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 write(gmeasure, name):
press, flow, force, hema = krebsutils.calc_vessel_hydrodynamics(
vesselgroup, True)
grp = gmeasure.create_group(name)
egrp = grp.create_group('edges')
ngrp = grp.create_group('nodes')
ngrp.create_dataset('h_press', data=press, compression=9)
egrp.create_dataset('h_flow', data=flow, compression=9)
egrp.create_dataset('h_hema', data=hema, compression=9)
egrp.create_dataset('h_force', data=force, compression=9)
def create_Y_sample(file_to_save):
radii = [2, 2, np.power(2**3 + 2**3, 1 / 3.)]
radii = [radius * 1.2 for radius in radii]
N_edges = len(radii)
file_to_save.create_group('vessels')
edgegrp = file_to_save['vessels'].create_group("edges")
edgegrp.attrs.create('COUNT', N_edges)
ds_nodeA = edgegrp.create_dataset('node_a_index', data=[0, 1, 3])
ds_nodeB = edgegrp.create_dataset('node_b_index', data=[3, 3, 2])
ds_radius = edgegrp.create_dataset('radius', data=radii)
ds_flags = edgegrp.create_dataset('flags',
data=[
int(krebsutils.VEIN),
int(krebsutils.VEIN),
int(krebsutils.VEIN)
])
points = []
points.append([-100, +100, 0])
points.append([-100, -100, 0])
points.append([0, 0, 100])
points.append([0, 0, 0])
N_nodes = len(points)
nodegrp = file_to_save['vessels'].create_group("nodes")
nodegrp.attrs.create('COUNT', N_nodes)
ds_roots = file_to_save['vessels/nodes'].create_dataset('roots',
data=[0, 1, 2])
ds_bc_node_index = file_to_save['vessels/nodes'].create_dataset(
'bc_node_index', data=[0, 1, 2])
#dummy pressure for compatiblility
#ds_pressure = f3['vessels/nodes'].create_dataset('roots_pressure', data = roots_pressure)
#this works
#ds_value_of_bc = f2['symetricA/vessels/nodes'].create_dataset('bc_value', data=[70*0.133,10*0.133])
ds_value_of_bc = file_to_save['vessels/nodes'].create_dataset(
'bc_value', data=[2, 2, 1])
ds_conductivity_of_bc = file_to_save['vessels/nodes'].create_dataset(
'bc_conductivity_value', data=[0, 0, 0])
ds_bctyp_of_roots = file_to_save['vessels/nodes'].create_dataset(
'bc_type', data=[1, 1, 1])
ds_world_pos = file_to_save['vessels/nodes'].create_dataset(
'world_pos', data=np.array(points))
file_to_save['vessels'].attrs.create('CLASS', 'REALWORLD')
#no bloodflowParams --> simple --> no hematocrit output
(pressure, flow, shearforce,
flags) = krebsutils.calc_vessel_hydrodynamics(file_to_save['vessels'],
return_flags=True)
# then we save the new data to complete the network copy
edgegrp.create_dataset('flow', data=flow, compression=9)
edgegrp.create_dataset('shearforce', data=shearforce, compression=9)
nodegrp.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 createMostBasic_world(fn):
points = []
points.append([-5, 0, 0])
p1 = [0, 0, 0]
p2 = [2.5, 3, 0]
p3 = [7.5, 3, 0]
p4 = [10, 0, 0]
p5 = [2.5, -3, 0]
p6 = [7.5, -3, 0]
p7 = [15, 0, 0]
points.append(p1)
points.append(p2)
points.append(p3)
points.append(p4)
points.append(p5)
points.append(p6)
points.append(p7)
node_a_index = [0, 1, 2, 3, 1, 5, 6, 4]
node_b_index = [1, 2, 3, 4, 5, 6, 4, 7]
flags = []
radii = []
flags.append(int(ku.ARTERY)) #0
radii.append(7)
flags.append(int(ku.ARTERY)) #1
radii.append(5)
flags.append(int(ku.CAPILLARY)) #2
radii.append(3)
flags.append(int(ku.VEIN)) #3
radii.append(6)
flags.append(int(ku.ARTERY)) #4
radii.append(5)
flags.append(int(ku.CAPILLARY)) #5
radii.append(3)
flags.append(int(ku.VEIN)) #6
radii.append(6)
flags.append(int(ku.VEIN)) #7
radii.append(10)
# flags.append(int(ku.VEIN))#8
# radii.append(level1)
# flags.append(int(ku.ARTERY))#9
# radii.append(level2)
# flags.append(int(ku.ARTERY))#10
# radii.append(level3)
# flags.append(int(ku.CAPILLARY))#11
# radii.append(level3)
# flags.append(int(ku.VEIN))#12
# radii.append(level3)
# flags.append(int(ku.ARTERY))#13
# radii.append(level3)
# flags.append(int(ku.CAPILLARY))#14
# radii.append(level3)
# flags.append(int(ku.VEIN))#15
# radii.append(level3)
# flags.append(int(ku.VEIN))#16
# radii.append(level2)
# flags.append(int(ku.CAPILLARY))#17
# radii.append(level3)
# #mirror x axis
# for i in range(len(points)):
# points.append([points[i][0],-points[i][1],points[i][2]])
#
#
# #double flags
# for i in range(len(flags)):
# flags.append(flags[i])
# radii.append(radii[i])
#
# #add entrence
