def parse_halo_catalog_internal(self):
"""
This parser works on the files output directly out of yt's internal
halo_finder. The parse_halo_catalog_external works with an
external version of FOF.
Examples
--------
>>> ds = load("DD0000/DD0000")
>>> halo_list = FOFHaloFinder(ds)
>>> halo_list.write_out("FOF/groups_00000.txt")
>>> halos_COM = parse_halo_catalog_internal()
"""
hp = []
for line in open("%s/groups_%05i.txt" % \
(self.FOF_directory, self.output_id)):
if line.startswith("# RED"):
self.redshift = float(line.split("=")[1])
continue
if line.strip() == "": continue # empty
if line[0] == "#": continue # comment
x, y, z = [float(f) for f in line.split()[7:10]] # COM x,y,z
hp.append([x, y, z])
if hp != []:
self.halo_positions = np.array(hp)
self.halo_kdtree = KDTree(self.halo_positions)
else:
self.halo_positions = None
self.halo_kdtree = None
return hp
def parse_halo_catalog_internal(self):
"""
This parser works on the files output directly out of yt's internal
halo_finder. The parse_halo_catalog_external works with an
external version of FOF.
Examples
--------
>>> ds = load("DD0000/DD0000")
>>> halo_list = FOFHaloFinder(ds)
>>> halo_list.write_out("FOF/groups_00000.txt")
>>> halos_COM = parse_halo_catalog_internal()
"""
hp = []
for line in open("%s/groups_%05i.txt" % \
(self.FOF_directory, self.output_id)):
if line.startswith("# RED"):
self.redshift = float(line.split("=")[1])
continue
if line.strip() == "": continue # empty
if line[0] == "#": continue # comment
x,y,z = [float(f) for f in line.split()[7:10]] # COM x,y,z
hp.append([x,y,z])
if hp != []:
self.halo_positions = np.array(hp)
self.halo_kdtree = KDTree(self.halo_positions)
else:
self.halo_positions = None
self.halo_kdtree = None
return hp
def parse_halo_catalog_external(self):
hp = []
for line in open("%s/groups_%05i.dat" % \
(self.FOF_directory, self.output_id)):
if line.strip() == "": continue # empty
if line.startswith("# Red"):
self.redshift = float(line.split("=")[1])
if line[0] == "#": continue # comment
if line[0] == "d": continue # datavar
x, y, z = [float(f) for f in line.split(None, 3)[:-1]]
hp.append([x, y, z])
if hp != []:
self.halo_positions = np.array(hp)
self.halo_kdtree = KDTree(self.halo_positions)
else:
self.halo_positions = None
self.halo_kdtree = None
return hp
def parse_halo_catalog_external(self):
hp = []
for line in open("%s/groups_%05i.dat" % \
(self.FOF_directory, self.output_id)):
if line.strip() == "": continue # empty
if line.startswith("# Red"):
self.redshift = float(line.split("=")[1])
if line[0] == "#": continue # comment
if line[0] == "d": continue # datavar
x,y,z = [float(f) for f in line.split(None, 3)[:-1]]
hp.append([x,y,z])
if hp != []:
self.halo_positions = np.array(hp)
self.halo_kdtree = KDTree(self.halo_positions)
else:
self.halo_positions = None
self.halo_kdtree = None
return hp
class HaloCatalog(object):
r"""A catalog of halos, parsed from EnzoFOF outputs.
This class will read in catalogs output by the Enzo FOF halo finder and
make available their positions, radii, etc. Enzo FOF was provided
starting with 2.0, and can be run either inline (with the correct
options) or as a postprocessing step using the `-F` command line
option. This class is mostly useful when calculating a merger tree,
and when the particle IDs for members of a given halo are output as
well.
Parameters
----------
output_id : int
This is the integer output id of the halo catalog to parse and
load.
cache : bool
Should we store, in between accesses, the particle IDs? If set to
true, the correct particle files must exist.
external_FOF : bool, optional
Are we building a tree from outputs generated by an
external FOF program, or an FOF internal to yt?
