def DoReadIn(filenames, pattern, fn_measure):
#read in lots of stuff
files = [h5files.open(fn, 'r') for fn in filenames]
output_f = h5py.File(fn_measure)
for afile in files:
#edges
index_of_circulated = np.bitwise_and(
np.asarray(afile[pattern + '/edges/flags']), ku.CIRCULATED) > 0
index_of_arteries = np.bitwise_and(
np.asarray(afile[pattern + '/edges/flags']), ku.ARTERY) > 0
index_of_veins = np.bitwise_and(
np.asarray(afile[pattern + '/edges/flags']), ku.VEIN) > 0
index_of_capillaries = np.bitwise_and(
np.asarray(afile[pattern + '/edges/flags']), ku.CAPILLARY) > 0
index_of_boundary = np.bitwise_and(
np.asarray(afile[pattern + '/edges/flags']), ku.BOUNDARY) > 0
indeces_of_circulated_arteries = np.bitwise_and(
index_of_circulated, index_of_arteries)
indeces_of_circulated_veins = np.bitwise_and(index_of_circulated,
index_of_veins)
indeces_of_circulated_capillaries = np.bitwise_and(
index_of_circulated, index_of_capillaries)
radii_of_capillaries = np.asarray(
afile[pattern +
'/edges/radius'])[indeces_of_circulated_capillaries]
#nodes
index_of_circulated_nodes = np.bitwise_and(
np.asarray(afile[pattern + '/nodes/nodeflags']), ku.CIRCULATED) > 0
indeces_of_roots = np.asarray(afile[pattern + '/nodes/roots'])
artery_roots = []
artery_roots_radii = []
artery_roots_pressure = []
venous_roots = []
venous_roots_radii = []
venous_roots_pressure = []
nodeflags = np.asarray(afile[pattern + '/nodes/nodeflags'])
for aIndex in indeces_of_roots:
if index_of_circulated_nodes[aIndex] and np.bitwise_and(
nodeflags[aIndex], ku.ARTERY):
artery_roots.append(aIndex)
artery_roots_pressure.append(
np.asarray(afile[pattern + '/nodes/pressure'])[aIndex])
if index_of_circulated_nodes[aIndex] and np.bitwise_and(
nodeflags[aIndex], ku.VEIN):
venous_roots.append(aIndex)
venous_roots_pressure.append(
np.asarray(afile[pattern + '/nodes/pressure'])[aIndex])
NodeAIndex = np.asarray(
afile[pattern + '/edges/node_a_index'])[index_of_boundary]
NodeBIndex = np.asarray(
afile[pattern + '/edges/node_b_index'])[index_of_boundary]
radii_of_boundary = np.asarray(
afile[pattern + '/edges/radius'])[index_of_boundary]
for (i, aNodeAIndex) in enumerate(NodeAIndex):
if (aNodeAIndex
in artery_roots) and not (aNodeAIndex in NodeBIndex):
artery_roots_radii.append(radii_of_boundary[i])
for (i, aNodeBIndex) in enumerate(NodeBIndex):
if aNodeBIndex in artery_roots:
artery_roots_radii.append(radii_of_boundary[i])
for (i, aNodeAIndex) in enumerate(NodeAIndex):
if aNodeAIndex in venous_roots and not (aNodeAIndex in NodeBIndex):
venous_roots_radii.append(radii_of_boundary[i])
for (i, aNodeBIndex) in enumerate(NodeBIndex):
if aNodeBIndex in venous_roots:
venous_roots_radii.append(radii_of_boundary[i])
if 1:
print("Circulated: %i " % np.sum(index_of_circulated))
print("Circulated Arteries: %i " %
np.sum(indeces_of_circulated_arteries))
print("Circulated Veins: %i " %
np.sum(indeces_of_circulated_veins))
print("Circulated Capillaries: %i " %
np.sum(indeces_of_circulated_capillaries))
if 1:
print("# Circulated Nodes: %i " %
np.sum(index_of_circulated_nodes))
print("# Arterious roots: %i " % len(artery_roots))
