|
#object PyArray_FromArray (ndarray, dtype, int)
|
|
object PyArray_FromInterface (object)
|
|
object PyArray_FromStructInterface (object)
|
|
#object PyArray_FromArrayAttr (object, dtype, object)
|
|
#NPY_SCALARKIND PyArray_ScalarKind (int, ndarray*)
|
|
int PyArray_CanCoerceScalar (int, int, NPY_SCALARKIND)
|
|
object PyArray_NewFlagsObject (object)
|
|
npy_bool PyArray_CanCastScalar (type, type)
|
|
#int PyArray_CompareUCS4 (npy_ucs4 *, npy_ucs4 *, register size_t)
|
|
int PyArray_RemoveSmallest (broadcast)
|
|
int PyArray_ElementStrides (object)
|
|
void PyArray_Item_INCREF (char *, dtype)
|
|
void PyArray_Item_XDECREF (char *, dtype)
|
|
object PyArray_FieldNames (object)
|
|
object PyArray_Transpose (ndarray, PyArray_Dims *)
|
|
object PyArray_TakeFrom (ndarray, object, int, ndarray, NPY_CLIPMODE)
|
|
object PyArray_PutTo (ndarray, object, object, NPY_CLIPMODE)
|
|
object PyArray_PutMask (ndarray, object, object)
|
|
object PyArray_Repeat (ndarray, object, int)
|
|
object PyArray_Choose (ndarray, object, ndarray, NPY_CLIPMODE)
|
|
int PyArray_Sort (ndarray, int, NPY_SORTKIND)
|
|
object PyArray_ArgSort (ndarray, int, NPY_SORTKIND)
|
|
object PyArray_SearchSorted (ndarray, object, NPY_SEARCHSIDE, PyObject *)
|
|
object PyArray_ArgMax (ndarray, int, ndarray)
|
|
object PyArray_ArgMin (ndarray, int, ndarray)
|
|
object PyArray_Reshape (ndarray, object)
|
|
object PyArray_Newshape (ndarray, PyArray_Dims *, NPY_ORDER)
|
|
object PyArray_Squeeze (ndarray)
|
|
#object PyArray_View (ndarray, dtype, type)
|
|
object PyArray_SwapAxes (ndarray, int, int)
|
|
object PyArray_Max (ndarray, int, ndarray)
|
|
object PyArray_Min (ndarray, int, ndarray)
|
|
object PyArray_Ptp (ndarray, int, ndarray)
|
|
object PyArray_Mean (ndarray, int, int, ndarray)
|
|
object PyArray_Trace (ndarray, int, int, int, int, ndarray)
|
|
object PyArray_Diagonal (ndarray, int, int, int)
|
|
object PyArray_Clip (ndarray, object, object, ndarray)
|
|
object PyArray_Conjugate (ndarray, ndarray)
|
|
object PyArray_Nonzero (ndarray)
|
|
object PyArray_Std (ndarray, int, int, ndarray, int)
|
|
object PyArray_Sum (ndarray, int, int, ndarray)
|
|
object PyArray_CumSum (ndarray, int, int, ndarray)
|
|
object PyArray_Prod (ndarray, int, int, ndarray)
|
|
object PyArray_CumProd (ndarray, int, int, ndarray)
|
|
object PyArray_All (ndarray, int, ndarray)
|
|
object PyArray_Any (ndarray, int, ndarray)
|
|
object PyArray_Compress (ndarray, object, int, ndarray)
|
|
object PyArray_Flatten (ndarray, NPY_ORDER)
|
|
object PyArray_Ravel (ndarray, NPY_ORDER)
|
|
npy_intp PyArray_MultiplyList (npy_intp *, int)
|
|
int PyArray_MultiplyIntList (int *, int)
|
|
