def load(filename, ds=None, obj=None, LoadHalo=1):
"""Function to load a CAESAR object from disk.
Parameters
----------
filename : str
Input file.
ds : yt dataset, optional
yt dataset to link to.
obj : :class:`main.CAESAR`, optional
For loading into an already created CAESAR object.
LoadHalo: int
Option to load halo information: 0=No; 1=Yes; 2=Yes, but not mass/radius info
Examples
--------
>>> import caesar
>>> import yt
>>> ds = yt.load('snapshot')
>>> obj = caesar.load(ds)
"""
from yt.funcs import mylog
mylog.info('Reading %s' % filename)
try:
infile = h5py.File(filename, 'r')
except IOError:
raise
if obj is None:
import os
from caesar.main import CAESAR
obj = CAESAR()
obj.data_file = os.path.abspath(filename)
unit_registry_json = infile.attrs['unit_registry_json']
obj.unit_registry = UnitRegistry.from_json(
unit_registry_json.decode('utf8'))
restore_global_attributes(obj, infile)
obj.simulation._unpack(obj, infile)
# restore halo data
if 'halo_data' in infile and LoadHalo:
mylog.info('Restoring halo attributes')
hd = infile['halo_data']
obj.halos = []
for i in range(0, obj.nhalos):
obj.halos.append(Halo(obj))
restore_object_attributes(obj.halos, hd, obj.unit_registry)
restore_object_dicts(obj.halos, hd, obj.unit_registry)
restore_object_list(obj.halos, 'galaxy_index_list', hd)
if LoadHalo == 1:
#Compute the virial/200/500/2500 masses
if hasattr(obj.simulation, 'Densities'):
PiFac = 4. / 3. * np.pi
h = obj.halos[0]
for h in obj.halos:
h.masses['virial'] = obj.simulation.Densities[
0] * PiFac * (h.radii['virial'] * h.radii['virial'] *
h.radii['virial'])
h.masses['m200c'] = (obj.simulation.Densities[1] * PiFac *
(h.radii['r200c'] * h.radii['r200c'] *
h.radii['r200c'])).to('Msun')
h.masses['m500c'] = (obj.simulation.Densities[2] * PiFac *
(h.radii['r500c'] * h.radii['r500c'] *
h.radii['r500c'])).to('Msun')
h.masses['m2500c'] = (
obj.simulation.Densities[3] * PiFac *
(h.radii['r2500c'] * h.radii['r2500c'] *
h.radii['r2500c'])).to('Msun')
# optional
for vals in ['dmlist', 'glist', 'slist', 'bhlist', 'dlist']:
restore_object_list(obj.halos, vals, hd)
# restore galaxy data
if 'galaxy_data' in infile:
mylog.info('Restoring galaxy attributes')
hd = infile['galaxy_data']
obj.galaxies = []
for i in range(0, obj.ngalaxies):
obj.galaxies.append(Galaxy(obj))
restore_object_attributes(obj.galaxies, hd, obj.unit_registry)
restore_object_dicts(obj.galaxies, hd, obj.unit_registry)
restore_object_list(obj.galaxies, 'cloud_index_list', hd)
# optional
for vals in ['glist', 'slist', 'bhlist', 'dlist']:
restore_object_list(obj.galaxies, vals, hd)
if 'cloud_data' in infile:
mylog.info('Restoring cloud attributes')
hd = infile['cloud_data']
obj.clouds = []
for i in range(0, obj.nclouds):
obj.clouds.append(Cloud(obj))
restore_object_attributes(obj.clouds, hd, obj.unit_registry)
restore_object_dicts(obj.clouds, hd, obj.unit_registry)
# optional
for vals in ['glist', 'slist', 'bhlist', 'dlist']:
restore_object_list(obj.clouds, vals, hd)
infile.close()
if LoadHalo:
obj._link_objects()
if ds is not None:
obj.yt_dataset = ds
return obj
def __init__(self, filename, skip_hash_check=False):
self._ds = None
self.data_file = os.path.abspath(filename)
self.skip_hash_check = skip_hash_check
self._halo_dmlist = LazyDataset(self, 'halo_data/lists/dmlist')
self._halo_slist = LazyDataset(self, 'halo_data/lists/slist')
self._halo_glist = LazyDataset(self, 'halo_data/lists/glist')
self._halo_bhlist = LazyDataset(self, 'halo_data/lists/bhlist')
self._halo_dlist = LazyDataset(self, 'halo_data/lists/dlist')
