mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 15:21:11 +00:00
Merged in python3 (pull request #5)
Port to python3, large code cleanup * Fixed command line for cosmotool * Fix path * Dump command line is log file * Fix important typo * Modify paths for example * Fix path again * Use an explicit constructor * Change file to open (python 2->3) * python3 fix for xrange in periodic_kdtree.py * Fixed index for Np, numPart, numZones, numZonesTot, partID, zoneID in catalogUtil.py
This commit is contained in:
parent
8249256508
commit
affb56ff48
392 changed files with 4092 additions and 260938 deletions
|
|
@ -1,290 +1,309 @@
|
|||
|
||||
# code for reading Subfind's subhalo_tab files
|
||||
# usage e.g.:
|
||||
#
|
||||
# import readsubf
|
||||
# cat = readsubf.subfind_catalog("./m_10002_h_94_501_z3_csf/",63,masstab=True)
|
||||
# print cat.nsubs
|
||||
# print "largest halo x position = ",cat.sub_pos[0][0]
|
||||
|
||||
import numpy as np
|
||||
import os
|
||||
import sys
|
||||
|
||||
class subfind_catalog:
|
||||
def __init__(self, basedir, snapnum, group_veldisp = False, masstab = False, long_ids = False, swap = False):
|
||||
self.filebase = basedir + "/groups_" + str(snapnum).zfill(3) + "/subhalo_tab_" + str(snapnum).zfill(3) + "."
|
||||
|
||||
#print
|
||||
#print "reading subfind catalog for snapshot",snapnum,"of",basedir
|
||||
|
||||
if long_ids: self.id_type = np.uint64
|
||||
else: self.id_type = np.uint32
|
||||
|
||||
self.group_veldisp = group_veldisp
|
||||
self.masstab = masstab
|
||||
|
||||
filenum = 0
|
||||
doneflag = False
|
||||
skip_gr = 0
|
||||
skip_sub = 0
|
||||
while not doneflag:
|
||||
curfile = self.filebase + str(filenum)
|
||||
|
||||
if (not os.path.exists(curfile)):
|
||||
print "file not found:", curfile
|
||||
sys.exit()
|
||||
|
||||
f = open(curfile,'rb')
|
||||
|
||||
ngroups = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
totngroups = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
nids = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
totnids = np.fromfile(f, dtype=np.uint64, count=1)[0]
|
||||
ntask = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
nsubs = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
totnsubs = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
|
||||
if swap:
|
||||
ngroups = ngroups.byteswap()
|
||||
totngroups = totngroups.byteswap()
|
||||
nids = nids.byteswap()
|
||||
totnids = totnids.byteswap()
|
||||
ntask = ntask.byteswap()
|
||||
nsubs = nsubs.byteswap()
|
||||
totnsubs = totnsubs.byteswap()
|
||||
|
||||
if filenum == 0:
|
||||
self.ngroups = totngroups
|
||||
self.nids = totnids
|
||||
self.nfiles = ntask
|
||||
self.nsubs = totnsubs
|
||||
|
||||
self.group_len = np.empty(totngroups, dtype=np.uint32)
|
||||
self.group_offset = np.empty(totngroups, dtype=np.uint32)
|
||||
self.group_mass = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_pos = np.empty(totngroups, dtype=np.dtype((np.float32,3)))
|
||||
self.group_m_mean200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_r_mean200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_m_crit200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_r_crit200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_m_tophat200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_r_tophat200 = np.empty(totngroups, dtype=np.float32)
