NSNAPSEARCH = treedata['Header']['TreeBuilder']['Temporal_linking_length']
TREEDIRECTION = treedata['Header']['TreeBuilder']['Tree_direction']
#alias tree data to halo data as forest file will combine the data
halodata = treedata
#store number of halos, scalefactors
numhalos = np.zeros(numsnaps, dtype=np.int64)
scalefactors = np.zeros(numsnaps)
#load halo properties file
print('Loading halo properties ...')
time1 = time.time()
mp = -1
for i in range(numsnaps):
fname = halocatalogdir + 'snap_%04d/snap_%04d.VELOCIraptor' % (i, i)
halos, numhalos[i] = vpt.ReadPropertyFile(fname, RAWPROPFORMAT, 0, 0,
requestedfields)
scalefactors[i] = halos['SimulationInfo']['ScaleFactor']
if (numhalos[i] > 0 and mp == -1):
mp = halos['Mass_tot'][0] / halos['npart'][0]
if (ireducememfootprintflag and numhalos[i] > 0):
for key in requestedfields:
if (halos[key].dtype == np.float64):
halos[key] = np.array(halos[key], dtype=np.float32)
halodata[i].update(halos)
print('Done', time.time() - time1)
#given walkable tree, determine the largest difference in snapshots between an object and its head
maxnsnapsearch = 0
for i in range(numsnaps):
if (numhalos[i] == 0): continue
headsnap = np.int64(halodata[i]['Head'] / TEMPORALHALOIDVAL)
def ReadVELOCIraptorTreeandHalodata(opt, inputfields):
start = time.time()
if (opt.iverbose): print("Reading the walkable tree")
sys.stdout.flush()
tree, numsnaps = VPT.ReadWalkableHDFTree(opt.inputtreefilename, False)
if (opt.iverbose):
print("Done reading the walkable tree in", time.time() - start)
sys.stdout.flush()
#Update the number of snapshots from the tree
opt.update_numsnaps(numsnaps)
#The fields that needs to be converted to physical
physconvertfields = [
inputfields[field] for field in inputfields.keys()
if field in ["X", "Y", "Z", "Radius", "Lx", "Ly", "Lz"]
]
#Open up the filelist and extract all the filenames
snapfilelist = open(opt.inputhalofilelistname, "r")
snapfilenames = [line.strip() for line in snapfilelist]
snapfilelist.close()
#Check the number of files in the VELOCIraptor filelist is the same as whats reported by the walkable tree
if (len(snapfilenames) != opt.numsnaps):
raise IOError(
"The number of input snapshots as reported by the walkable tree is not the same as the\n number of files in the input halo filelist, please correct this"
)
#extract the desiredfields from the inputfields
desiredfields = list(inputfields.values())
start = time.time()
if (opt.iverbose): print("Reading in the halo catalog")
sys.stdout.flush()
numhalos = np.zeros(opt.numsnaps, dtype=np.uint64)
halodata = [dict() for i in range(opt.numsnaps)]
atime = np.zeros(opt.numsnaps)
for i in range(opt.numsnaps):
start1 = time.time()
halodata[i], numhalos[i] = VPT.ReadPropertyFile(
snapfilenames[i], 2, 0, 0, desiredfields)
atime[i] = halodata[i]['SimulationInfo']['ScaleFactor']
for key in halodata[i].keys():
if (key == 'SimulationInfo' or key == 'UnitInfo'
or key == 'ConfigurationInfo'):
continue
#Reduce the precision of the datasets since OrbWeaver is all in float32
if (halodata[i][key].dtype == np.float64):
halodata[i][key].astype(np.float32,
casting="same_kind",
copy=False)
#Lets convert fields to physical if required
if ((key in physconvertfields) &
(halodata[i]['UnitInfo']["Comoving_or_Physical"] == 1)):
halodata[i][
