def addIsosurface(self, volumedata, level, style_object, clip_object,
clip_style_object):
vb = volumedata.value_bounds
wb = volumedata.worldbox
difference = vb[1] - vb[0]
if __debug__:
print('Adding Isosuface! See if threshold is reasonable:')
print('vb[1]-vb[0]: %f ' % difference)
threshold = -(level - vb[0]) / difference
if np.isnan(threshold) or np.isinf(threshold):
threshold = -1.
o = pv.Isosurface(
pv.Function('-%s(x,y,z)' % (volumedata.name)),
['max_gradient', volumedata.max_grad],
pv.ContainedBy(pv.Box(wb[:, 0], wb[:, 1])),
['threshold', threshold],
['all_intersections'],
#['scale', (wb[:,1]-wb[:,0])],
#['translate', (wb[:,0])],
)
o = pv.Object(o, style_object())
if clip_object:
s = krebsutils.povray_clip_object_str(clip_object,
str(clip_style_object))
if s:
o = pv.Intersection(o, s)
o.write(self.pvfile)
pigment {
color rgb<1,0.5, 0.1>
}
finish {
specular 0.1
ambient 1.
}
}'''
t1 = pv.Sphere((0, 0, 0), (tumRadius - shellHalfThickness) * trafo.w,
style)
t2 = pv.Sphere((0, 0, 0), (tumRadius + shellHalfThickness) * trafo.w,
style)
o = pv.Difference(t2, t1)
clipStyle = "pigment { color rgb<%0.2f,%0.2f,%0.2f> }" % defaultCrossSectionColor
clip = clipFactory(kwargs.get('tumor_clip', None))
s = krebsutils.povray_clip_object_str(clip, clipStyle)
if s:
o = pv.Intersection(o, s)
o.write(epv.pvfile)
CallPovrayAndOptionallyMakeMPLPlot(epv, imagefn, cm, label, **kwargs)
def renderScene(po2group, imagefn, options):
dataman = myutils.DataManager(2, [DataDetailedPO2(), DataBasicVessel()])
gvessels, gtumor = OpenVesselAndTumorGroups(po2group)
po2vessels, po2field_ld, po2field, parameters = dataman(
'detailedPO2', po2group)
po2vessels = np.average(po2vessels, axis=0)