FOF_directory : str, optional
Directory where FOF files are located
"""
cache = None
def __init__(self,
output_id,
cache=True,
external_FOF=True,
FOF_directory="FOF"):
self.output_id = output_id
self.external_FOF = external_FOF
self.redshift = 0.0
self.FOF_directory = FOF_directory
self.particle_file = h5py.File("%s/particles_%05i.h5" % \
(FOF_directory, output_id), "r")
if self.external_FOF:
self.parse_halo_catalog_external()
else:
self.parse_halo_catalog_internal()
if cache: self.cache = dict() #MaxLengthDict()
def __del__(self):
self.particle_file.close()
def parse_halo_catalog_external(self):
hp = []
for line in open("%s/groups_%05i.dat" % \
(self.FOF_directory, self.output_id)):
if line.strip() == "": continue # empty
if line.startswith("# Red"):
self.redshift = float(line.split("=")[1])
if line[0] == "#": continue # comment
if line[0] == "d": continue # datavar
x, y, z = [float(f) for f in line.split(None, 3)[:-1]]
hp.append([x, y, z])
if hp != []:
self.halo_positions = np.array(hp)
self.halo_kdtree = KDTree(self.halo_positions)
else:
self.halo_positions = None
self.halo_kdtree = None
return hp
def parse_halo_catalog_internal(self):
"""
This parser works on the files output directly out of yt's internal
halo_finder. The parse_halo_catalog_external works with an
external version of FOF.
Examples
--------
>>> ds = load("DD0000/DD0000")
>>> halo_list = FOFHaloFinder(ds)
>>> halo_list.write_out("FOF/groups_00000.txt")
>>> halos_COM = parse_halo_catalog_internal()
"""
hp = []
for line in open("%s/groups_%05i.txt" % \
(self.FOF_directory, self.output_id)):
if line.startswith("# RED"):
self.redshift = float(line.split("=")[1])
continue
if line.strip() == "": continue # empty
if line[0] == "#": continue # comment
x, y, z = [float(f) for f in line.split()[7:10]] # COM x,y,z
hp.append([x, y, z])
if hp != []:
self.halo_positions = np.array(hp)
self.halo_kdtree = KDTree(self.halo_positions)
else:
self.halo_positions = None
self.halo_kdtree = None
return hp
def read_particle_ids(self, halo_id):
if self.cache is not None:
if halo_id not in self.cache:
if self.external_FOF:
self.cache[halo_id] = \
self.particle_file["/Halo%08i/Particle ID" % halo_id][:]
else:
self.cache[halo_id] = \
self.particle_file["/Halo%08i/particle_index" % halo_id][:]
ids = self.cache[halo_id]
else:
if self.external_FOF:
ids = self.particle_file["/Halo%08i/Particle ID" % halo_id][:]
else:
ids = self.particle_file["/Halo%08i/particle_index" %
halo_id][:]
return HaloParticleList(halo_id, self.halo_positions[halo_id, :], ids)
def calculate_parentage_fractions(self, other_catalog, radius=0.10):
parentage_fractions = {}
if self.halo_positions is None or other_catalog.halo_positions is None:
return parentage_fractions
mylog.debug("Ball-tree query with radius %0.3e", radius)
all_nearest = self.halo_kdtree.query_ball_tree(
other_catalog.halo_kdtree, radius)
pbar = get_pbar("Halo Mergers", self.halo_positions.shape[0])
for hid1, nearest in enumerate(all_nearest):
pbar.update(hid1)
parentage_fractions[hid1] = {}
HPL1 = self.read_particle_ids(hid1)
for hid2 in sorted(nearest):
HPL2 = other_catalog.read_particle_ids(hid2)
p1, p2 = HPL1.find_relative_parentage(HPL2)
parentage_fractions[hid1][hid2] = (p1, p2,
HPL2.number_of_particles)
parentage_fractions[hid1][
"NumberOfParticles"] = HPL1.number_of_particles
pbar.finish()
return parentage_fractions
class HaloCatalog(object):
r"""A catalog of halos, parsed from EnzoFOF outputs.
This class will read in catalogs output by the Enzo FOF halo finder and
make available their positions, radii, etc. Enzo FOF was provided
starting with 2.0, and can be run either inline (with the correct
options) or as a postprocessing step using the `-F` command line
option. This class is mostly useful when calculating a merger tree,
and when the particle IDs for members of a given halo are output as
well.