# flags.append(int(ku.ARTERY))
# radii.append(level0)
# points.append([-13,0,0])
# flags.append(int(ku.VEIN))
# radii.append(level0)
# points.append([13,0,0])
#
# def reverse_xy(points):
# points2 = []
# scale = 100
# for point in points:
# points2.append([point[1]*scale,point[0]*scale,point[2]*scale])
# return points2
#
# #points = reverse_xy(points)
# points = scale_points(points)
# #add circulated flag
# flags2=[]
# for aflag in flags:
# flags2.append(np.bitwise_or(ku.CIRCULATED,aflag))
#
# #this datalist is after successfull adaption with all signals
# datalist=[13.301738,9.563003,7.1691427,7.108207,5.7596083,5.6054125,5.584573,6.330745,8.065095,9.596836,7.166868,
# 5.7524166,5.6175594,7.166868,5.7524166,5.6175594,6.354387,5.704988,13.301738,9.563003,7.1691427,7.108207,
# 5.7596083,5.6054125,5.584573,6.330745,8.065095,9.596836,7.166868,5.7524166,5.6175594,7.166868,5.7524166,
# 5.6175594,6.354387,5.704988,17.057396,9.972254]
# #radii = np.array(datalist)
# #radii=10*np.ones(len(node_a_index))
# #radii=6.5*np.ones(len(node_a_index))
# #write the data to a h5 file
# #f2 = h5files.open(fn,'w')
f2 = fn
f2.create_group('mostBasic_world/vessels')
#edge stuff
N_edges = len(radii)
edgegrp = f2['mostBasic_world/vessels'].create_group("edges")
edgegrp.attrs.create('COUNT', N_edges)
ds_nodeA = edgegrp.create_dataset('node_a_index', data=node_a_index)
ds_nodeB = edgegrp.create_dataset('node_b_index', data=node_b_index)
ds_radius = edgegrp.create_dataset('radius', data=radii)
#ds_hema = edgegrp.create_dataset('hematocrit', data=hema)
#ds_flow = edgegrp.create_dataset('flow', data=flow)
#mw_vessel_flags = get_flags_from_other_file()
ds_vesselflags = edgegrp.create_dataset('flags', data=flags)
#node stuff
N_nodes = len(points)
nodegrp = f2['mostBasic_world/vessels'].create_group("nodes")
nodegrp.attrs.create('COUNT', N_nodes)
ds_roots = f2['mostBasic_world/vessels/nodes'].create_dataset('roots',
data=[0, 7])
ds_bc_node_index = f2['mostBasic_world/vessels/nodes'].create_dataset(
'bc_node_index', data=[0, 7])
#dummy pressure for compatiblility
#ds_pressure = f3['vessels/nodes'].create_dataset('roots_pressure', data = roots_pressure)
#this works
#ds_value_of_bc = f2['symetricA/vessels/nodes'].create_dataset('bc_value', data=[70*0.133,10*0.133])
ds_value_of_bc = f2['mostBasic_world/vessels/nodes'].create_dataset(
'bc_value', data=[5, 3])
ds_bctyp_of_roots = f2['mostBasic_world/vessels/nodes'].create_dataset(
'bc_type', data=[1, 1])
ds_world_pos = f2['mostBasic_world/vessels/nodes'].create_dataset(
'world_pos', data=np.array(points))
f2['mostBasic_world/vessels'].attrs.create('CLASS', 'REALWORLD')
import krebsjobs.parameters.parameterSetsAdaption
#set_name = 'adaption_symetric_world'
set_name = 'adaption_symetricA_world_break'
#set_name = 'adaption_symetric_world'
adaptionParams = getattr(krebsjobs.parameters.parameterSetsAdaption,
set_name)
#CALCULATE!!!!
myutils.hdf_write_dict_hierarchy(f2['/'], 'mostBasic_world/parameters',
adaptionParams)
f2['mostBasic_world/parameters'].attrs.create('name', set_name)
f2['/'].file.flush()
dd = ku.calc_vessel_hydrodynamics(
f2['mostBasic_world/vessels'],
adaptionParams['calcflow']['includePhaseSeparationEffect'], False,
None, adaptionParams['calcflow'])
print('Calcflow done')
def createSymetricIrregular_world(fn):
points = []
points.append([-10, 0, 0])
p1 = [-6, 4, 0]
p2 = [-3, 6, 0]
p3 = [-1, 7, 0]
p4 = [-1, 5, 0]
p5 = [-3, 2, 0]
p6 = [-1, 3, 0]
p7 = [-1, 1, 0]
points.append(p1)
points.append(p2)
points.append(p3)
points.append(p4)
points.append(p5)
points.append(p6)
points.append(p7)
#mirror y axis
for i in range(len(points)):
points.append([-points[i][0], points[i][1], points[i][2]])
node_a_index = [
0, 1, 2, 2, 3, 11, 12, 10, 9, 1, 5, 6, 14, 5, 7, 15, 13, 4, 0, 17, 18,
18, 19, 27, 28, 26, 25, 17, 21, 22, 30, 21, 23, 31, 29, 20, 32, 8
]
node_b_index = [
1, 2, 3, 4, 11, 10, 10, 9, 8, 5, 6, 14, 13, 7, 15, 13, 9, 12, 17, 18,
19, 20, 27, 26, 26, 25, 8, 21, 22, 30, 29, 23, 31, 29, 25, 28, 0, 33
]
flags = []
radii = []
flags.append(int(ku.ARTERY)) #0
radii.append(9.5)
flags.append(int(ku.ARTERY)) #1
radii.append(8)
flags.append(int(ku.ARTERY)) #2
radii.append(7.5)
flags.append(int(ku.ARTERY)) #3
radii.append(7.)
