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"""MA: a facility for dealing with missing observations
MA is generally used as a Numeric.array look-alike.
There are some differences in semantics, see manual.
In particular note that slices are copies, not references.
by Paul F. Dubois
L-264
Lawrence Livermore National Laboratory
dubois@users.sourceforge.net
Copyright 1999, 2000, 2001 Regents of the University of California.
Released for unlimited redistribution; see file Legal.htm
Documentation is in the Numeric manual; see numpy.sourceforge.net
"""
import Numeric
import string, types, sys
from Precision import *
from Numeric import e, pi, NewAxis
MaskType=Int0
divide_tolerance = 1.e-35
class MAError (Exception):
def __init__ (self, args=None):
"Create an exception"
self.args = args
def __str__(self):
"Calculate the string representation"
return str(self.args)
__repr__ = __str__
class _MaskedPrintOption:
"One instance of this class, masked_print_option, is created."
def __init__ (self, display):
"Create the masked print option object."
self.set_display(display)
self._enabled = 1
def display (self):
"Show what prints for masked values."
return self._display
def set_display (self, s):
"set_display(s) sets what prints for masked values."
self._display = s
def enabled (self):
"Is the use of the display value enabled?"
return self._enabled
def enable(self, flag=1):
"Set the enabling flag to flag."
self._enabled = flag
def __str__ (self):
return str(self._display)
#if you single index into a masked location you get this object.
masked_print_option = _MaskedPrintOption('--')
# Use single element arrays or scalars.
default_real_fill_value = Numeric.array([1.0e20]).astype(Float32)
default_complex_fill_value = Numeric.array([1.0e20 + 0.0j]).astype(Complex32)
default_character_fill_value = '?'
default_integer_fill_value = Numeric.array([0]).astype(UnsignedInt8)
default_object_fill_value = '?'
def default_fill_value (obj):
"Function to calculate default fill value for an object."
if isinstance(obj, types.FloatType):
return default_real_fill_value
elif isinstance(obj, types.IntType) or isinstance(obj, types.LongType):
return default_integer_fill_value
elif isinstance(obj, types.StringType):
return default_character_fill_value
elif isinstance(obj, types.ComplexType):
return default_complex_fill_value
elif isinstance(obj, MaskedArray) or isinstance(obj, Numeric.arraytype):
x = obj.typecode()
if x in typecodes['Float']:
return default_real_fill_value
if x in typecodes['Integer']:
return default_integer_fill_value
if x in typecodes['Complex']:
return default_complex_fill_value
if x in typecodes['Character']:
return default_character_fill_value
if x in typecodes['UnsignedInteger']:
return Numeric.absolute(default_integer_fill_value)
return default_object_fill_value
else:
return default_object_fill_value
def minimum_fill_value (obj):
"Function to calculate default fill value suitable for taking minima."
if isinstance(obj, types.FloatType):
return default_real_fill_value
elif isinstance(obj, types.IntType) or isinstance(obj, types.LongType):
return sys.maxint
elif isinstance(obj, MaskedArray) or isinstance(obj, Numeric.arraytype):
x = obj.typecode()
if x in typecodes['Float']:
return default_real_fill_value
if x in typecodes['Integer']:
return sys.maxint
if x in typecodes['UnsignedInteger']:
return sys.maxint
else:
raise TypeError, 'Unsuitable type for calculating minimum.'
def maximum_fill_value (obj):
"Function to calculate default fill value suitable for taking maxima."
if isinstance(obj, types.FloatType):
return -default_real_fill_value
elif isinstance(obj, types.IntType) or isinstance(obj, types.LongType):
return -default_integer_fill_value
elif isinstance(obj, MaskedArray) or isinstance(obj, Numeric.arraytype):
x = obj.typecode()
if x in typecodes['Float']:
return -default_real_fill_value
if x in typecodes['Integer']:
return -sys.maxint
if x in typecodes['UnsignedInteger']:
return 0
else:
raise TypeError, 'Unsuitable type for calculating maximum.'
def set_fill_value (a, fill_value):
"Set fill value of a if it is a masked array."
if isMaskedArray(a):
a.set_fill_value (fill_value)
def getmask (a):
"""Mask of values in a; could be None.
Returns None if a is not a masked array.
To get an array for sure use getmaskarray."""
if isinstance(a, MaskedArray):
return a.raw_mask()
else:
return None
def getmaskarray (a):
"""Mask of values in a; an array of zeros if mask is None
or not a masked array. Caution: has savespace attribute,
and is a byte-sized integer.
Do not try to add up entries, for example.
"""
m = getmask(a)
if m is None:
return make_mask_none(shape(a))
else:
return m
def is_mask (m):
"""Is m a legal mask? Does not check contents, only type.
"""
if m is None or (isinstance(m, Numeric.ArrayType) and \
m.typecode() == MaskType):
return 1
else:
return 0
def make_mask (m, copy=0, flag=0):
"""make_mask(m, copy=0, flag=0)
return m as a mask, creating a copy if necessary or requested.
Can accept any sequence of integers or None. Does not check
that contents must be 0s and 1s.
if flag, return None if m contains no true elements.
"""
if m is None:
return None
elif isinstance(m, Numeric.ArrayType):
if m.typecode() == MaskType:
if copy:
result = Numeric.array(m, savespace=1)
else:
result = Numeric.array(m, copy=0, savespace=1)
else:
result = m.astype(MaskType)
result.savespace(1)
else:
result = Numeric.array(filled(m,1), MaskType, savespace=1)
if flag and not Numeric.sometrue(Numeric.ravel(result)):
return None
else:
return result
def make_mask_none (s):
"Return a mask of all zeros of shape s."
result = Numeric.zeros(s, MaskType)
result.savespace(1)
result.shape = s
return result
create_mask = make_mask_none #backwards compatibility
def mask_or (m1, m2):
"""Logical or of the mask candidates m1 and m2, treating None as false.
Result may equal m1 or m2 if the other is None.
"""
if m1 is None: return make_mask(m2)
if m2 is None: return make_mask(m1)
if m1 is m2 and is_mask(m1): return m1
return make_mask(Numeric.logical_or(m1, m2))
def filled (a, value = None):
"""a as a contiguous Numeric array with any masked areas replaced by value
if value is None or the special element "masked", fill_value(a)
is used instead.
If a is already a contiguous Numeric array, a itself is returned.
filled(a) can be used to be sure that the result is Numeric when
passing an object a to other software ignorant of MA, in particular to
Numeric itself.
"""
if isinstance(a, MaskedArray):
return a.filled(value)
elif isinstance(a, Numeric.ArrayType) and a.iscontiguous():
return a
elif isinstance(a, types.DictType):
return Numeric.array(a, 'O')
else:
return Numeric.array(a)
def fill_value (a):
"""
The fill value of a, if it has one; otherwise, the default fill value
for that type.
"""
if isMaskedArray(a):
result = a.fill_value()
else:
result = default_fill_value(a)
return result
def common_fill_value (a, b):
"The common fill_value of a and b, if there is one, or None"
t1 = fill_value(a)
t2 = fill_value(b)
if t1 == t2: return t1
return None
# Domain functions return 1 where the argument(s) are not in the domain.
class domain_check_interval:
"domain_check_interval(a,b)(x) = true where x < a or y > b"
def __init__(self, y1, y2):
"domain_check_interval(a,b)(x) = true where x < a or y > b"
self.y1 = y1
self.y2 = y2
def __call__ (self, x):
"Execute the call behavior."
return Numeric.logical_or(Numeric.greater (x, self.y2),
Numeric.less(x, self.y1)
)
class domain_tan:
"domain_tan(eps) = true where abs(cos(x)) < eps)"
def __init__(self, eps):
"domain_tan(eps) = true where abs(cos(x)) < eps)"
self.eps = eps
def __call__ (self, x):
"Execute the call behavior."
return Numeric.less(Numeric.absolute(Numeric.cos(x)), self.eps)
class domain_greater:
"domain_greater(v)(x) = true where x <= v"
def __init__(self, critical_value):
"domain_greater(v)(x) = true where x <= v"
self.critical_value = critical_value
def __call__ (self, x):
"Execute the call behavior."
return Numeric.less_equal (x, self.critical_value)
class domain_greater_equal:
"domain_greater_equal(v)(x) = true where x < v"
def __init__(self, critical_value):
"domain_greater_equal(v)(x) = true where x < v"
self.critical_value = critical_value
def __call__ (self, x):
"Execute the call behavior."
return Numeric.less (x, self.critical_value)
class masked_unary_operation:
def __init__ (self, aufunc, fill=0, domain=None):
""" masked_unary_operation(aufunc, fill=0, domain=None)
aufunc(fill) must be defined
self(x) returns aufunc(x)
with masked values where domain(x) is true or getmask(x) is true.
