"""
Implements reading HDF5 Gadget files, in various variants.
The gadget array names are mapped into pynbody array names according
to the mappings given by the config.ini section ``[gadgethdf-name-mapping]``.
The gadget particle groups are mapped into pynbody families according
to the mappings specified by the config.ini section ``[gadgethdf-type-mapping]``.
This can be many-to-one (many gadget particle types mapping into one
pynbody family), but only datasets which are common to all gadget types
will be available from pynbody.
Spanned files are supported. To load a range of files ``snap.0.hdf5``, ``snap.1.hdf5``, ... ``snap.n.hdf5``,
pass the filename ``snap``. If you pass e.g. ``snap.2.hdf5``, only file 2 will be loaded.
"""
import configparser
import functools
import itertools
import logging
import warnings
import numpy as np
from .. import config_parser, family, units, util
from . import SimSnap, namemapper
logger = logging.getLogger('pynbody.snapshot.gadgethdf')
try:
import h5py
except ImportError:
h5py = None
_default_type_map = {}
for x in family.family_names():
try:
_default_type_map[family.get_family(x)] = \
[q.strip() for q in config_parser.get('gadgethdf-type-mapping', x).split(",")]
except configparser.NoOptionError:
pass
_all_hdf_particle_groups = []
for hdf_groups in _default_type_map.values():
for hdf_group in hdf_groups:
_all_hdf_particle_groups.append(hdf_group)
class _DummyHDFData:
"""A stupid class to allow emulation of mass arrays for particles
whose mass is in the header"""
def __init__(self, value, length, dtype):
self.value = value
self.length = length
self.size = length
self.shape = (length, )
self.dtype = np.dtype(dtype)
def __len__(self):
return self.length
def read_direct(self, target):
target[:] = self.value
class _GadgetHdfMultiFileManager:
_nfiles_groupname = "Header"
_nfiles_attrname = "NumFilesPerSnapshot"
_size_from_hdf5_key = "ParticleIDs"
_subgroup_name = None
def __init__(self, filename, mode='r') :
filename = str(filename)
self._mode = mode
if h5py.is_hdf5(filename):
self._filenames = [filename]
self._numfiles = 1
else:
h1 = h5py.File(filename + ".0.hdf5", mode)
self._numfiles = self._get_num_files(h1)
if hasattr(self._numfiles, "__len__"):
assert len(self._numfiles) == 1
self._numfiles = self._numfiles[0]
self._filenames = [filename+"."+str(i)+".hdf5" for i in range(self._numfiles)]
self._open_files = {}
def _get_num_files(self, first_file):
return first_file[self._nfiles_groupname].attrs[self._nfiles_attrname]
def __len__(self):
return self._numfiles
def __iter__(self) :
for i in range(self._numfiles) :
if i not in self._open_files:
self._open_files[i] = h5py.File(self._filenames[i], self._mode)
if self._subgroup_name is not None:
self._open_files[i] = self._open_files[i][self._subgroup_name]
yield self._open_files[i]
def __getitem__(self, i) :
try :
return self._open_files[i]
except KeyError :
self._open_files[i] = next(itertools.islice(self,i,i+1))
return self._open_files[i]
def iter_particle_groups_with_name(self, hdf_family_name):
for hdf in self:
if hdf_family_name in hdf:
if self._size_from_hdf5_key in hdf[hdf_family_name]:
yield hdf[hdf_family_name]
def get_header_attrs(self):
return self[0].parent['Header'].attrs
def get_parameter_attrs(self):
try:
attrs = self[0].parent['Parameters'].attrs
except KeyError:
attrs = []
if len(attrs) == 0:
return self.get_header_attrs()
else:
return attrs
def get_unit_attrs(self):
return self[0].parent['Units'].attrs
def get_file0_root(self):
return self[0].parent
def iterroot(self):
for item in self:
yield item.parent
def reopen_in_mode(self, mode):
if mode!=self._mode:
self._open_files = {}
self._mode = mode
class _SubfindHdfMultiFileManager(_GadgetHdfMultiFileManager):
_nfiles_groupname = "FOF"
_nfiles_attrname = "NTask"
_subgroup_name = "FOF"
[docs]
class GadgetHDFSnap(SimSnap):
"""
Class that reads HDF Gadget snapshots.
"""
_multifile_manager_class = _GadgetHdfMultiFileManager
_readable_hdf5_test_key = "PartType?"
_readable_hdf5_test_attr = None # if None, no attribute is checked
_size_from_hdf5_key = "ParticleIDs"
_namemapper_config_section = "gadgethdf-name-mapping"
_softening_class_key = "SofteningClassOfPartType"
_softening_comoving_key = "SofteningComovingClass"
_softening_max_phys_key = "SofteningMaxPhysClass"
_mass_pynbody_name = "mass"
_eps_pynbody_name = "eps"
[docs]
def __init__(self, filename):
"""Initialise a Gadget HDF snapshot.
Spanned files are supported. To load a range of files ``snap.0.hdf5``, ``snap.1.hdf5``, ... ``snap.n.hdf5``,
pass the filename ``snap``. If you pass e.g. ``snap.2.hdf5``, only file 2 will be loaded.
