__all__ = ['record', 'recarray', 'format_parser'] import numeric as sb from defchararray import chararray import numerictypes as nt import types import stat, os _byteorderconv = {'b':'>', 'l':'<', 'n':'=', 'B':'>', 'L':'<', 'N':'=', 'S':'s', 's':'s', '>':'>', '<':'<', '=':'=', '|':'|', 'I':'|', 'i':'|'} # formats regular expression # allows multidimension spec with a tuple syntax in front # of the letter code '(2,3)f4' and ' ( 2 , 3 ) f4 ' # are equally allowed numfmt = nt.typeDict _typestr = nt._typestr def find_duplicate(list): """Find duplication in a list, return a list of duplicated elements""" dup = [] for i in range(len(list)): if (list[i] in list[i+1:]): if (list[i] not in dup): dup.append(list[i]) return dup class format_parser: def __init__(self, formats, names, titles, aligned=False): self._parseFormats(formats, aligned) self._setfieldnames(names, titles) self._createdescr() def _parseFormats(self, formats, aligned=0): """ Parse the field formats """ dtype = sb.dtype(formats, aligned) fields = dtype.fields keys = fields[-1] self._f_formats = [fields[key][0] for key in keys] self._offsets = [fields[key][1] for key in keys] self._nfields = len(keys) def _setfieldnames(self, names, titles): """convert input field names into a list and assign to the _names attribute """ if (names): if (type(names) in [types.ListType, types.TupleType]): pass elif (type(names) == types.StringType): names = names.split(',') else: raise NameError, "illegal input names %s" % `names` self._names = [n.strip() for n in names[:self._nfields]] else: self._names = [] # if the names are not specified, they will be assigned as "f1, f2,..." # if not enough names are specified, they will be assigned as "f[n+1], # f[n+2],..." etc. where n is the number of specified names..." self._names += ['f%d' % i for i in range(len(self._names)+1, self._nfields+1)] # check for redundant names _dup = find_duplicate(self._names) if _dup: raise ValueError, "Duplicate field names: %s" % _dup if (titles): self._titles = [n.strip() for n in titles[:self._nfields]] else: self._titles = [] titles = [] if (self._nfields > len(titles)): self._titles += [None]*(self._nfields-len(titles)) def _createdescr(self): self._descr = sb.dtype({'names':self._names, 'formats':self._f_formats, 'offsets':self._offsets, 'titles':self._titles}) class record(nt.void): def __repr__(self): return self.__str__() def __str__(self): return str(self.item()) def __getattribute__(self, attr): if attr in ['setfield', 'getfield', 'dtype']: return nt.void.__getattribute__(self, attr) fielddict = nt.void.__getattribute__(self, 'dtype').fields res = fielddict.get(attr,None) if res: return self.getfield(*res[:2]) return nt.void.__getattribute__(self, attr) def __setattr__(self, attr, val): if attr in ['setfield', 'getfield', 'dtype']: raise AttributeError, "Cannot set '%s' attribute" % attr; fielddict = nt.void.__getattribute__(self,'dtype').fields res = fielddict.get(attr,None) if res: return self.setfield(val,*res[:2]) return nt.void.__setattr__(self,attr,val) # The recarray is almost identical to a standard array (which supports # named fields already) The biggest difference is that it can use # attribute-lookup to find the fields and it is constructed using # a record. # If byteorder is given it forces a particular byteorder on all # the fields (and any subfields) class recarray(sb.ndarray): def __new__(subtype, shape, formats, names=None, titles=None, buf=None, offset=0, strides=None, byteorder=None, aligned=0): if isinstance(formats, sb.dtype): descr = formats else: parsed = format_parser(formats, names, titles, aligned) descr = parsed._descr if (byteorder is not None): byteorder = _byteorderconv[byteorder[0]] descr = descr.newbyteorder(byteorder) if buf is None: self = sb.ndarray.__new__(subtype, shape, (record, descr)) else: self = sb.ndarray.__new__(subtype, shape, (record, descr), buffer=buf, offset=offset, strides=strides) return self def __getattribute__(self, attr): fielddict = sb.ndarray.__getattribute__(self,'dtype').fields try: res = fielddict[attr][:2] except: return object.__getattribute__(self,attr) obj = self.getfield(*res) # if it has fields return a recarray, otherwise return # normal array if obj.dtype.fields: return obj if obj.dtype.char in 'SU': return obj.view(chararray) return obj.view(sb.ndarray) def __setattr__(self, attr, val): fielddict = sb.ndarray.__getattribute__(self,'dtype').fields try: res = fielddict[attr][:2] except: return object.__setattr__(self,attr,val) return self.setfield(val,*res) def field(self,attr, val=None): fielddict = sb.ndarray.__getattribute__(self,'dtype').fields if isinstance(attr,int): attr=fielddict[-1][attr] if val is None: return self.__getattribute__(attr) else: return self.