print("# Venous roots: %i " % len(venous_roots))
#print("Circulated Veins: %i " % np.sum(indeces_of_circulated_veins))
#print("Circulated Capillaries: %i " % np.sum(indeces_of_circulated_capillaries))
#write to file
if 1:
print("Working on file: %s" % afile.filename)
output_grp = output_f.create_group(os.path.basename(
afile.filename))
#output_grp.attrs.create("#circulated")
output_grp.attrs['#circulated'] = np.sum(index_of_circulated)
N = np.sum(index_of_circulated)
output_grp.attrs['#artery'] = np.sum(
indeces_of_circulated_arteries)
output_grp.attrs['#veins'] = np.sum(indeces_of_circulated_veins)
output_grp.attrs['#capillary'] = np.sum(
indeces_of_circulated_capillaries)
l = afile[pattern + '/lattice'].attrs['SCALE']
output_grp.attrs['length'] = l
if (np.var(radii_of_capillaries)) > 0.0001:
break
r_0 = np.mean(radii_of_capillaries)
output_grp.attrs['c_radius'] = r_0
output_grp.create_dataset('a_roots', data=artery_roots)
output_grp.create_dataset('a_roots_radius',
data=artery_roots_radii)
output_grp.create_dataset('a_roots_pressure',
data=artery_roots_pressure)
output_grp.create_dataset('v_roots', data=venous_roots)
output_grp.create_dataset('v_roots_radius', data=venous_roots)
output_grp.create_dataset('v_roots_pressure',
data=venous_roots_pressure)
dataman = myutils.DataManager(100, [DataBasicVessel()])
vessels = dataman.obtain_data(
'vessel_graph', afile['/' + pattern + '/'],
['flow', 'pressure', 'flags', 'radius', 'nodeflags'])
conductivities, avgVenousPressure, avgArterialPressure, totalFlow = ComputeVascularTreeBloodFlowResistances(
vessels)
output_grp.attrs['avgVenousPressure'] = avgVenousPressure
output_grp.attrs['avgArterialPressure'] = avgArterialPressure
output_grp.attrs['totalFlow_from_BloodFlowResistance'] = totalFlow
ax.set(xlabel=r'distance from rim [$\mu m$]',
ylabel=r'mvd [1/mm$^2$]')
ax.legend()
pdfpages.savefig(fig)
if __name__ == '__main__':
filenames = sys.argv[1:]
files = [h5files.open(fn, 'r') for fn in filenames]
fmeasure = h5files.open('analyzeBloodVolumeMeasurements.h5', 'a')
dataman = myutils.DataManager(10, [
DataTumorTissueSingle(),
DataVesselRadial(),
DataVesselSamples(),
DataBasicVessel(),
DataDistanceFromCenter()
])
#allgroups = sorted(filter(lambda k: k.startswith('out'), files[0].keys()))
allgroups = defaultdict(list)
for f in files:
keys = filter(lambda k: k.startswith('out'), f.keys())
for k in keys:
allgroups[k].append(f[k])
allgroups = [(k, allgroups[k]) for k in sorted(allgroups.keys())]
groupslist = [allgroups[-1], allgroups[len(allgroups) / 2]]
outfn = 'bloodVolume-%s.pdf' % splitext(basename(filenames[0]))[0]
pprint(groupslist)
print '-> %s' % (outfn)
with mpl_utils.PdfWriter(outfn) as pdfpages:
dest="force_flow_recompute",
help="recompute blood flow",
default=False,
action="store_true")
parser.add_option(
"--write-flow",
dest="write_flow",
help=
"writes the recomputed flow; note: hematocrit is completely ignored!",
default=False,
action="store_true")
options, args = parser.parse_args()
if options.write_flow:
options.force_flow_recompute = True
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,