flags.append(int(ku.CAPILLARY)) #4
radii.append(6.5)
flags.append(int(ku.VEIN)) #5
radii.append(7.)
flags.append(int(ku.VEIN)) #6
radii.append(7.5)
flags.append(int(ku.VEIN)) #7
radii.append(8)
flags.append(int(ku.VEIN)) #8
radii.append(9.5)
flags.append(int(ku.ARTERY)) #9
radii.append(8)
flags.append(int(ku.ARTERY)) #10
radii.append(7.5)
flags.append(int(ku.CAPILLARY)) #11
radii.append(6.5)
flags.append(int(ku.VEIN)) #12
radii.append(7.5)
flags.append(int(ku.ARTERY)) #13
radii.append(7.5)
flags.append(int(ku.CAPILLARY)) #14
radii.append(6.5)
flags.append(int(ku.VEIN)) #15
radii.append(7.5)
flags.append(int(ku.VEIN)) #16
radii.append(8)
flags.append(int(ku.CAPILLARY)) #17
radii.append(6.5)
#mirror x axis
for i in range(len(points)):
points.append([points[i][0], -points[i][1], points[i][2]])
#double flags
for i in range(len(flags)):
flags.append(flags[i])
radii.append(radii[i])
#add entrence
flags.append(int(ku.ARTERY))
radii.append(11.5)
points.append([-13, 0, 0])
flags.append(int(ku.VEIN))
radii.append(11.5)
points.append([13, 0, 0])
def reverse_xy(points):
points2 = []
scale = 100
for point in points:
points2.append([point[1] * scale, point[0] * scale, point[2]] *
scale)
return points2
def scale_points(points):
points2 = []
scale = 100
for point in points:
points2.append([point[0] * scale, point[1] * scale, point[2]] *
scale)
return points2
#points = reverse_xy(points)
points = scale_points(points)
#add circulated flag
flags2 = []
for aflag in flags:
flags2.append(np.bitwise_or(ku.CIRCULATED, aflag))
#radii=30*np.ones(len(node_a_index))
#radii=10*np.ones(len(node_a_index))
#now we will randomize the points a little bit
def screw_points(points, variation):
points2 = []
for point in points:
points2.append([
point[0] + point[0] * np.random.normal(0, variation),
point[1] + point[1] * np.random.normal(0, 2 * variation),
point[2] + point[2] * np.random.normal(0, variation)
])
return points2
if os.path.isfile('screwed_points.h5'):
f_out = h5py.File('screwed_points.h5', 'r')
points = np.asarray(f_out['screwed_points'])
else:
points = screw_points(points, 0.05)
f_out = h5py.File('screwed_points.h5', 'w')
f_out.create_dataset('screwed_points', data=points)
f_out.close()
#write the data to a h5 file
#f2 = h5files.open(fn,'w')
f2 = fn
f2.create_group('symetricIrregular/vessels')
#edge stuff
N_edges = len(radii)
edgegrp = f2['symetricIrregular/vessels'].create_group("edges")
edgegrp.attrs.create('COUNT', N_edges)
ds_nodeA = edgegrp.create_dataset('node_a_index', data=node_a_index)
ds_nodeB = edgegrp.create_dataset('node_b_index', data=node_b_index)
ds_radius = edgegrp.create_dataset('radius', data=radii)
#ds_hema = edgegrp.create_dataset('hematocrit', data=hema)
#ds_flow = edgegrp.create_dataset('flow', data=flow)
#mw_vessel_flags = get_flags_from_other_file()
ds_vesselflags = edgegrp.create_dataset('flags', data=flags2)
#node stuff
N_nodes = len(points)
nodegrp = f2['symetricIrregular/vessels'].create_group("nodes")
nodegrp.attrs.create('COUNT', N_nodes)
ds_roots = f2['symetricIrregular/vessels/nodes'].create_dataset(
'roots', data=[32, 33])
ds_bc_node_index = f2['symetricIrregular/vessels/nodes'].create_dataset(
'bc_node_index', data=[32, 33])
#dummy pressure for compatiblility
#ds_pressure = f3['vessels/nodes'].create_dataset('roots_pressure', data = roots_pressure)
ds_value_of_bc = f2['symetricIrregular/vessels/nodes'].create_dataset(
'bc_value', data=[70 * 0.133, 2.5e6])
ds_bctyp_of_roots = f2['symetricIrregular/vessels/nodes'].create_dataset(
'bc_type', data=[1, 2])
ds_world_pos = f2['symetricIrregular/vessels/nodes'].create_dataset(
'world_pos', data=np.array(points))
f2['symetricIrregular/vessels'].attrs.create('CLASS', 'REALWORLD')
import krebsjobs.parameters.parameterSetsAdaption
set_name = 'adaption_symetricIrregular_world'
adaptionParams = getattr(krebsjobs.parameters.parameterSetsAdaption,
set_name)
#CALCULATE!!!!
