""" A place for code to be called from core C-code. Some things are more easily handled Python. """ from __future__ import division, absolute_import, print_function import re import sys from numpy.compat import asbytes, basestring from .multiarray import dtype, array, ndarray import ctypes from .numerictypes import object_ if (sys.byteorder == 'little'): _nbo = asbytes('<') else: _nbo = asbytes('>') def _makenames_list(adict, align): allfields = [] fnames = list(adict.keys()) for fname in fnames: obj = adict[fname] n = len(obj) if not isinstance(obj, tuple) or n not in [2, 3]: raise ValueError("entry not a 2- or 3- tuple") if (n > 2) and (obj[2] == fname): continue num = int(obj[1]) if (num < 0): raise ValueError("invalid offset.") format = dtype(obj[0], align=align) if (format.itemsize == 0): raise ValueError("all itemsizes must be fixed.") if (n > 2): title = obj[2] else: title = None allfields.append((fname, format, num, title)) # sort by offsets allfields.sort(key=lambda x: x[2]) names = [x[0] for x in allfields] formats = [x[1] for x in allfields] offsets = [x[2] for x in allfields] titles = [x[3] for x in allfields] return names, formats, offsets, titles # Called in PyArray_DescrConverter function when # a dictionary without "names" and "formats" # fields is used as a data-type descriptor. def _usefields(adict, align): try: names = adict[-1] except KeyError: names = None if names is None: names, formats, offsets, titles = _makenames_list(adict, align) else: formats = [] offsets = [] titles = [] for name in names: res = adict[name] formats.append(res[0]) offsets.append(res[1]) if (len(res) > 2): titles.append(res[2]) else: titles.append(None) return dtype({"names": names, "formats": formats, "offsets": offsets, "titles": titles}, align) # construct an array_protocol descriptor list # from the fields attribute of a descriptor # This calls itself recursively but should eventually hit # a descriptor that has no fields and then return # a simple typestring def _array_descr(descriptor): fields = descriptor.fields if fields is None: subdtype = descriptor.subdtype if subdtype is None: if descriptor.metadata is None: return descriptor.str else: new = descriptor.metadata.copy() if new: return (descriptor.str, new) else: return descriptor.str else: return (_array_descr(subdtype[0]), subdtype[1]) names = descriptor.names ordered_fields = [fields[x] + (x,) for x in names] result = [] offset = 0 for field in ordered_fields: if field[1] > offset: num = field[1] - offset result.append(('', '|V%d' % num)) offset += num if len(field) > 3: name = (field[2], field[3]) else: name = field[2] if field[0].subdtype: tup = (name, _array_descr(field[0].subdtype[0]), field[0].subdtype[1]) else: tup = (name, _array_descr(field[0])) offset += field[0].itemsize result.append(tup) return result # Build a new array from the information in a pickle. # Note that the name numpy.core._internal._reconstruct is embedded in # pickles of ndarrays made with NumPy before release 1.0 # so don't remove the name here, or you'll # break backward compatibilty. def _reconstruct(subtype, shape, dtype): return ndarray.__new__(subtype, shape, dtype) # format_re was originally from numarray by J. Todd Miller format_re = re.compile(asbytes( r'(?P[<>|=]?)' r'(?P *[(]?[ ,0-9L]*[)]? *)' r'(?P[<>|=]?)' r'(?P[A-Za-z0-9.]*(?:\[[a-zA-Z0-9,.]+\])?)')) sep_re = re.compile(asbytes(r'\s*,\s*')) space_re = re.compile(asbytes(r'\s+$')) # astr is a string (perhaps comma separated) _convorder = {asbytes('='): _nbo} def _commastring(astr): startindex = 0 result = [] while startindex < len(astr): mo = format_re.match(astr, pos=startindex) try: (order1, repeats, order2, dtype) = mo.groups() except (TypeError, AttributeError): raise ValueError('format number %d of "%s" is not recognized' % (len(result)+1, astr)) startindex = mo.end() # Separator or ending padding if startindex < len(astr): if space_re.match(astr, pos=startindex): startindex = len(astr) else: mo = sep_re.match(astr, pos=startindex) if not mo: raise ValueError( 'format number %d of "%s" is not recognized' % (len(result)+1, astr)) startindex = mo.end() if order2 == asbytes(''): order = order1 elif order1 == asbytes(''): order = order2 else: order1 = _convorder.get(order1, order1) order2 = _convorder.get(order2, order2) if (order1 != order2): raise ValueError( 'inconsistent byte-order specification %s and %s' % (order1, order2)) order = order1 if order in [asbytes('|'), asbytes('='), _nbo]: order = asbytes('') dtype = order + dtype if (repeats == asbytes('')): newitem = dtype