"""
self.f = aufunc
self.fill = fill
self.domain = domain
self.__doc__ = getattr(aufunc, "__doc__", str(aufunc))
def __call__ (self, a, *args, **kwargs):
"Execute the call behavior."
# Numeric tries to return scalars rather than arrays when given scalars.
m = getmask(a)
d1 = filled(a, self.fill)
if self.domain is not None:
m = mask_or(m, self.domain(d1))
if m is None:
result = self.f(d1, *args, **kwargs)
if type(result) is Numeric.ArrayType:
return masked_array (result)
else:
return result
else:
dx = masked_array(d1, m)
result = self.f(filled(dx, self.fill), *args, **kwargs)
if type(result) is Numeric.ArrayType:
return masked_array(result, m)
elif m[...]:
return masked
else:
return result
def __str__ (self):
return "Masked version of " + str(self.f)
class domain_safe_divide:
def __init__ (self, tolerance=divide_tolerance):
self.tolerance = tolerance
def __call__ (self, a, b):
return Numeric.absolute(a) * self.tolerance >= Numeric.absolute(b)
class domained_binary_operation:
"""Binary operations that have a domain, like divide. These are complicated so they
are a separate class. They have no reduce, outer or accumulate.
"""
def __init__ (self, abfunc, domain, fillx=0, filly=0):
"""abfunc(fillx, filly) must be defined.
abfunc(x, filly) = x for all x to enable reduce.
"""
self.f = abfunc
self.domain = domain
self.fillx = fillx
self.filly = filly
self.__doc__ = getattr(abfunc, "__doc__", str(abfunc))
def __call__(self, a, b):
"Execute the call behavior."
ma = getmask(a)
mb = getmask(b)
d1 = filled(a, self.fillx)
d2 = filled(b, self.filly)
t = self.domain(d1, d2)
if Numeric.sometrue(t):
d2 = where(t, self.filly, d2)
mb = mask_or(mb, t)
m = mask_or(ma, mb)
if m is None:
result = self.f(d1, d2)
if type(result) is Numeric.ArrayType:
return masked_array(result)
else:
return result
result = self.f(d1, d2)
if type(result) is Numeric.ArrayType:
if m.shape != result.shape:
m = mask_or(getmaskarray(a), getmaskarray(b))
return masked_array(result, m)
elif m[...]:
return masked
else:
return result
def __str__ (self):
return "Masked version of " + str(self.f)
class masked_binary_operation:
def __init__ (self, abfunc, fillx=0, filly=0):
"""abfunc(fillx, filly) must be defined.
abfunc(x, filly) = x for all x to enable reduce.
"""
self.f = abfunc
self.fillx = fillx
self.filly = filly
self.__doc__ = getattr(abfunc, "__doc__", str(abfunc))
def __call__ (self, a, b, *args, **kwargs):
"Execute the call behavior."
m = mask_or(getmask(a), getmask(b))
if m is None:
d1 = filled(a, self.fillx)
d2 = filled(b, self.filly)
result = self.f(d1, d2, *args, **kwargs)
if type(result) is Numeric.ArrayType:
return masked_array(result)
else:
return result
d1 = filled(a, self.fillx)
d2 = filled(b, self.filly)
result = self.f(d1, d2, *args, **kwargs)
if type(result) is Numeric.ArrayType:
if m.shape != result.shape:
m = mask_or(getmaskarray(a), getmaskarray(b))
return masked_array(result, m)
elif m[...]:
return masked
else:
return result
def reduce (self, target, axis=0):
"""Reduce target along the given axis with this function."""
m = getmask(target)
t = filled(target, self.filly)
if t.shape == ():
t.shape = (1,)
if m is not None:
m = make_mask(m, copy=1)
m.shape = (1,)
if m is None:
return masked_array (self.f.reduce (t, axis))
else:
t = masked_array (t, m)
t = self.f.reduce(filled(t, self.filly), axis)
m = Numeric.logical_and.reduce(m, axis)
if isinstance(t, Numeric.ArrayType):
return masked_array(t, m, fill_value(target))
elif m:
return masked
else:
return t
def outer (self, a, b):
"Return the function applied to the outer product of a and b."
ma = getmask(a)
mb = getmask(b)
if ma is None and mb is None:
m = None
else:
ma = getmaskarray(a)
mb = getmaskarray(b)
m = logical_or.outer(ma, mb)
d = self.f.outer(filled(a, self.fillx), filled(b, self.filly))
return masked_array(d, m)
def accumulate (self, target, axis=0):
"""Accumulate target along axis after filling with y fill value."""
t = filled(target, self.filly)
return masked_array (self.f.accumulate (t, axis))
def __str__ (self):
return "Masked version of " + str(self.f)
sqrt = masked_unary_operation(Numeric.sqrt, 0.0, domain_greater_equal(0.0))
log = masked_unary_operation(Numeric.log, 1.0, domain_greater(0.0))
log10 = masked_unary_operation(Numeric.log10, 1.0, domain_greater(0.0))
exp = masked_unary_operation(Numeric.exp)
conjugate = masked_unary_operation(Numeric.conjugate)
sin = masked_unary_operation(Numeric.sin)
cos = masked_unary_operation(Numeric.cos)
tan = masked_unary_operation(Numeric.tan, 0.0, domain_tan(1.e-35))
arcsin = masked_unary_operation(Numeric.arcsin, 0.0, domain_check_interval(-1.0, 1.0))
arccos = masked_unary_operation(Numeric.arccos, 0.0, domain_check_interval(-1.0, 1.0))
arctan = masked_unary_operation(Numeric.arctan)
# Missing from Numeric
# arcsinh = masked_unary_operation(Numeric.arcsinh)
# arccosh = masked_unary_operation(Numeric.arccosh)
# arctanh = masked_unary_operation(Numeric.arctanh)
sinh = masked_unary_operation(Numeric.sinh)
cosh = masked_unary_operation(Numeric.cosh)
tanh = masked_unary_operation(Numeric.tanh)
absolute = masked_unary_operation(Numeric.absolute)
fabs = masked_unary_operation(Numeric.fabs)
negative = masked_unary_operation(Numeric.negative)
nonzero = masked_unary_operation(Numeric.nonzero)
around = masked_unary_operation(Numeric.around)
floor = masked_unary_operation(Numeric.floor)
ceil = masked_unary_operation(Numeric.ceil)
sometrue = masked_unary_operation(Numeric.sometrue)
alltrue = masked_unary_operation(Numeric.alltrue, 1)
logical_not = masked_unary_operation(Numeric.logical_not)
add = masked_binary_operation(Numeric.add)
subtract = masked_binary_operation(Numeric.subtract)
subtract.reduce = None
multiply = masked_binary_operation(Numeric.multiply, 1, 1)
divide = domained_binary_operation(Numeric.divide, domain_safe_divide(), 0, 1)
true_divide = domained_binary_operation(Numeric.true_divide, domain_safe_divide(), 0, 1)
floor_divide = domained_binary_operation(Numeric.floor_divide, domain_safe_divide(), 0, 1)
remainder = domained_binary_operation(Numeric.remainder, domain_safe_divide(), 0, 1)
fmod = domained_binary_operation(Numeric.fmod, domain_safe_divide(), 0, 1)
hypot = masked_binary_operation(Numeric.hypot)
arctan2 = masked_binary_operation(Numeric.arctan2, 0.0, 1.0)
arctan2.reduce = None
equal = masked_binary_operation(Numeric.equal)
equal.reduce = None
not_equal = masked_binary_operation(Numeric.not_equal)
not_equal.reduce = None
less_equal = masked_binary_operation(Numeric.less_equal)
less_equal.reduce = None
greater_equal = masked_binary_operation(Numeric.greater_equal)
greater_equal.reduce = None
less = masked_binary_operation(Numeric.less)
less.reduce = None
greater = masked_binary_operation(Numeric.greater)
greater.reduce = None
logical_and = masked_binary_operation(Numeric.logical_and)
logical_or = masked_binary_operation(Numeric.logical_or)
logical_xor = masked_binary_operation(Numeric.logical_xor)
bitwise_and = masked_binary_operation(Numeric.bitwise_and)
bitwise_or = masked_binary_operation(Numeric.bitwise_or)
bitwise_xor = masked_binary_operation(Numeric.bitwise_xor)
rank = Numeric.rank
shape = Numeric.shape
size = Numeric.size
class MaskedArray (object):
"""Arrays with possibly masked values.
