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#################### View.MemoryView ####################
# This utility provides cython.array and cython.view.memoryview
from __future__ import absolute_import
cimport cython
# from cpython cimport ...
cdef extern from "Python.h":
int PyIndex_Check(object)
object PyLong_FromVoidPtr(void *)
cdef extern from "pythread.h":
ctypedef void *PyThread_type_lock
PyThread_type_lock PyThread_allocate_lock()
void PyThread_free_lock(PyThread_type_lock)
int PyThread_acquire_lock(PyThread_type_lock, int mode) nogil
void PyThread_release_lock(PyThread_type_lock) nogil
cdef extern from "<string.h>":
void *memset(void *b, int c, size_t len)
cdef extern from *:
int __Pyx_GetBuffer(object, Py_buffer *, int) except -1
void __Pyx_ReleaseBuffer(Py_buffer *)
ctypedef struct PyObject
ctypedef Py_ssize_t Py_intptr_t
void Py_INCREF(PyObject *)
void Py_DECREF(PyObject *)
void* PyMem_Malloc(size_t n)
void PyMem_Free(void *p)
void* PyObject_Malloc(size_t n)
void PyObject_Free(void *p)
cdef struct __pyx_memoryview "__pyx_memoryview_obj":
Py_buffer view
PyObject *obj
__Pyx_TypeInfo *typeinfo
ctypedef struct {{memviewslice_name}}:
__pyx_memoryview *memview
char *data
Py_ssize_t shape[{{max_dims}}]
Py_ssize_t strides[{{max_dims}}]
Py_ssize_t suboffsets[{{max_dims}}]
void __PYX_INC_MEMVIEW({{memviewslice_name}} *memslice, int have_gil)
void __PYX_XDEC_MEMVIEW({{memviewslice_name}} *memslice, int have_gil)
ctypedef struct __pyx_buffer "Py_buffer":
PyObject *obj
PyObject *Py_None
cdef enum:
PyBUF_C_CONTIGUOUS,
PyBUF_F_CONTIGUOUS,
PyBUF_ANY_CONTIGUOUS
PyBUF_FORMAT
PyBUF_WRITABLE
PyBUF_STRIDES
PyBUF_INDIRECT
PyBUF_RECORDS
ctypedef struct __Pyx_TypeInfo:
pass
cdef object capsule "__pyx_capsule_create" (void *p, char *sig)
cdef int __pyx_array_getbuffer(PyObject *obj, Py_buffer view, int flags)
cdef int __pyx_memoryview_getbuffer(PyObject *obj, Py_buffer view, int flags)
cdef extern from *:
ctypedef int __pyx_atomic_int
{{memviewslice_name}} slice_copy_contig "__pyx_memoryview_copy_new_contig"(
__Pyx_memviewslice *from_mvs,
char *mode, int ndim,
size_t sizeof_dtype, int contig_flag,
bint dtype_is_object) nogil except *
bint slice_is_contig "__pyx_memviewslice_is_contig" (
{{memviewslice_name}} mvs, char order, int ndim) nogil
bint slices_overlap "__pyx_slices_overlap" ({{memviewslice_name}} *slice1,
{{memviewslice_name}} *slice2,
int ndim, size_t itemsize) nogil
cdef extern from "<stdlib.h>":
void *malloc(size_t) nogil
void free(void *) nogil
void *memcpy(void *dest, void *src, size_t n) nogil
#
### cython.array class
#
@cname("__pyx_array")
cdef class array:
cdef:
char *data
Py_ssize_t len
char *format
int ndim
Py_ssize_t *_shape
Py_ssize_t *_strides
Py_ssize_t itemsize
unicode mode # FIXME: this should have been a simple 'char'
bytes _format
void (*callback_free_data)(void *data)
# cdef object _memview
cdef bint free_data
cdef bint dtype_is_object
def __cinit__(array self, tuple shape, Py_ssize_t itemsize, format not None,
mode="c", bint allocate_buffer=True):
cdef int idx
cdef Py_ssize_t i, dim
cdef PyObject **p
self.ndim = <int> len(shape)
self.itemsize = itemsize
if not self.ndim:
raise ValueError("Empty shape tuple for cython.array")
if itemsize <= 0:
raise ValueError("itemsize <= 0 for cython.array")
if not isinstance(format, bytes):
format = format.encode('ASCII')
self._format = format # keep a reference to the byte string
self.format = self._format
# use single malloc() for both shape and strides
self._shape = <Py_ssize_t *> PyObject_Malloc(sizeof(Py_ssize_t)*self.ndim*2)
self._strides = self._shape + self.ndim
if not self._shape:
raise MemoryError("unable to allocate shape and strides.")
# cdef Py_ssize_t dim, stride
for idx, dim in enumerate(shape):
if dim <= 0:
raise ValueError("Invalid shape in axis %d: %d." % (idx, dim))
self._shape[idx] = dim
cdef char order
if mode == 'fortran':
order = b'F'
self.mode = u'fortran'
elif mode == 'c':
order = b'C'
self.mode = u'c'
else:
raise ValueError("Invalid mode, expected 'c' or 'fortran', got %s" % mode)
self.len = fill_contig_strides_array(self._shape, self._strides,
itemsize, self.ndim, order)
self.free_data = allocate_buffer
self.dtype_is_object = format == b'O'
if allocate_buffer:
# use malloc() for backwards compatibility
# in case external code wants to change the data pointer
self.data = <char *>malloc(self.len)
if not self.data:
raise MemoryError("unable to allocate array data.")
