def rem_run(id, confirm=True):
run = core.get_default_session().query(Creator).filter_by(id=id).first()
if run is None:
raise ValueError(" Run %i does not exist" % id)
print("You want to delete everything created by the following run:")
run.print_info()
if confirm:
print(""">>> type "yes" to continue""")
if (not confirm) or input(":").lower() == "yes":
#for y in run.halolinks:
# core.get_default_session().delete(y)
run.halolinks.delete()
run.halos.delete()
run.properties.delete()
run.timesteps.delete()
for s in run.simulations:
print(s)
core.get_default_session().delete(s)
core.get_default_session().commit()
core.get_default_session().delete(run)
core.get_default_session().commit()
print("OK")
else:
print("aborted")
def rem_simulation_timesteps(options):
basename = options.sims
from tangos.util.terminalcontroller import term
sim = core.get_default_session().query(Simulation).filter_by(
basename=basename).first()
if sim == None:
print(term.GREEN + "Simulation does not exist", term.NORMAL)
else:
print(term.RED + "Delete simulation", sim, term.NORMAL)
core.get_default_session().delete(sim)
def rollback(options):
if len(options.ids)>0:
for run_id in options.ids:
rem_run(run_id, not options.force)
else:
most_recent_id = core.get_default_session().query(Creator).order_by(
Creator.id.desc()).first().id
rem_run(most_recent_id, not options.force)
def _erase_run_content(run):
run.halolinks.delete()
run.halos.delete()
run.properties.delete()
run.timesteps.delete()
for s in run.simulations:
core.get_default_session().delete(s)
core.get_default_session().commit()
core.get_default_session().delete(run)
core.get_default_session().commit()
def db_import(options):
sims = options.sims
remote_db = options.file
global internal_session
engine2 = create_engine('sqlite:///' + remote_db, echo=False)
ext_session = sessionmaker(bind=engine2)()
_db_import_export(core.get_default_session(), ext_session, *sims)
def update_tracker_halos(sim=None):
from tangos import get_simulation
from tangos.core import get_default_session
from tangos.util.terminalcontroller import heading
if sim is None:
x = get_default_session().query(TrackData).all()
else:
x = get_simulation(sim).trackers.all()
for y in x:
heading(repr(y))
y.create_objects()
def rem_run(id, confirm=True):
run = core.get_default_session().query(Creator).filter_by(id=id).first()
if run is None:
raise ValueError(" Run %i does not exist" % id)
print("You want to delete everything created by the following run:")
run.print_info()
if confirm:
print(""">>> type "yes" to continue""")
if (not confirm) or input(":").lower() == "yes":
_erase_run_content(run)
print("OK")
else:
print("aborted")
def setup_module():
testing.init_blank_db_for_testing()
generator = SimulationGeneratorForTests()
generator.add_timestep()
generator.add_objects_to_timestep(10)
generator.add_properties_to_halos(Mvir=lambda i: 1. * i)
halo = tangos.get_halo(1)
session = core.get_default_session()
px = create_property(halo, "Mvir", -1., session)
session.add(px, session)
px = create_property(halo, "Mvir", -2., session)
session.add(px, session)
session.commit()
# Also create links between halos, including duplicates
halo2 = tangos.get_halo(2)
halo3 = tangos.get_halo(3)
halo9 = tangos.get_halo(9)
# two links between halo 1 to halo 2 with the same weight and name (maximal duplicate)
d_test = tangos.core.get_or_create_dictionary_item(session, "test")
l_obj = link.HaloLink(halo, halo2, d_test, 1.0)
session.add(l_obj)
l_obj = link.HaloLink(halo, halo2, d_test, 1.0)
session.add(l_obj)
# and another time but with same weight but different name (not a duplicate)
diff_name = tangos.core.get_or_create_dictionary_item(
session, "other_test")
l_obj = link.HaloLink(halo, halo2, diff_name, 1.0)
