def _initialize_index(self, data_file, regions):
pcount = sum(data_file.total_particles.values())
morton = np.empty(pcount, dtype='uint64')
if pcount == 0: return morton
mylog.debug("Initializing index % 5i (% 7i particles)",
data_file.file_id, pcount)
ind = 0
with h5py.File(data_file.filename, mode="r") as f:
if not f.keys(): return None
dx = np.finfo(f["FOF"]['CenterOfMass'].dtype).eps
dx = 2.0 * self.ds.quan(dx, "code_length")
for ptype in data_file.ds.particle_types_raw:
if data_file.total_particles[ptype] == 0: continue
pos = f[ptype]["CenterOfMass"][()].astype("float64")
pos = np.resize(pos, (data_file.total_particles[ptype], 3))
pos = data_file.ds.arr(pos, "code_length")
# These are 32 bit numbers, so we give a little lee-way.
# Otherwise, for big sets of particles, we often will bump into the
# domain edges. This helps alleviate that.
np.clip(pos, self.ds.domain_left_edge + dx,
self.ds.domain_right_edge - dx, pos)
if np.any(pos.min(axis=0) < self.ds.domain_left_edge) or \
np.any(pos.max(axis=0) > self.ds.domain_right_edge):
raise YTDomainOverflow(pos.min(axis=0), pos.max(axis=0),
self.ds.domain_left_edge,
self.ds.domain_right_edge)
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind + pos.shape[0]] = compute_morton(
pos[:, 0], pos[:, 1], pos[:, 2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge)
ind += pos.shape[0]
return morton
def _initialize_index(self, data_file, regions):
if self.index_ptype == "all":
ptypes = self.ds.particle_types_raw
pcount = sum(data_file.total_particles.values())
else:
ptypes = [self.index_ptype]
pcount = data_file.total_particles[self.index_ptype]
morton = np.empty(pcount, dtype='uint64')
if pcount == 0: return morton
mylog.debug("Initializing index % 5i (% 7i particles)",
data_file.file_id, pcount)
ind = 0
with h5py.File(data_file.filename, "r") as f:
if not f.keys(): return None
dx = np.finfo(f["Group"]["GroupPos"].dtype).eps
dx = 2.0 * self.ds.quan(dx, "code_length")
for ptype in ptypes:
if data_file.total_particles[ptype] == 0:
continue
pos = data_file._get_particle_positions(ptype, f=f)
pos = self.ds.arr(pos, "code_length")
if np.any(pos.min(axis=0) < self.ds.domain_left_edge) or \
np.any(pos.max(axis=0) > self.ds.domain_right_edge):
raise YTDomainOverflow(pos.min(axis=0), pos.max(axis=0),
self.ds.domain_left_edge,
self.ds.domain_right_edge)
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind + pos.shape[0]] = compute_morton(
pos[:, 0], pos[:, 1], pos[:, 2], self.ds.domain_left_edge,
self.ds.domain_right_edge)
ind += pos.shape[0]
return morton
def _initialize_index(self, data_file, regions):
pcount = data_file.header["num_halos"]
morton = np.empty(pcount, dtype='uint64')
mylog.debug("Initializing index % 5i (% 7i particles)",
data_file.file_id, pcount)
ind = 0
with h5py.File(data_file.filename, "r") as f:
if not f.keys(): return None
pos = np.empty((pcount, 3), dtype="float64")
pos = data_file.ds.arr(pos, "code_length")
dx = np.finfo(f['particle_position_x'].dtype).eps
dx = 2.0*self.ds.quan(dx, "code_length")
pos[:,0] = f["particle_position_x"].value
pos[:,1] = f["particle_position_y"].value
pos[:,2] = f["particle_position_z"].value
# These are 32 bit numbers, so we give a little lee-way.
# Otherwise, for big sets of particles, we often will bump into the
# domain edges. This helps alleviate that.
np.clip(pos, self.ds.domain_left_edge + dx,
self.ds.domain_right_edge - dx, pos)
if np.any(pos.min(axis=0) < self.ds.domain_left_edge) or \
np.any(pos.max(axis=0) > self.ds.domain_right_edge):
raise YTDomainOverflow(pos.min(axis=0),
pos.max(axis=0),
self.ds.domain_left_edge,
self.ds.domain_right_edge)
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind+pos.shape[0]] = compute_morton(
pos[:,0], pos[:,1], pos[:,2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge)
return morton
def _initialize_index(self, data_file, regions):
index_ptype = self.index_ptype
f = h5py.File(data_file.filename, "r")
if index_ptype == "all":
pcount = f["/Header"].attrs["NumPart_ThisFile"][:].sum()
keys = f.keys()
else:
pt = int(index_ptype[-1])
pcount = f["/Header"].attrs["NumPart_ThisFile"][pt]
keys = [index_ptype]
morton = np.empty(pcount, dtype='uint64')
ind = 0
for key in keys:
if not key.startswith("PartType"): continue
if "Coordinates" not in f[key]: continue
ds = f[key]["Coordinates"]
dt = ds.dtype.newbyteorder("N") # Native
pos = np.empty(ds.shape, dtype=dt)
pos[:] = ds
regions.add_data_file(pos, data_file.file_id,
data_file.ds.filter_bbox)
morton[ind:ind+pos.shape[0]] = compute_morton(
pos[:,0], pos[:,1], pos[:,2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge,
data_file.ds.filter_bbox)
ind += pos.shape[0]
f.close()
return morton
def _initialize_index(self, data_file, regions):
pcount = data_file.header["num_halos"]
morton = np.empty(pcount, dtype="uint64")
mylog.debug("Initializing index % 5i (% 7i particles)",
data_file.file_id, pcount)
if pcount == 0:
return morton
ind = 0
ptype = "halos"
with open(data_file.filename, "rb") as f:
pos = data_file._get_particle_positions(ptype, f=f)
pos = data_file.ds.arr(pos, "code_length")
if np.any(pos.min(axis=0) < self.ds.domain_left_edge) or np.any(
pos.max(axis=0) > self.ds.domain_right_edge):
raise YTDomainOverflow(
pos.min(axis=0),
pos.max(axis=0),
self.ds.domain_left_edge,
self.ds.domain_right_edge,
)
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind + pos.shape[0]] = compute_morton(
pos[:, 0],
pos[:, 1],
pos[:, 2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge,
)
return morton
def _initialize_index(self, data_file, regions):
