def DoTheRendering(fn, options):
with EasyPovRayRender(options) as epv:
epv.setBackground(options.background)
cam_fov = 60.
cam_distance_factor = ComputeCameraDistanceFactor(
cam_fov, options.res, wbbox)
epv.setCamera((0, 0, cam_distance_factor * 1.05),
lookat=(0, 0, 0),
fov=cam_fov,
up='y')
epv.addLight(10. * Vec3(1, 0.5, 2), 1.2)
options.vessel_clip = ('zslice', -150 * trafo.w, +150 * trafo.w)
pvcm = matplotlibColormapToPovray('DATACOLORMAP', cm)
epv.declareColorMap(pvcm)
if not options.not_render_volume:
epvvol = epv.declareVolumeData(volumedata,
volume_ld.GetWorldBox())
epv.addVolumeDataSlice(epvvol, (0, 0, planeZCoord), (0, 0, 1.),
pvcm)
if not options.not_render_vessels:
addVesselTree(epv, vessel_graph, trafo=trafo, options=options)
CallPovrayAndOptionallyMakeMPLPlot(epv, fn, cm, label, options)
def renderSliceWithDistribution(vesselgroup, imagefn, options):
vessel_ld = krebsutils.read_lattice_data_from_hdf(
vesselgroup['vessels/lattice'])
vessel_graph = krebsutils.read_vessels_from_hdf(
vesselgroup['vessels'],
['position', 'flags', 'radius', 'pressure', 'shearforce', 'nodeflags'],
return_graph=True)
vessel_graph.edges['radius'] *= 4.
#kwargs = deepcopy(kwargs)
wbbox = vessel_ld.worldBox
trafo = calc_centering_normalization_trafo(wbbox)
height = (wbbox[5] - wbbox[4]) * trafo.w
print('Vessel BBox:' + str(vessel_ld.worldBox))
print(vessel_ld)
print('Post Trafo Ld BBox:' + str(transform_ld(trafo, vessel_ld).worldBox))
hasGfField = 'field_ld' in vesselgroup and vessel_ld.shape[2] == 1
#hasGfField = False
if hasGfField:
volume_ld = krebsutils.read_lattice_data_from_hdf(
vesselgroup['field_ld'])
print('Volume BBox:' + str(volume_ld.worldBox))
print(volume_ld)
volumedata = np.asarray(vesselgroup['gf'])
#print volumedata.shape, volumedata.min(), volumedata.max()
volume_ld = transform_ld(trafo, volume_ld)
print('Post Trafo Volume BBox:' + str(volume_ld.worldBox))
print('volume data bounds:' + str(volumedata.min()),
str(volumedata.max()))
colorfactory(vessel_graph)
with EasyPovRayRender(**options) as epv:
epv.setBackground(options.pop('background', 0.0))
cam_fov = 60.
cam_distance_factor = ComputeCameraDistanceFactor(
cam_fov, options['res'], wbbox)
epv.setCamera((0, 0, cam_distance_factor * 1.05),
lookat=(0, 0, 0),
fov=cam_fov,
up='y')
epv.addLight(10. * Vec3(1, 0.5, 2), 1.2)
cm = matplotlib.cm.ScalarMappable(cmap=cm_gf)
cm.set_clim(-0.01, 1.01)
pvcm = matplotlibColormapToPovray('DATACOLORMAP', cm)
epv.declareColorMap(pvcm)
if hasGfField:
volumedata = epv.declareVolumeData(volumedata, volume_ld.worldBox,
volume_ld)
epv.addVolumeDataSlice(volumedata, (0, 0, 0), (0, 0, 1.), pvcm)
addVesselTree(epv, vessel_graph, trafo=trafo, **options)
imagefn = epv.render(imagefn)
cm = InsertGraphColors(vessel_graph, volumedata, data_name)
with EasyPovRayRender(options) as epv:
epv.setBackground(options.background)
cam_fov = 60.
cam_distance_factor = ComputeCameraDistanceFactor(
cam_fov, options.res, wbbox)
epv.setCamera((0, 0, cam_distance_factor * 1.05),
lookat=(0, 0, 0),
fov=cam_fov,
up='y')
epv.addLight(10. * Vec3(1, 0.5, 2), 1.2)
if (wbbox[1] - wbbox[0]) < (wbbox[5] - wbbox[4]) * 2.:
options.vessel_clip = ('zslice', -300 * trafo.w, +300 * trafo.w)
addVesselTree(epv, vessel_graph, trafo=trafo, options=options)
CallPovrayAndOptionallyMakeMPLPlot(epv, imagefn, cm, label, options)
def renderVasculatureWTumor(
(vessel_ld, vessel_graph, data_name), gtumor, imagefn, label, kwargs):
kwargs = deepcopy(kwargs)
wbbox = vessel_ld.worldBox
trafo = calc_centering_normalization_trafo(wbbox)
cm = InsertGraphColors(vessel_graph, None, data_name)
with EasyPovRayRender(**kwargs) as epv:
epv.setBackground(kwargs.pop('background', 1.0))