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from numpy import empty as numpy_empty
from numpy import frombuffer as numpy_frombuffer
from numpy import full as numpy_full
from numpy import load as numpy_load
from numpy import ndarray as numpy_ndarray
from numpy import save as numpy_save
from numpy.ma import array as numpy_ma_array
from numpy.ma import is_masked as numpy_ma_is_masked
from tempfile import mkstemp
from os import close
from multiprocessing import Array as multiprocessing_Array
from ..functions import parse_indices, get_subspace
from ..functions import inspect as cf_inspect
from ..constants import CONSTANTS
# ====================================================================
#
# FileArray object
#
# ====================================================================
class FileArray(object):
'''
A sub-array stored in a file.
'''
flags = {'C_CONTIGUOUS': True,
'OWNDATA' : True}
def __init__(self, **kwargs):
'''
**Initialization**
:Parameters:
file : str
The netCDF file name in normalized, absolute form.
dtype : numpy.dtype
The numpy data type of the data array.
ndim : int
Number of dimensions in the data array.
shape : tuple
The data array's dimension sizes.
size : int
Number of elements in the data array.
'''
self.__dict__ = kwargs
#--- End: def
def __array__(self, *dtype):
'''
Returns a numpy array copy the data array.
:Returns:
out : numpy.ndarray
The numpy array copy the data array.
:Examples:
>>> numpy.all(a[...] == numpy.array(a))
True
'''
if not dtype:
return self[...]
else:
return self[...].astype(dtype[0]) #, copy=False) OUght to work!
#--- End: def
def __deepcopy__(self, memo):
'''
Used if copy.deepcopy is called on the variable.
'''
return self.copy()
#--- End: def
def __getitem__(self, indices):
raise NotImplementedError(
"Class {0} must override the __getitem__ method".format(
self.__class__.__name))
def __repr__(self):
'''
x.__repr__() <==> repr(x)
'''
return "<CF %s: %s>" % (self.__class__.__name__, str(self))
#--- End: def
def __str__(self):
'''
x.__str__() <==> str(x)
'''
return "%s in %s" % (self.shape, self.file)
#--- End: def
@property
def array(self):
'''
'''
return self[...]
#--- End: def
@property
def base(self):
'''
'''
return
#--- End: def
def copy(self):
'''
Return a deep copy.
``f.copy() is equivalent to ``copy.deepcopy(f)``.
:Returns:
out :
A deep copy.
:Examples:
>>> g = f.copy()
'''
C = self.__class__
new = C.__new__(C)
new.__dict__ = self.__dict__.copy()
return new
#--- End: def
def inspect(self):
'''
Inspect the object for debugging.
.. seealso:: `cf.inspect`
:Returns:
None
'''
print cf_inspect(self)
#--- End: def
def close(self):
pass
#--- End: def
def open(self):
pass
#--- End: def
#--- End: class
# ====================================================================
#
# _TempFileArray object
#
# ====================================================================
class _TempFileArray(FileArray):
'''
A indexable N-dimensional array supporting masked values.
The array is stored on disk in a temporary file until it is
accessed. The directory containing the temporary file may be found and
set with the `cf.TEMPDIR` function.
'''
def __init__(self, array):
'''
**Initialization**
:Parameters:
array : numpy array
The array to be stored on disk in a temporary file.
:Examples:
>>> f = _TempFileArray(numpy.array([1, 2, 3, 4, 5]))
>>> f = _TempFileArray(numpy.ma.array([1, 2, 3, 4, 5]))
'''
# ------------------------------------------------------------
# Use mkstemp because we want to be responsible for deleting
# the temporary file when done with it.
# ------------------------------------------------------------
fd, _partition_file = mkstemp(prefix='cf_array_', suffix='.npy',
dir=CONSTANTS['TEMPDIR'])
close(fd)
# The name of the temporary file storing the array
self._partition_file = _partition_file
# Numpy data type of the array
self.dtype = array.dtype
# Tuple of the array's dimension sizes
self.shape = array.shape
# Number of elements in the array
self.size = array.size
# Number of dimensions in the array
self.ndim = array.ndim
numpy_save(_partition_file, self.saveable(array))
#--- End: def
def __del__(self):
'''
Called when the reference count reaches zero.
'''
if getrefcount is not None:
if getrefcount(self) > 2:
return
else:
# getrefcount has itself been deleted or is in the process
# of being torn down
return
# Remove the file from disk.
_remove_temporary_files(self._partition_file)
#--- End: def
def __getitem__(self, indices):
'''
x.__getitem__(indices) <==> x[indices]
Returns a numpy array.
'''
array = numpy_load(self._partition_file)
indices = parse_indices(array.shape, indices)
array = get_subspace(array, indices)
if self._masked_as_record:
# Convert a record array to a masked array
array = numpy_ma_array(array['_data'], mask=array['_mask'],
copy=False)
array.shrink_mask()
#--- End: if
# Return the numpy array
return array
#--- End: def
def __str__(self):
'''
x.__str__() <==> str(x)
'''
return '%s in %s' % (self.shape, self._partition_file)
#--- End: def
def close(self):
'''
Close all referenced open files.