dle = self.ds.domain_left_edge.in_units("code_length").d
dre = self.ds.domain_right_edge.in_units("code_length").d
pcount = 0
for dd in self.ds.midx.iter_bbox_data(
dle, dre,
['x']):
pcount += dd['x'].size
morton = np.empty(pcount, dtype='uint64')
ind = 0
chunk_id = 0
for dd in self.ds.midx.iter_bbox_data(
dle, dre,
['x','y','z']):
npart = dd['x'].size
pos = np.empty((npart, 3), dtype=dd['x'].dtype)
pos[:,0] = dd['x']
pos[:,1] = dd['y']
pos[:,2] = dd['z']
if np.any(pos.min(axis=0) < self.ds.domain_left_edge) or \
np.any(pos.max(axis=0) > self.ds.domain_right_edge):
raise YTDomainOverflow(pos.min(axis=0),
pos.max(axis=0),
self.ds.domain_left_edge,
self.ds.domain_right_edge)
regions.add_data_file(pos, chunk_id)
morton[ind:ind+npart] = compute_morton(
pos[:,0], pos[:,1], pos[:,2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge)
ind += npart
return morton
def _initialize_index(self, data_file, regions):
pcount = data_file.header["num_halos"]
morton = np.empty(pcount, dtype='uint64')
mylog.debug("Initializing index % 5i (% 7i particles)",
data_file.file_id, pcount)
ind = 0
with open(data_file.filename, "rb") as f:
f.seek(data_file._position_offset, os.SEEK_SET)
halos = np.fromfile(f, dtype=self._halo_dt, count = pcount)
pos = np.empty((halos.size, 3), dtype="float64")
# These positions are in Mpc, *not* "code" units
pos = data_file.ds.arr(pos, "code_length")
dx = np.finfo(halos['particle_position_x'].dtype).eps
dx = 2.0*self.ds.quan(dx, "code_length")
pos[:,0] = halos["particle_position_x"]
pos[:,1] = halos["particle_position_y"]
pos[:,2] = halos["particle_position_z"]
# These are 32 bit numbers, so we give a little lee-way.
# Otherwise, for big sets of particles, we often will bump into the
# domain edges. This helps alleviate that.
np.clip(pos, self.ds.domain_left_edge + dx,
self.ds.domain_right_edge - dx, pos)
#del halos
if np.any(pos.min(axis=0) < self.ds.domain_left_edge) or \
np.any(pos.max(axis=0) > self.ds.domain_right_edge):
raise YTDomainOverflow(pos.min(axis=0),
pos.max(axis=0),
self.ds.domain_left_edge,
self.ds.domain_right_edge)
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind+pos.shape[0]] = compute_morton(
pos[:,0], pos[:,1], pos[:,2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge)
return morton
def _initialize_index(self, data_file, regions):
pcount = data_file.ds.parameters["nhalos"] + data_file.ds.parameters[
"nsubs"]
morton = np.empty(pcount, dtype="uint64")
mylog.debug("Initializing index % 5i (% 7i particles)",
data_file.file_id, pcount)
if pcount == 0:
return morton
ind = 0
pos = self._get_particle_positions()
if np.any(pos.min(axis=0) < self.ds.domain_left_edge) or np.any(
pos.max(axis=0) > self.ds.domain_right_edge):
raise YTDomainOverflow(
pos.min(axis=0),
pos.max(axis=0),
self.ds.domain_left_edge,
self.ds.domain_right_edge,
)
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind + pos.shape[0]] = compute_morton(
pos[:, 0],
pos[:, 1],
pos[:, 2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge,
)
return morton
def _initialize_index(self, data_file, regions):
halos = data_file.read_data(usecols=['ID', 'Xc', 'Yc', 'Zc'])
pcount = len(halos['ID'])
morton = np.empty(pcount, dtype='uint64')
mylog.debug('Initializing index % 5i (% 7i particles)',
data_file.file_id, pcount)
if pcount == 0:
return morton
ind = 0
pos = np.empty((pcount, 3), dtype='float64')
pos = data_file.ds.arr(pos, 'code_length')
dx = np.finfo(halos['Xc'].dtype).eps
dx = 2.0 * self.ds.quan(dx, 'code_length')
pos[:, 0] = halos['Xc']
pos[:, 1] = halos['Yc']
pos[:, 2] = halos['Zc']
dle = self.ds.domain_left_edge
dre = self.ds.domain_right_edge
# These are 32 bit numbers, so we give a little lee-way.
# Otherwise, for big sets of particles, we often will bump into the
# domain edges. This helps alleviate that.
np.clip(pos, dle + dx, dre - dx, pos)
if np.any(pos.min(axis=0) < dle) or np.any(pos.max(axis=0) > dre):
raise YTDomainOverflow(pos.min(axis=0), pos.max(axis=0), dle, dre)
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind + pos.shape[0]] = compute_morton(
pos[:, 0], pos[:, 1], pos[:, 2], dle, dre)
return morton
def _initialize_index(self, data_file, regions):
dle = self.ds.domain_left_edge.in_units("code_length").d
dre = self.ds.domain_right_edge.in_units("code_length").d
pcount = 0
for dd in self.ds.midx.iter_bbox_data(dle, dre, ["x"]):
pcount += dd["x"].size
morton = np.empty(pcount, dtype="uint64")
ind = 0
chunk_id = 0
for dd in self.ds.midx.iter_bbox_data(dle, dre, ["x", "y", "z"]):
npart = dd["x"].size
pos = np.empty((npart, 3), dtype=dd["x"].dtype)
pos[:, 0] = dd["x"]
pos[:, 1] = dd["y"]
pos[:, 2] = dd["z"]
if np.any(pos.min(axis=0) < self.ds.domain_left_edge) or np.any(
pos.max(axis=0) > self.ds.domain_right_edge):
raise YTDomainOverflow(
pos.min(axis=0),
pos.max(axis=0),
self.ds.domain_left_edge,
self.ds.domain_right_edge,
)
regions.add_data_file(pos, chunk_id)
morton[ind:ind + npart] = compute_morton(
pos[:, 0],
pos[:, 1],
pos[:, 2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge,
)
ind += npart
return morton
def _initialize_index(self, data_file, regions):
pcount = data_file.header["num_halos"]
morton = np.empty(pcount, dtype='uint64')
mylog.debug("Initializing index % 5i (% 7i particles)",
data_file.file_id, pcount)
ind = 0
with h5py.File(data_file.filename, "r") as f:
if not f.keys(): return None
pos = np.empty((pcount, 3), dtype="float64")
pos = data_file.ds.arr(pos, "code_length")
dx = np.finfo(f['particle_position_x'].dtype).eps
dx = 2.0*self.ds.quan(dx, "code_length")