|
||||
if group_veldisp:
|
||||
self.group_veldisp_mean200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_veldisp_crit200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_veldisp_tophat200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_contamination_count = np.empty(totngroups, dtype=np.uint32)
|
||||
self.group_contamination_mass = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_nsubs = np.empty(totngroups, dtype=np.uint32)
|
||||
self.group_firstsub = np.empty(totngroups, dtype=np.uint32)
|
||||
|
||||
self.sub_len = np.empty(totnsubs, dtype=np.uint32)
|
||||
self.sub_offset = np.empty(totnsubs, dtype=np.uint32)
|
||||
self.sub_parent = np.empty(totnsubs, dtype=np.uint32)
|
||||
self.sub_mass = np.empty(totnsubs, dtype=np.float32)
|
||||
self.sub_pos = np.empty(totnsubs, dtype=np.dtype((np.float32,3)))
|
||||
self.sub_vel = np.empty(totnsubs, dtype=np.dtype((np.float32,3)))
|
||||
self.sub_cm = np.empty(totnsubs, dtype=np.dtype((np.float32,3)))
|
||||
self.sub_spin = np.empty(totnsubs, dtype=np.dtype((np.float32,3)))
|
||||
self.sub_veldisp = np.empty(totnsubs, dtype=np.float32)
|
||||
self.sub_vmax = np.empty(totnsubs, dtype=np.float32)
|
||||
self.sub_vmaxrad = np.empty(totnsubs, dtype=np.float32)
|
||||
self.sub_halfmassrad = np.empty(totnsubs, dtype=np.float32)
|
||||
self.sub_id_mostbound = np.empty(totnsubs, dtype=self.id_type)
|
||||
self.sub_grnr = np.empty(totnsubs, dtype=np.uint32)
|
||||
if masstab:
|
||||
self.sub_masstab = np.empty(totnsubs, dtype=np.dtype((np.float32,6)))
|
||||
|
||||
if ngroups > 0:
|
||||
locs = slice(skip_gr, skip_gr + ngroups)
|
||||
self.group_len[locs] = np.fromfile(f, dtype=np.uint32, count=ngroups)
|
||||
self.group_offset[locs] = np.fromfile(f, dtype=np.uint32, count=ngroups)
|
||||
self.group_mass[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_pos[locs] = np.fromfile(f, dtype=np.dtype((np.float32,3)), count=ngroups)
|
||||
self.group_m_mean200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_r_mean200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_m_crit200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_r_crit200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_m_tophat200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_r_tophat200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
if group_veldisp:
|
||||
self.group_veldisp_mean200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_veldisp_crit200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_veldisp_tophat200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_contamination_count[locs] = np.fromfile(f, dtype=np.uint32, count=ngroups)
|
||||
self.group_contamination_mass[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_nsubs[locs] = np.fromfile(f, dtype=np.uint32, count=ngroups)
|
||||
self.group_firstsub[locs] = np.fromfile(f, dtype=np.uint32, count=ngroups)
|
||||
skip_gr += ngroups
|
||||
|
||||
if nsubs > 0:
|
||||
locs = slice(skip_sub, skip_sub + nsubs)
|
||||
self.sub_len[locs] = np.fromfile(f, dtype=np.uint32, count=nsubs)
|
||||
self.sub_offset[locs] = np.fromfile(f, dtype=np.uint32, count=nsubs)
|
||||
self.sub_parent[locs] = np.fromfile(f, dtype=np.uint32, count=nsubs)
|
||||
self.sub_mass[locs] = np.fromfile(f, dtype=np.float32, count=nsubs)
|
||||