Masked values of 1 exclude element from the computation.
Construction:
x = array(data, typecode=None, copy=1, savespace=0,
mask = None, fill_value=None)
If copy=0, every effort is made not to copy the data:
If data is a MaskedArray, and argument mask=None,
then the candidate data is data.raw_data() and the
mask used is data.mask(). If data is a Numeric array,
it is used as the candidate raw data.
If savespace != data.spacesaver() or typecode is not None and
is != data.typecode() then a data copy is required.
Otherwise, the candidate is used.
If a data copy is required, raw data stored is the result of:
Numeric.array(data, typecode=typecode, copy=copy, savespace=savespace)
If mask is None there are no masked values. Otherwise mask must
be convertible to an array of integers of typecode MaskType,
with values 1 or 0, and of the same shape as x.
fill_value is used to fill in masked values when necessary,
such as when printing and in method/function filled().
The fill_value is not used for computation within this module.
If savespace is 1, the data is given the spacesaver property, and
the mask is replaced by None if all its elements are true.
"""
handler_cache_key = 'MA.MaskedArray'
def __init__(self, data, typecode=None,
copy=1, savespace=None, mask=None, fill_value=None,
):
"""array(data, typecode=None,copy=1, savespace=None,
mask=None, fill_value=None)
If data already a Numeric array, its typecode and spacesaver()
become the default values for typecode and savespace.
"""
tc = typecode
ss = savespace
need_data_copied = copy
if isinstance(data, MaskedArray):
c = data.raw_data()
ctc = c.typecode()
if tc is None:
tc = ctc
elif tc != ctc:
need_data_copied = 1
css = c.spacesaver()
if ss is None:
ss = css
elif ss != css:
need_data_copied = 1
else:
ss = 0
if mask is None:
mask = data.mask()
elif mask is not None: #attempting to change the mask
need_data_copied = 1
elif isinstance(data, Numeric.ArrayType):
c = data
ctc = c.typecode()
if tc is None:
tc = ctc
elif tc != ctc:
need_data_copied = 1
css = c.spacesaver()
if ss is None:
ss = css
elif ss != css:
need_data_copied = 1
else:
need_data_copied = 0 #because I'll do it now
if ss is None:
ss = 0
c = Numeric.array(data, tc, savespace=ss)
if need_data_copied:
if tc == ctc:
self._data = Numeric.array(c, copy=1, savespace = ss)
else:
self._data = c.astype(tc)
self._data.savespace(ss)
else:
self._data = c
if mask is None:
self._mask = None
self._shared_mask = 0
else:
self._mask = make_mask (mask, flag=ss)
if self._mask is None:
self._shared_mask = 0
else:
self._shared_mask = (self._mask is mask)
nm = size(self._mask)
nd = size(self._data)
if nm != nd:
if nm == 1:
self._mask = Numeric.resize(self._mask, self._data.shape)
self._shared_mask = 0
elif nd == 1:
self._data = Numeric.resize(self._data, self._mask.shape)
self._data.shape = self._mask.shape
else:
raise MAError, "Mask and data not compatible."
elif nm == 1 and shape(self._mask) != shape(self._data):
self.unshare_mask()
self._mask.shape = self._data.shape
self.set_fill_value(fill_value)
def __array__ (self, t = None):
"Special hook for Numeric. Converts to Numeric if possible."
if self._mask is not None:
if Numeric.sometrue(Numeric.ravel(self._mask)):
raise MAError, \
"""Cannot automatically convert masked array to Numeric because data
is masked in one or more locations.
"""
else: # Mask is all false
# Optimize to avoid future invocations of this section.
self._mask = None
self._shared_mask = 0
if t:
return self._data.astype(t)
else:
return self._data
def _get_shape(self):
"Return the current shape."
return self._data.shape
def _set_shape (self, newshape):
"Set the array's shape."
if not self._data.iscontiguous():
self._data = Numeric.array(self._data, self._data.typecode(),
1, self._data.spacesaver())
self._data.shape = newshape
if self._mask is not None:
self.unshare_mask()
if not self._mask.iscontiguous():
self._mask = Numeric.array(self._mask, MaskType, 1, 1)
self._mask.shape = newshape
def _get_flat(self):
"""Calculate the flat value.
"""
if self._mask is None:
return masked_array(self._data.flat, mask=None,
fill_value = self.fill_value())
else:
return masked_array(self._data.flat,
mask=self._mask.flat,
fill_value = self.fill_value())
def _set_flat (self, value):
"x.flat = value"
y = self.flat
y[:] = value
def _get_real(self):
"Get the real part of a complex array."
if self._mask is None:
return masked_array(self._data.real, mask=None,
fill_value = self.fill_value())
else:
return masked_array(self._data.real, mask=self.mask().flat,
fill_value = self.fill_value())
def _set_real (self, value):
"x.real = value"
y = self.real
y[...] = value
def _get_imaginary(self):
"Get the imaginary part of a complex array."
if self._mask is None:
return masked_array(self._data.imaginary, mask=None,
fill_value = self.fill_value())
else:
return masked_array(self._data.imaginary, mask=self.mask().flat,
fill_value = self.fill_value())
def _set_imaginary (self, value):
"x.imaginary = value"
y = self.imaginary
y[...] = value
def __str__(self):
"""Calculate the str representation, using masked for fill if
it is enabled. Otherwise fill with fill value.
"""
if masked_print_option.enabled():
f = masked_print_option
else:
f = self.fill_value()
return str(filled(self, f))
def __repr__(self):
"""Calculate the repr representation, using masked for fill if
it is enabled. Otherwise fill with fill value.
"""
with_mask = """\
array(data =
%(data)s,
mask =
%(mask)s,
fill_value=%(fill)s)
"""
with_mask1 = """\
array(data = %(data)s,
mask = %(mask)s,
fill_value=%(fill)s)
"""
without_mask = """array(
%(data)s)"""
without_mask1 = """array(%(data)s)"""
n = len(self.shape)
if self._mask is None:
if n <=1:
return without_mask1 % {'data':str(self.filled())}
return without_mask % {'data':str(self.filled())}
else:
if n <=1:
return with_mask % {
'data': str(self.filled()),
'mask': str(self.mask()),
'fill': str(self.fill_value())
}
return with_mask % {
'data': str(self.filled()),
'mask': str(self.mask()),
'fill': str(self.fill_value())
}
without_mask1 = """array(%(data)s)"""
if self._mask is None:
return without_mask % {'data':str(self.filled())}
else:
return with_mask % {
'data': str(self.filled()),
'mask': str(self.mask()),
'fill': str(self.fill_value())
}
def __float__(self):
"Convert self to float."
self.unmask()
if self._mask is not None:
raise MAError, 'Cannot convert masked element to a Python float.'
return float(self.raw_data()[...])
def __int__(self):
"Convert self to int."
self.unmask()
if self._mask is not None:
raise MAError, 'Cannot convert masked element to a Python int.'
return int(self.raw_data()[...])