if self.dtype_is_object:
p = <PyObject **> self.data
for i in range(self.len / itemsize):
p[i] = Py_None
Py_INCREF(Py_None)
@cname('getbuffer')
def __getbuffer__(self, Py_buffer *info, int flags):
cdef int bufmode = -1
if self.mode == u"c":
bufmode = PyBUF_C_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS
elif self.mode == u"fortran":
bufmode = PyBUF_F_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS
if not (flags & bufmode):
raise ValueError("Can only create a buffer that is contiguous in memory.")
info.buf = self.data
info.len = self.len
info.ndim = self.ndim
info.shape = self._shape
info.strides = self._strides
info.suboffsets = NULL
info.itemsize = self.itemsize
info.readonly = 0
if flags & PyBUF_FORMAT:
info.format = self.format
else:
info.format = NULL
info.obj = self
__pyx_getbuffer = capsule(<void *> &__pyx_array_getbuffer, "getbuffer(obj, view, flags)")
def __dealloc__(array self):
if self.callback_free_data != NULL:
self.callback_free_data(self.data)
elif self.free_data:
if self.dtype_is_object:
refcount_objects_in_slice(self.data, self._shape,
self._strides, self.ndim, False)
free(self.data)
PyObject_Free(self._shape)
@property
def memview(self):
return self.get_memview()
@cname('get_memview')
cdef get_memview(self):
flags = PyBUF_ANY_CONTIGUOUS|PyBUF_FORMAT|PyBUF_WRITABLE
return memoryview(self, flags, self.dtype_is_object)
def __len__(self):
return self._shape[0]
def __getattr__(self, attr):
return getattr(self.memview, attr)
def __getitem__(self, item):
return self.memview[item]
def __setitem__(self, item, value):
self.memview[item] = value
@cname("__pyx_array_new")
cdef array array_cwrapper(tuple shape, Py_ssize_t itemsize, char *format,
char *mode, char *buf):
cdef array result
if buf == NULL:
result = array(shape, itemsize, format, mode.decode('ASCII'))
else:
result = array(shape, itemsize, format, mode.decode('ASCII'),
allocate_buffer=False)
result.data = buf
return result
#
### Memoryview constants and cython.view.memoryview class
#
# Disable generic_contiguous, as it makes trouble verifying contiguity:
# - 'contiguous' or '::1' means the dimension is contiguous with dtype
# - 'indirect_contiguous' means a contiguous list of pointers
# - dtype contiguous must be contiguous in the first or last dimension
# from the start, or from the dimension following the last indirect dimension
#
# e.g.
# int[::indirect_contiguous, ::contiguous, :]
#
# is valid (list of pointers to 2d fortran-contiguous array), but
#
# int[::generic_contiguous, ::contiguous, :]
#
# would mean you'd have assert dimension 0 to be indirect (and pointer contiguous) at runtime.
# So it doesn't bring any performance benefit, and it's only confusing.
@cname('__pyx_MemviewEnum')
cdef class Enum(object):
cdef object name
def __init__(self, name):
self.name = name
def __repr__(self):
return self.name
cdef generic = Enum("<strided and direct or indirect>")
cdef strided = Enum("<strided and direct>") # default
cdef indirect = Enum("<strided and indirect>")
# Disable generic_contiguous, as it is a troublemaker
#cdef generic_contiguous = Enum("<contiguous and direct or indirect>")
cdef contiguous = Enum("<contiguous and direct>")
cdef indirect_contiguous = Enum("<contiguous and indirect>")
# 'follow' is implied when the first or last axis is ::1
@cname('__pyx_align_pointer')
cdef void *align_pointer(void *memory, size_t alignment) nogil:
"Align pointer memory on a given boundary"
cdef Py_intptr_t aligned_p = <Py_intptr_t> memory
cdef size_t offset
with cython.cdivision(True):
offset = aligned_p % alignment
if offset > 0:
aligned_p += alignment - offset
return <void *> aligned_p
# pre-allocate thread locks for reuse
## note that this could be implemented in a more beautiful way in "normal" Cython,
## but this code gets merged into the user module and not everything works there.
DEF THREAD_LOCKS_PREALLOCATED = 8
cdef int __pyx_memoryview_thread_locks_used = 0
cdef PyThread_type_lock[THREAD_LOCKS_PREALLOCATED] __pyx_memoryview_thread_locks = [
PyThread_allocate_lock(),
PyThread_allocate_lock(),
PyThread_allocate_lock(),
PyThread_allocate_lock(),
PyThread_allocate_lock(),
PyThread_allocate_lock(),
PyThread_allocate_lock(),
PyThread_allocate_lock(),
]
@cname('__pyx_memoryview')
cdef class memoryview(object):
cdef object obj
cdef object _size
cdef object _array_interface
cdef PyThread_type_lock lock
# the following array will contain a single __pyx_atomic int with
# suitable alignment
cdef __pyx_atomic_int acquisition_count[2]
cdef __pyx_atomic_int *acquisition_count_aligned_p
cdef Py_buffer view
cdef int flags
cdef bint dtype_is_object
cdef __Pyx_TypeInfo *typeinfo
def __cinit__(memoryview self, object obj, int flags, bint dtype_is_object=False):
self.obj = obj
self.flags = flags