session.add(l_obj)
# and another time, with same name but different weight
# (this is a non-maximal duplicate, oldest addition gets deleted and we keep the most recent link)
l_obj = link.HaloLink(halo, halo2, d_test, 0.5)
session.add(l_obj)
# and another time, with same weight and name as previous but linking to a different halo (not a duplicate)
l_obj = link.HaloLink(halo, halo3, d_test, 1.0)
session.add(l_obj)
# and now a completely independent link between halo 2 to halo 9
l_obj = link.HaloLink(halo2, halo9, d_test, 1.0)
session.add(l_obj)
def db_export(remote_db, *sims):
global internal_session
engine2 = create_engine('sqlite:///' + remote_db, echo=False)
int_session = core.get_default_session()
ext_session = sessionmaker(bind=engine2)()
Base.metadata.create_all(engine2)
_xcurrent_creator = core.creator.get_creator()
core.set_default_session(ext_session)
core.set_creator(ext_session.merge(Creator()))
_db_import_export(ext_session, int_session, *sims)
core.set_creator(_xcurrent_creator)
core.set_default_session(int_session)
def list_recent_runs(opts):
n = opts.num
run = core.get_default_session().query(Creator).order_by(
Creator.id.desc()).limit(n).all()
for r in run:
r.print_info()
def grep_run_info(opts):
matching_runs = core.get_default_session().query(Creator).filter(
Creator.command_line.like("%" + opts.query + "%")).all()
for r in matching_runs:
r.print_info()
return matching_runs
def grep_run_id(opts):
matching_runs = core.get_default_session().query(Creator).filter(
Creator.command_line.like("%" + opts.query + "%")).all()
for r in matching_runs:
print(r.id, end=' ')
print('\n')
def add_tracker(halo, size=None):
import pynbody
try:
halo = get_halo(halo)
except:
sim = get_simulation(halo)
print("Adding tracker for isolated run", sim)
halo = None
if halo is not None:
# check we can open the tracker file
hfile = halo.load()
hfile.physical_units()
use_iord = True
try:
hfile.dm['iord']
except:
use_iord = False
# get the centre
cen = halo.get('SSC', None)
if cen is None:
cen = pynbody.analysis.halo.shrink_sphere_center(hfile.dm)
hfile.ancestor.dm['pos'] -= cen
if size is None:
size = '500 pc'
size = pynbody.units.Unit(size)
try:
size.in_units("kpc")
X = hfile.ancestor.dm[pynbody.filt.Sphere(size)]
except:
size.in_units("kpc km s^-1")
X = hfile.ancestor.dm[pynbody.filt.LowPass("j2", size ** 2)]
size = str(size.in_units("kpc km s^-1")) + "_kks"
if len(X) < 2:
print("Alert! Track data is too short")
import pdb
pdb.set_trace()
# setup the tracker
tx = TrackData(halo.timestep.simulation)
print("Tracker halo ID is", tx.halo_number)
print("Length of track data is", len(X))
tx.select(X, use_iord)
ts_trigger = halo.timestep
else:
f = sim.timesteps[0].load()
tx = TrackData(sim)
if tx.halo_number != 1:
print("Already have a tracker for this simulation -> abort")
return
print("Tracker halo ID is", tx.halo_number)
tx.particles = np.array(
np.arange(0, len(f.dm) - 1, 1), dtype=int)
tx.use_iord = False
ts_trigger = None
core.get_default_session().add(tx)
tx.create_objects(first_timestep=ts_trigger)
if halo is not None:
targ = halo.timestep.halos.filter_by(
object_typecode=1, halo_number=tx.halo_number).first()
size = str(size).replace(" ", "")
halo["dm_central_" + size] = targ
print("Copying SSC...", end=' ')
sys.stdout.flush()
while halo is not None:
try:
targ['SSC'] = halo['SSC']
except KeyError:
pass
halo = halo.next
targ = targ.next
print("done")
core.get_default_session().commit()
def __init__(self, session=None):
self.session = session or core.get_default_session()
def grep_run(st):
run = core.get_default_session().query(Creator).filter(
Creator.command_line.like("%" + st + "%")).all()
for r in run:
print(r.id, end=' ')
