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readsubfHDF5.py
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readsubfHDF5.py
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# Python HDF5 subfind reader
# (requires util/hdf5lib.py)
#
# import readsubfHDF5
# cat = readsubfHDF5.subfind_catalog("./output/", 60)
# print cat.SubhaloPos
#
#
# Mark Vogelsberger ([email protected])
import numpy as np
import os
import sys
import hdf5lib
####################
#SUBHALO DATABLOCKS#
####################
#descriptions of subhalo datablocks -> add new datablocks here!
#format -> "HDF5_NAME":["DATATYPE", DIMENSION]
sub_datablocks = {"SubhaloLen":["INT",1],
"SubhaloMass":["FLOAT",1],
"SubhaloMassinRad":["FLOAT",1],
"SubhaloPos":["FLOAT",3],
"SubhaloVel":["FLOAT",3],
"SubhaloLenType":["INT",6],
"SubhaloMassType":["FLOAT",6],
"SubhaloCM":["FLOAT",3],
"SubhaloSpin":["FLOAT",3],
"SubhaloVelDisp":["FLOAT",1],
"SubhaloVmax":["FLOAT",1],
"SubhaloVmaxRad":["FLOAT",1],
"SubhaloHalfmassRad":["FLOAT",1],
"SubhaloHalfmassRadType":["FLOAT",6],
"SubhaloMassInRadType":["FLOAT", 6],
"SubhaloMassInRad":["FLOAT",1],
"SubhaloMassInHalfRadType":["FLOAT", 6],
"SubhaloMassInHalfRad":["FLOAT", 1],
"SubhaloIDMostbound":["ID",1],
"SubhaloGrNr":["INT",1],
"SubhaloParent":["INT",1],
"SubhaloSFR":["FLOAT",1],
"SubhaloSFRinRad":["FLOAT",1],
"SubhaloGasMetallicity":["FLOAT",1],
"SubhaloGasMetallicitySfr":["FLOAT",1],
"SubhaloStarMetallicity":["FLOAT",1],
"SubhaloGasMetalFractions":["FLOAT",9],
"SubhaloGasMetalFractionsSfr":["FLOAT",9],
"SubhaloGasMetalFractionsSfrWeighted":["FLOAT",9],
"SubhaloStarMetalFractions":["FLOAT",9],
"SubhaloStarMetallicityHalfRad":["FLOAT",1],
"SubhaloBHMass":["FLOAT",1],
"SubhaloBHMdot":["FLOAT",1],
"SubhaloStellarPhotometricsMassInRad":["FLOAT",1],
"SubhaloStellarPhotometrics":["FLOAT",8]} #band luminosities: U, B, V, K, g, r, i, z
##################
#GROUP DATABLOCKS#
##################
#descriptions of subhalo datablocks -> add new datablocks here!
#format -> "HDF5_NAME":["DATATYPE", DIMENSION]
grp_datablocks = {"GroupLen":["INT",1],
"GroupMass":["FLOAT",1],
"GroupPos":["FLOAT",3],
"GroupVel":["FLOAT",3],
"GroupLenType":["INT",6],
"GroupMassType":["FLOAT",6],
"Group_M_Mean200":["FLOAT",1],
"Group_R_Mean200":["FLOAT",1],
"Group_M_Crit200":["FLOAT",1],
"Group_R_Crit200":["FLOAT",1],
"Group_M_TopHat200":["FLOAT",1],
"Group_R_TopHat200":["FLOAT",1],
"Group_M_Crit500":["FLOAT",1],
"Group_R_Crit500":["FLOAT",1],
"GroupNsubs":["INT",1],
"GroupFirstSub":["INT",1],
"GroupSFR":["FLOAT",1],
"GroupGasMetallicity":["FLOAT",1],
"GroupStarMetallicity":["FLOAT",1],
"GroupGasMetalFractions":["FLOAT",9],
"GroupStarMetalFractions":["FLOAT",9],
"GroupBHMass":["FLOAT",1],
"GroupBHMdot":["FLOAT",1],
"GroupFuzzOffsetType":["INT64",6]}
class subfind_catalog:
def __init__(self, basedir, snapnum, long_ids = False, double_output = False, grpcat = True, subcat = True, name = "fof_subhalo_tab", keysel = None):
self.filebase = basedir + "/groups_" + str(snapnum).zfill(3) + "/" + name + "_" + str(snapnum).zfill(3) + "."