self.sub_pos[locs] = np.fromfile(f, dtype=np.dtype((np.float32,3)), count=nsubs)
|
||||
self.sub_vel[locs] = np.fromfile(f, dtype=np.dtype((np.float32,3)), count=nsubs)
|
||||
self.sub_cm[locs] = np.fromfile(f, dtype=np.dtype((np.float32,3)), count=nsubs)
|
||||
self.sub_spin[locs] = np.fromfile(f, dtype=np.dtype((np.float32,3)), count=nsubs)
|
||||
self.sub_veldisp[locs] = np.fromfile(f, dtype=np.float32, count=nsubs)
|
||||
self.sub_vmax[locs] = np.fromfile(f, dtype=np.float32, count=nsubs)
|
||||
self.sub_vmaxrad[locs] = np.fromfile(f, dtype=np.float32, count=nsubs)
|
||||
self.sub_halfmassrad[locs] = np.fromfile(f, dtype=np.float32, count=nsubs)
|
||||
self.sub_id_mostbound[locs] = np.fromfile(f, dtype=self.id_type, count=nsubs)
|
||||
self.sub_grnr[locs] = np.fromfile(f, dtype=np.uint32, count=nsubs)
|
||||
if masstab:
|
||||
self.sub_masstab[locs] = np.fromfile(f, dtype=np.dtype((np.float32,6)), count=nsubs)
|
||||
skip_sub += nsubs
|
||||
|
||||
curpos = f.tell()
|
||||
f.seek(0,os.SEEK_END)
|
||||
if curpos != f.tell(): print "Warning: finished reading before EOF for file",filenum
|
||||
f.close()
|
||||
#print 'finished with file number',filenum,"of",ntask
|
||||
filenum += 1
|
||||
if filenum == self.nfiles: doneflag = True
|
||||
|
||||
if swap:
|
||||
self.group_len.byteswap(True)
|
||||
self.group_offset.byteswap(True)
|
||||
self.group_mass.byteswap(True)
|
||||
self.group_pos.byteswap(True)
|
||||
self.group_m_mean200.byteswap(True)
|
||||
self.group_r_mean200.byteswap(True)
|
||||
self.group_m_crit200.byteswap(True)
|
||||
self.group_r_crit200.byteswap(True)
|
||||
self.group_m_tophat200.byteswap(True)
|
||||
self.group_r_tophat200.byteswap(True)
|
||||
if group_veldisp:
|
||||
self.group_veldisp_mean200.byteswap(True)
|
||||
self.group_veldisp_crit200.byteswap(True)
|
||||
self.group_veldisp_tophat200.byteswap(True)
|
||||
self.group_contamination_count.byteswap(True)
|
||||
self.group_contamination_mass.byteswap(True)
|
||||
self.group_nsubs.byteswap(True)
|
||||
self.group_firstsub.byteswap(True)
|
||||
|
||||
self.sub_len.byteswap(True)
|
||||
self.sub_offset.byteswap(True)
|
||||
self.sub_parent.byteswap(True)
|
||||
self.sub_mass.byteswap(True)
|
||||
self.sub_pos.byteswap(True)
|
||||
self.sub_vel.byteswap(True)
|
||||
self.sub_cm.byteswap(True)
|
||||
self.sub_spin.byteswap(True)
|
||||
self.sub_veldisp.byteswap(True)
|
||||
self.sub_vmax.byteswap(True)
|
||||
self.sub_vmaxrad.byteswap(True)
|
||||
self.sub_halfmassrad.byteswap(True)
|
||||
self.sub_id_mostbound.byteswap(True)
|
||||
self.sub_grnr.byteswap(True)
|
||||
if masstab:
|
||||
self.sub_masstab.byteswap(True)
|
||||
|
||||
#print
|
||||
#print "number of groups =", self.ngroups
|
||||
#print "number of subgroups =", self.nsubs
|
||||
#if self.nsubs > 0:
|
||||
# print "largest group of length",self.group_len[0],"has",self.group_nsubs[0],"subhalos"
|
||||
# print
|
||||
|
||||
|
||||
|
||||
# code for reading Subfind's ID files
|
||||
# usage e.g.:
|
||||
#
|
||||
# import readsubf
|
||||
# ids = readsubf.subf_ids("./m_10002_h_94_501_z3_csf/", 0, 100)
|
||||
|
||||
|
||||
class subf_ids:
|
||||
def __init__(self, basedir, snapnum, substart, sublen, swap = False, verbose = False, long_ids = False, read_all = False):
|
||||
self.filebase = basedir + "/groups_" + str(snapnum).zfill(3) + "/subhalo_ids_" + str(snapnum).zfill(3) + "."