key] *= atime[i] / halodata[i]["SimulationInfo"]["h_val"]
#Set the flag to physical
halodata[i]['UnitInfo']["Comoving_or_Physical"] = 0
if (opt.iverbose > 1):
print('Snapshot', i, 'done in', time.time() - start1)
sys.stdout.flush()
if (opt.iverbose):
print('Finished reading halo properties in', time.time() - start)
sys.stdout.flush()
VPT.AdjustforPeriod(opt.numsnaps, numhalos, halodata, tree)
unitdata = halodata[0]["UnitInfo"]
cosmodata = halodata[0]["SimulationInfo"]
cosmodata["ComovingBoxSize"] = np.round(
cosmodata["Period"] * cosmodata["h_val"] / cosmodata["ScaleFactor"], 1)
#Now it has been loaded the dictionary keys needs to be updated in the halodata so they are compatible with OrbWeaver
for i in range(opt.numsnaps):
for field in inputfields.keys():
halodata[i][field] = halodata[i].pop(inputfields[field])
return atime, numhalos, halodata, tree, unitdata, cosmodata
#for hdf input produce file listing input files
snaptreelist = open(basetreefname + '.snaptreelist.txt', 'w')
for i in range(numsnaps):
snaptreelist.write(basetreefname + '.snapshot_%03d.VELOCIraptor\n' % i)
snaptreelist.close()
rawtreedata = vpt.ReadHaloMergerTreeDescendant(
basetreefname + '.snaptreelist.txt', False, RAWTREEFORMAT, 1, True)
else:
rawtreedata = vpt.ReadHaloMergerTreeDescendant(basetreefname, False,
RAWTREEFORMAT, 0, True)
print('Finished reading raw tree')
numhalos = np.zeros(numsnaps, dtype=np.uint64)
halodata = [dict() for i in range(numsnaps)]
atime = np.zeros(numsnaps)
for i in range(numsnaps):
halodata[i], numhalos[i] = vpt.ReadPropertyFile(
basepropfname + '%03d.VELOCIraptor' % i, 2, 0, 1, requestedfields)
atime[i] = halodata[i]['SimulationInfo']['ScaleFactor']
for key in halodata[i].keys():
if (key == 'SimulationInfo' or key == 'UnitInfo'
or key == "ConfigurationInfo"):
continue
if (halodata[i][key].dtype == np.float64):
halodata[i][key] = np.array(halodata[i][key], dtype=np.float32)
print('Finished reading halo properties')
#produce head tail in ascending order
start = time.clock()
print("Building head/tail ")
vpt.BuildTemporalHeadTailDescendant(numsnaps, rawtreedata, numhalos, halodata,
TEMPORALHALOIDVAL)
print("Finished head/tail ", time.clock() - start)
1, True)
elif (TREEDIRECTION == 0):
print(
'Warning, progenitor based trees are less useful when building halo merger trees for SAMs.'
)
rawtreedata = vpt.ReadHaloMergerTree(fname, RAWTREEFORMAT, 1, True)
else:
print('Full graphs to walkable trees not implemented yet.')
print('Finished reading raw tree')
numhalos = np.zeros(numsnaps, dtype=np.uint64)
halodata = [dict() for i in range(numsnaps)]
atime = np.zeros(numsnaps)
for i in range(numsnaps):
halodata[i], numhalos[i] = vpt.ReadPropertyFile(
halocatalogdir + '/snapshot_%03d.VELOCIraptor' % i, 2, 0, 1,
requestedfields)
atime[i] = halodata[i]['SimulationInfo']['ScaleFactor']
for key in halodata[i].keys():
if (key == 'SimulationInfo' or key == 'UnitInfo'
or key == "ConfigurationInfo"):
continue
if (halodata[i][key].dtype == np.float64):
halodata[i][key] = np.array(halodata[i][key], dtype=np.float32)
print('Finished reading halo properties')
#produce head tail in ascending order
start = time.clock()
print("Building head/tail ")
vpt.BuildTemporalHeadTailDescendant(numsnaps, rawtreedata, numhalos, halodata,
TEMPORALHALOIDVAL)