pos[:,0] = f["particle_position_x"].value
pos[:,1] = f["particle_position_y"].value
pos[:,2] = f["particle_position_z"].value
# These are 32 bit numbers, so we give a little lee-way.
# Otherwise, for big sets of particles, we often will bump into the
# domain edges. This helps alleviate that.
np.clip(pos, self.ds.domain_left_edge + dx,
self.ds.domain_right_edge - dx, pos)
if np.any(pos.min(axis=0) < self.ds.domain_left_edge) or \
np.any(pos.max(axis=0) > self.ds.domain_right_edge):
raise YTDomainOverflow(pos.min(axis=0),
pos.max(axis=0),
self.ds.domain_left_edge,
self.ds.domain_right_edge)
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind+pos.shape[0]] = compute_morton(
pos[:,0], pos[:,1], pos[:,2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge)
return morton
def morton(self):
self.validate()
eps = np.finfo(self.dtype).eps
LE = self.min(axis=0)
LE -= np.abs(LE) * eps
RE = self.max(axis=0)
RE += np.abs(RE) * eps
morton = compute_morton(self[:, 0], self[:, 1], self[:, 2], LE, RE)
return morton
def morton(self):
self.validate()
eps = np.finfo(self.dtype).eps
LE = self.min(axis=0)
LE -= np.abs(LE) * eps
RE = self.max(axis=0)
RE += np.abs(RE) * eps
morton = compute_morton(
self[:,0], self[:,1], self[:,2],
LE, RE)
return morton
def _initialize_index(self, data_file, regions):
count = sum(data_file.total_particles.values())
DLE = data_file.ds.domain_left_edge
DRE = data_file.ds.domain_right_edge
with open(data_file.filename, "rb") as f:
# We add on an additionally 4 for the first record.
f.seek(data_file._position_offset + 4)
# The first total_particles * 3 values are positions
pp = np.fromfile(f, dtype = 'float32', count = count*3)
pp.shape = (count, 3)
regions.add_data_file(pp, data_file.file_id, data_file.ds.filter_bbox)
morton = compute_morton(pp[:,0], pp[:,1], pp[:,2], DLE, DRE,
data_file.ds.filter_bbox)
return morton
def _get_morton_from_position(self, data_file, count, offset_count,
regions, DLE, DRE):
with open(data_file.filename, "rb") as f:
# We add on an additionally 4 for the first record.
f.seek(data_file._position_offset + 4 + offset_count * 12)
# The first total_particles * 3 values are positions
pp = np.fromfile(f, dtype=self._endian + self._float_type,
count=count * 3)
pp.shape = (count, 3)
pp = pp.astype(self._float_type)
regions.add_data_file(pp, data_file.file_id,
data_file.ds.filter_bbox)
morton = compute_morton(pp[:, 0], pp[:, 1], pp[:, 2], DLE, DRE,
data_file.ds.filter_bbox)
return morton
def _initialize_index(self, data_file, regions):
totcount = 4096**2 #file is always this size
count = data_file.ds.parameters['lspecies'][-1]
DLE = data_file.ds.domain_left_edge
DRE = data_file.ds.domain_right_edge
dx = (DRE - DLE) / 2**_ORDER_MAX
with open(data_file.filename, "rb") as f:
# The first total_particles * 3 values are positions
pp = np.fromfile(f, dtype = '>f4', count = totcount*3)
pp.shape = (3, totcount)
pp = pp[:,:count] #remove zeros
pp = np.transpose(pp).astype(np.float32) #cast as float32 for compute_morton
pp = (pp - 1.)/data_file.ds.parameters['ng'] #correct the dm particle units
regions.add_data_file(pp, data_file.file_id)
morton = compute_morton(pp[:,0], pp[:,1], pp[:,2], DLE, DRE)
return morton
def _initialize_index(self, data_file, regions):
totcount = 4096**2 #file is always this size
count = data_file.ds.parameters['lspecies'][-1]
DLE = data_file.ds.domain_left_edge
DRE = data_file.ds.domain_right_edge
with open(data_file.filename, "rb") as f:
# The first total_particles * 3 values are positions
pp = np.fromfile(f, dtype='>f4', count=totcount * 3)
pp.shape = (3, totcount)
pp = pp[:, :count] #remove zeros
pp = np.transpose(pp).astype(
np.float32) #cast as float32 for compute_morton
pp = (pp - 1.) / data_file.ds.parameters[
'ng'] #correct the dm particle units
regions.add_data_file(pp, data_file.file_id)
morton = compute_morton(pp[:, 0], pp[:, 1], pp[:, 2], DLE, DRE)
return morton
def _initialize_index(self, data_file, regions):
header = self.ds.parameters
ptypes = header["particle_count"][data_file.file_id].keys()
pcount = sum(header["particle_count"][data_file.file_id].values())
morton = np.empty(pcount, dtype='uint64')
ind = 0
for ptype in ptypes:
s = self._open_stream(data_file, (ptype, "Coordinates"))
c = np.frombuffer(s, dtype="float64")
c.shape = (c.shape[0] / 3.0, 3)
regions.add_data_file(c, data_file.file_id,
data_file.ds.filter_bbox)
morton[ind:ind + c.shape[0]] = compute_morton(
c[:, 0], c[:, 1], c[:, 2], data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge, data_file.ds.filter_bbox)
ind += c.shape[0]
return morton
def _initialize_index(self, data_file, regions):
x, y, z = (self._handle[ax] for ax in 'xyz')
pcount = x.size
morton = np.empty(pcount, dtype='uint64')
ind = 0
while ind < pcount:
npart = min(CHUNKSIZE, pcount - ind)
pos = np.empty((npart, 3), dtype=x.dtype)
pos[:, 0] = x[ind:ind + npart]
pos[:, 1] = y[ind:ind + npart]
pos[:, 2] = z[ind:ind + npart]
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind + npart] = compute_morton(
pos[:, 0], pos[:, 1], pos[:, 2], data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge)
ind += CHUNKSIZE
return morton
def _morton_index(field, data):
"""This is the morton index, which is properly a uint64 field. Because
we make some assumptions that the fields returned by derived fields are
float64, this returns a "view" on the data that is float64. To get
back the original uint64, you need to call .view("uint64") on it;
however, it should be true that if you sort the uint64, you will get
the same order as if you sort the float64 view.
