def _generate_kdtree(self, fname):
from yt.utilities.lib.cykdtree import PyKDTree
if fname is not None:
if os.path.exists(fname):
mylog.info("Loading KDTree from %s", os.path.basename(fname))
kdtree = PyKDTree.from_file(fname)
if kdtree.data_version != self.ds._file_hash:
mylog.info("Detected hash mismatch, regenerating KDTree")
else:
self._kdtree = kdtree
return
positions = []
for data_file in self.data_files:
for _, ppos in self.io._yield_coordinates(
data_file, needed_ptype=self.ds._sph_ptypes[0]):
positions.append(ppos)
if positions == []:
self._kdtree = None
return
positions = np.concatenate(positions)
mylog.info("Allocating KDTree for %s particles", positions.shape[0])
num_neighbors = getattr(self.ds, "num_neighbors", 32)
self._kdtree = PyKDTree(
positions.astype("float64"),
left_edge=self.ds.domain_left_edge,
right_edge=self.ds.domain_right_edge,
periodic=np.array(self.ds.periodicity),
leafsize=2 * int(num_neighbors),
data_version=self.ds._file_hash,
)
if fname is not None:
self._kdtree.save(fname)
class SPHParticleIndex(ParticleIndex):
def _initialize_index(self):
ds = self.dataset
ds._file_hash = self._generate_hash()
if hasattr(self.io, '_generate_smoothing_length'):
self.io._generate_smoothing_length(self.data_files, self.kdtree)
super(SPHParticleIndex, self)._initialize_index()
def _generate_kdtree(self, fname):
from yt.utilities.lib.cykdtree import PyKDTree
if fname is not None:
if os.path.exists(fname):
mylog.info('Loading KDTree from %s' % os.path.basename(fname))
kdtree = PyKDTree.from_file(fname)
if kdtree.data_version != self.ds._file_hash:
mylog.info('Detected hash mismatch, regenerating KDTree')
else:
self._kdtree = kdtree
return
positions = []
for data_file in self.data_files:
for _, ppos in self.io._yield_coordinates(
data_file, needed_ptype=self.ds._sph_ptypes[0]):
positions.append(ppos)
if positions == []:
self._kdtree = None
return
positions = np.concatenate(positions)
mylog.info('Allocating KDTree for %s particles' % positions.shape[0])
self._kdtree = PyKDTree(positions.astype('float64'),
left_edge=self.ds.domain_left_edge,
right_edge=self.ds.domain_right_edge,
periodic=np.array(self.ds.periodicity),
leafsize=2 * int(self.ds.num_neighbors),
data_version=self.ds._file_hash)
if fname is not None:
self._kdtree.save(fname)
@property
def kdtree(self):
if hasattr(self, '_kdtree'):
return self._kdtree
ds = self.ds
if getattr(ds, 'kdtree_filename', None) is None:
if os.path.exists(ds.parameter_filename):
fname = ds.parameter_filename + ".kdtree"
else:
# we don't want to write to disk for in-memory data
fname = None
else:
fname = ds.kdtree_filename
self._generate_kdtree(fname)
return self._kdtree
def add_sph_fields(self, n_neighbors=32, kernel="cubic", sph_ptype="io"):
"""Add SPH fields for the specified particle type.
For a particle type with "particle_position" and "particle_mass" already
defined, this method adds the "smoothing_length" and "density" fields.
"smoothing_length" is computed as the distance to the nth nearest
neighbor. "density" is computed as the SPH (gather) smoothed mass. The
SPH fields are added only if they don't already exist.
Parameters
----------
n_neighbors : int
The number of neighbors to use in smoothing length computation.
kernel : str
The kernel function to use in density estimation.
sph_ptype : str
The SPH particle type. Each dataset has one sph_ptype only. This
method will overwrite existing sph_ptype of the dataset.
"""
mylog.info("Generating SPH fields")
# Unify units
l_unit = "code_length"
m_unit = "code_mass"
d_unit = "code_mass / code_length**3"
# Read basic fields
ad = self.all_data()
pos = ad[sph_ptype, "particle_position"].to(l_unit).d
mass = ad[sph_ptype, "particle_mass"].to(m_unit).d
# Construct k-d tree
kdtree = PyKDTree(
pos.astype("float64"),
left_edge=self.domain_left_edge.to_value(l_unit),
right_edge=self.domain_right_edge.to_value(l_unit),
periodic=self.periodicity,
leafsize=2 * int(n_neighbors),
)
order = np.argsort(kdtree.idx)
def exists(fname):
if (sph_ptype, fname) in self.derived_field_list:
mylog.info("Field ('%s','%s') already exists. Skipping",
sph_ptype, fname)
return True
else:
mylog.info("Generating field ('%s','%s')", sph_ptype, fname)
return False
data = {}
# Add smoothing length field
fname = "smoothing_length"
if not exists(fname):
hsml = generate_smoothing_length(pos[kdtree.idx], kdtree,
n_neighbors)
hsml = hsml[order]
data[(sph_ptype, "smoothing_length")] = (hsml, l_unit)
else:
hsml = ad[sph_ptype, fname].to(l_unit).d
# Add density field
fname = "density"
if not exists(fname):
dens = estimate_density(
pos[kdtree.idx],
mass[kdtree.idx],
hsml[kdtree.idx],
kdtree,
kernel_name=kernel,
)
dens = dens[order]
data[(sph_ptype, "density")] = (dens, d_unit)
# Add fields
self._sph_ptypes = (sph_ptype, )
self.index.update_data(data)
self.num_neighbors = n_neighbors