def __getitem__(self, index):
"""
Read PhysArray from file
"""
with Dataset(self._filepath, 'r') as ncfile:
# Get a reference to the variable
ncvar = ncfile.variables[self._variable]
# Get the attributes into a dictionary, for convenience
attrs = {a: ncvar.getncattr(a) for a in ncvar.ncattrs()}
# Read the variable units
units_attr = attrs.get('units', 1)
calendar_attr = attrs.get('calendar', None)
try:
units = Unit(units_attr, calendar=calendar_attr)
except ValueError:
msg = 'Units {!r} unrecognized in UDUNITS. Assuming unitless.'.format(
units_attr)
warn(msg, UnitsWarning)
units = Unit(1)
except:
raise
# Read the original variable dimensions
dimensions0 = ncvar.dimensions
# Read the original variable shape
shape0 = ncvar.shape
# Align the read-indices on dimensions
index1 = align_index(self._index, dimensions0)
# Get the dimensions after application of the first index
dimensions1 = tuple(d for d, i in zip(
dimensions0, index1) if isinstance(i, slice))
# Align the second index on the intermediate dimensions
index2 = align_index(index, dimensions1)
# Get the dimensions after application of the second index
dimensions2 = tuple(d for d, i in zip(
dimensions1, index2) if isinstance(i, slice))
# Compute the joined index object
index12 = join(shape0, index1, index2)
data = ncvar[index12]
# Upconvert, if possible
if issubclass(ncvar.dtype.type, numpy.float) and ncvar.dtype.itemsize < 8:
data = data.astype(numpy.float64)
# Read the positive attribute, if available
pos = attrs.get('positive', None)
return PhysArray(data, name=self.label, units=units, dimensions=dimensions2, positive=pos)
def test_dict(self):
indata = ({'a': slice(1, 5, 2), 'b': 6}, ('a', 'b', 'c'))
testname = 'align_index({}, {})'.format(*indata)
actual = align_index(*indata)
expected = (indata[0]['a'], indata[0]['b'], slice(None))
print_test_message(testname,
indata=indata,
actual=actual,
expected=expected)
self.assertEqual(actual, expected, '{} failed'.format(testname))
def test_tuple(self):
indata = ((4, slice(1, 5, 2)), ('a', 'b', 'c'))
testname = 'align_index({}, {})'.format(*indata)
actual = align_index(*indata)
expected = indata[0] + (slice(None), )
print_test_message(testname,
indata=indata,
actual=actual,
expected=expected)
self.assertEqual(actual, expected, '{} failed'.format(testname))
def __getitem__(self, index):
idx = align_index(index, self.dimensions)
if len(idx) == 0:
return self
else:
dimensions = tuple(d for i, d in zip(idx, self.dimensions) if isinstance(i, slice))
if dimensions != self.dimensions:
return PhysArray(super(PhysArray, self).__getitem__(idx), dimensions=dimensions)
else:
return super(PhysArray, self).__getitem__(idx)
def test_dict(self):
indata = ({"a": slice(1, 5, 2), "b": 6}, ("a", "b", "c"))
testname = "align_index({}, {})".format(*indata)
actual = align_index(*indata)
expected = (indata[0]["a"], indata[0]["b"], slice(None))
print_test_message(testname,
indata=indata,
actual=actual,
expected=expected)
self.assertEqual(actual, expected, "{} failed".format(testname))
def test_tuple(self):
indata = ((4, slice(1, 5, 2)), ("a", "b", "c"))
testname = "align_index({}, {})".format(*indata)
actual = align_index(*indata)
expected = indata[0] + (slice(None), )
print_test_message(testname,
indata=indata,
actual=actual,
expected=expected)
self.assertEqual(actual, expected, "{} failed".format(testname))
def __setitem__(self, index, values):
idx = align_index(index, self.dimensions)
if isinstance(values, PhysArray):
values = values.convert(self.units).transpose(self.dimensions)
super(PhysArray, self).__setitem__(idx, values)