|
||||
|
||||
if (verbose):
|
||||
print
|
||||
print "reading subhalo IDs for snapshot",snapnum,"of",basedir
|
||||
|
||||
if long_ids: self.id_type = np.uint64
|
||||
else: self.id_type = np.uint32
|
||||
|
||||
|
||||
filenum = 0
|
||||
doneflag = False
|
||||
count=substart
|
||||
found=0
|
||||
|
||||
|
||||
while not doneflag:
|
||||
curfile = self.filebase + str(filenum)
|
||||
|
||||
if (not os.path.exists(curfile)):
|
||||
print "file not found:", curfile
|
||||
sys.exit()
|
||||
|
||||
f = open(curfile,'rb')
|
||||
|
||||
Ngroups = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
TotNgroups = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
NIds = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
TotNids = np.fromfile(f, dtype=np.uint64, count=1)[0]
|
||||
NTask = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
Offset = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
|
||||
|
||||
if read_all:
|
||||
substart=0
|
||||
sublen=TotNids
|
||||
if swap:
|
||||
Ngroups = Ngroups.byteswap()
|
||||
TotNgroups = TotNgroups.byteswap()
|
||||
NIds = NIds.byteswap()
|
||||
TotNids = TotNids.byteswap()
|
||||
NTask = NTask.byteswap()
|
||||
Offset = Offset.byteswap()
|
||||
if filenum == 0:
|
||||
if (verbose):
|
||||
print "Ngroups = ", Ngroups
|
||||
print "TotNgroups = ", Ngroups
|
||||
print "NIds = ", NIds
|
||||
print "TotNids = ", TotNids
|
||||
print "NTask = ", NTask
|
||||
print "Offset = ", Offset
|
||||
self.nfiles = NTask
|
||||
self.SubLen=sublen
|
||||
self.SubIDs = np.empty(sublen, dtype=self.id_type)
|
||||
|
||||
|
||||
if count <= Offset+NIds:
|
||||
nskip = count - Offset
|
||||
nrem = Offset + NIds - count
|
||||
if sublen > nrem:
|
||||
n_to_read = nrem
|
||||
else:
|
||||
n_to_read = sublen
|
||||
if n_to_read > 0:
|
||||
if (verbose):
|
||||
print filenum, n_to_read
|
||||
if nskip > 0:
|
||||
dummy=np.fromfile(f, dtype=self.id_type, count=nskip)
|
||||
if (verbose):
|
||||
print dummy
|
||||
locs = slice(found, found + n_to_read)
|
||||
dummy2 = np.fromfile(f, dtype=self.id_type, count=n_to_read)
|
||||
if (verbose):
|
||||
print dummy2
|
||||
self.SubIDs[locs]=dummy2
|
||||
found += n_to_read
|
||||
count += n_to_read
|
||||
sublen -= n_to_read
|
||||
|
||||
f.close()
|
||||
filenum += 1
|
||||
if filenum == self.nfiles: doneflag = True
|
||||
|
||||
if swap:
|
||||
self.SubIDs.byteswap(True)
|
||||
|
||||
|
||||
#+
|
||||
# VIDE -- Void IDentification and Examination -- ./python_tools/fit_hod/readsubf.py
|
||||
# Copyright (C) 2010-2014 Guilhem Lavaux
|
||||
# Copyright (C) 2011-2014 P. M. Sutter
|
||||
#
|
||||
# This program is free software; you can redistribute it and/or modify
|
||||
# it under the terms of the GNU General Public License as published by
|
||||
# the Free Software Foundation; version 2 of the License.
|
||||
#
|
||||
#
|
||||
# This program is distributed in the hope that it will be useful,
|
||||
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
# GNU General Public License for more details.
|
||||
#
|
||||
# You should have received a copy of the GNU General Public License along
|
||||
# with this program; if not, write to the Free Software Foundation, Inc.,
|
||||
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
||||
#+
|
||||
|
||||
# code for reading Subfind's subhalo_tab files
|
||||
# usage e.g.:
|
||||
#
|
||||
# import readsubf
|
||||
# cat = readsubf.subfind_catalog("./m_10002_h_94_501_z3_csf/",63,masstab=True)
|
||||
# print cat.nsubs
|
||||
# print "largest halo x position = ",cat.sub_pos[0][0]
|
||||
|
||||
import numpy as np
|
||||
import os
|
||||
import sys
|
||||
|
||||
class subfind_catalog:
|
||||
def __init__(self, basedir, snapnum, group_veldisp = False, masstab = False, long_ids = False, swap = False):
|
||||
self.filebase = basedir + "/groups_" + str(snapnum).zfill(3) + "/subhalo_tab_" + str(snapnum).zfill(3) + "."