# Note copy semantics here differ from Numeric
def __getitem__(self, i):
"Get copy of item described by i."
m = self._mask
dout = self._data[i]
ss = self._data.spacesaver()
tc =self._data.typecode()
if type(dout) is Numeric.ArrayType:
if m is None:
result = array(dout, typecode=tc, copy = 1, savespace=ss)
else:
result = array(dout, typecode=tc, copy = 1, savespace=ss,
mask = m[i], fill_value=self.fill_value())
return result
elif m is None or not m[i]:
return dout #scalar
else: #scalar but masked
return masked
def __getslice__(self, i, j):
"Get copy of slice described by i, j"
m = self._mask
dout = self._data[i:j]
ss = self._data.spacesaver()
tc =self._data.typecode()
if m is None:
return array(dout, typecode=tc, copy = 1, savespace=ss)
else:
return array(dout, typecode=tc, copy = 1, savespace=ss,
mask = m[i:j], fill_value=self.fill_value())
# --------
# setitem and setslice notes
# note that if value is masked, it means to mask those locations.
# setting a value changes the mask to match the value in those locations.
def __setitem__(self, index, value):
"Set item described by index. If value is masked, mask those locations."
if self is masked:
raise MAError, 'Cannot alter the masked element.'
if value is masked:
if self._mask is None:
self._mask = make_mask_none(self._data.shape)
self._shared_mask = 0
else:
self.unshare_mask()
self._mask[index] = 1
return
m = getmask(value)
value = filled(value).astype(self._data.typecode())
self._data[index] = value
if m is None:
if self._mask is not None:
self.unshare_mask()
self._mask[index] = 0
else:
if self._mask is None:
self._mask = make_mask_none(self._data.shape)
self._shared_mask = 0
else:
self.unshare_mask()
self._mask[index] = m
def __setslice__(self, i, j, value):
"Set slice i:j; if value is masked, mask those locations."
if self is masked:
raise MAError, 'Cannot alter the masked element.'
if value is masked:
if self._mask is None:
self._mask = make_mask_none(self._data.shape)
self._shared_mask = 0
self._mask[i:j] = 1
return
m = getmask(value)
value = filled(value).astype(self._data.typecode())
self._data[i:j] = value
if m is None:
if self._mask is not None:
self.unshare_mask()
self._mask[i:j] = 0
else:
if self._mask is None:
self._mask = make_mask_none(self._data.shape)
self._shared_mask = 0
self._mask[i:j] = m
def __len__ (self):
"""Return length of first dimension. This is weird but Python's
slicing behavior depends on it."""
return len(self._data)
def __and__(self, other):
"Return bitwise_and"
return bitwise_and(self, other)
def __or__(self, other):
"Return bitwise_or"
return bitwise_or(self, other)
def __xor__(self, other):
"Return bitwise_xor"
return bitwise_xor(self, other)
__rand__ = __and__
__ror__ = __or__
__rxor__ = __xor__
def __abs__(self):
"Return absolute(self)"
return absolute(self)
def __neg__(self):
"Return negative(self)"
return negative(self)
def __pos__(self):
"Return array(self)"
return array(self)
def __add__(self, other):
"Return add(self, other)"
return add(self, other)
__radd__ = __add__
def __mod__ (self, other):
"Return remainder(self, other)"
return remainder(self, other)
def __rmod__ (self, other):
"Return remainder(other, self)"
return remainder(other, self)
def __lshift__ (self, n):
return left_shift(self, n)
def __rshift__ (self, n):
return right_shift(self, n)
def __sub__(self, other):
"Return subtract(self, other)"
return subtract(self, other)
def __rsub__(self, other):
"Return subtract(other, self)"
return subtract(other, self)
def __mul__(self, other):
"Return multiply(self, other)"
return multiply(self, other)
__rmul__ = __mul__
def __div__(self, other):
"Return divide(self, other)"
return divide(self, other)
def __rdiv__(self, other):
"Return divide(other, self)"
return divide(other, self)
def __truediv__(self, other):
"Return divide(self, other)"
return true_divide(self, other)
def __rtruediv__(self, other):
"Return divide(other, self)"
return true_divide(other, self)
def __floordiv__(self, other):
"Return divide(self, other)"
return floor_divide(self, other)
def __rfloordiv__(self, other):
"Return divide(other, self)"
return floor_divide(other, self)
def __pow__(self,other, third=None):
"Return power(self, other, third)"
return power(self, other, third)
def __sqrt__(self):
"Return sqrt(self)"
return sqrt(self)
def __iadd__(self, other):
"Add other to self in place."
t = self._data.typecode()
f = filled(other,0)
t1 = f.typecode()
if t == t1:
pass
elif t in typecodes['Integer']:
if t1 in typecodes['Integer']:
f = f.astype(t)
else:
raise TypeError, 'Incorrect type for in-place operation.'
elif t in typecodes['Float']:
if t1 in typecodes['Integer']:
f = f.astype(t)
elif t1 in typecodes['Float']:
f = f.astype(t)
else:
raise TypeError, 'Incorrect type for in-place operation.'
elif t in typecodes['Complex']:
if t1 in typecodes['Integer']:
f = f.astype(t)
elif t1 in typecodes['Float']:
f = f.astype(t)
elif t1 in typecodes['Complex']:
f = f.astype(t)
else:
raise TypeError, 'Incorrect type for in-place operation.'
else:
raise TypeError, 'Incorrect type for in-place operation.'
if self._mask is None:
self._data += f
m = getmask(other)
self._mask = m
self._shared_mask = m is not None
else:
result = add(self, masked_array(f, mask=getmask(other)))
self._data = result.raw_data()
self._mask = result.raw_mask()
self._shared_mask = 1
return self
def __imul__(self, other):
"Add other to self in place."
t = self._data.typecode()
f = filled(other,0)
t1 = f.typecode()
if t == t1:
pass
elif t in typecodes['Integer']:
if t1 in typecodes['Integer']:
f = f.astype(t)
else:
raise TypeError, 'Incorrect type for in-place operation.'
elif t in typecodes['Float']:
if t1 in typecodes['Integer']:
f = f.astype(t)
elif t1 in typecodes['Float']:
f = f.astype(t)
else:
raise TypeError, 'Incorrect type for in-place operation.'
elif t in typecodes['Complex']:
if t1 in typecodes['Integer']:
f = f.astype(t)
elif t1 in typecodes['Float']:
f = f.astype(t)
elif t1 in typecodes['Complex']:
f = f.astype(t)
else:
raise TypeError, 'Incorrect type for in-place operation.'
else:
raise TypeError, 'Incorrect type for in-place operation.'
if self._mask is None:
self._data *= f
m = getmask(other)
self._mask = m
self._shared_mask = m is not None
else:
result = multiply(self, masked_array(f, mask=getmask(other)))
self._data = result.raw_data()
self._mask = result.raw_mask()
self._shared_mask = 1
return self
def __isub__(self, other):
"Subtract other from self in place."
t = self._data.typecode()
f = filled(other,0)
t1 = f.typecode()
if t == t1:
pass
elif t in typecodes['Integer']:
if t1 in typecodes['Integer']:
f = f.astype(t)
else:
raise TypeError, 'Incorrect type for in-place operation.'
elif t in typecodes['Float']:
if t1 in typecodes['Integer']:
f = f.astype(t)
elif t1 in typecodes['Float']:
f = f.astype(t)
else:
raise TypeError, 'Incorrect type for in-place operation.'
