Source code for yt.frontends.halo_catalogs.halo_catalog.data_structures

"""
Data structures for HaloCatalog 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.
#-----------------------------------------------------------------------------

import h5py
import numpy as np
import stat
import weakref
import struct
import glob
import time
import os

from .fields import \
    HaloCatalogFieldInfo

from yt.utilities.cosmology import Cosmology
from yt.geometry.particle_geometry_handler import \
    ParticleIndex
from yt.data_objects.static_output import \
    Dataset, \
    ParticleFile
import yt.utilities.fortran_utils as fpu
from yt.units.yt_array import \
    YTArray, \
    YTQuantity
    
[docs]class HaloCatalogHDF5File(ParticleFile):
[docs] def __init__(self, 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()) super(HaloCatalogHDF5File, self).__init__(ds, io, filename, file_id)
[docs]class HaloCatalogDataset(Dataset): _index_class = ParticleIndex _file_class = HaloCatalogHDF5File _field_info_class = HaloCatalogFieldInfo _suffix = ".h5"
[docs] def __init__(self, filename, dataset_type="halocatalog_hdf5", n_ref = 16, over_refine_factor = 1): self.n_ref = n_ref self.over_refine_factor = over_refine_factor super(HaloCatalogDataset, self).__init__(filename, dataset_type)
def _parse_parameter_file(self): with h5py.File(self.parameter_filename, "r") as f: hvals = dict((key, f.attrs[key]) for key in f.attrs.keys()) self.dimensionality = 3 self.refine_by = 2 self.unique_identifier = \ int(os.stat(self.parameter_filename)[stat.ST_CTIME]) prefix = ".".join(self.parameter_filename.rsplit(".", 2)[:-2]) self.filename_template = "%s.%%(num)s%s" % (prefix, self._suffix) self.file_count = len(glob.glob(prefix + "*" + self._suffix)) for attr in ["cosmological_simulation", "current_time", "current_redshift", "hubble_constant", "omega_matter", "omega_lambda", "domain_left_edge", "domain_right_edge"]: setattr(self, attr, hvals[attr]) self.periodicity = (True, True, True) self.particle_types = ("halos") self.particle_types_raw = ("halos") nz = 1 << self.over_refine_factor self.domain_dimensions = np.ones(3, "int32") * nz self.parameters.update(hvals) def _set_code_unit_attributes(self): self.length_unit = self.quan(1.0, "cm") self.mass_unit = self.quan(1.0, "g") self.velocity_unit = self.quan(1.0, "cm / s") self.time_unit = self.quan(1.0, "s") @classmethod def _is_valid(self, *args, **kwargs): if not args[0].endswith(".h5"): return False with h5py.File(args[0], "r") as f: if "data_type" in f.attrs and \ f.attrs["data_type"] == "halo_catalog": return True return False