import glob
import os
from collections import defaultdict
import numpy as np
from yt.data_objects.static_output import ParticleDataset, ParticleFile
from yt.frontends.gadget.data_structures import _fix_unit_ordering
from yt.funcs import only_on_root, setdefaultattr
from yt.geometry.particle_geometry_handler import ParticleIndex
from yt.utilities.exceptions import YTException
from yt.utilities.logger import ytLogger as mylog
from yt.utilities.on_demand_imports import _h5py as h5py
from .fields import OWLSSubfindFieldInfo
[docs]
class OWLSSubfindParticleIndex(ParticleIndex):
chunksize = -1
def __init__(self, ds, dataset_type):
super().__init__(ds, dataset_type)
def _calculate_particle_index_starts(self):
# Halo indices are not saved in the file, so we must count by hand.
# File 0 has halos 0 to N_0 - 1, file 1 has halos N_0 to N_0 + N_1 - 1, etc.
particle_count = defaultdict(int)
offset_count = 0
for data_file in self.data_files:
data_file.index_start = {
ptype: particle_count[ptype] for ptype in data_file.total_particles
}
data_file.offset_start = offset_count
for ptype in data_file.total_particles:
particle_count[ptype] += data_file.total_particles[ptype]
offset_count += data_file.total_offset
def _calculate_file_offset_map(self):
# After the FOF is performed, a load-balancing step redistributes halos
# and then writes more fields. Here, for each file, we create a list of
# files which contain the rest of the redistributed particles.
ifof = np.array(
[data_file.total_particles["FOF"] for data_file in self.data_files]
)
isub = np.array([data_file.total_offset for data_file in self.data_files])
subend = isub.cumsum()
fofend = ifof.cumsum()
istart = np.digitize(fofend - ifof, subend - isub) - 1
iend = np.clip(np.digitize(fofend, subend), 0, ifof.size - 2)
for i, data_file in enumerate(self.data_files):
data_file.offset_files = self.data_files[istart[i] : iend[i] + 1]
def _detect_output_fields(self):
# TODO: Add additional fields
self._calculate_particle_index_starts()
self._calculate_file_offset_map()
dsl = []
units = {}
for dom in self.data_files:
fl, _units = self.io._identify_fields(dom)
units.update(_units)
for f in fl:
if f not in dsl:
dsl.append(f)
self.field_list = dsl
ds = self.dataset
ds.particle_types = tuple({pt for pt, ds in dsl})
# This is an attribute that means these particle types *actually*
# exist. As in, they are real, in the dataset.
ds.field_units.update(units)
ds.particle_types_raw = ds.particle_types
[docs]
class OWLSSubfindHDF5File(ParticleFile):
def __init__(self, ds, io, filename, file_id, bounds):
super().__init__(ds, io, filename, file_id, bounds)
with h5py.File(filename, mode="r") as f:
self.header = {field: f.attrs[field] for field in f.attrs.keys()}
[docs]
class OWLSSubfindDataset(ParticleDataset):
_load_requirements = ["h5py"]
_index_class = OWLSSubfindParticleIndex
_file_class = OWLSSubfindHDF5File
_field_info_class = OWLSSubfindFieldInfo
_suffix = ".hdf5"
def __init__(
self,
filename,
dataset_type="subfind_hdf5",
index_order=None,
index_filename=None,
units_override=None,
unit_system="cgs",
):
super().__init__(
filename,
dataset_type,
index_order=index_order,
index_filename=index_filename,
units_override=units_override,
unit_system=unit_system,
)
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
# Set standard values
if "Time_GYR" in hvals:
self.current_time = self.quan(hvals["Time_GYR"], "Gyr")
self.domain_left_edge = np.zeros(3, "float64")
self.domain_right_edge = np.ones(3, "float64") * hvals["BoxSize"]
self.domain_dimensions = np.ones(3, "int32")
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 = f"{prefix}.%(num)i.{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 _set_code_unit_attributes(self):
# Set a sane default for cosmological simulations.
if self._unit_base is None and self.cosmological_simulation == 1:
only_on_root(mylog.info, "Assuming length units are in Mpc/h (comoving)")
self._unit_base = {"length": (1.0, "Mpccm/h")}
# The other same defaults we will use from the standard Gadget
# defaults.
unit_base = self._unit_base or {}
if "length" in unit_base:
length_unit = unit_base["length"]
elif "UnitLength_in_cm" in unit_base:
if self.cosmological_simulation == 0:
length_unit = (unit_base["UnitLength_in_cm"], "cm")
else:
length_unit = (unit_base["UnitLength_in_cm"], "cmcm/h")
else:
raise RuntimeError
length_unit = _fix_unit_ordering(length_unit)
setdefaultattr(self, "length_unit", self.quan(length_unit[0], length_unit[1]))
if "velocity" in unit_base:
velocity_unit = unit_base["velocity"]
elif "UnitVelocity_in_cm_per_s" in unit_base:
velocity_unit = (unit_base["UnitVelocity_in_cm_per_s"], "cm/s")
else:
velocity_unit = (1e5, "cm/s * sqrt(a)")
velocity_unit = _fix_unit_ordering(velocity_unit)
setdefaultattr(
self, "velocity_unit", self.quan(velocity_unit[0], velocity_unit[1])
)
# We set hubble_constant = 1.0 for non-cosmology, so this is safe.
# Default to 1e10 Msun/h if mass is not specified.
if "mass" in unit_base:
mass_unit = unit_base["mass"]
elif "UnitMass_in_g" in unit_base:
if self.cosmological_simulation == 0:
mass_unit = (unit_base["UnitMass_in_g"], "g")
else:
mass_unit = (unit_base["UnitMass_in_g"], "g/h")
else:
# Sane default
mass_unit = (1.0, "1e10*Msun/h")
mass_unit = _fix_unit_ordering(mass_unit)
setdefaultattr(self, "mass_unit", self.quan(mass_unit[0], mass_unit[1]))
if "time" in unit_base:
time_unit = unit_base["time"]
elif "UnitTime_in_s" in unit_base:
time_unit = (unit_base["UnitTime_in_s"], "s")
else:
tu = (self.length_unit / self.velocity_unit).to("yr/h")
time_unit = (tu.d, tu.units)
setdefaultattr(self, "time_unit", self.quan(time_unit[0], time_unit[1]))
@classmethod
def _is_valid(cls, filename: str, *args, **kwargs) -> bool:
if cls._missing_load_requirements():
return False
need_groups = ["Constants", "Header", "Parameters", "Units", "FOF"]
valid = True
try:
fh = h5py.File(filename, mode="r")
valid = all(ng in fh["/"] for ng in need_groups)
fh.close()
except Exception:
valid = False
return valid