|
||||
|
||||
#print
|
||||
#print "reading subfind catalog for snapshot",snapnum,"of",basedir
|
||||
|
||||
if long_ids: self.id_type = np.uint64
|
||||
else: self.id_type = np.uint32
|
||||
|
||||
self.group_veldisp = group_veldisp
|
||||
self.masstab = masstab
|
||||
|
||||
filenum = 0
|
||||
doneflag = False
|
||||
skip_gr = 0
|
||||
skip_sub = 0
|
||||
while not doneflag:
|
||||
curfile = self.filebase + str(filenum)
|
||||
|
||||
if (not os.path.exists(curfile)):
|
||||
print("file not found:", curfile)
|
||||
sys.exit()
|
||||
|
||||
f = open(curfile,'rb')
|
||||
|
||||
ngroups = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
totngroups = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
nids = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
totnids = np.fromfile(f, dtype=np.uint64, count=1)[0]
|
||||
ntask = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
nsubs = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
totnsubs = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
|
||||
if swap:
|
||||
ngroups = ngroups.byteswap()
|
||||
totngroups = totngroups.byteswap()
|
||||
nids = nids.byteswap()
|
||||
totnids = totnids.byteswap()
|
||||
ntask = ntask.byteswap()
|
||||
nsubs = nsubs.byteswap()
|
||||
totnsubs = totnsubs.byteswap()
|
||||
|
||||
if filenum == 0:
|
||||
self.ngroups = totngroups
|
||||
self.nids = totnids
|
||||
self.nfiles = ntask
|
||||
self.nsubs = totnsubs
|
||||
|
||||
self.group_len = np.empty(totngroups, dtype=np.uint32)
|
||||
self.group_offset = np.empty(totngroups, dtype=np.uint32)
|
||||
self.group_mass = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_pos = np.empty(totngroups, dtype=np.dtype((np.float32,3)))
|
||||
self.group_m_mean200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_r_mean200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_m_crit200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_r_crit200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_m_tophat200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_r_tophat200 = np.empty(totngroups, dtype=np.float32)
|
||||
if group_veldisp:
|
||||
self.group_veldisp_mean200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_veldisp_crit200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_veldisp_tophat200 = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_contamination_count = np.empty(totngroups, dtype=np.uint32)
|
||||
self.group_contamination_mass = np.empty(totngroups, dtype=np.float32)
|
||||
self.group_nsubs = np.empty(totngroups, dtype=np.uint32)
|
||||
self.group_firstsub = np.empty(totngroups, dtype=np.uint32)
|
||||
|
||||
self.sub_len = np.empty(totnsubs, dtype=np.uint32)
|
||||
self.sub_offset = np.empty(totnsubs, dtype=np.uint32)
|
||||
self.sub_parent = np.empty(totnsubs, dtype=np.uint32)
|
||||
self.sub_mass = np.empty(totnsubs, dtype=np.float32)
|
||||
self.sub_pos = np.empty(totnsubs, dtype=np.dtype((np.float32,3)))
|
||||
self.sub_vel = np.empty(totnsubs, dtype=np.dtype((np.float32,3)))
|
||||
self.sub_cm = np.empty(totnsubs, dtype=np.dtype((np.float32,3)))
|
||||
self.sub_spin = np.empty(totnsubs, dtype=np.dtype((np.float32,3)))
|
||||
self.sub_veldisp = np.empty(totnsubs, dtype=np.float32)
|
||||
self.sub_vmax = np.empty(totnsubs, dtype=np.float32)
|
||||
self.sub_vmaxrad = np.empty(totnsubs, dtype=np.float32)
|
||||
self.sub_halfmassrad = np.empty(totnsubs, dtype=np.float32)
|
||||
self.sub_id_mostbound = np.empty(totnsubs, dtype=self.id_type)
|
||||
self.sub_grnr = np.empty(totnsubs, dtype=np.uint32)
|
||||
if masstab:
|
||||
self.sub_masstab = np.empty(totnsubs, dtype=np.dtype((np.float32,6)))
|
||||
|
||||
if ngroups > 0:
|
||||
locs = slice(skip_gr, skip_gr + ngroups)
|
||||
self.group_len[locs] = np.fromfile(f, dtype=np.uint32, count=ngroups)
|
||||
self.group_offset[locs] = np.fromfile(f, dtype=np.uint32, count=ngroups)
|
||||
self.group_mass[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_pos[locs] = np.fromfile(f, dtype=np.dtype((np.float32,3)), count=ngroups)
|
||||
self.group_m_mean200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_r_mean200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_m_crit200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_r_crit200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_m_tophat200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_r_tophat200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