if type(self) is memoryview or obj is not None:
__Pyx_GetBuffer(obj, &self.view, flags)
if <PyObject *> self.view.obj == NULL:
(<__pyx_buffer *> &self.view).obj = Py_None
Py_INCREF(Py_None)
global __pyx_memoryview_thread_locks_used
if __pyx_memoryview_thread_locks_used < THREAD_LOCKS_PREALLOCATED:
self.lock = __pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used]
__pyx_memoryview_thread_locks_used += 1
if self.lock is NULL:
self.lock = PyThread_allocate_lock()
if self.lock is NULL:
raise MemoryError
if flags & PyBUF_FORMAT:
self.dtype_is_object = (self.view.format[0] == b'O' and self.view.format[1] == b'\0')
else:
self.dtype_is_object = dtype_is_object
self.acquisition_count_aligned_p = <__pyx_atomic_int *> align_pointer(
<void *> &self.acquisition_count[0], sizeof(__pyx_atomic_int))
self.typeinfo = NULL
def __dealloc__(memoryview self):
if self.obj is not None:
__Pyx_ReleaseBuffer(&self.view)
cdef int i
global __pyx_memoryview_thread_locks_used
if self.lock != NULL:
for i in range(__pyx_memoryview_thread_locks_used):
if __pyx_memoryview_thread_locks[i] is self.lock:
__pyx_memoryview_thread_locks_used -= 1
if i != __pyx_memoryview_thread_locks_used:
__pyx_memoryview_thread_locks[i], __pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used] = (
__pyx_memoryview_thread_locks[__pyx_memoryview_thread_locks_used], __pyx_memoryview_thread_locks[i])
break
else:
PyThread_free_lock(self.lock)
cdef char *get_item_pointer(memoryview self, object index) except NULL:
cdef Py_ssize_t dim
cdef char *itemp = <char *> self.view.buf
for dim, idx in enumerate(index):
itemp = pybuffer_index(&self.view, itemp, idx, dim)
return itemp
#@cname('__pyx_memoryview_getitem')
def __getitem__(memoryview self, object index):
if index is Ellipsis:
return self
have_slices, indices = _unellipsify(index, self.view.ndim)
cdef char *itemp
if have_slices:
return memview_slice(self, indices)
else:
itemp = self.get_item_pointer(indices)
return self.convert_item_to_object(itemp)
def __setitem__(memoryview self, object index, object value):
have_slices, index = _unellipsify(index, self.view.ndim)
if have_slices:
obj = self.is_slice(value)
if obj:
self.setitem_slice_assignment(self[index], obj)
else:
self.setitem_slice_assign_scalar(self[index], value)
else:
self.setitem_indexed(index, value)
cdef is_slice(self, obj):
if not isinstance(obj, memoryview):
try:
obj = memoryview(obj, self.flags|PyBUF_ANY_CONTIGUOUS,
self.dtype_is_object)
except TypeError:
return None
return obj
cdef setitem_slice_assignment(self, dst, src):
cdef {{memviewslice_name}} dst_slice
cdef {{memviewslice_name}} src_slice
memoryview_copy_contents(get_slice_from_memview(src, &src_slice)[0],
get_slice_from_memview(dst, &dst_slice)[0],
src.ndim, dst.ndim, self.dtype_is_object)
cdef setitem_slice_assign_scalar(self, memoryview dst, value):
cdef int array[128]
cdef void *tmp = NULL
cdef void *item
cdef {{memviewslice_name}} *dst_slice
cdef {{memviewslice_name}} tmp_slice
dst_slice = get_slice_from_memview(dst, &tmp_slice)
if <size_t>self.view.itemsize > sizeof(array):
tmp = PyMem_Malloc(self.view.itemsize)
if tmp == NULL:
raise MemoryError
item = tmp
else:
item = <void *> array
try:
if self.dtype_is_object:
(<PyObject **> item)[0] = <PyObject *> value
else:
self.assign_item_from_object(<char *> item, value)
# It would be easy to support indirect dimensions, but it's easier
# to disallow :)
if self.view.suboffsets != NULL:
assert_direct_dimensions(self.view.suboffsets, self.view.ndim)
slice_assign_scalar(dst_slice, dst.view.ndim, self.view.itemsize,
item, self.dtype_is_object)
finally:
PyMem_Free(tmp)
cdef setitem_indexed(self, index, value):
cdef char *itemp = self.get_item_pointer(index)
self.assign_item_from_object(itemp, value)
cdef convert_item_to_object(self, char *itemp):
"""Only used if instantiated manually by the user, or if Cython doesn't
know how to convert the type"""
import struct
cdef bytes bytesitem
# Do a manual and complete check here instead of this easy hack
bytesitem = itemp[:self.view.itemsize]
try:
result = struct.unpack(self.view.format, bytesitem)
except struct.error:
raise ValueError("Unable to convert item to object")
else:
if len(self.view.format) == 1:
return result[0]
return result
cdef assign_item_from_object(self, char *itemp, object value):
"""Only used if instantiated manually by the user, or if Cython doesn't
know how to convert the type"""
import struct
cdef char c
cdef bytes bytesvalue
cdef Py_ssize_t i
if isinstance(value, tuple):
bytesvalue = struct.pack(self.view.format, *value)
else:
bytesvalue = struct.pack(self.view.format, value)
for i, c in enumerate(bytesvalue):
itemp[i] = c
@cname('getbuffer')
def __getbuffer__(self, Py_buffer *info, int flags):
if flags & PyBUF_STRIDES:
info.shape = self.view.shape
else:
info.shape = NULL
