""":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
"""
from __future__ import division, absolute_import, print_function
# 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 ?
import sys
import warnings
import numpy as np
import numpy.core.numerictypes as ntypes
from numpy.compat import basestring
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
_typestr = ntypes._typestr
import numpy.ma as ma
from numpy.ma import (
MAError, MaskedArray, masked, nomask, masked_array, getdata,
getmaskarray, filled
)
_check_fill_value = ma.core._check_fill_value
__all__ = [
'MaskedRecords', 'mrecarray', 'fromarrays', 'fromrecords',
'fromtextfile', 'addfield',
]
reserved_fields = ['_data', '_mask', '_fieldmask', 'dtype']
def _getformats(data):
"""
Returns the formats of arrays in arraylist as a comma-separated string.
"""
if hasattr(data, 'dtype'):
return ",".join([desc[1] for desc in data.dtype.descr])
formats = ''
for obj in data:
obj = np.asarray(obj)
formats += _typestr[obj.dtype.type]
if issubclass(obj.dtype.type, ntypes.flexible):
formats += repr(obj.itemsize)
formats += ','
return formats[:-1]
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("illegal input names %s" % repr(names))
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, object):
"""
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))
copy = True
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
def _getdata(self):
"""
Returns the data as a recarray.
"""
return ndarray.view(self, recarray)
_data = property(fget=_getdata)
def _getfieldmask(self):
"""
Alias to mask.
"""
return self._mask
_fieldmask = property(fget=_getfieldmask)
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):
raise AttributeError("record array has no attribute %s" % attr)
# So far, so good
_localdict = ndarray.__getattribute__(self, '__dict__')
_data = ndarray.view(self, _localdict['_baseclass'])
obj = _data.getfield(*res)
if obj.dtype.fields:
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
hasmasked = _mask.view((bool, (len(_mask.dtype) or 1))).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):
exctype, value = sys.exc_info()[:2]
raise exctype(value)
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):
raise AttributeError("record array has no attribute %s" % attr)
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, basestring):
# 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, basestring):
self._mask[indx] = ma.getmaskarray(value)
def __str__(self):
"""
Calculates the string representation.
"""
if self.size > 1:
mstr = ["(%s)" % ",".join([str(i) for i in s])
for s in zip(*[getattr(self, f) for f in self.dtype.names])]
return "[%s]" % ", ".join(mstr)
else:
mstr = ["%s" % ",".join([str(i) for i in s])
for s in zip([getattr(self, f) for f in self.dtype.names])]
return "(%s)" % ", ".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)
dtype = None
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 IOError:
raise IOError("No such file: '%s'" % fname)
if f.readline()[:2] != "\\x":
f.seek(0, 0)
return f
f.close()
raise NotImplementedError("Wow, binary file")
def fromtextfile(fname, delimitor=None, commentchar='#', missingchar='',
varnames=None, vartypes=None):
"""
Creates a mrecarray from data stored in the file `filename`.
Parameters
----------
fname : {file name/handle}
Handle of an opened file.
delimitor : {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"""
# 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(delimitor)
if len(_varnames) > 1:
break
if varnames is None:
varnames = _varnames
# Get the data.
_variables = masked_array([line.strip().split(delimitor) 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