myutils.hdf_write_dict_hierarchy(f2['/'], 'symetricIrregular/parameters',
adaptionParams)
f2['symetricIrregular/parameters'].attrs.create('name', set_name)
f2['/'].file.flush()
dd = ku.calc_vessel_hydrodynamics(
f2['symetricIrregular/vessels'],
adaptionParams['calcflow']['includePhaseSeparationEffect'], False,
None, adaptionParams['calcflow'])
print('Calcflow done')
#r = adap.computeAdaption(f3['vessels'], None, adaptionParams, adaptionParams['calcflow'], f3['/'] )
#dst_grp = f2['/symetric'].create_group('symetric/vessels_after_adaption')
dd = adap.computeAdaption_(
f2['/symetricIrregular'].create_group('vessels_after_adaption'),
f2['symetricIrregular/vessels'], adaptionParams)
a = os.system(
"python2 /localdisk/thierry/tumorcode/py/krebs/hdfvessels2vtk.py test_configs.h5 /symetricIrregular/vessels_after_adaption/vessels_after_adaption"
)
os.system(
"python2 /localdisk/thierry/tumorcode/py/krebs/povrayRenderVessels.py test_configs.h5 /symetricIrregular/vessels_after_adaption/vessels_after_adaption"
)
def createSymetric_worldB(fn):
points = []
points.append([-10, 0, 0])
p1 = [-6, 4, 0]
p2 = [-3, 6, 0]
p3 = [-1, 7, 0]
p4 = [-1, 5, 0]
p5 = [-3, 2, 0]
p6 = [-1, 3, 0]
p7 = [-1, 1, 0]
points.append(p1)
points.append(p2)
points.append(p3)
points.append(p4)
points.append(p5)
points.append(p6)
points.append(p7)
#mirror y axis
for i in range(len(points)):
points.append([-points[i][0], points[i][1], points[i][2]])
node_a_index = [
0, 1, 2, 2, 3, 11, 12, 10, 9, 1, 5, 6, 14, 5, 7, 15, 13, 4, 0, 17, 18,
18, 19, 27, 28, 26, 25, 17, 21, 22, 30, 21, 23, 31, 29, 20, 32, 8
]
node_b_index = [
1, 2, 3, 4, 11, 10, 10, 9, 8, 5, 6, 14, 13, 7, 15, 13, 9, 12, 17, 18,
19, 20, 27, 26, 26, 25, 8, 21, 22, 30, 29, 23, 31, 29, 25, 28, 0, 33
]
flags = []
radii = []
# level0 = 12.
# level1 = 10.1
# level2 = 8.5
# level3 = 7.1
level0 = 11.95
level1 = 9.55
level2 = 7.55
level3 = 6.0
flags.append(int(ku.ARTERY)) #0
radii.append(level1)
flags.append(int(ku.ARTERY)) #1
radii.append(level2)
flags.append(int(ku.ARTERY)) #2
radii.append(level3)
flags.append(int(ku.ARTERY)) #3
radii.append(level3)
flags.append(int(ku.CAPILLARY)) #4
radii.append(level3)
flags.append(int(ku.VEIN)) #5
radii.append(level3)
flags.append(int(ku.VEIN)) #6
radii.append(level3)
flags.append(int(ku.VEIN)) #7
radii.append(level2)
flags.append(int(ku.VEIN)) #8
radii.append(level1)
flags.append(int(ku.ARTERY)) #9
radii.append(level2)
flags.append(int(ku.ARTERY)) #10
radii.append(level3)
flags.append(int(ku.CAPILLARY)) #11
radii.append(level3)
flags.append(int(ku.VEIN)) #12
radii.append(level3)
flags.append(int(ku.ARTERY)) #13
radii.append(level3)
flags.append(int(ku.CAPILLARY)) #14
radii.append(level3)
flags.append(int(ku.VEIN)) #15
radii.append(level3)
flags.append(int(ku.VEIN)) #16
radii.append(level2)
flags.append(int(ku.CAPILLARY)) #17
radii.append(level3)
#mirror x axis
for i in range(len(points)):
points.append([points[i][0], -points[i][1], points[i][2]])
#double flags
for i in range(len(flags)):
flags.append(flags[i])
radii.append(radii[i])
#add entrence
flags.append(int(ku.ARTERY))
radii.append(level0)
points.append([-13, 0, 0])
flags.append(int(ku.VEIN))
radii.append(level0)
points.append([13, 0, 0])
def reverse_xy(points):
points2 = []
scale = 100
for point in points:
points2.append([point[1] * scale, point[0] * scale, point[2]] *
scale)
return points2
#points = reverse_xy(points)
points = scale_points(points)
#add circulated flag
flags2 = []
for aflag in flags:
flags2.append(np.bitwise_or(ku.CIRCULATED, aflag))
#this datalist is after successfull adaption with all signals
datalist = [
13.301738, 9.563003, 7.1691427, 7.108207, 5.7596083, 5.6054125,
5.584573, 6.330745, 8.065095, 9.596836, 7.166868, 5.7524166, 5.6175594,
7.166868, 5.7524166, 5.6175594, 6.354387, 5.704988, 13.301738,
9.563003, 7.1691427, 7.108207, 5.7596083, 5.6054125, 5.584573,
6.330745, 8.065095, 9.596836, 7.166868, 5.7524166, 5.6175594, 7.166868,
5.7524166, 5.6175594, 6.354387, 5.704988, 17.057396, 9.972254
]
#radii = np.array(datalist)
#radii=10*np.ones(len(node_a_index))
#radii=6.5*np.ones(len(node_a_index))