"""
super().__init__()
self._filename = filename
self._init_hdf_filemanager(filename)
self._translate_array_name = namemapper.AdaptiveNameMapper(self._namemapper_config_section,
return_all_format_names=True) # required for swift
self._init_unit_information()
self.__init_family_map()
self.__init_file_map()
self.__init_loadable_keys()
self.__infer_mass_dtype()
self._init_properties()
self._decorate()
def _have_softening_for_particle_type(self, particle_type):
attrs = self._get_hdf_parameter_attrs()
class_name = self._softening_class_key + str(particle_type)
return class_name in attrs
def _get_softening_for_particle_type(self, particle_type):
attrs = self._get_hdf_parameter_attrs()
class_name = self._softening_class_key + str(particle_type)
if class_name not in attrs:
return None
class_number = attrs[class_name]
comoving_softening = attrs[self._softening_comoving_key + str(class_number)]
max_physical_softening = attrs[self._softening_max_phys_key + str(class_number)]
if comoving_softening > max_physical_softening / self.properties['a']:
comoving_softening = max_physical_softening / self.properties['a']
return comoving_softening
def _have_softening_for_particle_group(self, particle_group):
return self._have_softening_for_particle_type(int(particle_group.name[-1]))
def _get_softening_for_particle_group(self, particle_group):
return self._get_softening_for_particle_type(int(particle_group.name[-1]))
def _get_hdf_header_attrs(self):
return self._hdf_files.get_header_attrs()
def _get_hdf_parameter_attrs(self):
return self._hdf_files.get_parameter_attrs()
def _get_hdf_unit_attrs(self):
return self._hdf_files.get_unit_attrs()
def _init_hdf_filemanager(self, filename):
self._hdf_files = self._multifile_manager_class(filename)
def __init_loadable_keys(self):
self._loadable_family_keys = {}
all_fams = self.families()
if len(all_fams)==0:
return
for fam in all_fams:
self._loadable_family_keys[fam] = {self._mass_pynbody_name}
can_get_eps = True
for hdf_group in self._all_hdf_groups_in_family(fam):
for this_key in self._get_hdf_allarray_keys(hdf_group):
ar_name = self._translate_array_name(this_key, reverse=True)
self._loadable_family_keys[fam].add(ar_name)
can_get_eps &= self._have_softening_for_particle_group(hdf_group)
if can_get_eps:
self._loadable_family_keys[fam].add(self._eps_pynbody_name)
self._loadable_family_keys[fam] = list(self._loadable_family_keys[fam])
self._loadable_keys = set(self._loadable_family_keys[all_fams[0]])
for fam_keys in self._loadable_family_keys.values():
self._loadable_keys.intersection_update(fam_keys)
self._loadable_keys = list(self._loadable_keys)
def _all_hdf_groups(self):
for hdf_family_name in _all_hdf_particle_groups:
yield from self._hdf_files.iter_particle_groups_with_name(hdf_family_name)
def _all_hdf_groups_in_family(self, fam):
for hdf_family_name in self._family_to_group_map[fam]:
yield from self._hdf_files.iter_particle_groups_with_name(hdf_family_name)
def __init_file_map(self):
family_slice_start = 0
all_families_sorted = self._families_ordered()
self._gadget_ptype_slice = {} # will map from gadget particle type to location in pynbody logical file map
for fam in all_families_sorted:
family_length = 0
# A simpler and more readable version of the code below would be:
#
# for hdf_group in self._all_hdf_groups_in_family(fam):
# family_length += hdf_group[self._size_from_hdf5_key].size
#
# However, occasionally we need to know where in the pynbody file map the gadget particle types lie.
# (Specifically this is used when loading subfind data.) So we need to expand that out a bit and also
# keep track of the slice for each gadget particle type.
ptype_slice_start = family_slice_start
for particle_type in self._family_to_group_map[fam]:
ptype_slice_len = 0
for hdf_group in self._hdf_files.iter_particle_groups_with_name(particle_type):
ptype_slice_len += hdf_group[self._size_from_hdf5_key].size
self._gadget_ptype_slice[particle_type] = slice(ptype_slice_start, ptype_slice_start + ptype_slice_len)
family_length += ptype_slice_len
ptype_slice_start += ptype_slice_len
self._family_slice[fam] = slice(family_slice_start, family_slice_start + family_length)
family_slice_start += family_length
self._num_particles = family_slice_start
def __infer_mass_dtype(self):
"""Some files have a mixture of header-based masses and, for other partile types, explicit mass
arrays. This routine decides in advance the correct dtype to assign to the mass array, whichever
particle type it is loaded for."""
mass_dtype = np.float64
for hdf in self._all_hdf_groups():
if "Coordinates" in hdf:
mass_dtype = hdf['Coordinates'].dtype
self._mass_dtype = mass_dtype
def _families_ordered(self):
# order by the PartTypeN
all_families = list(self._family_to_group_map.keys())
all_families_sorted = sorted(all_families, key=lambda v: self._family_to_group_map[v][0])
return all_families_sorted
def __init_family_map(self):
type_map = {}
for fam, g_types in _default_type_map.items():
my_types = []
for x in g_types:
# Get all keys from all hdf files
for hdf in self._hdf_files:
if x in list(hdf.keys()):
my_types.append(x)
break
if len(my_types):
type_map[fam] = my_types
self._family_to_group_map = type_map
def _family_has_loadable_array(self, fam, name):
"""Returns True if the array can be loaded for the specified family.
