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mrecords.py
""":mod:`numpy.ma..mrecords` Defines the equivalent of :class:`numpy.recarrays` for masked arrays, where fields can be accessed as attributes. Note that :class:`numpy.ma.MaskedArray` already supports structured datatypes and the masking of individual fields. .. moduleauthor:: Pierre Gerard-Marchant """ # We should make sure that no field is called '_mask','mask','_fieldmask', # or whatever restricted keywords. An idea would be to no bother in the # first place, and then rename the invalid fields with a trailing # underscore. Maybe we could just overload the parser function ? from numpy.ma import ( MAError, MaskedArray, masked, nomask, masked_array, getdata, getmaskarray, filled ) import numpy.ma as ma import warnings import numpy as np from numpy import ( bool_, dtype, ndarray, recarray, array as narray ) from numpy.core.records import ( fromarrays as recfromarrays, fromrecords as recfromrecords ) _byteorderconv = np.core.records._byteorderconv _check_fill_value = ma.core._check_fill_value __all__ = [ 'MaskedRecords', 'mrecarray', 'fromarrays', 'fromrecords', 'fromtextfile', 'addfield', ] reserved_fields = ['_data', '_mask', '_fieldmask', 'dtype'] def _checknames(descr, names=None): """ Checks that field names ``descr`` are not reserved keywords. If this is the case, a default 'f%i' is substituted. If the argument `names` is not None, updates the field names to valid names. """ ndescr = len(descr) default_names = ['f%i' % i for i in range(ndescr)] if names is None: new_names = default_names else: if isinstance(names, (tuple, list)): new_names = names elif isinstance(names, str): new_names = names.split(',') else: raise NameError(f'illegal input names {names!r}') nnames = len(new_names) if nnames < ndescr: new_names += default_names[nnames:] ndescr = [] for (n, d, t) in zip(new_names, default_names, descr.descr): if n in reserved_fields: if t[0] in reserved_fields: ndescr.append((d, t[1])) else: ndescr.append(t) else: ndescr.append((n, t[1])) return np.dtype(ndescr) def _get_fieldmask(self): mdescr = [(n, '|b1') for n in self.dtype.names] fdmask = np.empty(self.shape, dtype=mdescr) fdmask.flat = tuple([False] * len(mdescr)) return fdmask class MaskedRecords(MaskedArray): """ Attributes ---------- _data : recarray Underlying data, as a record array. _mask : boolean array Mask of the records. A record is masked when all its fields are masked. _fieldmask : boolean recarray Record array of booleans, setting the mask of each individual field of each record. _fill_value : record Filling values for each field. """ def __new__(cls, shape, dtype=None, buf=None, offset=0, strides=None, formats=None, names=None, titles=None, byteorder=None, aligned=False, mask=nomask, hard_mask=False, fill_value=None, keep_mask=True, copy=False, **options): self = recarray.__new__(cls, shape, dtype=dtype, buf=buf, offset=offset, strides=strides, formats=formats, names=names, titles=titles, byteorder=byteorder, aligned=aligned,) mdtype = ma.make_mask_descr(self.dtype) if mask is nomask or not np.size(mask): if not keep_mask: self._mask = tuple([False] * len(mdtype)) else: mask = np.array(mask, copy=copy) if mask.shape != self.shape: (nd, nm) = (self.size, mask.size) if nm == 1: mask = np.resize(mask, self.shape) elif nm == nd: mask = np.reshape(mask, self.shape) else: msg = "Mask and data not compatible: data size is %i, " + \ "mask size is %i." raise MAError(msg % (nd, nm)) if not keep_mask: self.__setmask__(mask) self._sharedmask = True else: if mask.dtype == mdtype: _mask = mask else: _mask = np.array([tuple([m] * len(mdtype)) for m in mask], dtype=mdtype) self._mask = _mask return self def __array_finalize__(self, obj): # Make sure we have a _fieldmask by default _mask = getattr(obj, '_mask', None) if _mask is None: objmask = getattr(obj, '_mask', nomask) _dtype = ndarray.__getattribute__(self, 'dtype') if objmask is nomask: _mask = ma.make_mask_none(self.shape, dtype=_dtype) else: mdescr = ma.make_mask_descr(_dtype) _mask = narray([tuple([m] * len(mdescr)) for m in objmask], dtype=mdescr).view(recarray) # Update some of the attributes _dict = self.