else: newitem = (dtype, eval(repeats)) result.append(newitem) return result def _getintp_ctype(): val = _getintp_ctype.cache if val is not None: return val char = dtype('p').char if (char == 'i'): val = ctypes.c_int elif char == 'l': val = ctypes.c_long elif char == 'q': val = ctypes.c_longlong else: val = ctypes.c_long _getintp_ctype.cache = val return val _getintp_ctype.cache = None # Used for .ctypes attribute of ndarray class _missing_ctypes(object): def cast(self, num, obj): return num def c_void_p(self, num): return num class _ctypes(object): def __init__(self, array, ptr=None): try: self._ctypes = ctypes except ImportError: self._ctypes = _missing_ctypes() self._arr = array self._data = ptr if self._arr.ndim == 0: self._zerod = True else: self._zerod = False def data_as(self, obj): return self._ctypes.cast(self._data, obj) def shape_as(self, obj): if self._zerod: return None return (obj*self._arr.ndim)(*self._arr.shape) def strides_as(self, obj): if self._zerod: return None return (obj*self._arr.ndim)(*self._arr.strides) def get_data(self): return self._data def get_shape(self): if self._zerod: return None return (_getintp_ctype()*self._arr.ndim)(*self._arr.shape) def get_strides(self): if self._zerod: return None return (_getintp_ctype()*self._arr.ndim)(*self._arr.strides) def get_as_parameter(self): return self._ctypes.c_void_p(self._data) data = property(get_data, None, doc="c-types data") shape = property(get_shape, None, doc="c-types shape") strides = property(get_strides, None, doc="c-types strides") _as_parameter_ = property(get_as_parameter, None, doc="_as parameter_") # Given a datatype and an order object # return a new names tuple # with the order indicated def _newnames(datatype, order): oldnames = datatype.names nameslist = list(oldnames) if isinstance(order, str): order = [order] if isinstance(order, (list, tuple)): for name in order: try: nameslist.remove(name) except ValueError: raise ValueError("unknown field name: %s" % (name,)) return tuple(list(order) + nameslist) raise ValueError("unsupported order value: %s" % (order,)) def _index_fields(ary, names): """ Given a structured array and a sequence of field names construct new array with just those fields. Parameters ---------- ary : ndarray Structured array being subscripted names : string or list of strings Either a single field name, or a list of field names Returns ------- sub_ary : ndarray If `names` is a single field name, the return value is identical to ary.getfield, a writeable view into `ary`. If `names` is a list of field names the return value is a copy of `ary` containing only those fields. This is planned to return a view in the future. Raises ------ ValueError If `ary` does not contain a field given in `names`. """ dt = ary.dtype #use getfield to index a single field if isinstance(names, basestring): try: return ary.getfield(dt.fields[names][0], dt.fields[names][1]) except KeyError: raise ValueError("no field of name %s" % names) for name in names: if name not in dt.fields: raise ValueError("no field of name %s" % name) formats = [dt.fields[name][0] for name in names] offsets = [dt.fields[name][1] for name in names] view_dtype = {'names': names, 'formats': formats, 'offsets': offsets, 'itemsize': dt.itemsize} # return copy for now (future plan to return ary.view(dtype=view_dtype)) copy_dtype = {'names': view_dtype['names'], 'formats': view_dtype['formats']} return array(ary.view(dtype=view_dtype), dtype=copy_dtype, copy=True) def _get_all_field_offsets(dtype, base_offset=0): """ Returns the types and offsets of all fields in a (possibly structured) data type, including nested fields and subarrays. Parameters ---------- dtype : data-type Data type to extract fields from. base_offset : int, optional Additional offset to add to all field offsets. Returns ------- fields : list of (data-type, int) pairs A flat list of (dtype, byte offset) pairs. """ fields = [] if dtype.fields is not None: for name in dtype.names: sub_dtype = dtype.fields[name][0] sub_offset = dtype.fields[name][1] + base_offset fields.extend(_get_all_field_offsets(sub_dtype, sub_offset)) else: if dtype.shape: sub_offsets = _get_all_field_offsets(dtype.base, base_offset) count = 1 for dim in dtype.shape: count *= dim fields.extend((typ, off + dtype.base.itemsize*j) for j in range(count) for (typ, off) in sub_offsets) else: fields.append((dtype, base_offset)) return fields def _check_field_overlap(new_fields, old_fields): """ Perform object memory overlap tests for two data-types (see _view_is_safe). This function checks that new