self._galaxy_slist = LazyDataset(self, 'galaxy_data/lists/slist')
self._galaxy_glist = LazyDataset(self, 'galaxy_data/lists/glist')
self._galaxy_bhlist = LazyDataset(self, 'galaxy_data/lists/bhlist')
self._galaxy_dlist = LazyDataset(self, 'galaxy_data/lists/dlist')
self._cloud_glist = LazyDataset(self, 'cloud_data/lists/glist')
self._cloud_dlist = LazyDataset(self, 'cloud_data/lists/dlist')
with h5py.File(filename, 'r') as hd:
mylog.info('Opening {}'.format(filename))
if 'hash' in hd.attrs:
self.hash = hd.attrs['hash']
else:
self.hash = None
if isinstance(self.hash, np.bytes_):
self.hash = self.hash.decode('utf8')
# This should probably be caesar_version or something
self.caesar = hd.attrs['caesar']
self.unit_registry = UnitRegistry.from_json(
hd.attrs['unit_registry_json'])
# Load the information about the simulation itself
self.simulation = SimulationAttributes()
self.simulation._unpack(self, hd)
# Halo data is loaded unconditionally, AFAICT it's always present
self._galaxy_index_list = None
if 'halo_data/lists/galaxy_index_list' in hd:
self._galaxy_index_list = LazyDataset(
self, 'halo_data/lists/galaxy_index_list')
self._halo_data = {}
for k, v in hd['halo_data'].items():
if type(v) is h5py.Dataset:
self._halo_data[k] = LazyDataset(self, 'halo_data/' + k)
self._halo_dicts = defaultdict(dict)
for k in hd['halo_data/dicts']:
dictname, arrname = k.split('.')
self._halo_dicts[dictname][arrname] = LazyDataset(
self, 'halo_data/dicts/' + k)
if 'tree_data/progen_halo_dm' in hd:
self._halo_data[
'progen_halo_dm'] = self._progen_halo_dm = LazyDataset(
self, 'tree_data/progen_halo_dm')
if 'tree_data/descend_halo_dm' in hd:
self._halo_data[
'descend_halo_dm'] = self._descend_halo_dm = LazyDataset(
self, 'tree_data/descend_halo_dm')
self.nhalos = hd.attrs['nhalos']
self.halos = LazyList(self.nhalos, lambda i: Halo(self, i))
mylog.info('Found {} halos'.format(len(self.halos)))
# Provide default values for everything, so that if a simulation
# without galaxies is loaded we get zero galaxies, not AttributeErrors
self._galaxy_data = {}
self._galaxy_dicts = defaultdict(dict)
self.ngalaxies = 0
self.galaxies = LazyList(self.ngalaxies, lambda i: Galaxy(self, i))
if 'galaxy_data' in hd:
self._cloud_index_list = None
if 'galaxy_data/lists/cloud_index_list' in hd:
self._cloud_index_list = LazyDataset(
self, 'galaxy_data/lists/cloud_index_list')
if 'tree_data/progen_galaxy_star' in hd:
self._galaxy_data[
'progen_galaxy_star'] = self._progen_galaxy_star = LazyDataset(
self, 'tree_data/progen_galaxy_star')
if 'tree_data/descend_galaxy_star' in hd:
self._galaxy_data[
'descend_galaxy_star'] = self._descend_galaxy_star = LazyDataset(
self, 'tree_data/descend_galaxy_star')
for k, v in hd['galaxy_data'].items():
if type(v) is h5py.Dataset:
self._galaxy_data[k] = LazyDataset(
self, 'galaxy_data/' + k)
for k in hd['galaxy_data/dicts']:
dictname, arrname = k.split('.')
self._galaxy_dicts[dictname][arrname] = LazyDataset(
self, 'galaxy_data/dicts/' + k)
self.ngalaxies = hd.attrs['ngalaxies']
self.galaxies = LazyList(self.ngalaxies,
lambda i: Galaxy(self, i))
mylog.info('Found {} galaxies'.format(len(self.galaxies)))
self._cloud_data = {}
self._cloud_dicts = defaultdict(dict)
self.nclouds = 0
self.clouds = LazyList(self.nclouds, lambda i: Cloud(self, i))
if 'cloud_data' in hd:
for k, v in hd['cloud_data'].items():
if type(v) is h5py.Dataset:
self._cloud_data[k] = LazyDataset(
self, 'cloud_data/' + k)
for k in hd['cloud_data/dicts']:
dictname, arrname = k.split('.')