__dict__ _dict.update(_mask=_mask) self._update_from(obj) if _dict['_baseclass'] == ndarray: _dict['_baseclass'] = recarray return @property def _data(self): """ Returns the data as a recarray. """ return ndarray.view(self, recarray) @property def _fieldmask(self): """ Alias to mask. """ return self._mask def __len__(self): """ Returns the length """ # We have more than one record if self.ndim: return len(self._data) # We have only one record: return the nb of fields return len(self.dtype) def __getattribute__(self, attr): try: return object.__getattribute__(self, attr) except AttributeError: # attr must be a fieldname pass fielddict = ndarray.__getattribute__(self, 'dtype').fields try: res = fielddict[attr][:2] except (TypeError, KeyError) as e: raise AttributeError( f'record array has no attribute {attr}') from e # So far, so good _localdict = ndarray.__getattribute__(self, '__dict__') _data = ndarray.view(self, _localdict['_baseclass']) obj = _data.getfield(*res) if obj.dtype.names is not None: raise NotImplementedError("MaskedRecords is currently limited to" "simple records.") # Get some special attributes # Reset the object's mask hasmasked = False _mask = _localdict.get('_mask', None) if _mask is not None: try: _mask = _mask[attr] except IndexError: # Couldn't find a mask: use the default (nomask) pass tp_len = len(_mask.dtype) hasmasked = _mask.view((bool, ((tp_len,) if tp_len else ()))).any() if (obj.shape or hasmasked): obj = obj.view(MaskedArray) obj._baseclass = ndarray obj._isfield = True obj._mask = _mask # Reset the field values _fill_value = _localdict.get('_fill_value', None) if _fill_value is not None: try: obj._fill_value = _fill_value[attr] except ValueError: obj._fill_value = None else: obj = obj.item() return obj def __setattr__(self, attr, val): """ Sets the attribute attr to the value val. """ # Should we call __setmask__ first ? if attr in ['mask', 'fieldmask']: self.__setmask__(val) return # Create a shortcut (so that we don't have to call getattr all the time) _localdict = object.__getattribute__(self, '__dict__') # Check whether we're creating a new field newattr = attr not in _localdict try: # Is attr a generic attribute ? ret = object.__setattr__(self, attr, val) except Exception: # Not a generic attribute: exit if it's not a valid field fielddict = ndarray.__getattribute__(self, 'dtype').fields or {} optinfo = ndarray.__getattribute__(self, '_optinfo') or {} if not (attr in fielddict or attr in optinfo): raise else: # Get the list of names fielddict = ndarray.__getattribute__(self, 'dtype').fields or {} # Check the attribute if attr not in fielddict: return ret if newattr: # We just added this one or this setattr worked on an # internal attribute. try: object.__delattr__(self, attr) except Exception: return ret # Let's try to set the field try: res = fielddict[attr][:2] except (TypeError, KeyError) as e: raise AttributeError( f'record array has no attribute {attr}') from e if val is masked: _fill_value = _localdict['_fill_value'] if _fill_value is not None: dval = _localdict['_fill_value'][attr] else: dval = val mval = True else: dval = filled(val) mval = getmaskarray(val) obj = ndarray.__getattribute__(self, '_data').setfield(dval, *res) _localdict['_mask'].__setitem__(attr, mval) return obj def __getitem__(self, indx): """ Returns all the fields sharing the same fieldname base. The fieldname base is either `_data` or `_mask`. """ _localdict = self.__dict__ _mask = ndarray.__getattribute__(self, '_mask') _data = ndarray.view(self, _localdict['_baseclass']) # We want a field if isinstance(indx, str): # Make sure _sharedmask is True to propagate back to _fieldmask # Don't use _set_mask, there are some copies being made that # break propagation Don't force the mask to nomask, that wreaks # easy masking obj = _data[indx].view(MaskedArray) obj._mask = _mask[indx] obj._sharedmask = True fval = _localdict['_fill_value'] if fval is not None: obj._fill_value = fval[indx] # Force to masked if the mask is True if not obj.ndim and obj._mask: return masked return obj # We want some elements. # First, the data. obj = np.array(_data[indx], copy=False).view(mrecarray) obj._mask = np.array(_mask[indx], copy=False).view(recarray) return obj def __setitem__(self, indx, value): """ Sets the given record to value. """ MaskedArray.__setitem__(self, indx, value) if isinstance(indx, str): self._mask[indx] = ma.getmaskarray(value) def __str__(self): """ Calculates the string representation. """ if self.size > 1: mstr = [f"({','.join([str(i) for i in s])})" for s in zip(*[getattr(self, f) for f in self.dtype.names])] return f"[{', '.join(mstr)}]" else: mstr = [f"{','.join([str(i) for i in s])}" for s in zip([getattr(self, f) for f in self.dtype.names])] return f"({', '.join(mstr)})" def __repr__(self): """ Calculates the repr representation. """ _names = self.dtype.names fmt = "%%%is : %%s" % (max([len(n) for n in _names]) + 4,) reprstr = [fmt % (f, getattr(self, f)) for f in self.dtype.names] reprstr.insert(0, 'masked_records(') reprstr.extend([fmt % (' fill_value', self.fill_value), ' )']) return str("\n".join(reprstr)) def view(self, dtype=None, type=None): """ Returns a view of the mrecarray. """ # OK, basic copy-paste from MaskedArray.view. if dtype is None: if type is None: output = ndarray.view(self) else: output = ndarray.view(self, type) # Here again. elif type is None: try: if issubclass(dtype, ndarray): output = ndarray.view(self, dtype) else: output = ndarray.view(self, dtype) # OK, there's the change except TypeError: dtype = np.dtype(dtype) # we need to revert to MaskedArray, but keeping the possibility # of subclasses (eg, TimeSeriesRecords), so we'll force a type # set to the first parent if dtype.fields is None: basetype = self.__class__.__bases__[0] output = self.__array__().view(dtype, basetype) output._update_from(self) else: output = ndarray.view(self, dtype) output._fill_value = None else: output = ndarray.view(self, dtype, type) # Update the mask, just like in MaskedArray.view if (getattr(output, '_mask', nomask) is not nomask): mdtype = ma.make_mask_descr(output.dtype) output._mask = self._mask.view(mdtype, ndarray) output._mask.shape = output.shape return output def harden_mask(self): """ Forces the mask to hard. """ self._hardmask = True def soften_mask(self): """ Forces the mask to soft """ self._hardmask = False def copy(self): """ Returns a copy of the masked record. """ copied = self._data.copy().view(type(self)) copied._mask = self._mask.copy() return copied def tolist(self, fill_value=None): """ Return the data portion of the array as a list. Data items are converted to the nearest compatible Python type. Masked values are converted to fill_value. If fill_value is None, the corresponding entries in the output list will be ``None``. """ if fill_value is not None: return self.filled(fill_value).tolist() result = narray(self.filled().tolist(), dtype=object) mask = narray(self._mask.tolist()) result[mask] = None return result.tolist() def __getstate__(self): """Return the internal state of the masked array. This is for pickling. """ state = (1, self.shape, self.dtype, self.flags.fnc, self._data.tobytes(), self._mask.tobytes(), self._fill_value, ) return state def __setstate__(self, state): """ Restore the internal state of the masked array. This is for pickling. ``state`` is typically the output of the ``__getstate__`` output, and is a 5-tuple: - class name - a tuple giving the shape of the data - a typecode for the data - a binary string for the data - a binary string for the mask. """ (ver, shp, typ, isf, raw, msk, flv) = state ndarray.__setstate__(self, (shp, typ, isf, raw)) mdtype = dtype([(k, bool_) for (k, _) in self.dtype.descr]) self.__dict__['_mask'].__setstate__((shp, mdtype, isf, msk)) self.fill_value = flv def __reduce__(self): """ Return a 3-tuple for pickling a MaskedArray. """ return (_mrreconstruct, (self.__class__, self._baseclass, (0,), 'b',), self.__getstate__()) def _mrreconstruct(subtype, baseclass, baseshape, basetype,): """ Build a new MaskedArray from the information stored in a pickle. """ _data = ndarray.__new__(baseclass, baseshape, basetype).view(subtype) _mask = ndarray.__new__(ndarray, baseshape, 'b1') return subtype.