:Returns:
None
:Examples:
>>> f.close()
'''
# No open files are referenced
pass
#--- End: def
def saveable(self, array):
'''
'''
if numpy_ma_isMaskedArray(array):
self._masked_as_record = True
return array.toflex()
mask = getattr(array, mask, None)
if mask is not None:
# Mimic numpy.ma.MaskedArray.toflex
self._masked_as_record = True
record = numpy_ndarray(array.shape,
dtype=[('_data', array.dtype),
('_mask', mask.dtype)])
record['_data'] = array
record['_mask'] = mask
array = record
else:
self._masked_as_record = False
#--- End: if
return array
#--- End: def
#--- End: class
class FilledArray(FileArray):
'''
**Initialization**
:Parameters:
dtype : numpy.dtype
The numpy data type of the data array.
ndim : int
Number of dimensions in the data array.
shape : tuple
The data array's dimension sizes.
size : int
Number of elements in the data array.
fill_value : scalar, optional
'''
def __getitem__(self, indices):
'''
x.__getitem__(indices) <==> x[indices]
Returns a numpy array.
'''
array_shape = []
for index in parse_indices(self.shape, indices):
if isinstance(index, slice):
step = index.step
if step == 1:
array_shape.append(index.stop - index.start)
elif step == -1:
stop = index.stop
if stop is None:
array_shape.append(index.start + 1)
else:
array_shape.append(index.start - index.stop)
else:
stop = index.stop
if stop is None:
stop = -1
a, b = divmod(stop - index.start, step)
if b:
a += 1
array_shape.append(a)
else:
array_shape.append(len(index))
#-- End: for
if self.fill_value is not None:
return numpy_full(array_shape, fill_value=self.fill_value, dtype=self.dtype)
else:
return numpy_empty(array_shape, dtype=self.dtype)
#--- End: def
def __repr__(self):
'''
x.__repr__() <==> repr(x)
'''
return "<CF {0}: shape={1}, dtype={2}, fill_value={3}>".format(
self.__class__.__name__, self.shape, self.dtype, self.fill_value)
#--- End: def
def __str__(self):
'''
x.__str__() <==> str(x)
'''
return repr(self)
#--- End: def
def reshape(self, newshape):
'''
'''
new = self.copy()
new.shape = newshape
new.ndim = len(newshape)
return new
#--- End: def
def resize(self, newshape):
'''
'''
self.shape = newshape
self.ndim = len(newshape)
#--- End: def
#--- End: class
class ArrayInterface(object):
'''
'''
def __init__(self, array):
'''
:Parameters:
array : numpy.ndarary
'''
self.__array_interface__ = array.__array_interface__
if numpy_ma_isMA(array):
self.mask = type(self)(array.mask)
else:
self.mask = None
self.dtype = array.dtype
self.shape = array.shape
self.size = array.size
self.ndim = array.ndim
self.flags = {'C_CONTIGUOUS': array.flags['C_CONTIGUOUS']}
#--- End: def
def __deepcopy__(self, memo):
'''
Used if copy.deepcopy is called on the variable.
'''
return self.copy()
#--- End: def
def __getitem__(self, indices):
'''
'''
array = self.array
indices = parse_indices(array.shape, indices)
return get_subspace(array, indices)
#--- End: def
def __repr__(self):
'''
'''
out = '<CF {0}: {1}'.format(self.__class__.__name__,
self.__array_interface__)
mask = self.mask
if mask:
out += ' MASK: {0}>'.format(mask.__array_interface__)
else:
out += '>'
return out
#--- End: def
def __str__(self):
'''
'''
return repr(self)
#--- End: def
@property
def array(self):
'''
'''
mask = self.mask
if not mask:
array = numpy_array(self, copy=False)
else:
array = numpy_ma_array(self, copy=False)
array.mask = numpy_array(mask, copy=False)
return array
#--- End: def
@property
def base(self):
'''
'''
return self
# return self.array.base
#--- End: def
def copy(self):
'''
Return a deep copy.
``f.copy() is equivalent to ``copy.deepcopy(f)``.
:Returns:
out :
A deep copy.
:Examples:
>>> g = f.copy()
'''
return type(self)(self.array.copy())
#--- End: def
def inspect(self):
'''
Inspect the object for debugging.
.. seealso:: `cf.inspect`
:Returns:
None
'''
print cf_inspect(self)
#--- End: def
def view(self):
return self.array.view()
#--- End: def
#--- End: class
class SharedMemoryArray(ArrayInterface):
'''
'''
def __init__(self, array):
'''
:Parameters:
array : numpy.ndarary
'''
# ------------------------------------------------------------
# Copy the array to a numpy array which accesses shared memory
# ------------------------------------------------------------
shape = array.shape
if numpy_ma_isMA(array):
mask = array.mask
array = array.data
else:
mask = None
dtype = array.dtype
mp_Array = multiprocessing_Array(_typecode[dtype.char], array.size)
a = numpy_frombuffer(mp_Array.get_obj(), dtype=dtype)
a.resize(shape)
a[...] = array
if mask is not None:
mask = array.mask
dtype = mask.dtype
mp_Array = multiprocessing_Array(_typecode[dtype.char], mask.size)
m = numpy_frombuffer(mp_Array.get_obj(), dtype=dtype)
m.resize(shape)
m[...] = mask
a = numpy_ma_array(a, copy=False)
a.mask = m
#--- End: if
#-------------------------------------------------------------
# Store the array interface of the numpy array
#-------------------------------------------------------------
super(SharedMemoryArray, self).__init__(a)
#--- End: def
#--- End: class
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