If fam is None, returns True if the array can be loaded for all families."""
return name in self.loadable_keys(fam)
def _get_all_particle_arrays(self, gtype):
"""Return all array names for a given gadget particle type"""
# this is a hack to flatten a list of lists
l = [item for sublist in [self._get_hdf_allarray_keys(x[gtype]) for x in self._hdf_files] for item in sublist]
# now just return the unique items by converting to a set
return list(set(l))
[docs]
def loadable_keys(self, fam=None):
if fam is None:
return self._loadable_keys
else:
return self._loadable_family_keys[fam]
@staticmethod
def _write(self, filename=None):
raise RuntimeError("Not implemented")
[docs]
def write_array(self, array_name, fam=None, overwrite=False):
translated_name = self._translate_array_name(array_name)[0]
self._hdf_files.reopen_in_mode('r+')
try:
if fam is None:
target = self
all_fams_to_write = self.families()
else:
target = self[fam]
all_fams_to_write = [fam]
for writing_fam in all_fams_to_write:
i0 = 0
target_array = self[writing_fam][array_name]
for hdf in self._all_hdf_groups_in_family(writing_fam):
npart = hdf['ParticleIDs'].size
i1 = i0 + npart
target_array_this = target_array[i0:i1]
dataset = self._get_or_create_hdf_dataset(hdf, translated_name,
target_array_this.shape,
target_array_this.dtype)
dataset.write_direct(target_array_this.reshape(dataset.shape))
i0 = i1
finally:
self._hdf_files.reopen_in_mode('r')
@staticmethod
def _get_hdf_allarray_keys(group):
"""Return all HDF array keys underneath group (includes nested groups)"""
keys = []
def _append_if_array(to_list, name, obj):
if not hasattr(obj, 'keys'):
to_list.append(name)
group.visititems(functools.partial(_append_if_array, keys))
return keys
def _get_or_create_hdf_dataset(self, particle_group, hdf_name, shape, dtype):
if self._translate_array_name(hdf_name,reverse=True) == self._mass_pynbody_name:
raise OSError("Unable to write the mass block due to Gadget header format")
ret = particle_group
for tpart in hdf_name.split("/")[:-1]:
ret =ret[tpart]
dataset_name = hdf_name.split("/")[-1]
return ret.require_dataset(dataset_name, shape, dtype, exact=True)
def _get_hdf_dataset(self, particle_group, hdf_name):
"""Return the HDF dataset resolving /'s into nested groups, and returning
an apparent Mass array even if the mass is actually stored in the header"""
if self._translate_array_name(hdf_name,reverse=True) == self._mass_pynbody_name:
try:
pgid = int(particle_group.name[-1])
mtab = particle_group.parent['Header'].attrs['MassTable'][pgid]
if mtab > 0:
return _DummyHDFData(mtab, particle_group[self._size_from_hdf5_key].size,
self._mass_dtype)
except (IndexError, KeyError):
pass
elif self._translate_array_name(hdf_name,reverse=True) == self._eps_pynbody_name:
eps = self._get_softening_for_particle_group(particle_group)
if eps is not None:
return _DummyHDFData(eps, particle_group[self._size_from_hdf5_key].size, self._mass_dtype)
ret = particle_group
for tpart in hdf_name.split("/"):
ret = ret[tpart]
return ret
@staticmethod
def _get_cosmo_factors(hdf, arr_name) :
"""Return the cosmological factors for a given array"""
match = [s for s in GadgetHDFSnap._get_hdf_allarray_keys(hdf) if ((s.endswith("/"+arr_name)) & ('PartType' in s))]
if (arr_name == 'Mass' or arr_name == 'Masses') and len(match) == 0:
# mass stored in header. We're out in the cold on our own.
warnings.warn("Masses are either stored in the header or have another dataset name; assuming the cosmological factor %s" % units.h**-1)
return units.Unit('1.0'), units.h**-1
if len(match) > 0 :
try:
aexp = hdf[match[0]].attrs['aexp-scale-exponent']
except KeyError:
# gadget4 <sigh>
aexp = hdf[match[0]].attrs['a_scaling']
try:
hexp = hdf[match[0]].attrs['h-scale-exponent']
except KeyError:
# gadget4 <sigh>
hexp = hdf[match[0]].attrs['h_scaling']
return units.a**util.fractions.Fraction.from_float(float(aexp)).limit_denominator(), units.h**util.fractions.Fraction.from_float(float(hexp)).limit_denominator()
else :
return units.Unit('1.0'), units.Unit('1.0')
def _get_units_from_hdf_attr(self, hdfattrs) :
"""Return the units based on HDF attributes VarDescription"""
if 'VarDescription' not in hdfattrs:
warnings.warn("Unable to infer units from HDF attributes")
return units.NoUnit()
VarDescription = str(hdfattrs['VarDescription'])
CGSConversionFactor = float(hdfattrs['CGSConversionFactor'])
aexp = hdfattrs['aexp-scale-exponent']
hexp = hdfattrs['h-scale-exponent']
arr_units = self._get_units_from_description(VarDescription, CGSConversionFactor)
if not np.allclose(aexp, 0.0):
arr_units *= (units.a) ** util.fractions.Fraction.from_float(float(aexp)).limit_denominator()
if not np.allclose(hexp, 0.0):
arr_units *= (units.h) ** util.fractions.Fraction.from_float(float(hexp)).limit_denominator()
return arr_units
def _get_units_from_description(self, description, expectedCgsConversionFactor=None):
arr_units = units.Unit('1.0')
conversion = 1.0
for unitname in list(self._hdf_unitvar.keys()):
power = 1.