__new__(subtype, _data, mask=_mask, dtype=basetype,) mrecarray = MaskedRecords ############################################################################### # Constructors # ############################################################################### def fromarrays(arraylist, dtype=None, shape=None, formats=None, names=None, titles=None, aligned=False, byteorder=None, fill_value=None): """ Creates a mrecarray from a (flat) list of masked arrays. Parameters ---------- arraylist : sequence A list of (masked) arrays. Each element of the sequence is first converted to a masked array if needed. If a 2D array is passed as argument, it is processed line by line dtype : {None, dtype}, optional Data type descriptor. shape : {None, integer}, optional Number of records. If None, shape is defined from the shape of the first array in the list. formats : {None, sequence}, optional Sequence of formats for each individual field. If None, the formats will be autodetected by inspecting the fields and selecting the highest dtype possible. names : {None, sequence}, optional Sequence of the names of each field. fill_value : {None, sequence}, optional Sequence of data to be used as filling values. Notes ----- Lists of tuples should be preferred over lists of lists for faster processing. """ datalist = [getdata(x) for x in arraylist] masklist = [np.atleast_1d(getmaskarray(x)) for x in arraylist] _array = recfromarrays(datalist, dtype=dtype, shape=shape, formats=formats, names=names, titles=titles, aligned=aligned, byteorder=byteorder).view(mrecarray) _array._mask.flat = list(zip(*masklist)) if fill_value is not None: _array.fill_value = fill_value return _array def fromrecords(reclist, dtype=None, shape=None, formats=None, names=None, titles=None, aligned=False, byteorder=None, fill_value=None, mask=nomask): """ Creates a MaskedRecords from a list of records. Parameters ---------- reclist : sequence A list of records. Each element of the sequence is first converted to a masked array if needed. If a 2D array is passed as argument, it is processed line by line dtype : {None, dtype}, optional Data type descriptor. shape : {None,int}, optional Number of records. If None, ``shape`` is defined from the shape of the first array in the list. formats : {None, sequence}, optional Sequence of formats for each individual field. If None, the formats will be autodetected by inspecting the fields and selecting the highest dtype possible. names : {None, sequence}, optional Sequence of the names of each field. fill_value : {None, sequence}, optional Sequence of data to be used as filling values. mask : {nomask, sequence}, optional. External mask to apply on the data. Notes ----- Lists of tuples should be preferred over lists of lists for faster processing. """ # Grab the initial _fieldmask, if needed: _mask = getattr(reclist, '_mask', None) # Get the list of records. if isinstance(reclist, ndarray): # Make sure we don't have some hidden mask if isinstance(reclist, MaskedArray): reclist = reclist.filled().view(ndarray) # Grab the initial dtype, just in case if dtype is None: dtype = reclist.dtype reclist = reclist.tolist() mrec = recfromrecords(reclist, dtype=dtype, shape=shape, formats=formats, names=names, titles=titles, aligned=aligned, byteorder=byteorder).view(mrecarray) # Set the fill_value if needed if fill_value is not None: mrec.fill_value = fill_value # Now, let's deal w/ the mask if mask is not nomask: mask = np.array(mask, copy=False) maskrecordlength = len(mask.dtype) if maskrecordlength: mrec._mask.flat = mask elif mask.ndim == 2: mrec._mask.flat = [tuple(m) for m in mask] else: mrec.__setmask__(mask) if _mask is not None: mrec._mask[:] = _mask return mrec def _guessvartypes(arr): """ Tries to guess the dtypes of the str_ ndarray `arr`. Guesses by testing element-wise conversion. Returns a list of dtypes. The array is first converted to ndarray. If the array is 2D, the test is performed on the first line. An exception is raised if the file is 3D or more. """ vartypes = [] arr = np.asarray(arr) if arr.ndim == 2: arr = arr[0] elif arr.ndim > 2: raise ValueError("The array should be 2D at most!") # Start the conversion loop. for f in arr: try: int(f) except (ValueError, TypeError): try: float(f) except (ValueError, TypeError): try: complex(f) except (ValueError, TypeError): vartypes.append(arr.dtype) else: vartypes.append(np.dtype(complex)) else: vartypes.append(np.dtype(float)) else: vartypes.append(np.dtype(int)) return vartypes def openfile(fname): """ Opens the file handle of file `fname`. """ # A file handle if hasattr(fname, 'readline'): return fname # Try to open the file and guess its type try: f = open(fname) except FileNotFoundError as e: raise FileNotFoundError(f"No such file: '{fname}'") from e if f.readline()[:2] != "\\x": f.seek(0, 0) return f f.close() raise NotImplementedError("Wow, binary file") def fromtextfile(fname, delimiter=None, commentchar='#', missingchar='', varnames=None, vartypes=None, *, delimitor=np._NoValue): # backwards compatibility """ Creates a mrecarray from data stored in the file `filename`. Parameters ---------- fname : {file name/handle} Handle of an opened file. delimiter : {None, string}, optional Alphanumeric character used to separate columns in the file. If None, any (group of) white spacestring(s) will be used. commentchar : {'#', string}, optional Alphanumeric character used to mark the start of a comment. missingchar : {'', string}, optional String indicating missing data, and used to create the masks. varnames : {None, sequence}, optional Sequence of the variable names. If None, a list will be created from the first non empty line of the file. vartypes : {None, sequence}, optional Sequence of the variables dtypes. If None, it will be estimated from the first non-commented line. Ultra simple: the varnames are in the header, one line""" if delimitor is not np._NoValue: if delimiter is not None: raise TypeError("fromtextfile() got multiple values for argument " "'delimiter'") # NumPy 1.22.0, 2021-09-23 warnings.warn("The 'delimitor' keyword argument of " "numpy.ma.mrecords.fromtextfile() is deprecated " "since NumPy 1.22.0, use 'delimiter' instead.", DeprecationWarning, stacklevel=2) delimiter = delimitor # Try to open the file. ftext = openfile(fname) # Get the first non-empty line as the varnames while True: line = ftext.readline() firstline = line[:line.find(commentchar)].strip() _varnames = firstline.split(delimiter) if len(_varnames) > 1: break if varnames is None: varnames = _varnames # Get the data. _variables = masked_array([line.strip().split(delimiter) for line in ftext if line[0] != commentchar and len(line) > 1]) (_, nfields) = _variables.shape ftext.close() # Try to guess the dtype. if vartypes is None: vartypes = _guessvartypes(_variables[0]) else: vartypes = [np.dtype(v) for v in vartypes] if len(vartypes) != nfields: msg = "Attempting to %i dtypes for %i fields!" msg += " Reverting to default." warnings.warn(msg % (len(vartypes), nfields), stacklevel=2) vartypes = _guessvartypes(_variables[0]) # Construct the descriptor. mdescr = [(n, f) for (n, f) in zip(varnames, vartypes)] mfillv = [ma.default_fill_value(f) for f in vartypes] # Get the data and the mask. # We just need a list of masked_arrays. It's easier to create it like that: _mask = (_variables.T == missingchar) _datalist = [masked_array(a, mask=m, dtype=t, fill_value=f) for (a, m, t, f) in zip(_variables.T, _mask, vartypes, mfillv)] return fromarrays(_datalist, dtype=mdescr) def addfield(mrecord, newfield, newfieldname=None): """Adds a new field to the masked record array Uses `newfield` as data and `newfieldname` as name. If `newfieldname` is None, the new field name is set to 'fi', where `i` is the number of existing fields. """ _data = mrecord._data _mask = mrecord._mask if newfieldname is None or newfieldname in reserved_fields: newfieldname = 'f%i' % len(_data.dtype) newfield = ma.array(newfield) # Get the new data. # Create a new empty recarray newdtype = np.dtype(_data.dtype.descr + [(newfieldname, newfield.dtype)]) newdata = recarray(_data.shape, newdtype) # Add the existing field [newdata.setfield(_data.getfield(*f), *f) for f in _data.dtype.fields.values()] # Add the new field newdata.setfield(newfield._data, *newdata.dtype.fields[newfieldname]) newdata = newdata.view(MaskedRecords) # Get the new mask # Create a new empty recarray newmdtype = np.dtype([(n, bool_) for n in newdtype.names]) newmask = recarray(_data.shape, newmdtype) # Add the old masks [newmask.setfield(_mask.getfield(*f), *f) for f in _mask.dtype.fields.values()] # Add the mask of the new field newmask.setfield(getmaskarray(newfield), *newmask.dtype.fields[newfieldname]) newdata._mask = newmask return newdata
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