void * PyArray_GetPtr (ndarray, npy_intp*)
|
|
int PyArray_CompareLists (npy_intp *, npy_intp *, int)
|
|
#int PyArray_AsCArray (object*, void *, npy_intp *, int, dtype)
|
|
#int PyArray_As1D (object*, char **, int *, int)
|
|
#int PyArray_As2D (object*, char ***, int *, int *, int)
|
|
int PyArray_Free (object, void *)
|
|
#int PyArray_Converter (object, object*)
|
|
int PyArray_IntpFromSequence (object, npy_intp *, int)
|
|
object PyArray_Concatenate (object, int)
|
|
object PyArray_InnerProduct (object, object)
|
|
object PyArray_MatrixProduct (object, object)
|
|
object PyArray_CopyAndTranspose (object)
|
|
object PyArray_Correlate (object, object, int)
|
|
int PyArray_TypestrConvert (int, int)
|
|
#int PyArray_DescrConverter (object, dtype*)
|
|
#int PyArray_DescrConverter2 (object, dtype*)
|
|
int PyArray_IntpConverter (object, PyArray_Dims *)
|
|
#int PyArray_BufferConverter (object, chunk)
|
|
int PyArray_AxisConverter (object, int *)
|
|
int PyArray_BoolConverter (object, npy_bool *)
|
|
int PyArray_ByteorderConverter (object, char *)
|
|
int PyArray_OrderConverter (object, NPY_ORDER *)
|
|
unsigned char PyArray_EquivTypes (dtype, dtype)
|
|
#object PyArray_Zeros (int, npy_intp *, dtype, int)
|
|
#object PyArray_Empty (int, npy_intp *, dtype, int)
|
|
object PyArray_Where (object, object, object)
|
|
object PyArray_Arange (double, double, double, int)
|
|
#object PyArray_ArangeObj (object, object, object, dtype)
|
|
int PyArray_SortkindConverter (object, NPY_SORTKIND *)
|
|
object PyArray_LexSort (object, int)
|
|
object PyArray_Round (ndarray, int, ndarray)
|
|
unsigned char PyArray_EquivTypenums (int, int)
|
|
int PyArray_RegisterDataType (dtype)
|
|
int PyArray_RegisterCastFunc (dtype, int, PyArray_VectorUnaryFunc *)
|
|
int PyArray_RegisterCanCast (dtype, int, NPY_SCALARKIND)
|
|
#void PyArray_InitArrFuncs (PyArray_ArrFuncs *)
|
|
object PyArray_IntTupleFromIntp (int, npy_intp *)
|
|
int PyArray_TypeNumFromName (char *)
|
|
int PyArray_ClipmodeConverter (object, NPY_CLIPMODE *)
|
|
#int PyArray_OutputConverter (object, ndarray*)
|
|
object PyArray_BroadcastToShape (object, npy_intp *, int)
|
|
void _PyArray_SigintHandler (int)
|
|
void* _PyArray_GetSigintBuf ()
|
|
#int PyArray_DescrAlignConverter (object, dtype*)
|
|
#int PyArray_DescrAlignConverter2 (object, dtype*)
|
|
int PyArray_SearchsideConverter (object, void *)
|
|
object PyArray_CheckAxis (ndarray, int *, int)
|
|
npy_intp PyArray_OverflowMultiplyList (npy_intp *, int)
|
|
int PyArray_CompareString (char *, char *, size_t)
|
|
int PyArray_SetBaseObject(ndarray, base) # NOTE: steals a reference to base! Use "set_array_base()" instead.