if long_ids: self.id_type = np.uint64
else: self.id_type = np.uint32
if double_output: self.double_type = np.float32
else: self.double_type = np.float64
filenum = 0
doneflag = False
skip_gr = 0
skip_sub = 0
vardict = {}
while not doneflag:
curfile = self.filebase + str(filenum) + ".hdf5"
if (not os.path.exists(curfile)):
self.filebase = basedir + "/" + name + "_" + str(snapnum).zfill(3)
curfile = self.filebase + ".hdf5"
if (not os.path.exists(curfile)):
print("file not found:", curfile)
sys.exit()
f=hdf5lib.OpenFile(curfile)
ngroups = hdf5lib.GetAttr(f, "Header", "Ngroups_ThisFile")
nsubs = hdf5lib.GetAttr(f, "Header", "Nsubgroups_ThisFile")
nfiles = hdf5lib.GetAttr(f, "Header", "NumFiles")
if filenum == 0:
self.ngroups = hdf5lib.GetAttr(f, "Header", "Ngroups_Total")
self.nids = hdf5lib.GetAttr(f, "Header", "Nids_Total")
self.nsubs = hdf5lib.GetAttr(f, "Header", "Nsubgroups_Total")
#GROUPS
if (grpcat==True):
if (keysel == None):
for key, val in list(grp_datablocks.items()):
if hdf5lib.Contains(f, "Group", key):
type = val[0]
dim = val[1]
if (type=='FLOAT'):
vars(self)[key]=np.empty(self.ngroups, dtype=np.dtype((self.double_type,dim)))
if (type=='INT'):
vars(self)[key]=np.empty(self.ngroups, dtype=np.dtype((np.int32,dim)))
if (type=='INT64'):
vars(self)[key]=np.empty(self.ngroups, dtype=np.dtype((np.int64,dim)))
if (type=='ID'):
vars(self)[key]=np.empty(self.ngroups, dtype=np.dtype((self.id_type,dim)))
vardict[key]=vars(self)[key]
else:
for key in keysel:
if hdf5lib.Contains(f, "Group", key):
val = grp_datablocks[key]
type = val[0]
dim = val[1]
if (type=='FLOAT'):
vars(self)[key]=np.empty(self.ngroups, dtype=np.dtype((self.double_type,dim)))
if (type=='INT'):
vars(self)[key]=np.empty(self.ngroups, dtype=np.dtype((np.int32,dim)))
if (type=='INT64'):
vars(self)[key]=np.empty(self.ngroups, dtype=np.dtype((np.int64,dim)))
if (type=='ID'):
vars(self)[key]=np.empty(self.ngroups, dtype=np.dtype((self.id_type,dim)))
vardict[key]=vars(self)[key]
#SUBHALOS
if (subcat==True):
if (keysel == None):
for key, val in list(sub_datablocks.items()):
if hdf5lib.Contains(f, "Subhalo", key):
type = val[0]
dim = val[1]
if (type=='FLOAT'):
vars(self)[key]=np.empty(self.nsubs, dtype=np.dtype((self.double_type,dim)))
if (type=='INT'):
vars(self)[key]=np.empty(self.nsubs, dtype=np.dtype((np.int32,dim)))
if (type=='INT64'):
vars(self)[key]=np.empty(self.nsubs, dtype=np.dtype((np.int32,dim)))
if (type=='ID'):
vars(self)[key]=np.empty(self.nsubs, dtype=np.dtype((self.id_type,dim)))
vardict[key]=vars(self)[key]
else:
for key in keysel:
if hdf5lib.Contains(f, "Subhalo", key):
val = sub_datablocks[key]
type = val[0]
dim = val[1]
if (type=='FLOAT'):
vars(self)[key]=np.empty(self.nsubs, dtype=np.dtype((self.double_type,dim)))
if (type=='INT'):
vars(self)[key]=np.empty(self.nsubs, dtype=np.dtype((np.int32,dim)))
if (type=='INT64'):
vars(self)[key]=np.empty(self.nsubs, dtype=np.dtype((np.int64,dim)))
if (type=='ID'):
vars(self)[key]=np.empty(self.nsubs, dtype=np.dtype((self.id_type,dim)))
vardict[key]=vars(self)[key]
#GROUPS
if (grpcat==True):
if ngroups > 0:
if (keysel == None):
for key, val in list(grp_datablocks.items()):
if hdf5lib.Contains(f, "Group", key):
type = val[0]
dim = val[1]
a=hdf5lib.GetData(f, "Group/"+key)
if dim==1:
vardict[key][skip_gr:skip_gr + ngroups]=a[:]
else:
for d in range(0,dim):
vardict[key][skip_gr:skip_gr + ngroups,d]=a[:,d]
else:
for key in keysel:
if hdf5lib.Contains(f, "Group", key):
val = grp_datablocks[key]
type = val[0]
dim = val[1]
a=hdf5lib.GetData(f, "Group/"+key)
if dim==1:
vardict[key][skip_gr:skip_gr + ngroups]=a[:]
else:
for d in range(0,dim):
vardict[key][skip_gr:skip_gr + ngroups,d]=a[:,d]
skip_gr += ngroups
#SUBHALOS
if (subcat==True):
if nsubs > 0:
if (keysel == None):
for key, val in list(sub_datablocks.items()):
if hdf5lib.Contains(f, "Subhalo", key):
type = val[0]
dim = val[1]
a=hdf5lib.GetData(f, "Subhalo/"+key)
if dim==1:
vardict[key][skip_sub:skip_sub + nsubs]=a[:]
else:
for d in range(0,dim):
vardict[key][skip_sub:skip_sub + nsubs,d]=a[:,d]
else:
for key in keysel:
if hdf5lib.Contains(f, "Subhalo", key):
val = sub_datablocks[key]
type = val[0]
dim = val[1]
a=hdf5lib.GetData(f, "Subhalo/"+key)
if dim==1:
vardict[key][skip_sub:skip_sub + nsubs]=a[:]
else:
for d in range(0,dim):
vardict[key][skip_sub:skip_sub + nsubs,d]=a[:,d]
skip_sub += nsubs
f.close()
filenum += 1
if filenum == nfiles: doneflag = True