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