"""
eps = np.finfo("f8").eps
uq = data.ds.domain_left_edge.uq
LE = data.ds.domain_left_edge - eps * uq
RE = data.ds.domain_right_edge + eps * uq
# .ravel() only copies if it needs to
morton = compute_morton(data["index", "x"].ravel(), data["index",
"y"].ravel(),
data["index", "z"].ravel(), LE, RE)
morton.shape = data["index", "x"].shape
return morton.view("f8")
def _initialize_index(self, data_file, regions):
halos = data_file.read_data(usecols=['ID'])
pcount = len(halos['ID'])
morton = np.empty(pcount, dtype='uint64')
mylog.debug('Initializing index % 5i (% 7i particles)',
data_file.file_id, pcount)
if pcount == 0:
return morton
ind = 0
pos = data_file._get_particle_positions('halos')
pos = data_file.ds.arr(pos, 'code_length')
dle = self.ds.domain_left_edge
dre = self.ds.domain_right_edge
if np.any(pos.min(axis=0) < dle) or np.any(pos.max(axis=0) > dre):
raise YTDomainOverflow(pos.min(axis=0), pos.max(axis=0), dle, dre)
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind + pos.shape[0]] = compute_morton(
pos[:, 0], pos[:, 1], pos[:, 2], dle, dre)
return morton
def _initialize_index(self, data_file, regions):
x, y, z = (self._handle[ax] for ax in 'xyz')
pcount = x.size
morton = np.empty(pcount, dtype='uint64')
ind = 0
while ind < pcount:
npart = min(CHUNKSIZE, pcount - ind)
pos = np.empty((npart, 3), dtype=x.dtype)
pos[:,0] = x[ind:ind+npart]
pos[:,1] = y[ind:ind+npart]
pos[:,2] = z[ind:ind+npart]
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind+npart] = compute_morton(
pos[:,0], pos[:,1], pos[:,2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge)
ind += CHUNKSIZE
return morton
def _initialize_index(self, data_file, regions):
header = self.ds.parameters
ptypes = header["particle_count"][data_file.file_id].keys()
pcount = sum(header["particle_count"][data_file.file_id].values())
morton = np.empty(pcount, dtype='uint64')
ind = 0
for ptype in ptypes:
s = self._open_stream(data_file, (ptype, "Coordinates"))
c = np.frombuffer(s, dtype="float64")
c.shape = (c.shape[0]/3.0, 3)
regions.add_data_file(c, data_file.file_id,
data_file.ds.filter_bbox)
morton[ind:ind+c.shape[0]] = compute_morton(
c[:,0], c[:,1], c[:,2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge,
data_file.ds.filter_bbox)
ind += c.shape[0]
return morton
def _initialize_index(self, data_file, regions):
p_fields = self._handle["/tracer particles"]
px, py, pz = self._position_fields
pcount = self._count_particles(data_file)["io"]
morton = np.empty(pcount, dtype='uint64')
ind = 0
while ind < pcount:
npart = min(self._chunksize, pcount - ind)
pos = np.empty((npart, 3), dtype="=f8")
pos[:, 0] = p_fields[ind:ind + npart, px]
pos[:, 1] = p_fields[ind:ind + npart, py]
pos[:, 2] = p_fields[ind:ind + npart, pz]
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind+npart] = \
compute_morton(pos[:,0], pos[:,1], pos[:,2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge)
ind += self._chunksize
return morton
def _initialize_index(self, data_file, regions):
all_count = self._count_particles(data_file)
pcount = sum(all_count.values())
morton = np.empty(pcount, dtype="uint64")
mylog.debug("Initializing index % 5i (% 7i particles)",
data_file.file_id, pcount)
ind = 0
with h5py.File(data_file.filename, mode="r") as f:
for ptype in all_count:
if ptype not in f or all_count[ptype] == 0:
continue
pos = np.empty((all_count[ptype], 3), dtype="float64")
units = _get_position_array_units(ptype, f, "x")
if ptype == "grid":
dx = f["grid"]["dx"][()].min()
dx = self.ds.quan(dx,
parse_h5_attr(f["grid"]["dx"],
"units")).to("code_length")
else:
dx = 2.0 * np.finfo(
f[ptype]["particle_position_x"].dtype).eps
dx = self.ds.quan(dx, units).to("code_length")
pos[:, 0] = _get_position_array(ptype, f, "x")
pos[:, 1] = _get_position_array(ptype, f, "y")
pos[:, 2] = _get_position_array(ptype, f, "z")
pos = self.ds.arr(pos, units).to("code_length")
dle = self.ds.domain_left_edge.to("code_length")
dre = self.ds.domain_right_edge.to("code_length")