self._cloud_dicts[dictname][arrname] = LazyDataset(
self, 'cloud_data/dicts/' + k)
if 'tree_data/progen_cloud_gas' in hd:
self._cloud_data[
'progen_cloud_gas'] = self._progen_cloud_gas = LazyDataset(
self, 'tree_data/progen_cloud_gas')
if 'tree_data/descend_cloud_gas' in hd:
self._cloud_data[
'descend_cloud_gas'] = self._descend_cloud_gas = LazyDataset(
self, 'tree_data/descend_cloud_gas')
self.nclouds = hd.attrs['nclouds']
self.clouds = LazyList(self.nclouds, lambda i: Cloud(self, i))
mylog.info('Found {} clouds'.format(len(self.clouds)))
def __init__(self, filename):
self._ds = None
self.data_file = os.path.abspath(filename)
self._halo_dmlist = LazyArray(self, 'halo_data/lists/dmlist')
self._halo_slist = LazyArray(self, 'halo_data/lists/slist')
self._halo_glist = LazyArray(self, 'halo_data/lists/glist')
self._halo_bhlist = LazyArray(self, 'halo_data/lists/bhlist')
self._halo_dlist = LazyArray(self, 'halo_data/lists/dlist')
self._galaxy_slist = LazyArray(self, 'galaxy_data/lists/slist')
self._galaxy_glist = LazyArray(self, 'galaxy_data/lists/glist')
self._galaxy_bhlist = LazyArray(self, 'galaxy_data/lists/bhlist')
self._galaxy_dlist = LazyArray(self, 'galaxy_data/lists/dlist')
self._cloud_glist = LazyArray(self, 'cloud_data/lists/glist')
self._cloud_dlist = LazyArray(self, 'cloud_data/lists/dlist')
with h5py.File(filename, 'r') as hd:
mylog.info('Reading {}'.format(filename))
self.hash = hd.attrs['hash']
self.caesar = hd.attrs['caesar']
self.unit_registry = UnitRegistry.from_json(
hd.attrs['unit_registry_json'].decode('utf8'))
# Load the information about the simulation itself
self.simulation = SimulationAttributes()
self.simulation._unpack(self, hd)
mylog.info('Loading halos')
self._galaxy_index_list = None
if 'halo_data/lists/galaxy_index_list' in hd:
self._galaxy_index_list = LazyArray(
self, 'halo_data/lists/galaxy_index_list')
self._halo_data = {}
for k, v in hd['halo_data'].items():
if type(v) is h5py.Dataset:
self._halo_data[k] = LazyArray(self, 'halo_data/' + k)
self._halo_dicts = defaultdict(dict)
for k in hd['halo_data/dicts']:
dictname, arrname = k.split('.')
self._halo_dicts[dictname][arrname] = LazyArray(
self, 'halo_data/dicts/' + k)
self.nhalos = hd.attrs['nhalos']
self.halos = LazyList(self.nhalos, lambda i: Halo(self, i))
mylog.info('Loaded {} halos'.format(len(self.halos)))
self._galaxy_data = {}
self._galaxy_dicts = defaultdict(dict)
self.ngalaxies = 0
self.galaxies = LazyList(self.ngalaxies, lambda i: Galaxy(self, i))
if 'galaxy_data' in hd:
mylog.info('Loading galaxies')
self._cloud_index_list = None
if 'galaxy_data/lists/cloud_index_list' in hd:
self._cloud_index_list = LazyArray(
self, 'galaxy_data/lists/cloud_index_list')
for k, v in hd['galaxy_data'].items():
if type(v) is h5py.Dataset:
self._galaxy_data[k] = LazyArray(
self, 'galaxy_data/' + k)
for k in hd['galaxy_data/dicts']:
dictname, arrname = k.split('.')
self._galaxy_dicts[dictname][arrname] = LazyArray(
self, 'galaxy_data/dicts/' + k)
self.ngalaxies = hd.attrs['ngalaxies']
self.galaxies = LazyList(self.ngalaxies,
lambda i: Galaxy(self, i))
mylog.info('Loaded {} galaxies'.format(len(self.galaxies)))
self._cloud_data = {}
self._cloud_dicts = defaultdict(dict)
self.nclouds = 0
self.clouds = LazyList(self.nclouds, lambda i: Cloud(self, i))
if 'cloud_data' in hd:
mylog.info('Loading clouds')
for k, v in hd['cloud_data'].items():
if type(v) is h5py.Dataset:
self._cloud_data[k] = LazyArray(
self, 'cloud_data/' + k)
for k in hd['cloud_data/dicts']:
dictname, arrname = k.split('.')
self._cloud_dicts[dictname][arrname] = LazyArray(
self, 'cloud_data/dicts/' + k)
self.nclouds = hd.attrs['nclouds']
self.clouds = LazyList(self.nclouds, lambda i: Cloud(self, i))
mylog.info('Loaded {} clouds'.format(len(self.clouds)))