__setattr__(attr,val) def fromarrays(arrayList, formats=None, names=None, titles=None, shape=None, aligned=0): """ create a record array from a (flat) list of arrays >>> x1=array([1,2,3,4]) >>> x2=array(['a','dd','xyz','12']) >>> x3=array([1.1,2,3,4]) >>> r=fromarrays([x1,x2,x3],names='a,b,c') >>> print r[1] (2, 'dd', 2.0) >>> x1[1]=34 >>> r.a array([1, 2, 3, 4]) """ if shape is None or shape == 0: shape = arrayList[0].shape if isinstance(shape, int): shape = (shape,) if formats is None: # go through each object in the list to see if it is an ndarray # and determine the formats. formats = '' for obj in arrayList: if not isinstance(obj, sb.ndarray): raise ValueError, "item in the array list must be an ndarray." formats += _typestr[obj.dtype.type] if issubclass(obj.dtype.type, nt.flexible): formats += `obj.itemsize` formats += ',' formats=formats[:-1] for obj in arrayList: if obj.shape != shape: raise ValueError, "array has different shape" parsed = format_parser(formats, names, titles, aligned) _names = parsed._names _array = recarray(shape, parsed._descr) # populate the record array (makes a copy) for i in range(len(arrayList)): _array[_names[i]] = arrayList[i] return _array # shape must be 1-d if you use list of lists... def fromrecords(recList, formats=None, names=None, titles=None, shape=None, aligned=0): """ create a recarray from a list of records in text form The data in the same field can be heterogeneous, they will be promoted to the highest data type. This method is intended for creating smaller record arrays. If used to create large array without formats defined r=fromrecords([(2,3.,'abc')]*100000) it can be slow. If formats is None, then this will auto-detect formats. Use list of tuples rather than list of lists for faster processing. >>> r=fromrecords([(456,'dbe',1.2),(2,'de',1.3)],names='col1,col2,col3') >>> print r[0] (456, 'dbe', 1.2) >>> r.col1 array([456, 2]) >>> r.col2 chararray(['dbe', 'de']) >>> import cPickle >>> print cPickle.loads(cPickle.dumps(r)) recarray[ (456, 'dbe', 1.2), (2, 'de', 1.3) ] """ nfields = len(recList[0]) if formats is None: # slower obj = sb.array(recList,dtype=object) arrlist = [sb.array(obj[...,i].tolist()) for i in xrange(nfields)] return fromarrays(arrlist, formats=formats, shape=shape, names=names, titles=titles, aligned=aligned) parsed = format_parser(formats, names, titles, aligned) try: retval = sb.array(recList, dtype = parsed._descr) except TypeError: # list of lists instead of list of tuples if (shape is None or shape == 0): shape = len(recList) if isinstance(shape, (int, long)): shape = (shape,) if len(shape) > 1: raise ValueError, "Can only deal with 1-d array." _array = recarray(shape, parsed._descr) for k in xrange(_array.size): _array[k] = tuple(recList[k]) return _array else: if shape is not None and retval.shape != shape: retval.shape = shape res = retval.view(recarray) res.dtype = sb.dtype((record, res.dtype)) return res def fromstring(datastring, formats, shape=None, names=None, titles=None, byteorder=None, aligned=0, offset=0): """ create a (read-only) record array from binary data contained in a string""" parsed = format_parser(formats, names, titles, aligned) itemsize = parsed._descr.itemsize if (shape is None or shape == 0 or shape == -1): shape = (len(datastring)-offset) / itemsize _array = recarray(shape, parsed._descr, names=names, titles=titles, buf=datastring, offset=offset, byteorder=byteorder) return _array def fromfile(fd, formats, shape=None, names=None, titles=None, byteorder=None, aligned=0, offset=0): """Create an array from binary file data If file is a string then that file is opened, else it is assumed to be a file object. >>> import testdata, sys >>> fd=open(testdata.filename) >>> fd.seek(2880*2) >>> r=fromfile(fd, formats='f8,i4,a5', shape=3, byteorder='big') >>> print r[0] (5.1000000000000005, 61, 'abcde') >>> r._shape (3,) """ if (shape is None or shape == 0): shape = (-1,) elif isinstance(shape, (int, long)): shape = (shape,) name = 0 if isinstance(fd, str): name = 1 fd = open(fd, 'rb') if (offset > 0): fd.seek(offset, 1) try: size = os.fstat(fd.fileno())[stat.ST_SIZE] - fd.tell() except: size = os.path.getsize(fd.name) - fd.tell() parsed = format_parser(formats, names, titles, aligned) itemsize = parsed._descr.itemsize shapeprod = sb.array(shape).prod() shapesize = shapeprod*itemsize if shapesize < 0: shape = list(shape) shape[ shape.index(-1) ] = size / -shapesize shape = tuple(shape) shapeprod = sb.array(shape).prod() nbytes = shapeprod*itemsize if nbytes > size: raise ValueError( "Not enough bytes left in file for specified shape and type") # create the array _array = recarray(shape, parsed._descr, byteorder=byteorder) nbytesread = fd.readinto(_array.data) if nbytesread != nbytes: raise IOError("Didn't read as many bytes as expected") if name: fd.close() return _array def array(obj, formats=None, names=None, titles=None, shape=None, byteorder=None, aligned=0, offset=0, strides=None): if isinstance(obj, (type(None), str, file)) and (formats is None): raise ValueError("Must define formats if object is "\ "None, string, or an open file") elif obj is None: if shape is None: raise ValueError("Must define a shape if obj is None") return recarray(shape, formats, names=names, titles=titles, buf=obj, offset=offset, strides=strides, byteorder=byteorder, aligned=aligned) elif isinstance(obj, str): return fromstring(obj, formats, names=names, titles=titles, shape=shape, byteorder=byteorder, aligned=aligned, offset=offset) elif isinstance(obj, (list, tuple)): if isinstance(obj[0], sb.ndarray): return fromarrays(obj, formats=formats, names=names, titles=titles, shape=shape, aligned=aligned) else: return fromrecords(obj, formats=formats, names=names, titles=titles, shape=shape, aligned=aligned) elif isinstance(obj, recarray): new = obj.copy() parsed = format_parser(formats, names, titles, aligned) new.dtype = parsed._descr return new elif isinstance(obj, file): return fromfile(obj, formats=formats, names=names, titles=titles, shape=shape, byteorder=byteorder, aligned=aligned, offset=offset) elif isinstance(obj, sb.ndarray): res = obj.view(recarray) if issubclass(res.dtype.type, nt.void): res.dtype = sb.dtype((record, res.dtype)) return res else: raise ValueError("Unknown input type")