def RunsOnClient(configstring_file, workdir, vesselfilename):
os.chdir(workdir)
if not os.path.exists(vesselfilename):
print 'GENERATING %s' % vesselfilename
with open(configstring_file, 'r') as f:
configstring = f.read()
krebsutils.run_vesselgen(configstring)
with h5py.File(vesselfilename, 'r+') as f:
# centering is needed because quantities are analyzed in dependence on the distance from the system origin!!
CenterTheLattice(f, 'field_ld')
CenterTheLattice(f, 'vessels/lattice')
f.flush()
ObtainDataOfVesselFile(f)
num_hierarchical_iterations=2,
# 2d sims take longer to converge since branches have to
# squeeze through narrow "corridors".
changeRateThreshold=0.1e-3, # lower than for 3d networks.
)
vd = VD(**paramset11)
vd = fix_worldsize(vd)
vd = generate_handmade1_config(vd, configs1dict['baumlecfg12'])
#vd = generate_alternating_config(vd, 1)
#vd = generate_handmade1_config_w_stems(vd, configs1dict['baumlecfg01'], vd.shape[0]*0.5, vd.shape[0]*0.8)
vd.outfilename = vd.name
#vd.full_debug_output = True
configstring = vd.generate_info_string()
print 'running: ', configstring
krebsutils.run_vesselgen(configstring)
if 0:
size = (10, 10, 10)
scale = 150.
pgrad = 0.2
p = pgrad * size[0] * scale
r = 6.
krebsutils.vesselgen_generate_single('vess-single-capillary.h5', size,
scale, 'quad', r, 0., p)
if 1:
scale = 150.
exponent_of_two = 1
import h5py
myFile = h5py.File('vess-cub.h5', 'w')
krebsutils.vesselgen_generate_symmetric(myFile, exponent_of_two, scale,
def run_vesselgen_client(configstring_file, workdir, vesselfilename):
qsub.printClientInfo()
os.chdir(workdir)
with open(configstring_file, 'r') as f:
configstring = f.read()
krebsutils.run_vesselgen(configstring)