if group_veldisp:
|
||||
self.group_veldisp_mean200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_veldisp_crit200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_veldisp_tophat200[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_contamination_count[locs] = np.fromfile(f, dtype=np.uint32, count=ngroups)
|
||||
self.group_contamination_mass[locs] = np.fromfile(f, dtype=np.float32, count=ngroups)
|
||||
self.group_nsubs[locs] = np.fromfile(f, dtype=np.uint32, count=ngroups)
|
||||
self.group_firstsub[locs] = np.fromfile(f, dtype=np.uint32, count=ngroups)
|
||||
skip_gr += ngroups
|
||||
|
||||
if nsubs > 0:
|
||||
locs = slice(skip_sub, skip_sub + nsubs)
|
||||
self.sub_len[locs] = np.fromfile(f, dtype=np.uint32, count=nsubs)
|
||||
self.sub_offset[locs] = np.fromfile(f, dtype=np.uint32, count=nsubs)
|
||||
self.sub_parent[locs] = np.fromfile(f, dtype=np.uint32, count=nsubs)
|
||||
self.sub_mass[locs] = np.fromfile(f, dtype=np.float32, count=nsubs)
|
||||
self.sub_pos[locs] = np.fromfile(f, dtype=np.dtype((np.float32,3)), count=nsubs)
|
||||
self.sub_vel[locs] = np.fromfile(f, dtype=np.dtype((np.float32,3)), count=nsubs)
|
||||
self.sub_cm[locs] = np.fromfile(f, dtype=np.dtype((np.float32,3)), count=nsubs)
|
||||
self.sub_spin[locs] = np.fromfile(f, dtype=np.dtype((np.float32,3)), count=nsubs)
|
||||
self.sub_veldisp[locs] = np.fromfile(f, dtype=np.float32, count=nsubs)
|
||||
self.sub_vmax[locs] = np.fromfile(f, dtype=np.float32, count=nsubs)
|
||||
self.sub_vmaxrad[locs] = np.fromfile(f, dtype=np.float32, count=nsubs)
|
||||
self.sub_halfmassrad[locs] = np.fromfile(f, dtype=np.float32, count=nsubs)
|
||||
self.sub_id_mostbound[locs] = np.fromfile(f, dtype=self.id_type, count=nsubs)
|
||||
self.sub_grnr[locs] = np.fromfile(f, dtype=np.uint32, count=nsubs)
|
||||
if masstab:
|
||||
self.sub_masstab[locs] = np.fromfile(f, dtype=np.dtype((np.float32,6)), count=nsubs)
|
||||
skip_sub += nsubs
|
||||
|
||||
curpos = f.tell()
|
||||
f.seek(0,os.SEEK_END)
|
||||
if curpos != f.tell(): print("Warning: finished reading before EOF for file",filenum)
|
||||
f.close()
|
||||
#print 'finished with file number',filenum,"of",ntask
|
||||
filenum += 1
|
||||
if filenum == self.nfiles: doneflag = True
|
||||
|
||||
if swap:
|
||||
self.group_len.byteswap(True)
|
||||
self.group_offset.byteswap(True)
|
||||
self.group_mass.byteswap(True)
|
||||
self.group_pos.byteswap(True)
|
||||
self.group_m_mean200.byteswap(True)
|
||||
self.group_r_mean200.byteswap(True)
|
||||
self.group_m_crit200.byteswap(True)
|
||||
self.group_r_crit200.byteswap(True)
|
||||
self.group_m_tophat200.byteswap(True)
|
||||
self.group_r_tophat200.byteswap(True)
|
||||
if group_veldisp:
|
||||
self.group_veldisp_mean200.byteswap(True)
|
||||
self.group_veldisp_crit200.byteswap(True)
|
||||
self.group_veldisp_tophat200.byteswap(True)
|
||||
self.group_contamination_count.byteswap(True)
|
||||
self.group_contamination_mass.byteswap(True)
|
||||
self.group_nsubs.byteswap(True)
|
||||
self.group_firstsub.byteswap(True)
|
||||
|
||||
self.sub_len.byteswap(True)
|
||||
self.sub_offset.byteswap(True)
|
||||
self.sub_parent.byteswap(True)
|
||||
self.sub_mass.byteswap(True)
|
||||
self.sub_pos.byteswap(True)
|
||||
self.sub_vel.byteswap(True)
|
||||
self.sub_cm.byteswap(True)
|
||||
self.sub_spin.byteswap(True)
|
||||
self.sub_veldisp.byteswap(True)
|
||||
self.sub_vmax.byteswap(True)
|
||||
self.sub_vmaxrad.byteswap(True)
|
||||
self.sub_halfmassrad.byteswap(True)
|
||||
self.sub_id_mostbound.byteswap(True)
|
||||
self.sub_grnr.byteswap(True)
|
||||
if masstab:
|
||||
self.sub_masstab.byteswap(True)
|
||||
|
||||
#print
|
||||
#print "number of groups =", self.ngroups
|
||||
#print "number of subgroups =", self.nsubs
|
||||
#if self.nsubs > 0:
|
||||
# print "largest group of length",self.group_len[0],"has",self.group_nsubs[0],"subhalos"
|
||||
# print
|
||||
|
||||
|
||||
|
||||
# code for reading Subfind's ID files
|
||||
# usage e.g.:
|
||||
#
|
||||
# import readsubf
|
||||
# ids = readsubf.subf_ids("./m_10002_h_94_501_z3_csf/", 0, 100)
|
||||
|
||||
|
||||
class subf_ids:
|
||||
def __init__(self, basedir, snapnum, substart, sublen, swap = False, verbose = False, long_ids = False, read_all = False):
|
||||
self.filebase = basedir + "/groups_" + str(snapnum).zfill(3) + "/subhalo_ids_" + str(snapnum).zfill(3) + "."