if unitname in description:
sstart = description.find(unitname)
if sstart > 0:
if description[sstart - 1] == "/":
power *= -1.
if len(description) > sstart + len(unitname):
# Just check we're not at the end of the line
if description[sstart + len(unitname)] == '^':
## Has an index, check if this is negative
if description[sstart + len(unitname) + 1] == "-":
power *= -1.
power *= float(
description[sstart + len(unitname) + 2:-1].split()[0]) ## Search for the power
else:
power *= float(
description[sstart + len(unitname) + 1:-1].split()[0]) ## Search for the power
if not np.allclose(power, 0.0):
arr_units *= self._hdf_unitvar[unitname] ** util.fractions.Fraction.from_float(
float(power)).limit_denominator()
if not np.allclose(power, 0.0):
conversion *= self._hdf_unitvar[unitname].in_units(
self._hdf_cgsvar[unitname]) ** util.fractions.Fraction.from_float(
float(power)).limit_denominator()
if expectedCgsConversionFactor is not None:
if not np.allclose(conversion, expectedCgsConversionFactor, rtol=1e-3):
raise units.UnitsException(
"Error with unit read out from HDF. Inferred CGS conversion factor is {!r} but HDF requires {!r}".format(
conversion, expectedCgsConversionFactor))
return arr_units
def _load_array(self, array_name, fam=None):
if not self._family_has_loadable_array(fam, array_name):
raise OSError("No such array on disk")
else:
translated_names = self._translate_array_name(array_name)
dtype, dy, units = self.__get_dtype_dims_and_units(fam, translated_names)
if array_name == self._mass_pynbody_name:
dtype = self._mass_dtype
# always load mass with this dtype, even if not the one in the file. This
# is to cope with cases where it's partly in the header and partly not.
# It also forces masses to the same dtype as the positions, which
# is important for the KDtree code.
if fam is None:
target = self
all_fams_to_load = self.families()
else:
target = self[fam]
all_fams_to_load = [fam]
target._create_array(array_name, dy, dtype=dtype)
if units is not None:
target[array_name].units = units
else:
target[array_name].set_default_units()
for loading_fam in all_fams_to_load:
i0 = 0
for hdf in self._all_hdf_groups_in_family(loading_fam):
npart = hdf['ParticleIDs'].size
if npart == 0:
continue
i1 = i0+npart
for translated_name in translated_names:
try:
dataset = self._get_hdf_dataset(hdf, translated_name)
except KeyError:
continue
target_array = self[loading_fam][array_name][i0:i1]
assert target_array.size == dataset.size
dataset.read_direct(target_array.reshape(dataset.shape))
i0 = i1
def __get_dtype_dims_and_units(self, fam, translated_names):
if fam is None:
fam = self.families()[0]
inferred_units = units.NoUnit()
representative_dset = None
representative_hdf = None
# not all arrays are present in all hdfs so need to loop
# until we find one
for hdf0 in self._hdf_files:
for translated_name in translated_names:
try:
representative_dset = self._get_hdf_dataset(hdf0[
self._family_to_group_map[fam][0]], translated_name)
break
except KeyError:
continue
if representative_dset is None:
continue
representative_hdf = hdf0
if hasattr(representative_dset, "attrs"):
inferred_units = self._get_units_from_hdf_attr(representative_dset.attrs)
if len(representative_dset)!=0:
# suitable for figuring out everything we need to know about this array
break
if representative_dset is None:
raise KeyError("Array is not present in HDF file")
assert len(representative_dset.shape) <= 2
if len(representative_dset.shape) > 1:
dy = representative_dset.shape[1]
else:
dy = 1
# Some versions of gadget fold the 3D arrays into 1D.
# So check if the dimensions make sense -- if not, assume we're looking at an array that
# is 3D and cross your fingers
npart = len(representative_hdf[self._family_to_group_map[fam][0]]['ParticleIDs'])
if len(representative_dset) != npart:
dy = len(representative_dset) // npart
dtype = representative_dset.dtype
if translated_name=="Mass":
dtype = self._mass_dtype
return dtype, dy, inferred_units
_velocity_unit_key = 'UnitVelocity_in_cm_per_s'
_length_unit_key = 'UnitLength_in_cm'
_mass_unit_key = 'UnitMass_in_g'
_time_unit_key = 'UnitTime_in_s'
def _init_unit_information(self):
try:
atr = self._hdf_files.get_unit_attrs()
except KeyError:
# Gadget 4 stores unit information in Parameters attr <sigh>
atr = self._hdf_files.get_parameter_attrs()
if self._velocity_unit_key not in atr.keys():
warnings.warn("No unit information found in GadgetHDF file. Using gadget default units.", RuntimeWarning)
vel_unit = config_parser.get('gadget-units', 'vel')
dist_unit = config_parser.get('gadget-units', 'pos')
mass_unit = config_parser.get('gadget-units', 'mass')
self._file_units_system = [units.Unit(x) for x in [
vel_unit, dist_unit, mass_unit, "K"]]
return
# Define the SubFind units, we will parse the attribute VarDescriptions for these
if self._velocity_unit_key is not None:
vel_unit = atr[self._velocity_unit_key]
else:
vel_unit = None
dist_unit = atr[self._length_unit_key]
mass_unit = atr[self._mass_unit_key]
try:
time_unit = atr[self._time_unit_key] * units.s
except KeyError:
# Gadget 4 seems not to store time units explicitly <sigh>
time_unit = dist_unit/vel_unit
if vel_unit is None:
# Swift files don't store the velocity explicitly
vel_unit = dist_unit / time_unit
temp_unit = 1.0
# Create a dictionary for the units, this will come in handy later
unitvar = {'U_V': vel_unit * units.cm/units.s, 'U_L': dist_unit * units.cm,
'U_M': mass_unit * units.g,
'U_T': time_unit,
'[K]': temp_unit * units.K,
'SEC_PER_YEAR': units.yr,
'SOLAR_MASS': units.Msol,
'solar masses / yr': units.Msol/units.yr,
'BH smoothing': dist_unit}
# Some arrays like StarFormationRate don't follow the pattern of U_ units
cgsvar = {'U_M': 'g', 'SOLAR_MASS': 'g', 'U_T': 's',
'SEC_PER_YEAR': 's', 'U_V': 'cm s**-1', 'U_L': 'cm', '[K]': 'K',
'solar masses / yr': 'g s**-1', 'BH smoothing': 'cm'}
self._hdf_cgsvar = cgsvar
self._hdf_unitvar = unitvar
cosmo = 'HubbleParam' in list(self._get_hdf_parameter_attrs().keys())
if cosmo:
try:
for fac in self._get_cosmo_factors(self._hdf_files[0], 'Coordinates'): dist_unit *= fac
except KeyError:
dist_unit *= units.a * units.h**-1
warnings.warn("Unable to find cosmological factors in HDF file; assuming position is %s" % dist_unit)
try:
for fac in self._get_cosmo_factors(self._hdf_files[0], 'Velocities'): vel_unit *= fac
except KeyError:
vel_unit *= units.a**(1,2)
warnings.warn("Unable to find cosmological factors in HDF file; assuming velocity is %s" % vel_unit)
try:
for fac in self._get_cosmo_factors(self._hdf_files[0], 'Mass'): mass_unit *= fac
except KeyError:
mass_unit *= units.h**-1
warnings.warn("Unable to find cosmological factors in HDF file; assuming mass is %s" % mass_unit)
self._file_units_system = [units.Unit(x) for x in [
vel_unit*units.cm/units.s, dist_unit*units.cm, mass_unit*units.g, "K"]]
@classmethod
def _test_for_hdf5_key(cls, f):
with h5py.File(f, "r") as h5test:
test_key = cls._readable_hdf5_test_key
found = False
if test_key[-1]=="?":
# try all particle numbers in turn
for p in range(6):
test_key = test_key[:-1]+str(p)
if test_key in h5test:
found = True
else:
found = test_key in h5test
if not found:
return False
if cls._readable_hdf5_test_attr is not None:
location, attrname = cls._readable_hdf5_test_attr
if location in h5test:
found = attrname in h5test[location].attrs
else:
found = False
return found
@classmethod
def _can_load(cls, f):
if hasattr(h5py, "is_hdf5"):
if h5py.is_hdf5(f):
return cls._test_for_hdf5_key(f)
elif h5py.is_hdf5(f.with_suffix(".0.hdf5")):
return cls._test_for_hdf5_key(f.with_suffix(".0.hdf5"))
else:
return False
else:
if "hdf5" in f:
warnings.warn(
"It looks like you're trying to load HDF5 files, but python's HDF support (h5py module) is missing.", RuntimeWarning)
return False
def _init_properties(self):
atr = self._get_hdf_header_attrs()
# expansion factor could be saved as redshift
if 'ExpansionFactor' in atr:
self.properties['a'] = atr['ExpansionFactor']
elif 'Redshift' in atr:
self.properties['a'] = 1. / (1 + atr['Redshift'])
# Gadget 4 stores parameters in a separate dictionary <sigh>. For older formats, this will point back to the same
# as the header attributes.
atr = self._get_hdf_parameter_attrs()
# not all omegas need to be specified in the attributes
if 'OmegaBaryon' in atr:
self.properties['omegaB0'] = atr['OmegaBaryon']
if 'Omega0' in atr:
self.properties['omegaM0'] = atr['Omega0']
if 'OmegaLambda' in atr:
self.properties['omegaL0'] = atr['OmegaLambda']
if 'BoxSize' in atr:
self.properties['boxsize'] = atr['BoxSize'] * self.infer_original_units('cm')
if 'HubbleParam' in atr:
self.properties['h'] = atr['HubbleParam']
if 'a' in self.properties:
self.properties['z'] = (1. / self.properties['a']) - 1
# time unit might not be set in the attributes
if "Time_GYR" in atr:
self.properties['time'] = units.Gyr * atr['Time_GYR']
else:
from .. import analysis
self.properties['time'] = analysis.cosmology.age(self) * units.Gyr
for s,value in self._get_hdf_header_attrs().items():
if s not in ['ExpansionFactor', 'Time_GYR', 'Time', 'Omega0', 'OmegaBaryon', 'OmegaLambda', 'BoxSize', 'HubbleParam']:
self.properties[s] = value
[docs]
class ArepoHDFSnap(GadgetHDFSnap):
"""
Reads Arepo HDF snapshots.