|
|
|
|
|
|
# Typedefs that matches the runtime dtype objects in
|
|
# the numpy module.
|
|
|
|
# The ones that are commented out needs an IFDEF function
|
|
# in Cython to enable them only on the right systems.
|
|
|
|
ctypedef npy_int8 int8_t
|
|
ctypedef npy_int16 int16_t
|
|
ctypedef npy_int32 int32_t
|
|
ctypedef npy_int64 int64_t
|
|
#ctypedef npy_int96 int96_t
|
|
#ctypedef npy_int128 int128_t
|
|
|
|
ctypedef npy_uint8 uint8_t
|
|
ctypedef npy_uint16 uint16_t
|
|
ctypedef npy_uint32 uint32_t
|
|
ctypedef npy_uint64 uint64_t
|
|
#ctypedef npy_uint96 uint96_t
|
|
#ctypedef npy_uint128 uint128_t
|
|
|
|
ctypedef npy_float32 float32_t
|
|
ctypedef npy_float64 float64_t
|
|
#ctypedef npy_float80 float80_t
|
|
#ctypedef npy_float128 float128_t
|
|
|
|
ctypedef float complex complex64_t
|
|
ctypedef double complex complex128_t
|
|
|
|
# The int types are mapped a bit surprising --
|
|
# numpy.int corresponds to 'l' and numpy.long to 'q'
|
|
ctypedef npy_long int_t
|
|
ctypedef npy_longlong long_t
|
|
ctypedef npy_longlong longlong_t
|
|
|
|
ctypedef npy_ulong uint_t
|
|
ctypedef npy_ulonglong ulong_t
|
|
ctypedef npy_ulonglong ulonglong_t
|
|
|
|
ctypedef npy_intp intp_t
|
|
ctypedef npy_uintp uintp_t
|
|
|
|
ctypedef npy_double float_t
|
|
ctypedef npy_double double_t
|
|
ctypedef npy_longdouble longdouble_t
|
|
|
|
ctypedef npy_cfloat cfloat_t
|
|
ctypedef npy_cdouble cdouble_t
|
|
ctypedef npy_clongdouble clongdouble_t
|
|
|
|
ctypedef npy_cdouble complex_t
|
|
|
|
cdef inline object PyArray_MultiIterNew1(a):
|
|
return PyArray_MultiIterNew(1, <void*>a)
|
|
|
|
cdef inline object PyArray_MultiIterNew2(a, b):
|
|
return PyArray_MultiIterNew(2, <void*>a, <void*>b)
|
|
|
|
cdef inline object PyArray_MultiIterNew3(a, b, c):
|
|
return PyArray_MultiIterNew(3, <void*>a, <void*>b, <void*> c)
|
|
|
|
cdef inline object PyArray_MultiIterNew4(a, b, c, d):
|
|
return PyArray_MultiIterNew(4, <void*>a, <void*>b, <void*>c, <void*> d)
|
|
|
|
cdef inline object PyArray_MultiIterNew5(a, b, c, d, e):
|
|
return PyArray_MultiIterNew(5, <void*>a, <void*>b, <void*>c, <void*> d, <void*> e)
|
|
|
|
cdef inline tuple PyDataType_SHAPE(dtype d):
|
|
if PyDataType_HASSUBARRAY(d):
|
|
return <tuple>d.subarray.shape
|
|
else:
|
|
return ()
|
|
|
|
|
|
#
|
|
# ufunc API
|
|
#
|
|
|
|
cdef extern from "numpy/ufuncobject.h":
|
|
|
|
ctypedef void (*PyUFuncGenericFunction) (char **, npy_intp *, npy_intp *, void *)
|
|
|
|
ctypedef class numpy.ufunc [object PyUFuncObject, check_size ignore]:
|
|
cdef:
|
|
int nin, nout, nargs
|
|
int identity
|
|
PyUFuncGenericFunction *functions
|
|
void **data
|
|
int ntypes
|
|
int check_return
|
|
char *name
|
|
char *types
|
|
char *doc
|
|
void *ptr
|
|
PyObject *obj
|
|
PyObject *userloops
|
|
|
|
cdef enum:
|
|
PyUFunc_Zero
|
|
PyUFunc_One
|
|
PyUFunc_None
|
|
UFUNC_ERR_IGNORE
|
|
UFUNC_ERR_WARN
|
|
UFUNC_ERR_RAISE
|
|
UFUNC_ERR_CALL
|
|
UFUNC_ERR_PRINT
|
|
UFUNC_ERR_LOG
|
|
UFUNC_MASK_DIVIDEBYZERO
|
|
UFUNC_MASK_OVERFLOW
|
|
UFUNC_MASK_UNDERFLOW
|
|
UFUNC_MASK_INVALID
|
|
UFUNC_SHIFT_DIVIDEBYZERO
|
|
UFUNC_SHIFT_OVERFLOW
|
|
UFUNC_SHIFT_UNDERFLOW
|
|
UFUNC_SHIFT_INVALID
|
|
UFUNC_FPE_DIVIDEBYZERO
|
|
UFUNC_FPE_OVERFLOW
|
|
UFUNC_FPE_UNDERFLOW
|
|
UFUNC_FPE_INVALID
|
|
UFUNC_ERR_DEFAULT
|
|
UFUNC_ERR_DEFAULT2
|
|
|
|
object PyUFunc_FromFuncAndData(PyUFuncGenericFunction *,
|
|
void **, char *, int, int, int, int, char *, char *, int)
|
|