#write the data to a h5 file
#f2 = h5files.open(fn,'w')
f2 = fn
f2.create_group('symetricB/vessels')
#edge stuff
N_edges = len(radii)
edgegrp = f2['symetricB/vessels'].create_group("edges")
edgegrp.attrs.create('COUNT', N_edges)
ds_nodeA = edgegrp.create_dataset('node_a_index', data=node_a_index)
ds_nodeB = edgegrp.create_dataset('node_b_index', data=node_b_index)
ds_radius = edgegrp.create_dataset('radius', data=radii)
#ds_hema = edgegrp.create_dataset('hematocrit', data=hema)
#ds_flow = edgegrp.create_dataset('flow', data=flow)
#mw_vessel_flags = get_flags_from_other_file()
ds_vesselflags = edgegrp.create_dataset('flags', data=flags2)
#node stuff
N_nodes = len(points)
nodegrp = f2['symetricB/vessels'].create_group("nodes")
nodegrp.attrs.create('COUNT', N_nodes)
ds_roots = f2['symetricB/vessels/nodes'].create_dataset('roots',
data=[32, 33])
ds_bc_node_index = f2['symetricB/vessels/nodes'].create_dataset(
'bc_node_index', data=[32, 33])
#dummy pressure for compatiblility
#ds_pressure = f3['vessels/nodes'].create_dataset('roots_pressure', data = roots_pressure)
ds_value_of_bc = f2['symetricB/vessels/nodes'].create_dataset(
'bc_value', data=[70 * 0.133, 0.5e6])
ds_bctyp_of_roots = f2['symetricB/vessels/nodes'].create_dataset(
'bc_type', data=[1, 2])
ds_world_pos = f2['symetricB/vessels/nodes'].create_dataset(
'world_pos', data=np.array(points))
f2['symetricB/vessels'].attrs.create('CLASS', 'REALWORLD')
import krebsjobs.parameters.parameterSetsAdaption
set_name = 'adaption_symetricB_world'
adaptionParams = getattr(krebsjobs.parameters.parameterSetsAdaption,
set_name)
#CALCULATE!!!!
myutils.hdf_write_dict_hierarchy(f2['/'], 'symetricB/parameters',
adaptionParams)
f2['symetricB/parameters'].attrs.create('name', set_name)
f2['/'].file.flush()
dd = ku.calc_vessel_hydrodynamics(
f2['symetricB/vessels'],
adaptionParams['calcflow']['includePhaseSeparationEffect'], False,
None, adaptionParams['calcflow'])
print('Calcflow done')
#r = adap.computeAdaption(f3['vessels'], None, adaptionParams, adaptionParams['calcflow'], f3['/'] )
#dst_grp = f2['/symetric'].create_group('symetric/vessels_after_adaption')
dd = adap.computeAdaption_(
f2['/symetricB'].create_group('vessels_after_adaption'),
f2['symetricB/vessels'], adaptionParams)
a = os.system(
"python2 /localdisk/thierry/tumorcode/py/krebs/hdfvessels2vtk.py test_configs.h5 /symetricB/vessels_after_adaption/vessels_after_adaption"
)
os.system(
"python2 /localdisk/thierry/tumorcode/py/krebs/povrayRenderVessels.py test_configs.h5 /symetricB/vessels_after_adaption/vessels_after_adaption"
)
def createAsymetric_world(fn):
points = []
points.append([0, 0, 0])
points.append([200, 0, 0])
points.append([400, 0, 0])
points.append([600, 0, 0])
points.append([800, 0, 0])
points.append([1000, 0, 0])
points.append([1200, 0, 0])
points.append([1400, 0, 0])
points.append([1450, 120, 0])
points.append([1500, 240, 0])
points.append([1500, 360, 0])
points.append([1450, 480, 0])
points.append([1400, 600, 0])
points.append([1350, 480, 0])
points.append([1300, 360, 0])
points.append([1300, 240, 0])
points.append([1350, 120, 0])
points.append([1200, 600, 0])
points.append([1000, 600, 0])
points.append([800, 600, 0])
points.append([600, 600, 0])
points.append([400, 600, 0])
points.append([200, 600, 0])
points.append([0, 600, 0])
points.append([1200, 360, 0])
points.append([1000, 360, 0])
points.append([800, 360, 0])
points.append([600, 360, 0])
points.append([400, 360, 0])
points.append([200, 360, 0])
points.append([1200, 240, 0])
points.append([1000, 240, 0])
points.append([800, 240, 0])
points.append([600, 240, 0])
points.append([400, 240, 0])
points.append([200, 240, 0])
def scale_points(points):
points2 = []
scale = 1
for point in points:
points2.append([-point[0] * scale, -point[1] * scale, point[2]] *
scale)
return points2
#points = reverse_xy(points)
points = scale_points(points)
node_a_index = []
node_b_index = []
flags = []
radii = []
#1
node_a_index.append(0)
node_b_index.append(1)
flags.append(int(ku.ARTERY))
radii.append(7.5)
#2
node_a_index.append(1)
node_b_index.append(2)
flags.append(int(ku.ARTERY))
radii.append(7.)
#3
node_a_index.append(2)
node_b_index.append(3)
flags.append(int(ku.ARTERY))
radii.append(6.5)
#4
node_a_index.append(3)
node_b_index.append(4)
flags.append(int(ku.ARTERY))
radii.append(6.0)
#5
node_a_index.append(4)
node_b_index.append(5)
flags.append(int(ku.ARTERY))
radii.append(5.8)
#6
node_a_index.append(5)
node_b_index.append(6)
flags.append(int(ku.ARTERY))
radii.append(5.6)
#7
node_a_index.append(6)
node_b_index.append(7)
flags.append(int(ku.ARTERY))
radii.append(5.4)
#8
node_a_index.append(7)
node_b_index.append(8)
flags.append(int(ku.ARTERY))
radii.append(5.2)
#9
node_a_index.append(8)
node_b_index.append(9)
flags.append(int(ku.ARTERY))
radii.append(5.)
#10
node_a_index.append(9)
node_b_index.append(10)
flags.append(int(ku.CAPILLARY))
radii.append(4.5)
#11
node_a_index.append(10)
node_b_index.append(11)
flags.append(int(ku.VEIN))
radii.append(7.)
#12
node_a_index.append(11)
node_b_index.append(12)
flags.append(int(ku.VEIN))
radii.append(7.)
#13
node_a_index.append(12)
node_b_index.append(13)
flags.append(int(ku.VEIN))
radii.append(7.)
#14
node_a_index.append(13)
node_b_index.append(14)
flags.append(int(ku.VEIN))
radii.append(7.)
#15
node_a_index.append(14)
node_b_index.append(15)
flags.append(int(ku.CAPILLARY))
radii.append(4.5)
#16
node_a_index.append(15)
node_b_index.append(16)
flags.append(int(ku.ARTERY))
radii.append(7.)
#17
node_a_index.append(16)
node_b_index.append(7)
flags.append(int(ku.ARTERY))
radii.append(7.)
#18
node_a_index.append(12)
node_b_index.append(17)
flags.append(int(ku.VEIN))
radii.append(7.)
#19
node_a_index.append(17)
node_b_index.append(18)
flags.append(int(ku.VEIN))
radii.append(7.)
#20
node_a_index.append(18)
node_b_index.append(19)
flags.append(int(ku.VEIN))
radii.append(7.)
#21
node_a_index.append(19)
node_b_index.append(20)
flags.append(int(ku.VEIN))
radii.append(7.)
#22
node_a_index.append(20)
node_b_index.append(21)
flags.append(int(ku.VEIN))
radii.append(7.)
#23
node_a_index.append(21)
node_b_index.append(22)
flags.append(int(ku.VEIN))
radii.append(7.)
#24
node_a_index.append(22)
node_b_index.append(23)
flags.append(int(ku.VEIN))
radii.append(7.)
#25
node_a_index.append(17)
node_b_index.append(24)
flags.append(int(ku.VEIN))
radii.append(7.)
#26
node_a_index.append(18)
node_b_index.append(25)
flags.append(int(ku.VEIN))
radii.append(7.)
#27
node_a_index.append(19)
node_b_index.append(26)
flags.append(int(ku.VEIN))
radii.append(7.)
#28
node_a_index.append(20)
node_b_index.append(27)
flags.append(int(ku.VEIN))
radii.append(7.)
#29
node_a_index.append(21)
node_b_index.append(28)
flags.append(int(ku.VEIN))
radii.append(7.)
#30
node_a_index.append(22)
node_b_index.append(29)
flags.append(int(ku.VEIN))
radii.append(7.)
#31
node_a_index.append(24)
node_b_index.append(30)
flags.append(int(ku.CAPILLARY))
radii.append(4.5)
#32
node_a_index.append(25)
node_b_index.append(31)
flags.append(int(ku.CAPILLARY))
radii.append(4.5)
#33
node_a_index.append(26)
node_b_index.append(32)
flags.append(int(ku.CAPILLARY))
radii.append(4.5)
#34
node_a_index.append(27)
node_b_index.append(33)
flags.append(int(ku.CAPILLARY))
radii.append(4.5)
#35
node_a_index.append(28)
node_b_index.append(34)
flags.append(int(ku.CAPILLARY))
radii.append(4.5)
#36
node_a_index.append(29)
node_b_index.append(35)
flags.append(int(ku.CAPILLARY))
radii.append(4.5)
#37
node_a_index.append(30)
node_b_index.append(6)
flags.append(int(ku.ARTERY))
radii.append(7.)
#38
node_a_index.append(31)
node_b_index.append(5)
flags.append(int(ku.ARTERY))
radii.append(7.)
#39
node_a_index.append(32)
node_b_index.append(4)
flags.append(int(ku.ARTERY))
radii.append(7.)
#40
node_a_index.append(33)
node_b_index.append(3)
flags.append(int(ku.ARTERY))
radii.append(7.)
#41
node_a_index.append(34)
node_b_index.append(2)
flags.append(int(ku.ARTERY))
radii.append(7.)
#42
node_a_index.append(35)
node_b_index.append(1)
flags.append(int(ku.ARTERY))
radii.append(7.)
#add circulated flag
flags2 = []
for aflag in flags:
flags2.append(np.bitwise_or(ku.CIRCULATED, aflag))
#radii=30*np.ones(len(node_a_index))
#write the data to a h5 file
#f3 = h5files.open(fn,'w')
f3 = fn
f3.create_group('Asymetric/vessels')
#edge stuff
N_edges = len(radii)
edgegrp = f3['Asymetric/vessels'].create_group("edges")
edgegrp.attrs.create('COUNT', N_edges)
ds_nodeA = edgegrp.create_dataset('node_a_index', data=node_a_index)
ds_nodeB = edgegrp.create_dataset('node_b_index', data=node_b_index)
ds_radius = edgegrp.create_dataset('radius', data=radii)
#ds_hema = edgegrp.create_dataset('hematocrit', data=hema)
#ds_flow = edgegrp.create_dataset('flow', data=flow)
#mw_vessel_flags = get_flags_from_other_file()
ds_vesselflags = edgegrp.create_dataset('flags', data=flags2)
#node stuff
N_nodes = len(points)
nodegrp = f3['Asymetric/vessels'].create_group("nodes")
nodegrp.attrs.create('COUNT', N_nodes)
ds_bc_node_index = f3['Asymetric/vessels/nodes'].create_dataset(
'bc_node_index', data=[0, 23])
ds_roots = f3['Asymetric/vessels/nodes'].create_dataset('roots',
data=[0, 23])
#dummy pressure for compatiblility
#ds_pressure = f3['vessels/nodes'].create_dataset('roots_pressure', data = roots_pressure)
ds_value_of_bc = f3['Asymetric/vessels/nodes'].create_dataset(
'bc_value', data=[70 * 0.133, 2.5e6])
""" Michael 1: press, 2, flow,
Secomb 0: press, 2, flow
"""
ds_bctyp_of_roots = f3['Asymetric/vessels/nodes'].create_dataset(
'bc_type', data=[1, 2])
ds_world_pos = f3['Asymetric/vessels/nodes'].create_dataset(
'world_pos', data=np.array(points))
f3['Asymetric/vessels'].attrs.create('CLASS', 'REALWORLD')
import krebsjobs.parameters.parameterSetsAdaption
set_name = 'adaption_asymetric_world'
adaptionParams = getattr(krebsjobs.parameters.parameterSetsAdaption,
set_name)
#CALCULATE!!!!
myutils.hdf_write_dict_hierarchy(f3['/'], 'Asymetric/parameters',
adaptionParams)
f3['Asymetric/parameters'].attrs.create('name', set_name)
f3['/'].file.flush()
dd = ku.calc_vessel_hydrodynamics(
f3['Asymetric/vessels'],
adaptionParams['calcflow']['includePhaseSeparationEffect'], False,
None, adaptionParams['calcflow'])
print('Calcflow done')
#r = adap.computeAdaption(f3['vessels'], None, adaptionParams, adaptionParams['calcflow'], f3['/'] )
dd = adap.computeAdaption_(
f3['Asymetric'].create_group('vessels_after_adaption'),
f3['Asymetric/vessels'], adaptionParams)
dataman = myutils.DataManager(100, [DataBasicVessel()])
filenames, pattern = args[:-1], args[-1]
files = [
h5files.open(fn, 'a' if options.add_resistor_bc else 'r+')
for fn in filenames
]
groups = list(
itertools.chain.from_iterable(
myutils.walkh5(f, pattern, return_h5objects=True) for f in files))
for vesselgroup in groups:
if options.force_flow_recompute and not options.add_resistor_bc:
(pressure, flow,
shearforce) = krebsutils.calc_vessel_hydrodynamics(vesselgroup)
vessels = dataman.obtain_data('vessel_graph', vesselgroup,
['flags', 'radius'])
vessels.edges['flow'] = flow
vessels.nodes['pressure'] = pressure
else:
vessels = dataman.obtain_data(
'vessel_graph', vesselgroup,
['flow', 'pressure', 'flags', 'radius'])
def DoBC():
conductivities, avgVenousPressure, avgArterialPressure, totalFlow = ComputeVascularTreeBloodFlowResistances(
vessels)
avgConductivity = (totalFlow /
(avgArterialPressure - avgVenousPressure))
print 'avgVenousPressure', avgVenousPressure
def createMostBasic_world(fn):
points = []
points.append([-5, 0, 0])
p1 = [0, 0, 0]
p2 = [2.5, 3, 0]
p3 = [7.5, 3, 0]
p4 = [10, 0, 0]
p5 = [2.5, -3, 0]
p6 = [7.5, -3, 0]
p7 = [15, 0, 0]
points.append(p1)
points.append(p2)
points.append(p3)
points.append(p4)
points.append(p5)
points.append(p6)
points.append(p7)
node_a_index = [0, 1, 2, 3, 1, 5, 6, 4]
node_b_index = [1, 2, 3, 4, 5, 6, 4, 7]
flags = []
radii = []
flags.append(int(ku.ARTERY)) #0
radii.append(7)
flags.append(int(ku.ARTERY)) #1
radii.append(5)
flags.append(int(ku.CAPILLARY)) #2
radii.append(3)
flags.append(int(ku.VEIN)) #3
radii.append(6)
flags.append(int(ku.ARTERY)) #4
radii.append(5)
flags.append(int(ku.CAPILLARY)) #5
radii.append(3)
flags.append(int(ku.VEIN)) #6
radii.append(6)
flags.append(int(ku.VEIN)) #7
radii.append(10)
f2 = fn
f2.create_group('mostBasic_world/vessels')
#edge stuff
N_edges = len(radii)
edgegrp = f2['mostBasic_world/vessels'].create_group("edges")
edgegrp.attrs.create('COUNT', N_edges)
ds_nodeA = edgegrp.create_dataset('node_a_index', data=node_a_index)
ds_nodeB = edgegrp.create_dataset('node_b_index', data=node_b_index)
ds_radius = edgegrp.create_dataset('radius', data=radii)
#ds_hema = edgegrp.create_dataset('hematocrit', data=hema)
#ds_flow = edgegrp.create_dataset('flow', data=flow)
ds_vesselflags = edgegrp.create_dataset('flags', data=flags)
#node stuff
N_nodes = len(points)
nodegrp = f2['mostBasic_world/vessels'].create_group("nodes")
nodegrp.attrs.create('COUNT', N_nodes)
ds_roots = f2['mostBasic_world/vessels/nodes'].create_dataset('roots',
data=[0, 7])
ds_bc_node_index = f2['mostBasic_world/vessels/nodes'].create_dataset(
'bc_node_index', data=[0, 7])
ds_value_of_bc = f2['mostBasic_world/vessels/nodes'].create_dataset(
'bc_value', data=[5, 3])
ds_bctyp_of_roots = f2['mostBasic_world/vessels/nodes'].create_dataset(
'bc_type', data=[1, 1])
ds_world_pos = f2['mostBasic_world/vessels/nodes'].create_dataset(
'world_pos', data=np.array(points))
f2['mostBasic_world/vessels'].attrs.create('CLASS', 'REALWORLD')
'''get some hydrodynamics parameters'''
import krebsjobs.parameters.parameterSetsVesselGen
set_name = 'default'
vesselGenParams = getattr(krebsjobs.parameters.parameterSetsVesselGen,
set_name)
#CALCULATE!!!!
myutils.hdf_write_dict_hierarchy(f2['/'], 'mostBasic_world/parameters',
vesselGenParams['calcflow'])
f2['mostBasic_world/parameters'].attrs.create('name', set_name)
f2['/'].file.flush()
#calc_vessel_hydrodynamics(vesselgroup, calc_hematocrit=False, return_flags=False, override_hematocrit = None, bloodflowparams = dict(),storeCalculationInHDF=False)
dd = ku.calc_vessel_hydrodynamics(
f2['mostBasic_world/vessels'],
bloodflowparams=vesselGenParams['calcflow'],
storeCalculationInHDF=True)
print('Calcflow done')
vesselgrp.create_dataset('edges/hematocrit', data=hema_new)
print("done... deleting double entries")
if __name__ == '__main__':
#write the data to a h5 file
fn = 'apj.h5'
f3 = h5files.open(fn, 'w')
vesselgrp = f3.create_group('vessels')
vesselgrp.attrs.create('CLASS', 'REALWORLD')
'''***** INPUT *****'''
'''path to apj_network_546_segments.txt
this might change during your installation'''
path_to_txt = '/home/usersHR/thierry/tumorcode/py/krebs/adaption'
get_network_from_file(vesselgrp, path_to_txt)
node_label2index = get_nodes_from_file(vesselgrp, path_to_txt)
delete_double_edges(vesselgrp)
correct_vessel_indeces(node_label2index, vesselgrp)
'''***** tumorcode stuff *****'''
import krebsjobs.parameters.parameterSetsAdaption
adaptionParams = getattr(krebsjobs.parameters.parameterSetsAdaption, 'apj')
##CALCULATE!!!!
#pressure, flow, force, hema, flags = ku.calc_vessel_hydrodynamics(f3['vessels'], False, False, None, adaptionParams['calcflow'],storeCalculationInHDF=True)
dd = ku.calc_vessel_hydrodynamics(
f3['vessels'],
return_flags=True,
bloodflowparams=adaptionParams['calcflow'],
storeCalculationInHDF=True)
f3.close