"""
_readable_hdf5_test_attr = "Config", "VORONOI"
_softening_class_key = "SofteningTypeOfPartType"
_softening_comoving_key = "SofteningComovingType"
_softening_max_phys_key = "SofteningMaxPhysType"
def _get_units_from_hdf_attr(self, hdfattrs):
if 'length_scaling' not in hdfattrs:
warnings.warn("Unable to infer units from HDF attributes")
return units.NoUnit()
l, m, v, a, h = (float(hdfattrs[x]) for x in ['length_scaling', 'mass_scaling', 'velocity_scaling', 'a_scaling', 'h_scaling'])
base_units = [units.cm, units.g, units.cm/units.s, units.a, units.h]
if float(hdfattrs['to_cgs'])==0.0:
# 0.0 is used in dimensionless cases
arr_units = units.Unit(1.0)
else:
arr_units = units.Unit(float(hdfattrs['to_cgs']))
for exponent, base_unit in zip([l, m, v, a, h], base_units):
if not np.allclose(exponent, 0.0):
arr_units *= base_unit ** util.fractions.Fraction.from_float(float(exponent)).limit_denominator()
return arr_units
[docs]
class SubFindHDFSnap(GadgetHDFSnap) :
"""
Reads the variant of Gadget HDF snapshots that include SubFind output inside the snapshot itself.
"""
_multifile_manager_class = _SubfindHdfMultiFileManager
_readable_hdf5_test_key = "FOF"
[docs]
class EagleLikeHDFSnap(GadgetHDFSnap):
"""Reads Eagle-like HDF snapshots (download at http://data.cosma.dur.ac.uk:8080/eagle-snapshots/)"""
_readable_hdf5_test_key = "PartType1/SubGroupNumber"
[docs]
def halos(self, subs=None):
"""Load the Eagle FOF halos, or if subs is specified the Subhalos of the given FOF halo number.
*subs* should be an integer specifying the parent FoF number"""
from .. import halo
if subs:
if not np.issubdtype(type(subs), np.integer):
raise ValueError("The subs argument must specify the group number")
parent_group = self[self['GroupNumber']==subs]
if len(parent_group)==0:
raise ValueError("No group found with id %d"%subs)
cat = halo.number_array.HaloNumberCatalogue(parent_group,
array="SubGroupNumber", ignore=np.max(self['SubGroupNumber']))
cat._keep_subsnap_alive = parent_group # by default, HaloCatalogue only keeps a weakref (should this be changed?)
return cat
else:
return halo.number_array.HaloNumberCatalogue(self, array="GroupNumber", ignore=np.max(self['GroupNumber']))
## Gadget has internal energy variable
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def u(self) :
"""Gas internal energy derived from snapshot variable or temperature"""
try:
u = self['InternalEnergy']
except KeyError:
gamma = 5./3
u = self['temp']*units.k/(self['mu']*units.m_p*(gamma-1))
return u
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def p(sim) :
"""Calculate the pressure for gas particles, including polytropic equation of state gas"""
critpres = 2300. * units.K * units.m_p / units.cm**3 ## m_p K cm^-3
critdens = 0.1 * units.m_p / units.cm**3 ## m_p cm^-3
gammaeff = 4./3.
oneos = sim.g['OnEquationOfState'] == 1.
p = sim.g['rho'].in_units('m_p cm**-3') * sim.g['temp'].in_units('K')
p[oneos] = critpres * (sim.g['rho'][oneos].in_units('m_p cm**-3')/critdens)**gammaeff
return p
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def HII(sim) :
"""Number of HII ions per proton mass"""
return sim.g["hydrogen"] - sim.g["HI"]
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def HeIII(sim) :
"""Number of HeIII ions per proton mass"""
return sim.g["hetot"] - sim.g["HeII"] - sim.g["HeI"]
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def ne(sim) :
"""Number of electrons per proton mass, ignoring the contribution from He!"""
ne = sim.g["HII"] #+ sim["HeII"] + 2*sim["HeIII"]
ne.units = units.m_p**-1
return ne
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def rho_ne(sim) :
"""Electron number density per SPH particle, currently ignoring the contribution from He!"""
return sim.g["ne"].in_units("m_p**-1") * sim.g["rho"].in_units("m_p cm**-3")
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def dm(sim) :
"""Dispersion measure per SPH particle currently ignoring n_e contribution from He """
return sim.g["rho_ne"]
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def cosmodm(sim) :
"""Cosmological Dispersion measure per SPH particle includes (1+z) factor, currently ignoring n_e contribution from He """
return sim.g["rho_ne"] * (1. + sim.g["redshift"])
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def redshift(sim) :
"""Redshift from LoS Velocity 'losvel' """
return np.exp( sim['losvel'].in_units('c') ) - 1.