if flags & PyBUF_STRIDES:
info.strides = self.view.strides
else:
info.strides = NULL
if flags & PyBUF_INDIRECT:
info.suboffsets = self.view.suboffsets
else:
info.suboffsets = NULL
if flags & PyBUF_FORMAT:
info.format = self.view.format
else:
info.format = NULL
info.buf = self.view.buf
info.ndim = self.view.ndim
info.itemsize = self.view.itemsize
info.len = self.view.len
info.readonly = 0
info.obj = self
__pyx_getbuffer = capsule(<void *> &__pyx_memoryview_getbuffer, "getbuffer(obj, view, flags)")
# Some properties that have the same sematics as in NumPy
@property
def T(self):
cdef _memoryviewslice result = memoryview_copy(self)
transpose_memslice(&result.from_slice)
return result
@property
def base(self):
return self.obj
@property
def shape(self):
return tuple([length for length in self.view.shape[:self.view.ndim]])
@property
def strides(self):
if self.view.strides == NULL:
# Note: we always ask for strides, so if this is not set it's a bug
raise ValueError("Buffer view does not expose strides")
return tuple([stride for stride in self.view.strides[:self.view.ndim]])
@property
def suboffsets(self):
if self.view.suboffsets == NULL:
return (-1,) * self.view.ndim
return tuple([suboffset for suboffset in self.view.suboffsets[:self.view.ndim]])
@property
def ndim(self):
return self.view.ndim
@property
def itemsize(self):
return self.view.itemsize
@property
def nbytes(self):
return self.size * self.view.itemsize
@property
def size(self):
if self._size is None:
result = 1
for length in self.view.shape[:self.view.ndim]:
result *= length
self._size = result
return self._size
def __len__(self):
if self.view.ndim >= 1:
return self.view.shape[0]
return 0
def __repr__(self):
return "<MemoryView of %r at 0x%x>" % (self.base.__class__.__name__,
id(self))
def __str__(self):
return "<MemoryView of %r object>" % (self.base.__class__.__name__,)
# Support the same attributes as memoryview slices
def is_c_contig(self):
cdef {{memviewslice_name}} *mslice
cdef {{memviewslice_name}} tmp
mslice = get_slice_from_memview(self, &tmp)
return slice_is_contig(mslice[0], 'C', self.view.ndim)
def is_f_contig(self):
cdef {{memviewslice_name}} *mslice
cdef {{memviewslice_name}} tmp
mslice = get_slice_from_memview(self, &tmp)
return slice_is_contig(mslice[0], 'F', self.view.ndim)
def copy(self):
cdef {{memviewslice_name}} mslice
cdef int flags = self.flags & ~PyBUF_F_CONTIGUOUS
slice_copy(self, &mslice)
mslice = slice_copy_contig(&mslice, "c", self.view.ndim,
self.view.itemsize,
flags|PyBUF_C_CONTIGUOUS,
self.dtype_is_object)
return memoryview_copy_from_slice(self, &mslice)
def copy_fortran(self):
cdef {{memviewslice_name}} src, dst
cdef int flags = self.flags & ~PyBUF_C_CONTIGUOUS
slice_copy(self, &src)
dst = slice_copy_contig(&src, "fortran", self.view.ndim,
self.view.itemsize,
flags|PyBUF_F_CONTIGUOUS,
self.dtype_is_object)
return memoryview_copy_from_slice(self, &dst)
@cname('__pyx_memoryview_new')
cdef memoryview_cwrapper(object o, int flags, bint dtype_is_object, __Pyx_TypeInfo *typeinfo):
cdef memoryview result = memoryview(o, flags, dtype_is_object)
result.typeinfo = typeinfo
return result
@cname('__pyx_memoryview_check')
cdef inline bint memoryview_check(object o):
return isinstance(o, memoryview)
cdef tuple _unellipsify(object index, int ndim):
"""
Replace all ellipses with full slices and fill incomplete indices with
full slices.
"""
if not isinstance(index, tuple):
tup = (index,)
else:
tup = index
result = []
have_slices = False
seen_ellipsis = False
for idx, item in enumerate(tup):
if item is Ellipsis:
if not seen_ellipsis:
result.extend([slice(None)] * (ndim - len(tup) + 1))
seen_ellipsis = True
else:
result.append(slice(None))
have_slices = True
else:
if not isinstance(item, slice) and not PyIndex_Check(item):
raise TypeError("Cannot index with type '%s'" % type(item))
have_slices = have_slices or isinstance(item, slice)
result.append(item)
nslices = ndim - len(result)
if nslices:
result.extend([slice(None)] * nslices)
return have_slices or nslices, tuple(result)
cdef assert_direct_dimensions(Py_ssize_t *suboffsets, int ndim):
for suboffset in suboffsets[:ndim]:
if suboffset >= 0:
raise ValueError("Indirect dimensions not supported")
#
### Slicing a memoryview
#
@cname('__pyx_memview_slice')
cdef memoryview memview_slice(memoryview memview, object indices):
cdef int new_ndim = 0, suboffset_dim = -1, dim
cdef bint negative_step
cdef {{memviewslice_name}} src, dst
cdef {{memviewslice_name}} *p_src
# dst is copied by value in memoryview_fromslice -- initialize it
# src is never copied
memset(&dst, 0, sizeof(dst))
cdef _memoryviewslice memviewsliceobj
assert memview.view.ndim > 0
if isinstance(memview, _memoryviewslice):
memviewsliceobj = memview
p_src = &memviewsliceobj.from_slice
else:
slice_copy(memview, &src)