# These are 32 bit numbers, so we give a little lee-way.
# Otherwise, for big sets of particles, we often will bump into the
# domain edges. This helps alleviate that.
np.clip(pos, dle + dx, dre - dx, pos)
if np.any(pos.min(axis=0) < dle) or np.any(
pos.max(axis=0) > dre):
raise YTDomainOverflow(pos.min(axis=0), pos.max(axis=0),
dle, dre)
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind + pos.shape[0]] = compute_morton(
pos[:, 0], pos[:, 1], pos[:, 2], dle, dre)
ind += pos.shape[0]
return morton
def _initialize_index(self, data_file, regions):
# self.fields[g.id][fname] is the pattern here
morton = []
for ptype in self.ds.particle_types_raw:
try:
pos = np.column_stack(self.fields[data_file.filename][
(ptype, "particle_position_%s" % ax)] for ax in 'xyz')
except KeyError:
pos = self.fields[data_file.filename][ptype, "particle_position"]
if np.any(pos.min(axis=0) < data_file.ds.domain_left_edge) or \
np.any(pos.max(axis=0) > data_file.ds.domain_right_edge):
raise YTDomainOverflow(pos.min(axis=0), pos.max(axis=0),
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge)
regions.add_data_file(pos, data_file.file_id)
morton.append(compute_morton(
pos[:,0], pos[:,1], pos[:,2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge))
return np.concatenate(morton)
def _initialize_index(self, data_file, regions):
# self.fields[g.id][fname] is the pattern here
morton = []
for ptype in self.ds.particle_types_raw:
try:
pos = np.column_stack(self.fields[data_file.filename][
(ptype, "particle_position_%s" % ax)] for ax in 'xyz')
except KeyError:
pos = self.fields[data_file.filename][ptype, "particle_position"]
if np.any(pos.min(axis=0) < data_file.ds.domain_left_edge) or \
np.any(pos.max(axis=0) > data_file.ds.domain_right_edge):
raise YTDomainOverflow(pos.min(axis=0), pos.max(axis=0),
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge)
regions.add_data_file(pos, data_file.file_id)
morton.append(compute_morton(
pos[:,0], pos[:,1], pos[:,2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge))
return np.concatenate(morton)
def _initialize_index(self, data_file, regions):
ds = data_file.ds
morton = np.empty(sum(data_file.total_particles.values()),
dtype="uint64")
ind = 0
DLE, DRE = ds.domain_left_edge, ds.domain_right_edge
dx = (DRE - DLE) / (2**_ORDER_MAX)
self.domain_left_edge = DLE.in_units("code_length").ndarray_view()
self.domain_right_edge = DRE.in_units("code_length").ndarray_view()
with open(data_file.filename, "rb") as f:
f.seek(ds._header_offset)
for iptype, ptype in enumerate(self._ptypes):
# We'll just add the individual types separately
count = data_file.total_particles[ptype]
if count == 0: continue
start, stop = ind, ind + count
while ind < stop:
c = min(CHUNKSIZE, stop - ind)
pp = np.fromfile(f, dtype = self._pdtypes[ptype],
count = c)
mis = np.empty(3, dtype="float64")
mas = np.empty(3, dtype="float64")
for axi, ax in enumerate('xyz'):
mi = pp["Coordinates"][ax].min()
ma = pp["Coordinates"][ax].max()
mylog.debug("Spanning: %0.3e .. %0.3e in %s", mi, ma, ax)
mis[axi] = mi
mas[axi] = ma
pos = np.empty((pp.size, 3), dtype="float64")
for i, ax in enumerate("xyz"):
eps = np.finfo(pp["Coordinates"][ax].dtype).eps
pos[:,i] = pp["Coordinates"][ax]
regions.add_data_file(pos, data_file.file_id,
data_file.ds.filter_bbox)
morton[ind:ind+c] = compute_morton(
pos[:,0], pos[:,1], pos[:,2],
DLE, DRE, data_file.ds.filter_bbox)
ind += c
mylog.info("Adding %0.3e particles", morton.size)
return morton
def _initialize_index(self, data_file, regions):
ds = data_file.ds
morton = np.empty(sum(data_file.total_particles.values()),
dtype="uint64")
ind = 0
DLE, DRE = ds.domain_left_edge, ds.domain_right_edge
dx = (DRE - DLE) / (2**_ORDER_MAX)
self.domain_left_edge = DLE.in_units("code_length").ndarray_view()
self.domain_right_edge = DRE.in_units("code_length").ndarray_view()
with open(data_file.filename, "rb") as f:
f.seek(ds._header_offset)
for iptype, ptype in enumerate(self._ptypes):
# We'll just add the individual types separately
count = data_file.total_particles[ptype]
if count == 0: continue
start, stop = ind, ind + count
while ind < stop:
c = min(CHUNKSIZE, stop - ind)
pp = np.fromfile(f, dtype=self._pdtypes[ptype], count=c)
mis = np.empty(3, dtype="float64")
mas = np.empty(3, dtype="float64")
for axi, ax in enumerate('xyz'):
mi = pp["Coordinates"][ax].min()
ma = pp["Coordinates"][ax].max()
mylog.debug("Spanning: %0.3e .. %0.3e in %s", mi, ma,
ax)
mis[axi] = mi
mas[axi] = ma
pos = np.empty((pp.size, 3), dtype="float64")
for i, ax in enumerate("xyz"):
eps = np.finfo(pp["Coordinates"][ax].dtype).eps
pos[:, i] = pp["Coordinates"][ax]
regions.add_data_file(pos, data_file.file_id,
data_file.ds.filter_bbox)
morton[ind:ind + c] = compute_morton(
pos[:, 0], pos[:, 1], pos[:, 2], DLE, DRE,
data_file.ds.filter_bbox)
ind += c
mylog.info("Adding %0.3e particles", morton.size)
return morton
def _initialize_index(self, data_file, regions):
f = _get_h5_handle(data_file.filename)
pcount = f["/Header"].attrs["NumPart_ThisFile"][:].sum()
morton = np.empty(pcount, dtype='uint64')
ind = 0
for key in f.keys():
if not key.startswith("PartType"): continue
if "Coordinates" not in f[key]: continue
ds = f[key]["Coordinates"]
dt = ds.dtype.newbyteorder("N") # Native
pos = np.empty(ds.shape, dtype=dt)
pos[:] = ds
regions.add_data_file(pos, data_file.file_id,
data_file.ds.filter_bbox)
morton[ind:ind+pos.shape[0]] = compute_morton(
pos[:,0], pos[:,1], pos[:,2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge,
data_file.ds.filter_bbox)
ind += pos.shape[0]
f.close()
return morton
def _initialize_index(self, data_file, regions):
all_count = self._count_particles(data_file)
pcount = sum(all_count.values())
morton = np.empty(pcount, dtype='uint64')
mylog.debug("Initializing index % 5i (% 7i particles)",
data_file.file_id, pcount)
ind = 0
with h5py.File(data_file.filename, "r") as f:
for ptype in all_count:
if ptype not in f or all_count[ptype] == 0: continue
pos = np.empty((all_count[ptype], 3), dtype="float64")
pos = data_file.ds.arr(pos, "code_length")
if ptype == "grid":
dx = f["grid"]["pdx"].value.min()
else:
raise NotImplementedError
dx = self.ds.quan(dx, "code_length")
pos[:, 0] = _get_position_array(ptype, f, "px")
pos[:, 1] = _get_position_array(ptype, f, "py")