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def doppler_redshift(sim) :
"""Doppler Redshift from LoS Velocity 'losvel' using SR """
return np.sqrt( (1. + sim['losvel'].in_units('c')) / (1. - sim['losvel'].in_units('c')) ) - 1.
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def em(sim) :
"""Emission Measure (n_e^2) per particle to be integrated along LoS"""
return sim.g["rho_ne"]*sim.g["rho_ne"]
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def halpha(sim) :
"""H alpha intensity (based on Emission Measure n_e^2) per particle to be integrated along LoS"""
## Rate at which recombining electrons and protons produce Halpha photons.
## Case B recombination assumed from Draine (2011)
#alpha = 2.54e-13 * (sim.g['temp'].in_units('K') / 1e4)**(-0.8163-0.0208*np.log(sim.g['temp'].in_units('K') / 1e4))
#alpha.units = units.cm**(3) * units.s**(-1)
## H alpha intensity = coeff * EM
## where coeff is h (c / Lambda_Halpha) / 4Pi) and EM is int rho_e * rho_p * alpha
## alpha = 7.864e-14 T_1e4K from http://astro.berkeley.edu/~ay216/08/NOTES/Lecture08-08.pdf
coeff = (6.6260755e-27) * (299792458. / 656.281e-9) / (4.*np.pi) ## units are erg sr^-1
alpha = coeff * 7.864e-14 * (1e4 / sim.g['temp'].in_units('K'))
alpha.units = units.erg * units.cm**(3) * units.s**(-1) * units.sr**(-1) ## It's intensity in erg cm^3 s^-1 sr^-1
return alpha * sim["em"] # Flux erg cm^-3 s^-1 sr^-1
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def c_n_sq(sim) :
"""Turbulent amplitude C_N^2 for use in SM calculations (e.g. Eqn 20 of Macquart & Koay 2013 ApJ 776 2) """
## Spectrum of turbulence below the SPH resolution, assume Kolmogorov
beta = 11./3.
L_min = 0.1*units.Mpc
c_n_sq = ((beta - 3.)/((2.)*(2.*np.pi)**(4.-beta)))*L_min**(3.-beta)*sim["em"]
c_n_sq.units = units.m**(-20,3)
return c_n_sq
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def hetot(self) :
return self["He"]
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def hydrogen(self) :
return self["H"]
## Need to use the ionisation fraction calculation here which gives ionisation fraction
## based on the gas temperature, density and redshift for a CLOUDY table
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def HI(sim) :
"""Fraction of Neutral Hydrogen HI use limited CLOUDY table"""
import pynbody.analysis.hifrac
return pynbody.analysis.hifrac.calculate(sim.g,ion='hi')
## Need to use the ionisation fraction calculation here which gives ionisation fraction
## based on the gas temperature, density and redshift for a CLOUDY table, then applying
## selfshielding for the dense, star forming gas on the equation of state
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def HIeos(sim) :
"""Fraction of Neutral Hydrogen HI use limited CLOUDY table, assuming dense EoS gas is selfshielded"""
import pynbody.analysis.hifrac
return pynbody.analysis.hifrac.calculate(sim.g,ion='hi', selfshield='eos')
## Need to use the ionisation fraction calculation here which gives ionisation fraction
## based on the gas temperature, density and redshift for a CLOUDY table, then applying
## selfshielding for the dense, star forming gas on the equation of state AND a further
## pressure based limit for
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def HID12(sim) :
"""Fraction of Neutral Hydrogen HI use limited CLOUDY table, using the Duffy +12a prescription for selfshielding"""
import pynbody.analysis.hifrac
return pynbody.analysis.hifrac.calculate(sim.g,ion='hi', selfshield='duffy12')
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def HeI(sim) :
"""Fraction of Helium HeI"""
import pynbody.analysis.ionfrac
return pynbody.analysis.ionfrac.calculate(sim.g,ion='hei')
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def HeII(sim) :
"""Fraction of Helium HeII"""
import pynbody.analysis.ionfrac
return pynbody.analysis.ionfrac.calculate(sim.g,ion='heii')
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def OI(sim) :
"""Fraction of Oxygen OI"""
import pynbody.analysis.ionfrac
return pynbody.analysis.ionfrac.calculate(sim.g,ion='oi')
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def OII(sim) :
"""Fraction of Oxygen OII"""
import pynbody.analysis.ionfrac
return pynbody.analysis.ionfrac.calculate(sim.g,ion='oii')
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def OVI(sim) :
"""Fraction of Oxygen OVI"""
import pynbody.analysis.ionfrac
return pynbody.analysis.ionfrac.calculate(sim.g,ion='ovi')
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def CIV(sim) :
"""Fraction of Carbon CIV"""