elif t in typecodes['Complex']:
if t1 in typecodes['Integer']:
f = f.astype(t)
elif t1 in typecodes['Float']:
f = f.astype(t)
elif t1 in typecodes['Complex']:
f = f.astype(t)
else:
raise TypeError, 'Incorrect type for in-place operation.'
else:
raise TypeError, 'Incorrect type for in-place operation.'
if self._mask is None:
self._data -= f
m = getmask(other)
self._mask = m
self._shared_mask = m is not None
else:
result = subtract(self, masked_array(f, mask=getmask(other)))
self._data = result.raw_data()
self._mask = result.raw_mask()
self._shared_mask = 1
return self
def __idiv__(self, other):
"Divide self by other in place."
t = self._data.typecode()
f = filled(other,0)
t1 = f.typecode()
if t == t1:
pass
elif t in typecodes['Integer']:
if t1 in typecodes['Integer']:
f = f.astype(t)
else:
raise TypeError, 'Incorrect type for in-place operation.'
elif t in typecodes['Float']:
if t1 in typecodes['Integer']:
f = f.astype(t)
elif t1 in typecodes['Float']:
f = f.astype(t)
else:
raise TypeError, 'Incorrect type for in-place operation.'
elif t in typecodes['Complex']:
if t1 in typecodes['Integer']:
f = f.astype(t)
elif t1 in typecodes['Float']:
f = f.astype(t)
elif t1 in typecodes['Complex']:
f = f.astype(t)
else:
raise TypeError, 'Incorrect type for in-place operation.'
else:
raise TypeError, 'Incorrect type for in-place operation.'
mo = getmask(other)
result = divide(self, masked_array(f, mask=mo))
self._data = result.raw_data()
dm = result.raw_mask()
if dm is not self._mask:
self._mask = dm
self._shared_mask = 1
return self
def __eq__(self,other):
return equal(self,other)
def __ne__(self,other):
return not_equal(self,other)
def __lt__(self,other):
return less(self,other)
def __le__(self,other):
return less_equal(self,other)
def __gt__(self,other):
return greater(self,other)
def __ge__(self,other):
return greater_equal(self,other)
def astype (self, tc):
"return self as array of given type."
d = self._data.astype(tc)
d.savespace(self._data.spacesaver())
return array(d, mask=self._mask)
def byte_swapped(self):
"""Returns the raw data field, byte_swapped. Included for consistency
with Numeric but doesn't make sense in this context.
"""
return self._data.byte_swapped()
def compressed (self):
"A 1-D array of all the non-masked data."
d = Numeric.ravel(self._data)
if self._mask is None:
return array(d)
else:
m = 1 - Numeric.ravel(self._mask)
c = Numeric.compress(m, d)
return array(c, copy=0)
def count (self, axis = None):
"Count of the non-masked elements in a, or along a certain axis."
m = self._mask
s = self._data.shape
ls = len(s)
if m is None:
if ls == 0:
return 1
if ls == 1:
return s[0]
if axis is None:
return reduce(lambda x,y:x*y, s)
else:
n = s[axis]
t = list(s)
del t[axis]
return ones(t) * n
if axis is None:
w = Numeric.ravel(m).astype(Int) #avoid savespace truncation
n1 = size(w)
if n1 == 1:
n2 = w[0]
else:
n2 = Numeric.add.reduce(w)
return n1 - n2
else:
n1 = size(m, axis)
n2 = sum(m.astype(Int), axis)
return n1 - n2
def dot (self, other):
"s.dot(other) = innerproduct(s, other)"
return innerproduct(self, other)
def fill_value(self):
"Get the current fill value."
return self._fill_value
def filled (self, fill_value=None):
"""A Numeric array with masked values filled. If fill_value is None,
use self.fill_value().
If mask is None, copy data only if not contiguous.
Result is always a contiguous, Numeric array.
"""
d = self._data
m = self._mask
if m is None:
if d.iscontiguous():
return d
else:
return Numeric.array(d, typecode=d.typecode(), copy=1,
savespace = d.spacesaver())
value = fill_value
if value is None:
value = self._fill_value
if self is masked:
result = Numeric.array(value)
result.shape = d.shape
else:
try:
result = Numeric.array(d, typecode=d.typecode(), copy=1,
savespace = d.spacesaver())
Numeric.putmask(result, m, value)
except:
result = Numeric.choose(m, (d, value))
return result
def ids (self):
"""Return the ids of the data and mask areas"""
return (id(self._data), id(self._mask))
def iscontiguous (self):
"Is the data contiguous?"
return self._data.iscontiguous()
def itemsize(self):
"Item size of each data item."
return self._data.itemsize()
def mask(self):
"Return the data mask, or None. Result contiguous."
m = self._mask
if m is None:
return m
elif m.iscontiguous():
return m
else:
return Numeric.array(self._mask)
def outer(self, other):
"s.outer(other) = outerproduct(s, other)"
return outerproduct(self, other)
def put (self, values):
"""Set the non-masked entries of self to filled(values).
No change to mask
"""
iota = Numeric.arange(self.size())
if self._mask is None:
ind = iota
else:
ind = Numeric.compress(1 - self._mask, iota)
if len(ind) != size(values):
raise MAError, "x.put(values) incorrect count of values."
Numeric.put (self._data, ind, filled(values))
def putmask (self, values):
"""Set the masked entries of self to filled(values).
Mask changed to None.
"""
if self._mask is not None:
iota = Numeric.arange(self.size())
ind = Numeric.compress(self._mask, iota)
if len(ind) != size(values):
raise MAError, "x.put(values) incorrect count of values."
Numeric.put (self._data, ind, filled(values))
self._mask = None
self._shared_mask = 0
def raw_data (self):
""" The raw data; portions may be meaningless.
May be noncontiguous. Expert use only."""
return self._data
def raw_mask (self):
""" The raw mask; portions may be meaningless.
May be noncontiguous. Expert use only.
"""
return self._mask
def spacesaver (self):
"Get the spacesaver attribute."
return self._data.spacesaver()
def savespace (self, value):
"Set the spacesaver attribute to value"
self._data.savespace(value)
def set_fill_value (self, v=None):
"Set the fill value to v. Omit v to restore default."
if v is None:
v = default_fill_value (self.raw_data())
self._fill_value = v
def size (self, axis = None):
"Number of elements in array, or in a particular axis."
s = self._data.shape
if axis is None:
if len(s) == 0:
return 1
else:
return reduce(lambda x,y: x*y, s)
else:
return s[axis]
def spacesaver (self):
"spacesaver() queries the spacesaver attribute."
return self._data.spacesaver()
def typecode(self):
return self._data.typecode()
def tolist(self, fill_value=None):
"Convert to list"
return self.filled(fill_value).tolist()
def tostring(self, fill_value=None):
"Convert to string"
return self.filled(fill_value).tostring()
def unmask (self):
"Replace the mask by None if possible."
if self._mask is None: return
m = make_mask(self._mask, flag=1)
if m is None:
self._mask = None
self._shared_mask = 0
def unshare_mask (self):
"If currently sharing mask, make a copy."
if self._shared_mask:
self._mask = make_mask (self._mask, copy=1, flag=0)
self._shared_mask = 0
shape = property(_get_shape, _set_shape,
doc = 'tuple giving the shape of the array')
flat = property(_get_flat, _set_flat,
doc = 'Access array in flat form.')
real = property(_get_real, _set_real,
doc = 'Access the real part of the array')
imaginary = property(_get_imaginary, _set_imaginary,
doc = 'Access the imaginary part of the array')
imag = imaginary
array = MaskedArray
class MaskedScalar (MaskedArray):
def __init__ (self):
MaskedArray.__init__ (self, [0], mask=[1])
self._data.shape = ()
self._mask.shape = ()
shape = property(MaskedArray._get_shape)
masked = MaskedScalar()
def isMaskedArray (x):
"Is x a masked array, that is, an instance of MaskedArray?"
return isinstance(x, MaskedArray)
isarray = isMaskedArray
isMA = isMaskedArray #backward compatibility
def allclose (a, b, fill_value=1, rtol=1.e-5, atol=1.e-8):
""" Returns true if all components of a and b are equal
subject to given tolerances.