pos[:,2] = np.zeros(all_count[ptype], dtype="float64") + \
self.ds.domain_left_edge[2].in_cgs().d
# These are 32 bit numbers, so we give a little lee-way.
# Otherwise, for big sets of particles, we often will bump into the
# domain edges. This helps alleviate that.
np.clip(pos, self.ds.domain_left_edge + dx,
self.ds.domain_right_edge - dx, pos)
if np.any(pos.min(axis=0) < self.ds.domain_left_edge) or \
np.any(pos.max(axis=0) > self.ds.domain_right_edge):
raise YTDomainOverflow(pos.min(axis=0), pos.max(axis=0),
self.ds.domain_left_edge,
self.ds.domain_right_edge)
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind + pos.shape[0]] = compute_morton(
pos[:, 0], pos[:, 1], pos[:, 2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge)
ind += pos.shape[0]
return morton
def _initialize_index(self, data_file, regions):
pcount = data_file.header["num_halos"]
morton = np.empty(pcount, dtype='uint64')
mylog.debug("Initializing index % 5i (% 7i particles)",
data_file.file_id, pcount)
ind = 0
if pcount == 0: return None
ptype = 'halos'
with h5py.File(data_file.filename, "r") as f:
if not f.keys(): return None
units = parse_h5_attr(f["particle_position_x"], "units")
pos = data_file._get_particle_positions(ptype, f=f)
pos = data_file.ds.arr(pos, units).to("code_length")
dle = self.ds.domain_left_edge.to("code_length")
dre = self.ds.domain_right_edge.to("code_length")
if np.any(pos.min(axis=0) < dle) or \
np.any(pos.max(axis=0) > dre):
raise YTDomainOverflow(pos.min(axis=0), pos.max(axis=0), dle,
dre)
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind + pos.shape[0]] = compute_morton(
pos[:, 0], pos[:, 1], pos[:, 2], dle, dre)
return morton
def _initialize_index(self, data_file, regions):
pcount = data_file.header["num_halos"]
morton = np.empty(pcount, dtype='uint64')
mylog.debug("Initializing index % 5i (% 7i particles)",
data_file.file_id, pcount)
if pcount == 0: return morton
ind = 0
with open(data_file.filename, "rb") as f:
f.seek(data_file._position_offset, os.SEEK_SET)
halos = np.fromfile(f, dtype=self._halo_dt, count = pcount)
pos = np.empty((halos.size, 3), dtype="float64")
# These positions are in Mpc, *not* "code" units
pos = data_file.ds.arr(pos, "code_length")
dx = np.finfo(halos['particle_position_x'].dtype).eps
dx = 2.0*self.ds.quan(dx, "code_length")
pos[:,0] = halos["particle_position_x"]
pos[:,1] = halos["particle_position_y"]
pos[:,2] = halos["particle_position_z"]
# These are 32 bit numbers, so we give a little lee-way.
# Otherwise, for big sets of particles, we often will bump into the
# domain edges. This helps alleviate that.
np.clip(pos, self.ds.domain_left_edge + dx,
self.ds.domain_right_edge - dx, pos)
del halos
if np.any(pos.min(axis=0) < self.ds.domain_left_edge) or \
np.any(pos.max(axis=0) > self.ds.domain_right_edge):
raise YTDomainOverflow(pos.min(axis=0),
pos.max(axis=0),
self.ds.domain_left_edge,
self.ds.domain_right_edge)
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind+pos.shape[0]] = compute_morton(
pos[:,0], pos[:,1], pos[:,2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge)
return morton
def _initialize_index(self, data_file, regions):
pcount = sum(data_file.total_particles.values())
morton = np.empty(pcount, dtype='uint64')
if pcount == 0: return morton
mylog.debug("Initializing index % 5i (% 7i particles)",
data_file.file_id, pcount)
ind = 0
with h5py.File(data_file.filename, "r") as f:
if not f.keys(): return None
dx = np.finfo(f["Group"]["GroupPos"].dtype).eps
dx = 2.0*self.ds.quan(dx, "code_length")
for ptype in data_file.ds.particle_types_raw:
if data_file.total_particles[ptype] == 0: continue
pos = f[ptype]["%sPos" % ptype].value.astype("float64")
pos = np.resize(pos, (data_file.total_particles[ptype], 3))
pos = data_file.ds.arr(pos, "code_length")
# These are 32 bit numbers, so we give a little lee-way.
# Otherwise, for big sets of particles, we often will bump into the
# domain edges. This helps alleviate that.
np.clip(pos, self.ds.domain_left_edge + dx,
self.ds.domain_right_edge - dx, pos)
if np.any(pos.min(axis=0) < self.ds.domain_left_edge) or \
np.any(pos.max(axis=0) > self.ds.domain_right_edge):
raise YTDomainOverflow(pos.min(axis=0),
pos.max(axis=0),
self.ds.domain_left_edge,
self.ds.domain_right_edge)
regions.add_data_file(pos, data_file.file_id)
morton[ind:ind+pos.shape[0]] = compute_morton(
pos[:,0], pos[:,1], pos[:,2],
data_file.ds.domain_left_edge,
data_file.ds.domain_right_edge)
ind += pos.shape[0]
return morton
def smooth(self, positions, fields = None, index_fields = None,
method = None, create_octree = False, nneighbors = 64):
r"""Operate on the mesh, in a particle-against-mesh fashion, with
non-local input.