p_src = &src
# Note: don't use variable src at this point
# SubNote: we should be able to declare variables in blocks...
# memoryview_fromslice() will inc our dst slice
dst.memview = p_src.memview
dst.data = p_src.data
# Put everything in temps to avoid this bloody warning:
# "Argument evaluation order in C function call is undefined and
# may not be as expected"
cdef {{memviewslice_name}} *p_dst = &dst
cdef int *p_suboffset_dim = &suboffset_dim
cdef Py_ssize_t start, stop, step
cdef bint have_start, have_stop, have_step
for dim, index in enumerate(indices):
if PyIndex_Check(index):
slice_memviewslice(
p_dst, p_src.shape[dim], p_src.strides[dim], p_src.suboffsets[dim],
dim, new_ndim, p_suboffset_dim,
index, 0, 0, # start, stop, step
0, 0, 0, # have_{start,stop,step}
False)
elif index is None:
p_dst.shape[new_ndim] = 1
p_dst.strides[new_ndim] = 0
p_dst.suboffsets[new_ndim] = -1
new_ndim += 1
else:
start = index.start or 0
stop = index.stop or 0
step = index.step or 0
have_start = index.start is not None
have_stop = index.stop is not None
have_step = index.step is not None
slice_memviewslice(
p_dst, p_src.shape[dim], p_src.strides[dim], p_src.suboffsets[dim],
dim, new_ndim, p_suboffset_dim,
start, stop, step,
have_start, have_stop, have_step,
True)
new_ndim += 1
if isinstance(memview, _memoryviewslice):
return memoryview_fromslice(dst, new_ndim,
memviewsliceobj.to_object_func,
memviewsliceobj.to_dtype_func,
memview.dtype_is_object)
else:
return memoryview_fromslice(dst, new_ndim, NULL, NULL,
memview.dtype_is_object)
#
### Slicing in a single dimension of a memoryviewslice
#
cdef extern from "<stdlib.h>":
void abort() nogil
void printf(char *s, ...) nogil
cdef extern from "<stdio.h>":
ctypedef struct FILE
FILE *stderr
int fputs(char *s, FILE *stream)
cdef extern from "pystate.h":
void PyThreadState_Get() nogil
# These are not actually nogil, but we check for the GIL before calling them
void PyErr_SetString(PyObject *type, char *msg) nogil
PyObject *PyErr_Format(PyObject *exc, char *msg, ...) nogil
@cname('__pyx_memoryview_slice_memviewslice')
cdef int slice_memviewslice(
{{memviewslice_name}} *dst,
Py_ssize_t shape, Py_ssize_t stride, Py_ssize_t suboffset,
int dim, int new_ndim, int *suboffset_dim,
Py_ssize_t start, Py_ssize_t stop, Py_ssize_t step,
int have_start, int have_stop, int have_step,
bint is_slice) nogil except -1:
"""
Create a new slice dst given slice src.
dim - the current src dimension (indexing will make dimensions
disappear)
new_dim - the new dst dimension
suboffset_dim - pointer to a single int initialized to -1 to keep track of
where slicing offsets should be added
"""
cdef Py_ssize_t new_shape
cdef bint negative_step
if not is_slice:
# index is a normal integer-like index
if start < 0:
start += shape
if not 0 <= start < shape:
_err_dim(IndexError, "Index out of bounds (axis %d)", dim)
else:
# index is a slice
negative_step = have_step != 0 and step < 0
if have_step and step == 0:
_err_dim(ValueError, "Step may not be zero (axis %d)", dim)
# check our bounds and set defaults
if have_start:
if start < 0:
start += shape
if start < 0:
start = 0
elif start >= shape:
if negative_step:
start = shape - 1
else:
start = shape
else:
if negative_step:
start = shape - 1
else:
start = 0
if have_stop:
if stop < 0:
stop += shape
if stop < 0:
stop = 0
elif stop > shape:
stop = shape
else:
if negative_step:
stop = -1
else:
stop = shape
if not have_step:
step = 1
# len = ceil( (stop - start) / step )
with cython.cdivision(True):
new_shape = (stop - start) // step
if (stop - start) - step * new_shape:
new_shape += 1
if new_shape < 0:
new_shape = 0
# shape/strides/suboffsets
dst.strides[new_ndim] = stride * step
dst.shape[new_ndim] = new_shape
dst.suboffsets[new_ndim] = suboffset
# Add the slicing or idexing offsets to the right suboffset or base data *
if suboffset_dim[0] < 0:
dst.data += start * stride
else:
dst.suboffsets[suboffset_dim[0]] += start * stride
if suboffset >= 0:
if not is_slice:
if new_ndim == 0:
dst.data = (<char **> dst.data)[0] + suboffset
else:
_err_dim(IndexError, "All dimensions preceding dimension %d "
"must be indexed and not sliced", dim)
else:
suboffset_dim[0] = new_ndim
return 0
#
### Index a memoryview
#
@cname('__pyx_pybuffer_index')
cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index,
Py_ssize_t dim) except NULL:
cdef Py_ssize_t shape, stride, suboffset = -1
cdef Py_ssize_t itemsize = view.itemsize
cdef char *resultp
if view.ndim == 0:
shape = view.len / itemsize
stride = itemsize
else:
shape = view.shape[dim]
stride = view.strides[dim]
if view.suboffsets != NULL:
suboffset = view.suboffsets[dim]
if index < 0:
index += view.shape[dim]
if index < 0:
raise IndexError("Out of bounds on buffer access (axis %d)" % dim)
if index >= shape:
raise IndexError("Out of bounds on buffer access (axis %d)" % dim)
resultp = bufp + index * stride
if suboffset >= 0:
resultp = (<char **> resultp)[0] + suboffset
return resultp
#
### Transposing a memoryviewslice
#
@cname('__pyx_memslice_transpose')