If fill_value is 1, masked values considered equal.
If fill_value is 0, masked values considered unequal.
The relative error rtol should be positive and << 1.0
The absolute error atol comes into play for those elements
of b that are very small or zero; it says how small a must be also.
"""
m = mask_or(getmask(a), getmask(b))
d1 = filled(a)
d2 = filled(b)
x = filled(array(d1, copy=0, mask=m), fill_value).astype(Float)
y = filled(array(d2, copy=0, mask=m), 1).astype(Float)
d = Numeric.less_equal(Numeric.absolute(x-y), atol + rtol * Numeric.absolute(y))
return Numeric.alltrue(Numeric.ravel(d))
def allequal (a, b, fill_value=1):
"""
True if all entries of a and b are equal, using
fill_value as a truth value where either or both are masked.
"""
m = mask_or(getmask(a), getmask(b))
if m is None:
x = filled(a)
y = filled(b)
d = Numeric.equal(x, y)
return Numeric.alltrue(Numeric.ravel(d))
elif fill_value:
x = filled(a)
y = filled(b)
d = Numeric.equal(x, y)
dm = array(d, mask=m, copy=0)
return Numeric.alltrue(Numeric.ravel(filled(dm, 1)))
else:
return 0
def masked_values (data, value, rtol=1.e-5, atol=1.e-8, copy=1,
savespace=0):
"""
masked_values(data, value, rtol=1.e-5, atol=1.e-8)
Create a masked array; mask is None if possible.
If copy==0, and otherwise possible, result
may share data values with original array.
Let d = filled(data, value). Returns d
masked where abs(data-value)<= atol + rtol * abs(value)
if d is of a floating point type. Otherwise returns
masked_object(d, value, copy, savespace)
"""
abs = Numeric.absolute
d = filled(data, value)
if d.typecode() in typecodes['Float']:
m = Numeric.less_equal(abs(d-value), atol+rtol*abs(value))
m = make_mask(m, flag=1)
return array(d, mask = m, savespace=savespace, copy=copy,
fill_value=value)
else:
return masked_object(d, value, copy, savespace)
def masked_object (data, value, copy=1, savespace=0):
"Create array masked where exactly data equal to value"
d = filled(data, value)
dm = make_mask(Numeric.equal(d, value), flag=1)
return array(d, mask=dm, copy=copy, savespace=savespace,
fill_value=value)
def arrayrange(start, stop=None, step=1, typecode=None):
"""Just like range() except it returns a array whose type can be specfied
by the keyword argument typecode.
"""
return array(Numeric.arrayrange(start, stop, step, typecode))
arange = arrayrange
def fromstring (s, t):
"Construct a masked array from a string. Result will have no mask."
return masked_array(Numeric.fromstring(s, t))
def left_shift (a, n):
"Left shift n bits"
m = getmask(a)
if m is None:
d = Numeric.left_shift(filled(a), n)
return masked_array(d)
else:
d = Numeric.left_shift(filled(a,0), n)
return masked_array(d, m)
def right_shift (a, n):
"Right shift n bits"
m = getmask(a)
if m is None:
d = Numeric.right_shift(filled(a), n)
return masked_array(d)
else:
d = Numeric.right_shift(filled(a,0), n)
return masked_array(d, m)
def resize (a, new_shape):
"""resize(a, new_shape) returns a new array with the specified shape.
The original array's total size can be any size."""
m = getmask(a)
if m is not None:
m = Numeric.resize(m, new_shape)
result = array(Numeric.resize(filled(a), new_shape), mask=m)
result.set_fill_value(fill_value(a))
return result
def repeat(a, repeats, axis=0):
"""repeat elements of a repeats times along axis
repeats is a sequence of length a.shape[axis]
telling how many times to repeat each element.
"""
af = filled(a)
if isinstance(repeats, types.IntType):
repeats = tuple([repeats]*(shape(af)[axis]))
m = getmask(a)
if m is not None:
m = Numeric.repeat(m, repeats, axis)
d = Numeric.repeat(af, repeats, axis)
result = masked_array(d, m)
result.set_fill_value(fill_value(a))
return result
def identity(n):
"""identity(n) returns the identity matrix of shape n x n.
"""
return array(Numeric.identity(n))
def indices (dimensions, typecode=None):
"""indices(dimensions,typecode=None) returns an array representing a grid
of indices with row-only, and column-only variation.
"""
return array(Numeric.indices(dimensions, typecode))
def zeros (shape, typecode=Int, savespace=0):
"""zeros(n, typecode=Int, savespace=0) =
an array of all zeros of the given length or shape."""
return array(Numeric.zeros(shape, typecode, savespace))
def ones (shape, typecode=Int, savespace=0):
"""ones(n, typecode=Int, savespace=0) =
an array of all ones of the given length or shape."""
return array(Numeric.ones(shape, typecode, savespace))
def count (a, axis = None):
"Count of the non-masked elements in a, or along a certain axis."
a = masked_array(a)
return a.count(axis)
def power (a, b, third=None):
"a**b"
if third is not None:
raise MAError, "3-argument power not supported."
ma = getmask(a)
mb = getmask(b)
m = mask_or(ma, mb)
fa = filled(a, 1)
fb = filled(b, 1)
if fb.typecode() in typecodes["Integer"]:
return masked_array(Numeric.power(fa, fb), m)
md = make_mask(Numeric.less_equal (fa, 0), flag=1)
m = mask_or(m, md)
if m is None:
return masked_array(Numeric.power(fa, fb))
else:
fa = Numeric.where(m, 1, fa)
return masked_array(Numeric.power(fa, fb), m)
def masked_array (a, mask=None, fill_value=None):
"""masked_array(a, mask=None) =
array(a, mask=mask, copy=0, fill_value=fill_value)
Use fill_value(a) if None.
"""
#
# This is an unfortunate copy of what is in fill_value
# but I want the name fill_value as a parameter.
#
if fill_value is None:
if isMaskedArray(a):
fill_value = a.fill_value()
else:
fill_value = default_fill_value(a)
return array(a, mask=mask, copy=0, fill_value=fill_value)
sum = add.reduce
product = multiply.reduce
def average (a, axis=0, weights=None, returned = 0):
"""average(a, axis=0, weights=None)
Computes average along indicated axis.
If axis is None, average over the entire array
Inputs can be integer or floating types; result is of type Float.
If weights are given, result is sum(a*weights)/(sum(weights)*1.0)
weights must have a's shape or be the 1-d with length the size
of a in the given axis.
