def surface2Volume(vesselgroup):
vessels = krebsutils.read_vesselgraph(vesselgroup, ['flags', 'radius', 'length'])
flags = RemoveArteriovenousFlagsFromCapillaries(vessels['flags'])
flags = flags[:,0]
mask1 = myutils.bbitwise_and(flags, krebsutils.CIRCULATED)
totalvol = totalLdVolume(vesselgroup)
def compute(flagMask):
if flagMask:
mask = mask1 & myutils.bbitwise_and(flags, flagMask)
else:
mask = mask1
length = np.asarray(vessels['length'][mask], dtype = np.float64)
radius = np.asarray(vessels['radius'][mask], dtype = np.float64)
radius = radius[:,0]
vol = math.pi * np.power(radius, 2.) * length
surface = 2* math.pi* radius* length
#surface = np.sum(surface)
#vol = np.sum(vol)
s2v = surface/vol
mystd = np.std(s2v)
myavg = np.average(s2v)
myrel = mystd/myavg
print("spread: %f" % myrel)
return np.average(surface/vol)
return compute(0), compute(krebsutils.ARTERY), compute(krebsutils.VEIN), compute(krebsutils.CAPILLARY)
def cylinderCollectionLineDensity(vesselgroup):
vessels = krebsutils.read_vesselgraph(vesselgroup, ['flags', 'length'])
flags = RemoveArteriovenousFlagsFromCapillaries(vessels['flags'])
flags = flags[:,0]
mask1 = myutils.bbitwise_and(flags, krebsutils.CIRCULATED)
totalvol = totalLdVolume(vesselgroup)
def compute(flagMask):
if flagMask:
mask = mask1 & myutils.bbitwise_and(flags, flagMask)
else:
mask = mask1
length = np.asarray(vessels['length'][mask], dtype = np.float64)
total = np.sum(length)
return total/totalvol
return compute(0), compute(krebsutils.ARTERY), compute(krebsutils.VEIN), compute(krebsutils.CAPILLARY)