def from_cell_str(cls, unit_cell_str, sub=slice(None)):
sub = fix_slice(sub)
if "," in unit_cell_str:
parameters = list(parse_unit(word) for word in unit_cell_str.split(",") if len(word) > 0)
if len(parameters) == 1:
a = parameters[0]
single = numpy.array([[a,0,0],[0,a,0],[0,0,a]], float)
elif len(parameters) == 3:
a,b,c = parameters
single = numpy.array([[[a,0,0],[0,b,0],[0,0,c]]], float)
elif len(parameters) == 6:
a,b,c,alpha,beta,gamma = parameters
uc = UnitCell(
numpy.array([[1,0,0],[0,1,0],[0,0,1]], float),
numpy.array([True, True, True]),
)
uc.set_parameterst(numpy.array([a,b,c]), numpy.array([alpha,beta,gamma]))
single = uc.cell
elif len(parameters) == 9:
single = numpy.array(parameters,float).reshape((3,3)).transpose()
else:
raise ValueError("If the --cell option contains comma's, one, three, six or nine value(s) are expected.")
data = single.reshape((3,3,1))
else:
data = [
[
load_track("%s.%s.%s" % (unit_cell_str, v, c), sub)
for v in "abc"
]
for c in "xyz"
]
return cls(data)
def read_into(self, destination, sub=None):
sub = fix_slice(sub)
dtype, f = self._get_read_buffer(sub.start)
stop_bytes = min(sub.stop*dtype.itemsize, self._get_data_size())
length = stop_bytes/dtype.itemsize - sub.start
tmp = numpy.fromfile(f, dtype, length, '')[::sub.step]
length = (length-1)/sub.step+1
destination[:length] = tmp
f.close()
return length
def read(self, sub=None):
sub = fix_slice(sub)
dtype, f = self._get_read_buffer(sub.start)
stop_bytes = min(sub.stop*dtype.itemsize, self._get_data_size())
length = stop_bytes/dtype.itemsize - sub.start
result = numpy.fromfile(f, dtype, length, '')[::sub.step]
if not result.flags["C_CONTIGUOUS"]:
result = result.copy()
f.close()
return result
def __init__(self, filenames, dtype, buffer_size=None, dot_interval=None, sub=slice(None)):
MultiTrackBase.__init__(self)
if buffer_size is None:
buffer_size = context.default_buffer_size
if dot_interval is None:
dot_interval = context.default_dot_interval
# some residual parameters
self.dot_interval = dot_interval
self.row_counter = 0
self.sub = fix_slice(sub)
self.init_buffer(buffer_size, dtype)
self.init_tracks(filenames, dtype)
self.init_shortest()
def iter_unit_cells(unit_cell_str, sub=None):
sub = fix_slice(sub)
if len(unit_cell_str) == 0:
uc = UnitCell(
numpy.array([[1,0,0],[0,1,0],[0,0,1]], float),
numpy.array([False,False,False]),
)
while True:
yield uc
if "," in unit_cell_str:
parameters = list(parse_unit(word) for word in unit_cell_str.split(",") if len(word) > 0)
if len(parameters) == 1:
a= parameters[0]
uc = UnitCell(
numpy.array([[a,0,0],[0,a,0],[0,0,a]], float),
numpy.array([True, True, True]),
)
elif len(parameters) == 3:
a,b,c = parameters
uc = UnitCell(
numpy.array([[a,0,0],[0,b,0],[0,0,c]], float),
numpy.array([True, True, True]),
)
elif len(parameters) == 6:
a,b,c,alpha,beta,gamma = parameters
uc = UnitCell.from_parameters3(
numpy.array([a,b,c]),
numpy.array([alpha,beta,gamma])
)
elif len(parameters) == 9:
uc = UnitCell(
numpy.array(parameters, float).reshape((3,3)),
numpy.array([True, True, True]),
)
else:
raise ValueError("If the --cell option contains comma's, one, three, six or nine value(s) are expected.")
while True:
yield uc
else:
filenames = ["%s.%s" % (unit_cell_str, suffix) for suffix in ["a.x", "a.y", "a.z", "b.x", "b.y", "b.z", "c.x", "c.y", "c.z"]]
dtype = numpy.dtype([("cell", float, (3,3))])
mtr = MultiTracksReader(filenames, dtype, sub=sub)
for row in mtr:
yield UnitCell(
numpy.array(row["cell"], float),
numpy.array([True, True, True]),
)