cdef int transpose_memslice({{memviewslice_name}} *memslice) nogil except 0:
cdef int ndim = memslice.memview.view.ndim
cdef Py_ssize_t *shape = memslice.shape
cdef Py_ssize_t *strides = memslice.strides
# reverse strides and shape
cdef int i, j
for i in range(ndim / 2):
j = ndim - 1 - i
strides[i], strides[j] = strides[j], strides[i]
shape[i], shape[j] = shape[j], shape[i]
if memslice.suboffsets[i] >= 0 or memslice.suboffsets[j] >= 0:
_err(ValueError, "Cannot transpose memoryview with indirect dimensions")
return 1
#
### Creating new memoryview objects from slices and memoryviews
#
@cname('__pyx_memoryviewslice')
cdef class _memoryviewslice(memoryview):
"Internal class for passing memoryview slices to Python"
# We need this to keep our shape/strides/suboffset pointers valid
cdef {{memviewslice_name}} from_slice
# We need this only to print it's class' name
cdef object from_object
cdef object (*to_object_func)(char *)
cdef int (*to_dtype_func)(char *, object) except 0
def __dealloc__(self):
__PYX_XDEC_MEMVIEW(&self.from_slice, 1)
cdef convert_item_to_object(self, char *itemp):
if self.to_object_func != NULL:
return self.to_object_func(itemp)
else:
return memoryview.convert_item_to_object(self, itemp)
cdef assign_item_from_object(self, char *itemp, object value):
if self.to_dtype_func != NULL:
self.to_dtype_func(itemp, value)
else:
memoryview.assign_item_from_object(self, itemp, value)
@property
def base(self):
return self.from_object
__pyx_getbuffer = capsule(<void *> &__pyx_memoryview_getbuffer, "getbuffer(obj, view, flags)")
@cname('__pyx_memoryview_fromslice')
cdef memoryview_fromslice({{memviewslice_name}} memviewslice,
int ndim,
object (*to_object_func)(char *),
int (*to_dtype_func)(char *, object) except 0,
bint dtype_is_object):
cdef _memoryviewslice result
if <PyObject *> memviewslice.memview == Py_None:
return None
# assert 0 < ndim <= memviewslice.memview.view.ndim, (
# ndim, memviewslice.memview.view.ndim)
result = _memoryviewslice(None, 0, dtype_is_object)
result.from_slice = memviewslice
__PYX_INC_MEMVIEW(&memviewslice, 1)
result.from_object = (<memoryview> memviewslice.memview).base
result.typeinfo = memviewslice.memview.typeinfo
result.view = memviewslice.memview.view
result.view.buf = <void *> memviewslice.data
result.view.ndim = ndim
(<__pyx_buffer *> &result.view).obj = Py_None
Py_INCREF(Py_None)
result.flags = PyBUF_RECORDS
result.view.shape = <Py_ssize_t *> result.from_slice.shape
result.view.strides = <Py_ssize_t *> result.from_slice.strides
# only set suboffsets if actually used, otherwise set to NULL to improve compatibility
result.view.suboffsets = NULL
for suboffset in result.from_slice.suboffsets[:ndim]:
if suboffset >= 0:
result.view.suboffsets = <Py_ssize_t *> result.from_slice.suboffsets
break
result.view.len = result.view.itemsize
for length in result.view.shape[:ndim]:
result.view.len *= length
result.to_object_func = to_object_func
result.to_dtype_func = to_dtype_func
return result
@cname('__pyx_memoryview_get_slice_from_memoryview')
cdef {{memviewslice_name}} *get_slice_from_memview(memoryview memview,
{{memviewslice_name}} *mslice):
cdef _memoryviewslice obj
if isinstance(memview, _memoryviewslice):
obj = memview
return &obj.from_slice
else:
slice_copy(memview, mslice)
return mslice
@cname('__pyx_memoryview_slice_copy')
cdef void slice_copy(memoryview memview, {{memviewslice_name}} *dst):
cdef int dim
cdef (Py_ssize_t*) shape, strides, suboffsets
shape = memview.view.shape
strides = memview.view.strides
suboffsets = memview.view.suboffsets
dst.memview = <__pyx_memoryview *> memview
dst.data = <char *> memview.view.buf
for dim in range(memview.view.ndim):
dst.shape[dim] = shape[dim]
dst.strides[dim] = strides[dim]
dst.suboffsets[dim] = suboffsets[dim] if suboffsets else -1
@cname('__pyx_memoryview_copy_object')
cdef memoryview_copy(memoryview memview):
"Create a new memoryview object"
cdef {{memviewslice_name}} memviewslice
slice_copy(memview, &memviewslice)
return memoryview_copy_from_slice(memview, &memviewslice)
@cname('__pyx_memoryview_copy_object_from_slice')
cdef memoryview_copy_from_slice(memoryview memview, {{memviewslice_name}} *memviewslice):
"""
Create a new memoryview object from a given memoryview object and slice.
"""
cdef object (*to_object_func)(char *)
cdef int (*to_dtype_func)(char *, object) except 0
if isinstance(memview, _memoryviewslice):
to_object_func = (<_memoryviewslice> memview).to_object_func
to_dtype_func = (<_memoryviewslice> memview).to_dtype_func
else:
to_object_func = NULL
to_dtype_func = NULL
return memoryview_fromslice(memviewslice[0], memview.view.ndim,
to_object_func, to_dtype_func,
memview.dtype_is_object)
#
### Copy the contents of a memoryview slices
#
cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil:
if arg < 0:
return -arg
else:
return arg
@cname('__pyx_get_best_slice_order')
cdef char get_best_order({{memviewslice_name}} *mslice, int ndim) nogil:
"""
Figure out the best memory access order for a given slice.