import pynbody.analysis.ionfrac
return pynbody.analysis.ionfrac.calculate(sim.g,ion='civ')
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def NV(sim) :
"""Fraction of Nitrogen NV"""
import pynbody.analysis.ionfrac
return pynbody.analysis.ionfrac.calculate(sim.g,ion='nv')
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def SIV(sim) :
"""Fraction of Silicon SiIV"""
import pynbody.analysis.ionfrac
return pynbody.analysis.ionfrac.calculate(sim.g,ion='siiv')
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def MGII(sim) :
"""Fraction of Magnesium MgII"""
import pynbody.analysis.ionfrac
return pynbody.analysis.ionfrac.calculate(sim.g,ion='mgii')
# The Solar Abundances used in Gadget-3 OWLS / Eagle / Smaug sims
XSOLH=0.70649785
XSOLHe=0.28055534
XSOLC=2.0665436E-3
XSOLN=8.3562563E-4
XSOLO=5.4926244E-3
XSOLNe=1.4144605E-3
XSOLMg=5.907064E-4
XSOLSi=6.825874E-4
XSOLS=4.0898522E-4
XSOLCa=6.4355E-5
XSOLFe=1.1032152E-3
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def feh(self) :
minfe = np.amin(self['Fe'][np.where(self['Fe'] > 0)])
self['Fe'][np.where(self['Fe'] == 0)]=minfe
return np.log10(self['Fe']/self['H']) - np.log10(XSOLFe/XSOLH)
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def sixh(self) :
minsi = np.amin(self['Si'][np.where(self['Si'] > 0)])
self['Si'][np.where(self['Si'] == 0)]=minsi
return np.log10(self['Si']/self['Si']) - np.log10(XSOLSi/XSOLH)
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def sxh(self) :
minsx = np.amin(self['S'][np.where(self['S'] > 0)])
self['S'][np.where(self['S'] == 0)]=minsx
return np.log10(self['S']/self['S']) - np.log10(XSOLS/XSOLH)
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def mgxh(self) :
minmg = np.amin(self['Mg'][np.where(self['Mg'] > 0)])
self['Mg'][np.where(self['Mg'] == 0)]=minmg
return np.log10(self['Mg']/self['Mg']) - np.log10(XSOLMg/XSOLH)
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def oxh(self) :
minox = np.amin(self['O'][np.where(self['O'] > 0)])
self['O'][np.where(self['O'] == 0)]=minox
return np.log10(self['O']/self['H']) - np.log10(XSOLO/XSOLH)
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def nexh(self) :
minne = np.amin(self['Ne'][np.where(self['Ne'] > 0)])
self['Ne'][np.where(self['Ne'] == 0)]=minne
return np.log10(self['Ne']/self['Ne']) - np.log10(XSOLNe/XSOLH)
[docs]
@SubFindHDFSnap.derived_array
def hexh(self) :
minhe = np.amin(self['He'][np.where(self['He'] > 0)])
self['He'][np.where(self['He'] == 0)]=minhe
return np.log10(self['He']/self['He']) - np.log10(XSOLHe/XSOLH)
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def cxh(self) :
mincx = np.amin(self['C'][np.where(self['C'] > 0)])
self['C'][np.where(self['C'] == 0)]=mincx
return np.log10(self['C']/self['H']) - np.log10(XSOLC/XSOLH)
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def caxh(self) :
mincax = np.amin(self['Ca'][np.where(self['Ca'] > 0)])
self['Ca'][np.where(self['Ca'] == 0)]=mincax
return np.log10(self['Ca']/self['H']) - np.log10(XSOLCa/XSOLH)
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def nxh(self) :
minnx = np.amin(self['N'][np.where(self['N'] > 0)])
self['N'][np.where(self['N'] == 0)]=minnx
return np.log10(self['N']/self['H']) - np.log10(XSOLH/XSOLH)
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def ofe(self) :
minox = np.amin(self['O'][np.where(self['O'] > 0)])
self['O'][np.where(self['O'] == 0)]=minox
minfe = np.amin(self['Fe'][np.where(self['Fe'] > 0)])
self['Fe'][np.where(self['Fe'] == 0)]=minfe
return np.log10(self['O']/self['Fe']) - np.log10(XSOLO/XSOLFe)
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def mgfe(sim) :
minmg = np.amin(sim['Mg'][np.where(sim['Mg'] > 0)])
sim['Mg'][np.where(sim['Mg'] == 0)]=minmg
minfe = np.amin(sim['Fe'][np.where(sim['Fe'] > 0)])
sim['Fe'][np.where(sim['Fe'] == 0)]=minfe
return np.log10(sim['Mg']/sim['Fe']) - np.log10(XSOLMg/XSOLFe)
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def nefe(sim) :
minne = np.amin(sim['Ne'][np.where(sim['Ne'] > 0)])
sim['Ne'][np.where(sim['Ne'] == 0)]=minne
minfe = np.amin(sim['Fe'][np.where(sim['Fe'] > 0)])
sim['Fe'][np.where(sim['Fe'] == 0)]=minfe
return np.log10(sim['Ne']/sim['Fe']) - np.log10(XSOLNe/XSOLFe)
[docs]
@GadgetHDFSnap.derived_array
@SubFindHDFSnap.derived_array
def sife(sim) :
minsi = np.amin(sim['Si'][np.where(sim['Si'] > 0)])
sim['Si'][np.where(sim['Si'] == 0)]=minsi
minfe = np.amin(sim['Fe'][np.where(sim['Fe'] > 0)])
sim['Fe'][np.where(sim['Fe'] == 0)]=minfe
return np.log10(sim['Si']/sim['Fe']) - np.log10(XSOLSi/XSOLFe)
