def copyVesselnetworkAndComputeFlow(gvdst, gv, bloodflowparams):
'''gdst = group where the data is placed in, does not create a 'vesse' folder in it but writes nodes, edges directly;
gv = source vessel group
'''
myutils.buildLink(gvdst, 'CLASS', gv)
myutils.buildLink(gvdst, 'SOURCE', gv)
# first we need to copy some of the vessel data
gvedst = gvdst.create_group('edges')
gvndst = gvdst.create_group('nodes')
gvedst.attrs['COUNT'] = gv['edges'].attrs['COUNT']
gvndst.attrs['COUNT'] = gv['nodes'].attrs['COUNT']
if (gv.attrs.__contains__('CLASS')):
#special things if it is lattice based
if (gv.attrs['CLASS'] == 'GRAPH'):
gv.copy('lattice', gvdst)
gvedst.attrs['CLASS'] = 'GRAPH'
for name in ['lattice_pos', 'roots']:
gv['nodes'].copy(name, gvndst)
if (gv.attrs['CLASS'] == 'REALWORLD'):
gvedst.attrs['CLASS'] = 'REALWORLD'
for name in [
'world_pos', 'roots', 'bc_node_index', 'bc_type',
'bc_value'
]:
gv['nodes'].copy(name, gvndst)
for name in ['radius', 'node_a_index', 'node_b_index']:
gv['edges'].copy(name, gvedst)
# then we recompute blood flow because the alorithm has changed and we may or may not want hematocrit
if bloodflowparams['includePhaseSeparationEffect'] == True:
pressure, flow, shearforce, hematocrit, flags = _ku.calc_vessel_hydrodynamics(
gv, return_flags=True, bloodflowparams=bloodflowparams)
gvedst.create_dataset('flow', data=flow, compression=9)
gvedst.create_dataset('shearforce', data=shearforce, compression=9)
gvedst.create_dataset('hematocrit', data=hematocrit, compression=9)
gvedst.create_dataset('flags', data=flags, compression=9)
gvndst.create_dataset('pressure', data=pressure, compression=9)
else:
print("Computing without phase seperation effect")
pressure, flow, shearforce, hematocrit, flags = _ku.calc_vessel_hydrodynamics(
gv, return_flags=True, bloodflowparams=bloodflowparams)
gvedst.create_dataset('flow', data=flow, compression=9)
gvedst.create_dataset('shearforce', data=shearforce, compression=9)
gvedst.create_dataset('hematocrit', data=hematocrit, compression=9)
gvedst.create_dataset('flags', data=flags, compression=9)
gvndst.create_dataset('pressure', data=pressure, compression=9)
def enlarge_vessels(factor, gv_filename, bloodflowparams):
'''gvdst = group where the data is placed in, does not create a 'vesse' folder in it but writes nodes, edges directly;
gv = source vessel group
'''
inFile = h5files.open(gv_filename, 'r')
gv = inFile['vessels']
fac_as_percent = int(np.ceil(float(factor) * 100 - 100))
dest_file = h5files.open(
myutils.strip_from_end(gv_filename, '.h5') +
'_growth_by_%02i.h5' % fac_as_percent, 'a')
dest_file.attrs.create('enlargeFactor', data=fac_as_percent)
gvdst = dest_file.create_group('vessels')
gvdst.attrs['CLASS'] = 'GRAPH'
myutils.buildLink(gvdst, 'SOURCE', gv)
# first we need to copy some of the vessel data
gvedst = gvdst.create_group('edges')
gvndst = gvdst.create_group('nodes')
gvedst.attrs['COUNT'] = gv['edges'].attrs['COUNT']
gvndst.attrs['COUNT'] = gv['nodes'].attrs['COUNT']
gv.copy('lattice', gvdst)
for name in [
'lattice_pos', 'roots', 'nodeflags', 'gf', 'bc_conductivity_value',
'bc_node_index', 'bc_type', 'bc_value'
]:
gv['nodes'].copy(name, gvndst)
for name in ['radius', 'node_a_index', 'node_b_index', 'flags']:
if name == 'radius':
radii = gv['edges/' + name]
radii = factor * np.asarray(radii)
gvedst.create_dataset(name, data=radii)
else:
gv['edges'].copy(name, gvedst)
# then we recompute blood flow because the alorithm has changed and we may or may not want hematocrit
(pressure, flow, shearforce, hematocrit,
flags) = krebsutils.calc_vessel_hydrodynamics(
gvdst, return_flags=True, bloodflowparams=bloodflowparams)
# then we save the new data to complete the network copy
gvedst.create_dataset('flow', data=flow, compression=9)
gvedst.create_dataset('shearforce', data=shearforce, compression=9)
gvedst.create_dataset('hematocrit', data=hematocrit, compression=9)
gvndst.create_dataset('pressure', data=pressure, compression=9)
def copyVesselnetworkAndComputeFlow(gvdst, gv, bloodflowparams):
'''gdst = group where the data is placed in, does not create a 'vesse' folder in it but writes nodes, edges directly;
gv = source vessel group
'''
if gv.attrs['CLASS'] == 'GRAPH':
gvdst.attrs['CLASS'] = 'GRAPH'
myutils.buildLink(gvdst, 'SOURCE', gv)
# first we need to copy some of the vessel data
gvedst = gvdst.create_group('edges')
gvndst = gvdst.create_group('nodes')
gvedst.attrs['COUNT'] = gv['edges'].attrs['COUNT']
gvndst.attrs['COUNT'] = gv['nodes'].attrs['COUNT']
gv.copy('lattice',gvdst)
for name in ['lattice_pos', 'roots','bc_conductivity_value','bc_node_index','bc_type','bc_value']:
gv['nodes'].copy(name, gvndst)
for name in ['radius', 'node_a_index', 'node_b_index']:
gv['edges'].copy(name, gvedst)
if gv.attrs['CLASS'] == 'REALWORLD':
gvdst.attrs['CLASS'] = 'REALWORLD'
myutils.buildLink(gvdst, 'SOURCE', gv)
# first we need to copy some of the vessel data
gvedst = gvdst.create_group('edges')
gvndst = gvdst.create_group('nodes')
gvedst.attrs['COUNT'] = gv['edges'].attrs['COUNT']
gvndst.attrs['COUNT'] = gv['nodes'].attrs['COUNT']
#gv.copy('lattice',gvdst)
for name in ['world_pos', 'roots','bc_conductivity_value','bc_node_index','bc_type','bc_value']:
gv['nodes'].copy(name, gvndst)
for name in ['radius', 'node_a_index', 'node_b_index']:
gv['edges'].copy(name, gvedst)
# then we recompute blood flow because the alorithm has changed and we may or may not want hematocrit
pressure, flow, shearforce, hematocrit, flags = krebsutils.calc_vessel_hydrodynamics_(gv, calc_hematocrit=True, return_flags = True, override_hematocrit= True, bloodflowparams = bloodflowparams,storeCalculationInHDF=False)
# then we save the new data to complete the network copy
gvedst.create_dataset('flow' , data = flow , compression = 9)
gvedst.create_dataset('shearforce', data = shearforce , compression = 9)
gvedst.create_dataset('hematocrit', data = hematocrit , compression = 9)
gvedst.create_dataset('flags' , data = flags , compression = 9)
gvndst.create_dataset('pressure' , data = pressure , compression = 9)