"""
cdef int i
cdef Py_ssize_t c_stride = 0
cdef Py_ssize_t f_stride = 0
for i in range(ndim - 1, -1, -1):
if mslice.shape[i] > 1:
c_stride = mslice.strides[i]
break
for i in range(ndim):
if mslice.shape[i] > 1:
f_stride = mslice.strides[i]
break
if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride):
return 'C'
else:
return 'F'
@cython.cdivision(True)
cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides,
char *dst_data, Py_ssize_t *dst_strides,
Py_ssize_t *src_shape, Py_ssize_t *dst_shape,
int ndim, size_t itemsize) nogil:
# Note: src_extent is 1 if we're broadcasting
# dst_extent always >= src_extent as we don't do reductions
cdef Py_ssize_t i
cdef Py_ssize_t src_extent = src_shape[0]
cdef Py_ssize_t dst_extent = dst_shape[0]
cdef Py_ssize_t src_stride = src_strides[0]
cdef Py_ssize_t dst_stride = dst_strides[0]
if ndim == 1:
if (src_stride > 0 and dst_stride > 0 and
<size_t> src_stride == itemsize == <size_t> dst_stride):
memcpy(dst_data, src_data, itemsize * dst_extent)
else:
for i in range(dst_extent):
memcpy(dst_data, src_data, itemsize)
src_data += src_stride
dst_data += dst_stride
else:
for i in range(dst_extent):
_copy_strided_to_strided(src_data, src_strides + 1,
dst_data, dst_strides + 1,
src_shape + 1, dst_shape + 1,
ndim - 1, itemsize)
src_data += src_stride
dst_data += dst_stride
cdef void copy_strided_to_strided({{memviewslice_name}} *src,
{{memviewslice_name}} *dst,
int ndim, size_t itemsize) nogil:
_copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides,
src.shape, dst.shape, ndim, itemsize)
@cname('__pyx_memoryview_slice_get_size')
cdef Py_ssize_t slice_get_size({{memviewslice_name}} *src, int ndim) nogil:
"Return the size of the memory occupied by the slice in number of bytes"
cdef int i
cdef Py_ssize_t size = src.memview.view.itemsize
for i in range(ndim):
size *= src.shape[i]
return size
@cname('__pyx_fill_contig_strides_array')
cdef Py_ssize_t fill_contig_strides_array(
Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride,
int ndim, char order) nogil:
"""
Fill the strides array for a slice with C or F contiguous strides.
This is like PyBuffer_FillContiguousStrides, but compatible with py < 2.6
"""
cdef int idx
if order == 'F':
for idx in range(ndim):
strides[idx] = stride
stride = stride * shape[idx]
else:
for idx in range(ndim - 1, -1, -1):
strides[idx] = stride
stride = stride * shape[idx]
return stride
@cname('__pyx_memoryview_copy_data_to_temp')
cdef void *copy_data_to_temp({{memviewslice_name}} *src,
{{memviewslice_name}} *tmpslice,
char order,
int ndim) nogil except NULL:
"""
Copy a direct slice to temporary contiguous memory. The caller should free
the result when done.
"""
cdef int i
cdef void *result
cdef size_t itemsize = src.memview.view.itemsize
cdef size_t size = slice_get_size(src, ndim)
result = malloc(size)
if not result:
_err(MemoryError, NULL)
# tmpslice[0] = src
tmpslice.data = <char *> result
tmpslice.memview = src.memview
for i in range(ndim):
tmpslice.shape[i] = src.shape[i]
tmpslice.suboffsets[i] = -1
fill_contig_strides_array(&tmpslice.shape[0], &tmpslice.strides[0], itemsize,
ndim, order)
# We need to broadcast strides again
for i in range(ndim):
if tmpslice.shape[i] == 1:
tmpslice.strides[i] = 0
if slice_is_contig(src[0], order, ndim):
memcpy(result, src.data, size)
else:
copy_strided_to_strided(src, tmpslice, ndim, itemsize)
return result
# Use 'with gil' functions and avoid 'with gil' blocks, as the code within the blocks
# has temporaries that need the GIL to clean up
@cname('__pyx_memoryview_err_extents')
cdef int _err_extents(int i, Py_ssize_t extent1,
Py_ssize_t extent2) except -1 with gil:
raise ValueError("got differing extents in dimension %d (got %d and %d)" %
(i, extent1, extent2))
@cname('__pyx_memoryview_err_dim')
cdef int _err_dim(object error, char *msg, int dim) except -1 with gil:
raise error(msg.decode('ascii') % dim)
@cname('__pyx_memoryview_err')
cdef int _err(object error, char *msg) except -1 with gil:
if msg != NULL:
raise error(msg.decode('ascii'))
else:
raise error
@cname('__pyx_memoryview_copy_contents')
cdef int memoryview_copy_contents({{memviewslice_name}} src,
{{memviewslice_name}} dst,
int src_ndim, int dst_ndim,
bint dtype_is_object) nogil except -1:
"""
Copy memory from slice src to slice dst.
Check for overlapping memory and verify the shapes.
"""
cdef void *tmpdata = NULL
cdef size_t itemsize = src.memview.view.itemsize
cdef int i
cdef char order = get_best_order(&src, src_ndim)
cdef bint broadcasting = False
cdef bint direct_copy = False
cdef {{memviewslice_name}} tmp
if src_ndim < dst_ndim:
broadcast_leading(&src, src_ndim, dst_ndim)
elif dst_ndim < src_ndim:
broadcast_leading(&dst, dst_ndim, src_ndim)
cdef int ndim = max(src_ndim, dst_ndim)
for i in range(ndim):
if src.shape[i] != dst.shape[i]:
if src.shape[i] == 1:
broadcasting = True
src.strides[i] = 0
else:
_err_extents(i, dst.shape[i], src.shape[i])
if src.suboffsets[i] >= 0:
_err_dim(ValueError, "Dimension %d is not direct", i)
if slices_overlap(&src, &dst, ndim, itemsize):
# slices overlap, copy to temp, copy temp to dst
if not slice_is_contig(src, order, ndim):
order = get_best_order(&dst, ndim)
tmpdata = copy_data_to_temp(&src, &tmp, order, ndim)
src = tmp
if not broadcasting:
# See if both slices have equal contiguity, in that case perform a
# direct copy. This only works when we are not broadcasting.
if slice_is_contig(src, 'C', ndim):
direct_copy = slice_is_contig(dst, 'C', ndim)
elif slice_is_contig(src, 'F', ndim):
direct_copy = slice_is_contig(dst, 'F', ndim)
if direct_copy:
# Contiguous slices with same order
refcount_copying(&dst, dtype_is_object, ndim, False)
memcpy(dst.data, src.data, slice_get_size(&src, ndim))
refcount_copying(&dst, dtype_is_object, ndim, True)
free(tmpdata)
return 0
if order == 'F' == get_best_order(&dst, ndim):
# see if both slices have Fortran order, transpose them to match our
# C-style indexing order
transpose_memslice(&src)
transpose_memslice(&dst)
refcount_copying(&dst, dtype_is_object, ndim, False)
copy_strided_to_strided(&src, &dst, ndim, itemsize)
refcount_copying(&dst, dtype_is_object, ndim, True)
free(tmpdata)
return 0
@cname('__pyx_memoryview_broadcast_leading')
cdef void broadcast_leading({{memviewslice_name}} *mslice,
int ndim,
int ndim_other) nogil:
cdef int i
cdef int offset = ndim_other - ndim
for i in range(ndim - 1, -1, -1):
mslice.shape[i + offset] = mslice.shape[i]
mslice.strides[i + offset] = mslice.strides[i]
mslice.suboffsets[i + offset] = mslice.suboffsets[i]
for i in range(offset):
mslice.shape[i] = 1
mslice.strides[i] = mslice.strides[0]
mslice.suboffsets[i] = -1
#
### Take care of refcounting the objects in slices. Do this seperately from any copying,
### to minimize acquiring the GIL
#
@cname('__pyx_memoryview_refcount_copying')
cdef void refcount_copying({{memviewslice_name}} *dst, bint dtype_is_object,
int ndim, bint inc) nogil:
# incref or decref the objects in the destination slice if the dtype is
# object
if dtype_is_object:
refcount_objects_in_slice_with_gil(dst.data, dst.shape,
dst.strides, ndim, inc)
@cname('__pyx_memoryview_refcount_objects_in_slice_with_gil')
cdef void refcount_objects_in_slice_with_gil(char *data, Py_ssize_t *shape,
Py_ssize_t *strides, int ndim,
bint inc) with gil:
refcount_objects_in_slice(data, shape, strides, ndim, inc)
@cname('__pyx_memoryview_refcount_objects_in_slice')
cdef void refcount_objects_in_slice(char *data, Py_ssize_t *shape,
Py_ssize_t *strides, int ndim, bint inc):
cdef Py_ssize_t i
for i in range(shape[0]):
if ndim == 1:
if inc:
Py_INCREF((<PyObject **> data)[0])
else:
Py_DECREF((<PyObject **> data)[0])
else:
refcount_objects_in_slice(data, shape + 1, strides + 1,
ndim - 1, inc)
data += strides[0]
#
### Scalar to slice assignment
#
@cname('__pyx_memoryview_slice_assign_scalar')
cdef void slice_assign_scalar({{memviewslice_name}} *dst, int ndim,
size_t itemsize, void *item,
bint dtype_is_object) nogil:
refcount_copying(dst, dtype_is_object, ndim, False)
_slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim,
itemsize, item)
refcount_copying(dst, dtype_is_object, ndim, True)
@cname('__pyx_memoryview__slice_assign_scalar')
cdef void _slice_assign_scalar(char *data, Py_ssize_t *shape,
Py_ssize_t *strides, int ndim,
size_t itemsize, void *item) nogil:
cdef Py_ssize_t i
cdef Py_ssize_t stride = strides[0]
cdef Py_ssize_t extent = shape[0]
if ndim == 1:
for i in range(extent):
memcpy(data, item, itemsize)
data += stride
else:
for i in range(extent):
_slice_assign_scalar(data, shape + 1, strides + 1,
ndim - 1, itemsize, item)
data += stride
############### BufferFormatFromTypeInfo ###############
cdef extern from *:
ctypedef struct __Pyx_StructField
cdef enum:
__PYX_BUF_FLAGS_PACKED_STRUCT
__PYX_BUF_FLAGS_INTEGER_COMPLEX
ctypedef struct __Pyx_TypeInfo:
char* name
__Pyx_StructField* fields
size_t size
size_t arraysize[8]
int ndim
char typegroup
char is_unsigned
int flags
ctypedef struct __Pyx_StructField:
__Pyx_TypeInfo* type
char* name
size_t offset
ctypedef struct __Pyx_BufFmt_StackElem:
__Pyx_StructField* field
size_t parent_offset
#ctypedef struct __Pyx_BufFmt_Context:
# __Pyx_StructField root
__Pyx_BufFmt_StackElem* head
struct __pyx_typeinfo_string:
char string[3]
__pyx_typeinfo_string __Pyx_TypeInfoToFormat(__Pyx_TypeInfo *)
@cname('__pyx_format_from_typeinfo')
cdef bytes format_from_typeinfo(__Pyx_TypeInfo *type):
cdef __Pyx_StructField *field
cdef __pyx_typeinfo_string fmt
cdef bytes part, result
if type.typegroup == 'S':
assert type.fields != NULL and type.fields.type != NULL
if type.flags & __PYX_BUF_FLAGS_PACKED_STRUCT:
alignment = b'^'
else:
alignment = b''
parts = [b"T{"]
field = type.fields
while field.type:
part = format_from_typeinfo(field.type)
parts.append(part + b':' + field.name + b':')
field += 1
result = alignment.join(parts) + b'}'
else:
fmt = __Pyx_TypeInfoToFormat(type)
if type.arraysize[0]:
extents = [unicode(type.arraysize[i]) for i in range(type.ndim)]
result = (u"(%s)" % u','.join(extents)).encode('ascii') + fmt.string
else:
result = fmt.string
return result