If returned, return a tuple: the result and the sum of the weights
or count of values. Results will have the same shape.
masked values in the weights will be set to 0.0
"""
a = masked_array(a)
mask = a.mask()
ash = a.shape
if ash == ():
ash = (1,)
if axis is None:
if mask is None:
if weights is None:
n = add.reduce(a.raw_data().flat)
d = reduce(lambda x, y: x * y, ash, 1.0)
else:
w = filled(weights, 0.0).flat
n = Numeric.add.reduce(a.raw_data().flat * w)
d = Numeric.add.reduce(w)
del w
else:
if weights is None:
n = add.reduce(a.flat)
w = Numeric.choose(mask, (1.0,0.0)).flat
d = Numeric.add.reduce(w)
del w
else:
w = array(filled(weights, 0.0), Numeric.Float, mask=mask).flat
n = add.reduce(a.flat * w)
d = add.reduce(w)
del w
else:
if mask is None:
if weights is None:
d = ash[axis] * 1.0
n = Numeric.add.reduce(a.raw_data(), axis)
else:
w = filled(weights, 0.0)
wsh = w.shape
if wsh == ():
wsh = (1,)
if wsh == ash:
w = Numeric.array(w, Float, copy=0)
n = add.reduce(a*w, axis)
d = add.reduce(w, axis)
del w
elif wsh == (ash[axis],):
ni = ash[axis]
r = [NewAxis]*len(ash)
r[axis] = slice(None,None,1)
w = eval ("w["+ repr(tuple(r)) + "] * ones(ash, Float)")
n = add.reduce(a*w, axis)
d = add.reduce(w, axis)
del w, r
else:
raise ValueError, 'average: weights wrong shape.'
else:
if weights is None:
n = add.reduce(a, axis)
w = Numeric.choose(mask, (1.0, 0.0))
d = Numeric.add.reduce(w, axis)
del w
else:
w = filled(weights, 0.0)
wsh = w.shape
if wsh == ():
wsh = (1,)
if wsh == ash:
w = array(w, Float, mask=mask, copy=0)
n = add.reduce(a*w, axis)
d = add.reduce(w, axis)
elif wsh == (ash[axis],):
ni = ash[axis]
r = [NewAxis]*len(ash)
r[axis] = slice(None,None,1)
w = eval ("w["+ repr(tuple(r)) + "] * masked_array(ones(ash, Float), mask)")
n = add.reduce(a*w, axis)
d = add.reduce(w, axis)
else:
raise ValueError, 'average: weights wrong shape.'
del w
# print n, d, repr(mask), repr(weights)
result = divide (n, d)
del n
if isinstance(result, MaskedArray):
result.unmask()
if returned:
if not isinstance(d, MaskedArray):
d = masked_array(d)
if not d.shape == result.shape:
d = ones(result.shape, Float) * d
d.unmask()
if returned:
return result, d
else:
return result
def where (condition, x, y):
"""where(condition, x, y) is x where condition is nonzero, y otherwise.
condition must be convertible to an integer array.
Answer is always the shape of condition.
The type depends on x and y. It is integer if both x and y are
the value masked.
"""
fc = filled(not_equal(condition,0), 0)
if x is masked:
xv = 0
xm = 1
else:
xv = filled(x)
xm = getmask(x)
if xm is None: xm = 0
if y is masked:
yv = 0
ym = 1
else:
yv = filled(y)
ym = getmask(y)
if ym is None: ym = 0
d = Numeric.choose(fc, (yv, xv))
md = Numeric.choose(fc, (ym, xm))
m = getmask(condition)
m = make_mask(mask_or(m, md), copy=0, flag=1)
return masked_array(d, m)
def choose (indices, t):
"Returns array shaped like indices with elements chosen from t"
def fmask (x):
if x is masked: return 1
return filled(x)
def nmask (x):
if x is masked: return 1
m = getmask(x)
if m is None: return 0
return m
c = filled(indices,0)
masks = [nmask(x) for x in t]
a = [fmask(x) for x in t]
d = Numeric.choose(c, a)
m = Numeric.choose(c, masks)
m = make_mask(mask_or(m, getmask(indices)), copy=0, flag=1)
return masked_array(d, m)
def masked_where(condition, x, copy=1):
"""Return x as an array masked where condition is true.
Also masked where x or condition masked.
"""
cm = filled(condition,1)
m = mask_or(getmask(x), cm)
return array(filled(x), copy=copy, mask=m)
def masked_greater(x, value, copy=1):
"masked_greater(x, value) = x masked where x > value"
return masked_where(greater(x, value), x, copy)
def masked_greater_equal(x, value, copy=1):
"masked_greater_equal(x, value) = x masked where x >= value"
return masked_where(greater_equal(x, value), x, copy)
def masked_less(x, value, copy=1):
"masked_less(x, value) = x masked where x < value"
return masked_where(less(x, value), x, copy)
def masked_less_equal(x, value, copy=1):
"masked_less_equal(x, value) = x masked where x <= value"
return masked_where(less_equal(x, value), x, copy)
def masked_not_equal(x, value, copy=1):
"masked_not_equal(x, value) = x masked where x != value"
d = filled(x,0)
c = Numeric.not_equal(d, value)
m = mask_or(c, getmask(x))
return array(d, mask=m, copy=copy)
def masked_equal(x, value, copy=1):
"""masked_equal(x, value) = x masked where x == value
For floating point consider masked_values(x, value) instead.
"""
d = filled(x,0)
c = Numeric.equal(d, value)
m = mask_or(c, getmask(x))
return array(d, mask=m, copy=copy)
def masked_inside(x, v1, v2, copy=1):
"""x with mask of all values of x that are inside [v1,v2]
v1 and v2 can be given in either order.
"""
if v2 < v1:
t = v2
v2 = v1
v1 = t
d=filled(x, 0)
c = Numeric.logical_and(Numeric.less_equal(d, v2), Numeric.greater_equal(d, v1))
m = mask_or(c, getmask(x))
return array(d, mask = m, copy=copy)
def masked_outside(x, v1, v2, copy=1):
"""x with mask of all values of x that are outside [v1,v2]
v1 and v2 can be given in either order.
"""
if v2 < v1:
t = v2
v2 = v1
v1 = t
d = filled(x,0)
c = Numeric.logical_or(Numeric.less(d, v1), Numeric.greater(d, v2))
m = mask_or(c, getmask(x))
return array(d, mask = m, copy=copy)
def reshape (a, newshape):
"Copy of a with a new shape."
m = getmask(a)
d = Numeric.reshape(filled(a), newshape)
if m is None:
return masked_array(d)
else:
return masked_array(d, mask=Numeric.reshape(m, newshape))
def ravel (a):
"a as one-dimensional, may share data and mask"
m = getmask(a)
d = Numeric.ravel(filled(a))
if m is None:
return masked_array(d)
else:
return masked_array(d, mask=Numeric.ravel(m))
def concatenate (arrays, axis=0):
"Concatenate the arrays along the given axis"
d = []
for x in arrays:
d.append(filled(x))
d = Numeric.concatenate(d, axis)
for x in arrays:
if getmask(x) is not None: break
else:
return masked_array(d)
dm = []
for x in arrays:
dm.append(getmaskarray(x))
dm = Numeric.concatenate(dm, axis)
return masked_array(d, mask=dm)
def take (a, indices, axis=0):
"take(a, indices, axis=0) returns selection of items from a."
m = getmask(a)
d = masked_array(a).raw_data()
if m is None:
return masked_array(Numeric.take(d, indices, axis))
else:
return masked_array(Numeric.take(d, indices, axis),
mask = Numeric.take(m, indices, axis))
def transpose(a, axes=None):
"transpose(a, axes=None) reorder dimensions per tuple axes"
m = getmask(a)
d = filled(a)
if m is None:
return masked_array(Numeric.transpose(d, axes))
else:
return masked_array(Numeric.transpose(d, axes),
mask = Numeric.transpose(m, axes))
def put (a, indices, values):
"put(a, indices, values) sets storage-indexed locations to corresponding values. values and indices are filled if necessary."
d = a.raw_data()
ind = filled(indices)
v = filled(values)
Numeric.put (d, ind, v)
m = getmask(a)
if m is not None:
a.unshare_mask()
Numeric.put(a.raw_mask(), ind, 0)
def putmask (a, mask, values):
"put (a, mask, values) sets a where mask is true."
if mask is None:
return
Numeric.putmask(a.raw_data(), mask, values)
m = getmask(a)
if m is None: return
a.unshare_mask()
Numeric.putmask(a.raw_mask(), mask, 0)
def innerproduct(a,b):
"""innerproduct(a,b) returns the dot product of two arrays, which has
shape a.shape[:-1] + b.shape[:-1] with elements computed by summing the
product of the elements from the last dimensions of a and b.
Masked elements are replace by zeros.