fields only access memory contained in old fields, and that non-object fields are not interpreted as objects and vice versa. Parameters ---------- new_fields : list of (data-type, int) pairs Flat list of (dtype, byte offset) pairs for the new data type, as returned by _get_all_field_offsets. old_fields: list of (data-type, int) pairs Flat list of (dtype, byte offset) pairs for the old data type, as returned by _get_all_field_offsets. Raises ------ TypeError If the new fields are incompatible with the old fields """ #first go byte by byte and check we do not access bytes not in old_fields new_bytes = set() for tp, off in new_fields: new_bytes.update(set(range(off, off+tp.itemsize))) old_bytes = set() for tp, off in old_fields: old_bytes.update(set(range(off, off+tp.itemsize))) if new_bytes.difference(old_bytes): raise TypeError("view would access data parent array doesn't own") #next check that we do not interpret non-Objects as Objects, and vv obj_offsets = [off for (tp, off) in old_fields if tp.type is object_] obj_size = dtype(object_).itemsize for fld_dtype, fld_offset in new_fields: if fld_dtype.type is object_: # check we do not create object views where # there are no objects. if fld_offset not in obj_offsets: raise TypeError("cannot view non-Object data as Object type") else: # next check we do not create non-object views # where there are already objects. # see validate_object_field_overlap for a similar computation. for obj_offset in obj_offsets: if (fld_offset < obj_offset + obj_size and obj_offset < fld_offset + fld_dtype.itemsize): raise TypeError("cannot view Object as non-Object type") def _getfield_is_safe(oldtype, newtype, offset): """ Checks safety of getfield for object arrays. As in _view_is_safe, we need to check that memory containing objects is not reinterpreted as a non-object datatype and vice versa. Parameters ---------- oldtype : data-type Data type of the original ndarray. newtype : data-type Data type of the field being accessed by ndarray.getfield offset : int Offset of the field being accessed by ndarray.getfield Raises ------ TypeError If the field access is invalid """ new_fields = _get_all_field_offsets(newtype, offset) old_fields = _get_all_field_offsets(oldtype) # raises if there is a problem _check_field_overlap(new_fields, old_fields) def _view_is_safe(oldtype, newtype): """ Checks safety of a view involving object arrays, for example when doing:: np.zeros(10, dtype=oldtype).view(newtype) We need to check that 1) No memory that is not an object will be interpreted as a object, 2) No memory containing an object will be interpreted as an arbitrary type. Both cases can cause segfaults, eg in the case the view is written to. Strategy here is to also disallow views where newtype has any field in a place oldtype doesn't. Parameters ---------- oldtype : data-type Data type of original ndarray newtype : data-type Data type of the view Raises ------ TypeError If the new type is incompatible with the old type. """ new_fields = _get_all_field_offsets(newtype) new_size = newtype.itemsize old_fields = _get_all_field_offsets(oldtype) old_size = oldtype.itemsize # if the itemsizes are not equal, we need to check that all the # 'tiled positions' of the object match up. Here, we allow # for arbirary itemsizes (even those possibly disallowed # due to stride/data length issues). if old_size == new_size: new_num = old_num = 1 else: gcd_new_old = _gcd(new_size, old_size) new_num = old_size // gcd_new_old old_num = new_size // gcd_new_old # get position of fields within the tiling new_fieldtile = [(tp, off + new_size*j) for j in range(new_num) for (tp, off) in new_fields] old_fieldtile = [(tp, off + old_size*j) for j in range(old_num) for (tp, off) in old_fields] # raises if there is a problem _check_field_overlap(new_fieldtile, old_fieldtile) # Given a string containing a PEP 3118 format specifier, # construct a Numpy dtype _pep3118_native_map = { '?': '?', 'b': 'b', 'B': 'B', 'h': 'h', 'H': 'H', 'i': 'i', 'I': 'I', 'l': 'l', 'L': 'L', 'q': 'q', 'Q': 'Q', 'e': 'e', 'f': 'f', 'd': 'd', 'g': 'g', 'Zf': 'F', 'Zd': 'D', 'Zg': 'G', 's': 'S', 'w': 'U', 'O': 'O', 'x': 'V', # padding } _pep3118_native_typechars = ''.join(_pep3118_native_map.keys()) _pep3118_standard_map = { '?': '?', 'b': 'b', 'B': 'B', 'h': 'i2', 'H': 'u2', 'i': 'i4', 'I': 'u4', 'l': 'i4', 'L': 'u4', 'q': 'i8', 'Q': 'u8', 'e': 'f2', 'f': 'f', 'd': 'd', 'Zf': 'F', 'Zd': 'D', 's': 'S', 'w': 'U', 'O': 'O', 'x': 'V', # padding } _pep3118_standard_typechars = ''.join(_pep3118_standard_map.keys()) def _dtype_from_pep3118(spec, byteorder='@', is_subdtype=False): fields = {} offset = 0 explicit_name = False this_explicit_name = False common_alignment = 1 is_padding = False dummy_name_index = [0] def next_dummy_name(): dummy_name_index[0] += 1 def get_dummy_name(): while True: name = 'f%d' % dummy_name_index[0] if name not in fields: return name next_dummy_name() # Parse spec while spec: value = None # End of structure, bail out to upper level if spec[0] == '}': spec = spec[1:] break # Sub-arrays (1) shape = None if spec[0] == '(': j = spec.index(')') shape = tuple(map(int, spec[1:j].split(','))) spec = spec[j+1:] # Byte order if spec[0] in ('@', '=', '<', '>', '^', '!'): byteorder = spec[0] if byteorder == '!': byteorder = '>' spec = spec[1:] # Byte order characters also control native vs. standard type sizes if byteorder in ('@', '^'): type_map = _pep3118_native_map type_map_chars = _pep3118_native_typechars else: type_map = _pep3118_standard_map type_map_chars = _pep3118_standard_typechars # Item sizes itemsize = 1 if spec[0].isdigit(): j = 1 for j in range(1, len(spec)): if not spec[j].isdigit(): break itemsize = int(spec[:j]) spec = spec[j:] # Data types is_padding = False if spec[:2] == 'T{': value, spec, align, next_byteorder = _dtype_from_pep3118( spec[2:], byteorder=byteorder, is_subdtype=True) elif spec[0] in type_map_chars: next_byteorder = byteorder if spec[0] == 'Z': j = 2 else: j = 1 typechar = spec[:j] spec = spec[j:] is_padding = (typechar == 'x') dtypechar = type_map[typechar] if dtypechar in 'USV': dtypechar += '%d' % itemsize itemsize = 1 numpy_byteorder = {'@': '=', '^': '='}.get(byteorder, byteorder) value = dtype(numpy_byteorder + dtypechar) align = value.alignment else: raise ValueError("Unknown PEP 3118 data type specifier %r" % spec) # # Native alignment may require padding # # Here we assume that the presence of a '@' character implicitly implies # that the start of the array is *already* aligned. # extra_offset = 0 if byteorder == '@': start_padding = (-offset) % align intra_padding = (-value.itemsize) % align offset += start_padding if intra_padding != 0: if itemsize > 1 or (shape is not None and _prod(shape) > 1): # Inject internal padding to the end of the sub-item value = _add_trailing_padding(value, intra_padding) else: # We can postpone the injection of internal padding, # as the item appears at most once extra_offset += intra_padding # Update common alignment common_alignment = (align*common_alignment / _gcd(align, common_alignment)) # Convert itemsize to sub-array if itemsize != 1: value = dtype((value, (itemsize,))) # Sub-arrays (2) if shape is not None: value = dtype((value, shape)) # Field name this_explicit_name = False if spec and spec.startswith(':'): i = spec[1:].index(':') + 1 name = spec[1:i] spec = spec[i+1:] explicit_name = True this_explicit_name = True else: name = get_dummy_name() if not is_padding or this_explicit_name: if name in fields: raise RuntimeError("Duplicate field name '%s' in PEP3118 format" % name) fields[name] = (value, offset) if not this_explicit_name: next_dummy_name() byteorder = next_byteorder offset += value.itemsize offset += extra_offset # Check if this was a simple 1-item type if (len(fields) == 1 and not explicit_name and fields['f0'][1] == 0 and not is_subdtype): ret = fields['f0'][0] else: ret = dtype(fields) # Trailing padding must be explicitly added padding = offset - ret.itemsize if byteorder == '@': padding += (-offset) % common_alignment if is_padding and not this_explicit_name: ret = _add_trailing_padding(ret, padding) # Finished if is_subdtype: return ret, spec, common_alignment, byteorder else: return ret def _add_trailing_padding(value, padding): """Inject the specified number of padding bytes at the end of a dtype""" if value.fields is None: vfields = {'f0': (value, 0)} else: vfields = dict(value.fields) if (value.names and value.names[-1] == '' and value[''].char == 'V'): # A trailing padding field is already present vfields[''] = ('V%d' % (vfields[''][0].itemsize + padding), vfields[''][1]) value = dtype(vfields) else: # Get a free name for the padding field j = 0 while True: name = 'pad%d' % j if name not in vfields: vfields[name] = ('V%d' % padding, value.itemsize) break j += 1 value = dtype(vfields) if '' not in vfields: # Strip out the name of the padding field names = list(value.names) names[-1] = '' value.names = tuple(names) return value def _prod(a): p = 1 for x in a: p *= x return p def _gcd(a, b): """Calculate the greatest common divisor of a and b""" while b: a, b = b, a % b return a