This uses the octree indexing system to call a "smoothing" operation
(defined in yt/geometry/particle_smooth.pyx) that can take input from
several (non-local) particles and construct some value on the mesh.
The canonical example is to conduct a smoothing kernel operation on the
mesh.
Parameters
----------
positions : array_like (Nx3)
The positions of all of the particles to be examined. A new
indexed octree will be constructed on these particles.
fields : list of arrays
All the necessary fields for computing the particle operation. For
instance, this might include mass, velocity, etc.
index_fields : list of arrays
All of the fields defined on the mesh that may be used as input to
the operation.
method : string
This is the "method name" which will be looked up in the
`particle_smooth` namespace as `methodname_smooth`. Current
methods include `volume_weighted`, `nearest`, `idw`,
`nth_neighbor`, and `density`.
create_octree : bool
Should we construct a new octree for indexing the particles? In
cases where we are applying an operation on a subset of the
particles used to construct the mesh octree, this will ensure that
we are able to find and identify all relevant particles.
nneighbors : int, default 64
The number of neighbors to examine during the process.
Returns
-------
List of fortran-ordered, mesh-like arrays.
"""
# Here we perform our particle deposition.
positions.convert_to_units("code_length")
if create_octree:
morton = compute_morton(
positions[:,0], positions[:,1], positions[:,2],
self.ds.domain_left_edge,
self.ds.domain_right_edge)
morton.sort()
particle_octree = ParticleOctreeContainer([1, 1, 1],
self.ds.domain_left_edge,
self.ds.domain_right_edge,
over_refine = self._oref)
# This should ensure we get everything within one neighbor of home.
particle_octree.n_ref = nneighbors * 2
particle_octree.add(morton)
particle_octree.finalize()
pdom_ind = particle_octree.domain_ind(self.selector)
else:
particle_octree = self.oct_handler
pdom_ind = self.domain_ind
if fields is None: fields = []
if index_fields is None: index_fields = []
cls = getattr(particle_smooth, "%s_smooth" % method, None)
if cls is None:
raise YTParticleDepositionNotImplemented(method)
nz = self.nz
mdom_ind = self.domain_ind
nvals = (nz, nz, nz, (mdom_ind >= 0).sum())
op = cls(nvals, len(fields), nneighbors)
op.initialize()
mylog.debug("Smoothing %s particles into %s Octs",
positions.shape[0], nvals[-1])
op.process_octree(self.oct_handler, mdom_ind, positions,
self.fcoords, fields,
self.domain_id, self._domain_offset, self.ds.periodicity,
index_fields, particle_octree, pdom_ind, self.ds.geometry)
# If there are 0s in the smoothing field this will not throw an error,
# but silently return nans for vals where dividing by 0
# Same as what is currently occurring, but suppressing the div by zero
# error.
with np.errstate(invalid='ignore'):
vals = op.finalize()
if vals is None: return
if isinstance(vals, list):
vals = [np.asfortranarray(v) for v in vals]
else:
vals = np.asfortranarray(vals)
return vals
def particle_operation(self,
positions,
fields=None,
method=None,
nneighbors=64,
kernel_name='cubic'):
r"""Operate on particles, in a particle-against-particle fashion.
This uses the octree indexing system to call a "smoothing" operation
(defined in yt/geometry/particle_smooth.pyx) that expects to be called
in a particle-by-particle fashion. For instance, the canonical example
of this would be to compute the Nth nearest neighbor, or to compute the
density for a given particle based on some kernel operation.
Many of the arguments to this are identical to those used in the smooth
and deposit functions. Note that the `fields` argument must not be
empty, as these fields will be modified in place.
Parameters
----------
positions : array_like (Nx3)
The positions of all of the particles to be examined. A new
indexed octree will be constructed on these particles.
fields : list of arrays
All the necessary fields for computing the particle operation. For
instance, this might include mass, velocity, etc. One of these
will likely be modified in place.
method : string
This is the "method name" which will be looked up in the
`particle_smooth` namespace as `methodname_smooth`.
nneighbors : int, default 64
The number of neighbors to examine during the process.
kernel_name : string, default 'cubic'
This is the name of the smoothing kernel to use. Current supported
kernel names include `cubic`, `quartic`, `quintic`, `wendland2`,
`wendland4`, and `wendland6`.
Returns
-------
Nothing.
"""
# Here we perform our particle deposition.
positions.convert_to_units("code_length")
morton = compute_morton(positions[:, 0], positions[:, 1],
positions[:, 2], self.ds.domain_left_edge,
self.ds.domain_right_edge)
morton.sort()
particle_octree = ParticleOctreeContainer([1, 1, 1],
self.ds.domain_left_edge,
self.ds.domain_right_edge,
over_refine=1)
particle_octree.n_ref = nneighbors * 2
particle_octree.add(morton)
particle_octree.finalize()
pdom_ind = particle_octree.domain_ind(self.selector)
if fields is None: fields = []
cls = getattr(particle_smooth, "%s_smooth" % method, None)
if cls is None:
raise YTParticleDepositionNotImplemented(method)
nz = self.nz
mdom_ind = self.domain_ind
nvals = (nz, nz, nz, (mdom_ind >= 0).sum())
op = cls(nvals, len(fields), nneighbors, kernel_name)
op.initialize()
mylog.debug("Smoothing %s particles into %s Octs", positions.shape[0],
nvals[-1])
op.process_particles(particle_octree, pdom_ind, positions, fields,
self.domain_id, self._domain_offset,
self.ds.periodicity, self.ds.geometry)
vals = op.finalize()
if vals is None: return
if isinstance(vals, list):
vals = [np.asfortranarray(v) for v in vals]
else:
vals = np.asfortranarray(vals)
return vals
def smooth(self,
positions,
fields=None,
index_fields=None,
method=None,
create_octree=False,
nneighbors=64,
kernel_name='cubic'):
r"""Operate on the mesh, in a particle-against-mesh fashion, with
non-local input.