"""
fa = filled(a, 0)
fb = filled(b, 0)
if len(fa.shape) == 0: fa.shape = (1,)
if len(fb.shape) == 0: fb.shape = (1,)
return masked_array(Numeric.innerproduct(fa, fb))
def outerproduct(a, b):
"""outerproduct(a,b) = {a[i]*b[j]}, has shape (len(a),len(b))"""
fa = filled(a,0).flat
fb = filled(b,0).flat
d = Numeric.outerproduct(fa, fb)
ma = getmask(a)
mb = getmask(b)
if ma is None and mb is None:
return masked_array(d)
ma = getmaskarray(a)
mb = getmaskarray(b)
m = make_mask(1-Numeric.outerproduct(1-ma,1-mb), copy=0)
return masked_array(d, m)
def dot(a, b):
"""dot(a,b) returns matrix-multiplication between a and b. The product-sum
is over the last dimension of a and the second-to-last dimension of b.
Masked values are replaced by zeros. See also innerproduct.
"""
return innerproduct(filled(a,0), Numeric.swapaxes(filled(b,0), -1, -2))
def compress(condition, x, dimension=-1):
"""Select those parts of x for which condition is true.
Masked values in condition are considered false.
"""
c = filled(condition, 0)
m = getmask(x)
if m is not None:
m=Numeric.compress(c, m, dimension)
d = Numeric.compress(c, filled(x), dimension)
return masked_array(d, m)
class _minimum_operation:
"Object to calculate minima"
def __init__ (self):
"""minimum(a, b) or minimum(a)
In one argument case returns the scalar minimum.
"""
pass
def __call__ (self, a, b=None):
"Execute the call behavior."
if b is None:
m = getmask(a)
if m is None:
d = min(filled(a).flat)
return d
ac = a.compressed()
if len(ac) == 0:
return masked
else:
return min(ac.raw_data())
else:
return where(less(a, b), a, b)[...]
def reduce (self, target, axis=0):
"""Reduce target along the given axis."""
m = getmask(target)
if m is None:
t = filled(target)
return masked_array (Numeric.minimum.reduce (t, axis))
else:
t = Numeric.minimum.reduce(filled(target, minimum_fill_value(target)), axis)
m = Numeric.logical_and.reduce(m, axis)
return masked_array(t, m, fill_value(target))
def outer (self, a, b):
"Return the function applied to the outer product of a and b."
ma = getmask(a)
mb = getmask(b)
if ma is None and mb is None:
m = None
else:
ma = getmaskarray(a)
mb = getmaskarray(b)
m = logical_or.outer(ma, mb)
d = Numeric.minimum.outer(filled(a), filled(b))
return masked_array(d, m)
minimum = _minimum_operation ()
class _maximum_operation:
"Object to calculate maxima"
def __init__ (self):
"""maximum(a, b) or maximum(a)
In one argument case returns the scalar maximum.
"""
pass
def __call__ (self, a, b=None):
"Execute the call behavior."
if b is None:
m = getmask(a)
if m is None:
d = max(filled(a).flat)
return d
ac = a.compressed()
if len(ac) == 0:
return masked
else:
return max(ac.raw_data())
else:
return where(greater(a, b), a, b)[...]
def reduce (self, target, axis=0):
"""Reduce target along the given axis."""
m = getmask(target)
if m is None:
t = filled(target)
return masked_array (Numeric.maximum.reduce (t, axis))
else:
t = Numeric.maximum.reduce(filled(target, maximum_fill_value(target)), axis)
m = Numeric.logical_and.reduce(m, axis)
return masked_array(t, m, fill_value(target))
def outer (self, a, b):
"Return the function applied to the outer product of a and b."
ma = getmask(a)
mb = getmask(b)
if ma is None and mb is None:
m = None
else:
ma = getmaskarray(a)
mb = getmaskarray(b)
m = logical_or.outer(ma, mb)
d = Numeric.maximum.outer(filled(a), filled(b))
return masked_array(d, m)
maximum = _maximum_operation ()
def sort (x, axis = -1, fill_value=None):
"""If x does not have a mask, return a masked array formed from the
result of Numeric.sort(x, axis).
Otherwise, fill x with fill_value. Sort it.
Set a mask where the result is equal to fill_value.
Note that this may have unintended consequences if the data contains the
fill value at a non-masked site.
If fill_value is not given the default fill value for x's type will be
used.
"""
if fill_value is None:
fill_value = default_fill_value (x)
d = filled(x, fill_value)
s = Numeric.sort(d, axis)
if getmask(x) is None:
return masked_array(s)
return masked_values(s, fill_value, copy=0)
def diagonal(a, k = 0, axis1=0, axis2=1):
"""diagonal(a,k=0,axis1=0, axis2=1) = the k'th diagonal of a"""
d = Numeric.diagonal(filled(a), k, axis1, axis2)
m = getmask(a)
if m is None:
return masked_array(d, m)
else:
return masked_array(d, Numeric.diagonal(m, k, axis1, axis2))
def argsort (x, axis = -1, fill_value=None):
"""Treating masked values as if they have the value fill_value,
return sort indices for sorting along given axis.
if fill_value is None, use fill_value(x)
Returns a Numeric array.
"""
d = filled(x, fill_value)
return Numeric.argsort(d, axis)
def argmin (x, axis = -1, fill_value=None):
"""Treating masked values as if they have the value fill_value,
return indices for minimum values along given axis.
if fill_value is None, use fill_value(x).
Returns a Numeric array if x has more than one dimension.
Otherwise, returns a scalar index.
"""
d = filled(x, fill_value)
return Numeric.argmin(d, axis)
def argmax (x, axis = -1, fill_value=None):
"""Treating masked values as if they have the value fill_value,
return sort indices for maximum along given axis.
if fill_value is None, use -fill_value(x) if it exists.
Returns a Numeric array if x has more than one dimension.
Otherwise, returns a scalar index.
"""
if fill_value is None:
fill_value = default_fill_value (x)
try:
fill_value = - fill_value
except:
pass
d = filled(x, fill_value)
return Numeric.argmax(d, axis)
def fromfunction (f, s):
"""apply f to s to create array as in Numeric."""
return masked_array(Numeric.fromfunction(f,s))
def asarray(data, typecode=None):
"""asarray(data, typecode=None) = array(data, typecode=None, copy=0)
Returns data if typecode if data is a MaskedArray and typecode None
or the same.
"""
if isinstance(data, MaskedArray) and \
(typecode is None or typecode == data.typecode()):
return data
return array(data, typecode=typecode, copy=0)
# This section is stolen from a post about how to limit array printing.
__MaxElements = 300 #Maximum size for printing
def limitedArrayRepr(a, max_line_width = None, precision = None, suppress_small = None):
"Calculate string representation, limiting size of output."
global __MaxElements
s = a.shape
elems = Numeric.multiply.reduce(s)
if elems > __MaxElements:
if len(s) > 1:
return 'array (%s) , type = %s, has %d elements' % \
(string.join(map(str, s), ","), a.typecode(), elems)
else:
return Numeric.array2string (a[:__MaxElements], max_line_width, precision,
suppress_small,',',0) + \
('\n + %d more elements' % (elems - __MaxElements))
else:
return Numeric.array2string (a, max_line_width, precision,
suppress_small,',',0)
__original_str = Numeric.array_str
__original_repr = Numeric.array_repr
def set_print_limit (m=0):
"Set the maximum # of elements for printing arrays. <=0 = no limit"
import multiarray
global __MaxElements
n = int(m)
__MaxElements = n
if n <= 0:
Numeric.array_str = __original_str
Numeric.array_repr = __original_repr
multiarray.set_string_function(__original_str, 0)
multiarray.set_string_function(__original_repr, 1)
else:
Numeric.array_str = limitedArrayRepr
Numeric.array_repr = limitedArrayRepr
multiarray.set_string_function(limitedArrayRepr, 0)
multiarray.set_string_function(limitedArrayRepr, 1)
def get_print_limit ():
"Get the maximum # of elements for printing arrays. "
return __MaxElements
set_print_limit(__MaxElements)
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