int PyUFunc_RegisterLoopForType(ufunc, int,
|
|
PyUFuncGenericFunction, int *, void *)
|
|
int PyUFunc_GenericFunction \
|
|
(ufunc, PyObject *, PyObject *, PyArrayObject **)
|
|
void PyUFunc_f_f_As_d_d \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_d_d \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_f_f \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_g_g \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_F_F_As_D_D \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_F_F \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_D_D \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_G_G \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_O_O \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_ff_f_As_dd_d \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_ff_f \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_dd_d \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_gg_g \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_FF_F_As_DD_D \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_DD_D \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_FF_F \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_GG_G \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_OO_O \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_O_O_method \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_OO_O_method \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
void PyUFunc_On_Om \
|
|
(char **, npy_intp *, npy_intp *, void *)
|
|
int PyUFunc_GetPyValues \
|
|
(char *, int *, int *, PyObject **)
|
|
int PyUFunc_checkfperr \
|
|
(int, PyObject *, int *)
|
|
void PyUFunc_clearfperr()
|
|
int PyUFunc_getfperr()
|
|
int PyUFunc_handlefperr \
|
|
(int, PyObject *, int, int *)
|
|
int PyUFunc_ReplaceLoopBySignature \
|
|
(ufunc, PyUFuncGenericFunction, int *, PyUFuncGenericFunction *)
|
|
object PyUFunc_FromFuncAndDataAndSignature \
|
|
(PyUFuncGenericFunction *, void **, char *, int, int, int,
|
|
int, char *, char *, int, char *)
|
|
|
|
int _import_umath() except -1
|
|
|
|
cdef inline void set_array_base(ndarray arr, object base):
|
|
Py_INCREF(base) # important to do this before stealing the reference below!
|
|
PyArray_SetBaseObject(arr, base)
|
|
|
|
cdef inline object get_array_base(ndarray arr):
|
|
base = PyArray_BASE(arr)
|
|
if base is NULL:
|
|
return None
|
|
return <object>base
|
|
|
|
# Versions of the import_* functions which are more suitable for
|
|
# Cython code.
|
|
cdef inline int import_array() except -1:
|
|
try:
|
|
__pyx_import_array()
|
|
except Exception:
|
|
raise ImportError("numpy.core.multiarray failed to import")
|
|
|
|
cdef inline int import_umath() except -1:
|
|
try:
|
|
_import_umath()
|
|
except Exception:
|
|
raise ImportError("numpy.core.umath failed to import")
|
|
|
|
cdef inline int import_ufunc() except -1:
|
|
try:
|
|
_import_umath()
|
|
except Exception:
|
|
raise ImportError("numpy.core.umath failed to import")
|
|
|
|
cdef extern from *:
|
|
# Leave a marker that the NumPy declarations came from this file
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# See https://github.com/cython/cython/issues/3573
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"""
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/* NumPy API declarations from "numpy/__init__.pxd" */
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"""
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