Source code for yt.frontends.owls_subfind.data_structures

"""
Data structures for OWLSSubfind frontend.




"""

#-----------------------------------------------------------------------------
# Copyright (c) 2013, yt Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------

from collections import defaultdict
from yt.utilities.on_demand_imports import _h5py as h5py
import numpy as np
import stat
import glob
import os

from .fields import \
    OWLSSubfindFieldInfo

from yt.funcs import \
    only_on_root, \
    setdefaultattr
from yt.utilities.exceptions import \
    YTException
from yt.utilities.logger import ytLogger as \
    mylog
from yt.geometry.particle_geometry_handler import \
    ParticleIndex
from yt.data_objects.static_output import \
    Dataset, \
    ParticleFile
from yt.frontends.gadget.data_structures import \
    _fix_unit_ordering

[docs]class OWLSSubfindParticleIndex(ParticleIndex): def __init__(self, ds, dataset_type): super(OWLSSubfindParticleIndex, self).__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 = dict([(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 dsl = [] units = {} for dom in self.data_files: fl, _units = self.io._identify_fields(dom) units.update(_units) dom._calculate_offsets(fl) for f in fl: if f not in dsl: dsl.append(f) self.field_list = dsl ds = self.dataset ds.particle_types = tuple(set(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 def _setup_geometry(self): super(OWLSSubfindParticleIndex, self)._setup_geometry() self._calculate_particle_index_starts() self._calculate_file_offset_map()
[docs]class OWLSSubfindHDF5File(ParticleFile): def __init__(self, ds, io, filename, file_id): super(OWLSSubfindHDF5File, self).__init__(ds, io, filename, file_id) with h5py.File(filename, "r") as f: self.header = dict((field, f.attrs[field]) \ for field in f.attrs.keys())
[docs]class OWLSSubfindDataset(Dataset): _index_class = OWLSSubfindParticleIndex _file_class = OWLSSubfindHDF5File _field_info_class = OWLSSubfindFieldInfo _suffix = ".hdf5" def __init__(self, filename, dataset_type="subfind_hdf5", n_ref = 16, over_refine_factor = 1, units_override=None, unit_system="cgs"): self.n_ref = n_ref self.over_refine_factor = over_refine_factor super(OWLSSubfindDataset, self).__init__(filename, dataset_type, 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 self.unique_identifier = \ int(os.stat(self.parameter_filename)[stat.ST_CTIME]) # Set standard values 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"] 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 _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 = dict(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") 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: time_unit = (1., "s") setdefaultattr(self, 'time_unit', self.quan(time_unit[0], time_unit[1])) @classmethod def _is_valid(self, *args, **kwargs): need_groups = ['Constants', 'Header', 'Parameters', 'Units', 'FOF'] veto_groups = [] valid = True try: fh = h5py.File(args[0], mode='r') valid = all(ng in fh["/"] for ng in need_groups) and \ not any(vg in fh["/"] for vg in veto_groups) fh.close() except: valid = False pass return valid