This uses the octree indexing system to call a "smoothing" operation
(defined in yt/geometry/particle_smooth.pyx) that can take input from
several (non-local) particles and construct some value on the mesh.
The canonical example is to conduct a smoothing kernel operation on the
mesh.
Parameters
----------
positions : array_like (Nx3)
The positions of all of the particles to be examined. A new
indexed octree will be constructed on these particles.
fields : list of arrays
All the necessary fields for computing the particle operation. For
instance, this might include mass, velocity, etc.
index_fields : list of arrays
All of the fields defined on the mesh that may be used as input to
the operation.
method : string
This is the "method name" which will be looked up in the
`particle_smooth` namespace as `methodname_smooth`. Current
methods include `volume_weighted`, `nearest`, `idw`,
`nth_neighbor`, and `density`.
create_octree : bool
Should we construct a new octree for indexing the particles? In
cases where we are applying an operation on a subset of the
particles used to construct the mesh octree, this will ensure that
we are able to find and identify all relevant particles.
nneighbors : int, default 64
The number of neighbors to examine during the process.
kernel_name : string, default 'cubic'
This is the name of the smoothing kernel to use. Current supported
kernel names include `cubic`, `quartic`, `quintic`, `wendland2`,
`wendland4`, and `wendland6`.
Returns
-------
List of fortran-ordered, mesh-like arrays.
"""
# Here we perform our particle deposition.
positions.convert_to_units("code_length")
if create_octree:
morton = compute_morton(positions[:, 0], positions[:, 1],
positions[:, 2], self.ds.domain_left_edge,
self.ds.domain_right_edge)
morton.sort()
particle_octree = ParticleOctreeContainer(
[1, 1, 1],
self.ds.domain_left_edge,
self.ds.domain_right_edge,
over_refine=self._oref)
# This should ensure we get everything within one neighbor of home.
particle_octree.n_ref = nneighbors * 2
particle_octree.add(morton)
particle_octree.finalize()
pdom_ind = particle_octree.domain_ind(self.selector)
else:
particle_octree = self.oct_handler
pdom_ind = self.domain_ind
if fields is None: fields = []
if index_fields is None: index_fields = []
cls = getattr(particle_smooth, "%s_smooth" % method, None)
if cls is None:
raise YTParticleDepositionNotImplemented(method)
nz = self.nz
mdom_ind = self.domain_ind
nvals = (nz, nz, nz, (mdom_ind >= 0).sum())
op = cls(nvals, len(fields), nneighbors, kernel_name)
op.initialize()
mylog.debug("Smoothing %s particles into %s Octs", positions.shape[0],
nvals[-1])
# Pointer operations within 'process_octree' require arrays to be
# contiguous cf. https://bitbucket.org/yt_analysis/yt/issues/1079
fields = [np.ascontiguousarray(f, dtype="float64") for f in fields]
op.process_octree(self.oct_handler, mdom_ind, positions, self.fcoords,
fields, self.domain_id, self._domain_offset,
self.ds.periodicity, index_fields, particle_octree,
pdom_ind, self.ds.geometry)
# If there are 0s in the smoothing field this will not throw an error,
# but silently return nans for vals where dividing by 0
# Same as what is currently occurring, but suppressing the div by zero
# error.
with np.errstate(invalid='ignore'):
vals = op.finalize()
if vals is None: return
if isinstance(vals, list):
vals = [np.asfortranarray(v) for v in vals]
else:
vals = np.asfortranarray(vals)
return vals
def particle_operation(self, positions, fields = None,
method = None, nneighbors = 64):
r"""Operate on particles, in a particle-against-particle fashion.
This uses the octree indexing system to call a "smoothing" operation
(defined in yt/geometry/particle_smooth.pyx) that expects to be called
in a particle-by-particle fashion. For instance, the canonical example
of this would be to compute the Nth nearest neighbor, or to compute the
density for a given particle based on some kernel operation.
Many of the arguments to this are identical to those used in the smooth
and deposit functions. Note that the `fields` argument must not be
empty, as these fields will be modified in place.
Parameters
----------
positions : array_like (Nx3)
The positions of all of the particles to be examined. A new
indexed octree will be constructed on these particles.
fields : list of arrays
All the necessary fields for computing the particle operation. For
instance, this might include mass, velocity, etc. One of these
will likely be modified in place.
method : string
This is the "method name" which will be looked up in the
`particle_smooth` namespace as `methodname_smooth`.
nneighbors : int, default 64
The number of neighbors to examine during the process.
Returns
-------
Nothing.
"""
# Here we perform our particle deposition.
positions.convert_to_units("code_length")
morton = compute_morton(
positions[:,0], positions[:,1], positions[:,2],
self.ds.domain_left_edge,
self.ds.domain_right_edge)
morton.sort()
particle_octree = ParticleOctreeContainer([1, 1, 1],
self.ds.domain_left_edge,
self.ds.domain_right_edge,
over_refine = 1)
particle_octree.n_ref = nneighbors * 2
particle_octree.add(morton)
particle_octree.finalize()
pdom_ind = particle_octree.domain_ind(self.selector)
if fields is None: fields = []
cls = getattr(particle_smooth, "%s_smooth" % method, None)
if cls is None:
raise YTParticleDepositionNotImplemented(method)
nz = self.nz
mdom_ind = self.domain_ind
nvals = (nz, nz, nz, (mdom_ind >= 0).sum())
op = cls(nvals, len(fields), nneighbors)
op.initialize()
mylog.debug("Smoothing %s particles into %s Octs",
positions.shape[0], nvals[-1])
op.process_particles(particle_octree, pdom_ind, positions,
fields, self.domain_id, self._domain_offset, self.ds.periodicity,
self.ds.geometry)
vals = op.finalize()
if vals is None: return
if isinstance(vals, list):
vals = [np.asfortranarray(v) for v in vals]
else:
vals = np.asfortranarray(vals)
return vals