|
||||
|
||||
if (verbose):
|
||||
print()
|
||||
print("reading subhalo IDs for snapshot",snapnum,"of",basedir)
|
||||
|
||||
if long_ids: self.id_type = np.uint64
|
||||
else: self.id_type = np.uint32
|
||||
|
||||
|
||||
filenum = 0
|
||||
doneflag = False
|
||||
count=substart
|
||||
found=0
|
||||
|
||||
|
||||
while not doneflag:
|
||||
curfile = self.filebase + str(filenum)
|
||||
|
||||
if (not os.path.exists(curfile)):
|
||||
print("file not found:", curfile)
|
||||
sys.exit()
|
||||
|
||||
f = open(curfile,'rb')
|
||||
|
||||
Ngroups = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
TotNgroups = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
NIds = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
TotNids = np.fromfile(f, dtype=np.uint64, count=1)[0]
|
||||
NTask = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
Offset = np.fromfile(f, dtype=np.uint32, count=1)[0]
|
||||
|
||||
|
||||
if read_all:
|
||||
substart=0
|
||||
sublen=TotNids
|
||||
if swap:
|
||||
Ngroups = Ngroups.byteswap()
|
||||
TotNgroups = TotNgroups.byteswap()
|
||||
NIds = NIds.byteswap()
|
||||
TotNids = TotNids.byteswap()
|
||||
NTask = NTask.byteswap()
|
||||
Offset = Offset.byteswap()
|
||||
if filenum == 0:
|
||||
if (verbose):
|
||||
print("Ngroups = ", Ngroups)
|
||||
print("TotNgroups = ", Ngroups)
|
||||
print("NIds = ", NIds)
|
||||
print("TotNids = ", TotNids)
|
||||
print("NTask = ", NTask)
|
||||
print("Offset = ", Offset)
|
||||
self.nfiles = NTask
|
||||
self.SubLen=sublen
|
||||
self.SubIDs = np.empty(sublen, dtype=self.id_type)
|
||||
|
||||
|
||||
if count <= Offset+NIds:
|
||||
nskip = count - Offset
|
||||
nrem = Offset + NIds - count
|
||||
if sublen > nrem:
|
||||
n_to_read = nrem
|
||||
else:
|
||||
n_to_read = sublen
|
||||
if n_to_read > 0:
|
||||
if (verbose):
|
||||
print(filenum, n_to_read)
|
||||
if nskip > 0:
|
||||
dummy=np.fromfile(f, dtype=self.id_type, count=nskip)
|
||||
if (verbose):
|
||||
print(dummy)
|
||||
locs = slice(found, found + n_to_read)
|
||||
dummy2 = np.fromfile(f, dtype=self.id_type, count=n_to_read)
|
||||
if (verbose):
|
||||
print(dummy2)
|
||||
self.SubIDs[locs]=dummy2
|
||||
found += n_to_read
|
||||
count += n_to_read
|
||||
sublen -= n_to_read
|
||||
|
||||
f.close()
|
||||
filenum += 1
|
||||
if filenum == self.nfiles: doneflag = True
|
||||
|
||||
if swap:
|
||||
self.SubIDs.byteswap(True)
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue