def analyzeTumorShape(dataset,
do_curvature=True,
do_integrals=True,
do_linecomps=False,
contourspec=('S', 0.)):
out = Struct()
#generate tumorsurface
contour_name, contour_value = contourspec
assert contour_value in (0., 0.5)
dataset.GetPointData().SetActiveScalars(contour_name)
iso = vtkcommon.vtkContour(dataset, contour_value)
# measurement
if do_linecomps:
lc, pts = vtkcommon.vtkGetLineComponents(iso)
out['lines'] = lc
out['points'] = pts
if do_curvature:
# curvature
tmp = vtkcommon.vtkCurvature(iso, 9)
out['curvature'] = np.asarray(vtkcommon.fromVtkArray(
tmp.GetPointData().GetArray("curvature")),
dtype=np.float32)
del tmp
if do_integrals:
# integrate volume (area, length)
_, _, out['iso_area'] = vtkcommon.vtkIntegrateData(iso)
# integrated data
cd, pd, volume = vtkcommon.vtkIntegrateData(dataset)
cd = dict((dataset.GetCellData().GetArray(i).GetName(), cd[i])
for i in xrange(dataset.GetCellData().GetNumberOfArrays()))
pd = dict((dataset.GetPointData().GetArray(i).GetName(), pd[i])
for i in xrange(dataset.GetPointData().GetNumberOfArrays()))
data = cd.copy()
data.update(pd)
out['tumor_volume'] = (
data[contour_name] +
volume) * 0.5 if contour_value == 0 else data[contour_name]
out['radius_estimate'] = math.sqrt(out.tumor_volume / math.pi)
out['area_estimate'] = 2. * math.pi * out.radius_estimate
return out
size = (401, 41, 41),
scale = 10., # gives 4 x 0.4 x 0.4 mm^3 length
pgrad = PressureGradientFromFlowRate(3.3e6, 50., _paramsbf),
r = 50.,
ld_type = 'quad',
direction_mode = 0,
)
basecase = namedtuple('Params', 'paramsbf, paramspo2, paramsTube')(_paramsbf, _paramspo2, _paramstube)
basecase.paramspo2['massTransferCoefficientModelNumber'] = 1
basecase.paramspo2['conductivity_coeff1'] = 7.2
basecase.paramspo2['conductivity_coeff2'] = 4.0
basecase.paramspo2['conductivity_coeff3'] = 0.0
literature_cases = Struct()
# this is supposed to reproduce the cases from nair 1989
# where o2 diffuses from a perfused pipe through a block
# of rubber.
nair_release = deepcopy(basecase)
nair_release.paramsTube['size'] = (401, 19, 19)
nair_release.paramsTube['r'] = 27*0.5 # FUUUU ... paper gives diameter, must convert to radius
nair_release.paramsTube['pgrad'] = PressureGradientFromFlowRate(3.3e6, 27.*0.5, _paramsbf) # flow rate of 12 ul /hr
nair_release.paramspo2['tissue_po2_boundary_condition'] = 'dirichlet_yz'
nair_release.paramspo2['po2init_r0'] = 160
nair_release.paramspo2['po2init_cutoff'] = 160
nair_release.paramspo2['mmcons_m0_tum'] = 0
nair_release.paramspo2['mmcons_m0_norm'] = 0
nair_release.paramspo2['solubility_tissue'] = 1
nair_release.paramspo2['D_tissue'] = 0.94
def __init__(self):
self.data = Struct(rBV_by_iter=[],
radii_prob=[],
lengths_by_rad=[],
lengths_prob=[],
num_branches_by_rad=[])
import os, sys
import h5py
import os, sys
import posixpath
import numpy as np
import collections
import matplotlib
import matplotlib.pyplot as plt
import mpl_utils
import extensions
from mystruct import Struct
import myutils
dataconfigs = [
Struct(name='kdiff_cells', rng='auto', title=r'kdiff_cells'),
Struct(name='kdiff_obst', rng='auto', title=r'kdiff_obst'),
Struct(name='necro', rng=(-0.1, 1.1), title=r'necro'),
Struct(name='totalconc', rng=None, title=r'vol. ratio $\phi + m$'),
Struct(name='conc', rng=(-0.1, 1.1), title=r'vol. ratio $\phi$'),
Struct(name='conc_necro', rng=(-0.1, 1.1), title=r'vol. ratio $d$'),
Struct(name='obstacle', rng=(-0.1, 1.1), title=r'obst. ratio $m$'),
Struct(name='oxy', rng=(-0.1, 1.1), title=r'O$_2\, c$'),
Struct(name='oxy_sources', rng=(-0.1, 1.1), title=r'$\Gamma_c$'),
Struct(name='fieldOxy', rng=(-0.1, 1.1), title=r'O$_2$'),
Struct(name='vel_0', rng='auto', coords='xface', title=r'$v_x$'),
Struct(name='ls', rng='zero-centered', title=r'$\theta$'),
Struct(name='vel', rng='zero-centered', title=r'$v_x$'),
Struct(name='press', rng='auto', title=r'pressure $\Sigma$'),
Struct(name='ptc', rng=(0., 1.), title=r'$\Theta_\epsilon(\theta)$'),
Struct(name='sources',
def H5PrintOpt():
return Struct(recursive=False,
print_full_dataset=0,
print_attributes=False,
print_eval=None)