def __init__(self,
points,
ds=None,
field_parameters=None,
data_source=None):
validate_object(ds, Dataset)
validate_object(field_parameters, dict)
validate_object(data_source, YTSelectionContainer)
validate_object(points, YTArray)
points = fix_length(points, ds)
if len(points) < 2:
raise YTException(
"Not enough points. Expected at least 2, got %s" % len(points))
mylog.debug('Building minimal sphere around points.')
mb = _miniball.Miniball(points)
if not mb.is_valid():
raise YTException("Could not build valid sphere around points.")
center = ds.arr(mb.center(), points.units)
radius = ds.quan(np.sqrt(mb.squared_radius()), points.units)
super(YTMinimalSphere, self).__init__(center, ds, field_parameters,
data_source)
self.set_field_parameter('radius', radius)
self.set_field_parameter("center", self.center)
self.radius = radius
def _validate_unit_vectors(normal_vector, north_vector):
# Make sure vectors are unitless
if north_vector is not None:
north_vector = YTArray(north_vector, "", dtype='float64')
if normal_vector is not None:
normal_vector = YTArray(normal_vector, "", dtype='float64')
if not np.dot(normal_vector, normal_vector) > 0:
raise YTException("normal_vector cannot be the zero vector.")
if north_vector is not None and _aligned(north_vector, normal_vector):
raise YTException("normal_vector and north_vector cannot be aligned.")
return normal_vector, north_vector
def _read_field_names(self, grid):
if grid.filename is None: return []
f = h5py.File(grid.filename, "r")
try:
group = f[grid.block_name]
except KeyError:
raise YTException(message="Grid %s is missing from data file %s." %
(grid.block_name, grid.filename),
ds=self.ds)
fields = []
dtypes = set([])
for name, v in iteritems(group):
if not hasattr(v, "shape") or v.dtype == "O":
continue
# mesh fields are "field <name>"
if name.startswith("field"):
dummy, fname = name.split(" ", 1)
fields.append(("enzop", fname))
dtypes.add(v.dtype)
# particle fields are "particle <type> <name>"
else:
dummy, ftype, fname = name.split(" ", 2)
fields.append((ftype, fname))
if len(dtypes) == 1:
# Now, if everything we saw was the same dtype, we can go ahead and
# set it here. We do this because it is a HUGE savings for 32 bit
# floats, since our numpy copying/casting is way faster than
# h5py's, for some reason I don't understand. This does *not* need
# to be correct -- it will get fixed later -- it just needs to be
# okay for now.
self._field_dtype = list(dtypes)[0]
f.close()
return fields
def _parse_parameter_file(self):
handle = h5py.File(self.parameter_filename, mode="r")
hvals = {}
hvals.update((str(k), v) for k, v in handle["/Header"].attrs.items())
hvals["NumFiles"] = hvals["NumFilesPerSnapshot"]
hvals["Massarr"] = hvals["MassTable"]
self.dimensionality = 3
self.refine_by = 2
self.unique_identifier = \
int(os.stat(self.parameter_filename)[stat.ST_CTIME])
# Set standard values
self.current_time = self.quan(
hvals["Time_GYR"] * sec_conversion["Gyr"], "s")
self.domain_left_edge = np.zeros(3, "float64")
self.domain_right_edge = np.ones(3, "float64") * hvals["BoxSize"]
nz = 1 << self.over_refine_factor
self.domain_dimensions = np.ones(3, "int32") * nz
self.cosmological_simulation = 1
self.periodicity = (True, True, True)
self.current_redshift = hvals["Redshift"]
self.omega_lambda = hvals["OmegaLambda"]
self.omega_matter = hvals["Omega0"]
self.hubble_constant = hvals["HubbleParam"]
self.parameters = hvals
prefix = os.path.abspath(
os.path.join(
os.path.dirname(self.parameter_filename),
os.path.basename(self.parameter_filename).split(".", 1)[0]))
suffix = self.parameter_filename.rsplit(".", 1)[-1]
self.filename_template = "%s.%%(num)i.%s" % (prefix, suffix)
self.file_count = len(glob.glob(prefix + "*" + self._suffix))
if self.file_count == 0:
raise YTException(message="No data files found.", ds=self)
self.particle_types = ("FOF", "SUBFIND")
self.particle_types_raw = ("FOF", "SUBFIND")
# To avoid having to open files twice
self._unit_base = {}
self._unit_base.update(
(str(k), v) for k, v in handle["/Units"].attrs.items())
handle.close()
def _parse_parameter_file(self):
handle = h5py.File(self.parameter_filename, mode="r")
hvals = {}
hvals.update((str(k), v) for k, v in handle["/Header"].attrs.items())
hvals["NumFiles"] = hvals["NumFiles"]
self.dimensionality = 3
self.refine_by = 2
self.unique_identifier = \
int(os.stat(self.parameter_filename)[stat.ST_CTIME])
# Set standard values
self.domain_left_edge = np.zeros(3, "float64")
self.domain_right_edge = np.ones(3, "float64") * hvals["BoxSize"]
nz = 1 << self.over_refine_factor
self.domain_dimensions = np.ones(3, "int32") * nz
self.cosmological_simulation = 1
self.periodicity = (True, True, True)
self.current_redshift = hvals["Redshift"]
self.omega_lambda = hvals["OmegaLambda"]
self.omega_matter = hvals["Omega0"]
self.hubble_constant = hvals["HubbleParam"]
cosmology = Cosmology(hubble_constant=self.hubble_constant,
omega_matter=self.omega_matter,
omega_lambda=self.omega_lambda)
self.current_time = cosmology.t_from_z(self.current_redshift)
self.parameters = hvals
prefix = os.path.abspath(
os.path.join(
os.path.dirname(self.parameter_filename),
os.path.basename(self.parameter_filename).split(".", 1)[0]))
suffix = self.parameter_filename.rsplit(".", 1)[-1]
self.filename_template = "%s.%%(num)i.%s" % (prefix, suffix)
self.file_count = len(glob.glob(prefix + "*" + self._suffix))
if self.file_count == 0:
raise YTException(message="No data files found.", ds=self)
self.particle_types = ("Group", "Subhalo")
self.particle_types_raw = ("Group", "Subhalo")
handle.close()