Parameters
----------
output_id : int
This is the integer output id of the halo catalog to parse and
load.
cache : bool
Should we store, in between accesses, the particle IDs? If set to
true, the correct particle files must exist.
external_FOF : bool, optional
Are we building a tree from outputs generated by an
external FOF program, or an FOF internal to yt?
FOF_directory : str, optional
Directory where FOF files are located
"""
cache = None
def __init__(self, output_id, cache = True, external_FOF=True, FOF_directory="FOF"):
self.output_id = output_id
self.external_FOF = external_FOF
self.redshift = 0.0
self.FOF_directory = FOF_directory
self.particle_file = h5py.File("%s/particles_%05i.h5" % \
(FOF_directory, output_id), "r")
if self.external_FOF:
self.parse_halo_catalog_external()
else:
self.parse_halo_catalog_internal()
if cache: self.cache = dict()#MaxLengthDict()
def __del__(self):
self.particle_file.close()
def parse_halo_catalog_external(self):
hp = []
for line in open("%s/groups_%05i.dat" % \
(self.FOF_directory, self.output_id)):
if line.strip() == "": continue # empty
if line.startswith("# Red"):
self.redshift = float(line.split("=")[1])
if line[0] == "#": continue # comment
if line[0] == "d": continue # datavar
x,y,z = [float(f) for f in line.split(None, 3)[:-1]]
hp.append([x,y,z])
if hp != []:
self.halo_positions = np.array(hp)
self.halo_kdtree = KDTree(self.halo_positions)
else:
self.halo_positions = None
self.halo_kdtree = None
return hp
def parse_halo_catalog_internal(self):
"""
This parser works on the files output directly out of yt's internal
halo_finder. The parse_halo_catalog_external works with an
external version of FOF.
Examples
--------
>>> ds = load("DD0000/DD0000")
>>> halo_list = FOFHaloFinder(ds)
>>> halo_list.write_out("FOF/groups_00000.txt")
>>> halos_COM = parse_halo_catalog_internal()
"""
hp = []
for line in open("%s/groups_%05i.txt" % \
(self.FOF_directory, self.output_id)):
if line.startswith("# RED"):
self.redshift = float(line.split("=")[1])
continue
if line.strip() == "": continue # empty
if line[0] == "#": continue # comment
x,y,z = [float(f) for f in line.split()[7:10]] # COM x,y,z
hp.append([x,y,z])
if hp != []:
self.halo_positions = np.array(hp)
self.halo_kdtree = KDTree(self.halo_positions)
else:
self.halo_positions = None
self.halo_kdtree = None
return hp
def read_particle_ids(self, halo_id):
if self.cache is not None:
if halo_id not in self.cache:
if self.external_FOF:
self.cache[halo_id] = \
self.particle_file["/Halo%08i/Particle ID" % halo_id][:]
else:
self.cache[halo_id] = \
self.particle_file["/Halo%08i/particle_index" % halo_id][:]
ids = self.cache[halo_id]
else:
if self.external_FOF:
ids = self.particle_file["/Halo%08i/Particle ID" % halo_id][:]
else:
ids = self.particle_file["/Halo%08i/particle_index" % halo_id][:]
return HaloParticleList(halo_id, self.halo_positions[halo_id,:], ids)
def calculate_parentage_fractions(self, other_catalog, radius = 0.10):
parentage_fractions = {}
if self.halo_positions == None or other_catalog.halo_positions == None:
return parentage_fractions
mylog.debug("Ball-tree query with radius %0.3e", radius)
all_nearest = self.halo_kdtree.query_ball_tree(
other_catalog.halo_kdtree, radius)
pbar = get_pbar("Halo Mergers", self.halo_positions.shape[0])
for hid1, nearest in enumerate(all_nearest):
pbar.update(hid1)
parentage_fractions[hid1] = {}
HPL1 = self.read_particle_ids(hid1)
for hid2 in sorted(nearest):
HPL2 = other_catalog.read_particle_ids(hid2)
p1, p2 = HPL1.find_relative_parentage(HPL2)
parentage_fractions[hid1][hid2] = (p1, p2, HPL2.number_of_particles)
parentage_fractions[hid1]["NumberOfParticles"] = HPL1.number_of_particles
pbar.finish()
return parentage_fractions
