def __init(self, d_thr=2.0):
from VascGraph.GraphIO import ReadPajek
try:
g = ReadPajek(self.g_path).GetOutput()
if self.fix_rad:
self.g = self.fixRad(g)
else:
self.g = g
self.gtrue = ReadPajek(self.gtrue_path).GetOutput()
except:
g = ReadPajek(os.getcwd() + '/' + self.g_path).GetOutput()
self.g = self.fixRad(g)
self.gtrue = ReadPajek(os.getcwd() + '/' +
self.gtrue_path).GetOutput()
self.g_path = os.getcwd() + '/' + self.g_path
self.gtrue_path = os.getcwd() + '/' + self.gtrue_path
nodes_exp = np.array(self.g.GetNodesPos())
nodes_real = np.array(self.gtrue.GetNodesPos())
radius_exp = np.array(self.g.GetRadii())[:, None]
radius_real = np.array(self.gtrue.GetRadii())[:, None]
dist1 = []
for idx, i in enumerate(nodes_real):
dist1.append(np.sum((i - nodes_exp)**2, axis=1))
#real nodes with the corresponding exp. ones
idx1 = np.argmin(dist1, axis=1)
d1 = np.array([i[idx1[j]]**.5 for j, i in enumerate(dist1)])
radius_exp_m = radius_exp[idx1]
self.rad_real = radius_real[d1 < d_thr]
self.rad_exp_m = radius_exp_m[d1 < d_thr]
dist2 = []
for idx, i in enumerate(nodes_exp):
dist2.append(np.sum((i - nodes_real)**2, axis=1))
#exp nodes with the corresponding real. ones
idx2 = np.argmin(dist2, axis=1)
d2 = np.array([i[idx2[j]]**.5 for j, i in enumerate(dist2)])
radius_real_m = radius_real[idx2]
self.rad_exp = radius_exp[d2 < d_thr]
self.rad_real_m = radius_real_m[d2 < d_thr]
Item('reset_nodes', show_label=False),
Item('nodes_list', style='readonly', label='Selected nodes'),
Item('connect_nodes', show_label=False),
orientation='horizontal'
),
Group('_', Item('save', show_label=False),'_'),
label='Edit', orientation='vertical', layout='split',show_border = True,
)
# The layout of the dialog created
view = View(
Group(
Group(Item('scene', editor=SceneEditor(scene_class=MayaviScene),
height=600, width=400, show_label=False)),
Group(control_group,
editing_group, layout='tabbed'),
layout='split'),
resizable=True, title = 'Nodes selection'
)
if __name__=='__main__':
g=ReadPajek('/home/rdamseh/GraphPaper2018V1/1.pajek')
window=ModifyGraph(fixG(g.GetOutput()))
window.configure_traits()
import numpy as np
import networkx as nx
import skimage as sk
from VascGraph.Skeletonize import GenerateGraph, ContractGraph, RefineGraph
from VascGraph.GeomGraph import DiGraph
from VascGraph.GraphIO import ReadPajek, WritePajek
from VascGraph.GraphLab import GraphPlot
from matplotlib import pyplot as plt
from mayavi import mlab
from VascGraph.Tools.VisTools import *
from VascGraph.Tools.CalcTools import *
from GraphFlowSimulation import GraphObject, GraphFlowSimulation
if __name__ == "__main__":
g = ReadPajek('/home/rdamseh/GraphPaper2018V1' +
'/flow/test_network.di.pajek').GetOutput()
metadata = sio.loadmat('/home/rdamseh/GraphPaper2018V1' +
'/flow/test_network.di.pajek.metadata.mat')
g_object = GraphObject(g)
g_object.InitGraph()
g = g_object.GetGraph()
# g_object.UpdateReducedGraph()
# g=g_object.GetReducedGraph()
# ----------- assigne resistances ---------- #
print('Computes resistances ...')
flow = GraphFlowSimulation(g, metadata)
flow.ComputeResistance()
flow.GetCloseGraph()
g = flow.Graph
import numpy as np
import networkx as nx
import skimage as sk
from VascGraph.Skeletonize import GenerateGraph, ContractGraph, RefineGraph
from VascGraph.GeomGraph import DiGraph
from VascGraph.GraphIO import ReadPajek, WritePajek
from VascGraph.GraphLab import GraphPlot
from matplotlib import pyplot as plt
from mayavi import mlab
from VascGraph.Tools.VisTools import *
from VascGraph.Tools.CalcTools import *
from GraphFlowSimulation import GraphObject, GraphFlowSimulation
if __name__ == "__main__":
g = ReadPajek('/home/rdamseh/GraphPaper2018V1' +
'/flow/test_network_flow.di.pajek').GetOutput()
arteriol_pressure = 60
venule_pressure = 25
intra_cranial_pressure = 10
input_so2 = .94 # arteriol o2 saturation
alpha = 1.275 * 10e-12 # bunsen solubility
po2_tissue = 15 # o2 partial pressure in tissue
rho = 30 * 1e-6 # effective radius for o2 consumbtion rate
Kappa_w = 5 * 10e-8 #o2 premiability on vascular wall
C_Hb = 150 # hemoglobin concentration g/mL
gamma_Hb = 2.3 * 10 - 9 # mL of Hb to moles
def so2_to_Cb(so2):
class ValidateRadius:
def __init__(self, g_path, gtrue_path, fix_rad=True, mode='mean'):
self.g_path = g_path
self.gtrue_path = gtrue_path
self.mode = mode
self.fix_rad = fix_rad
def __init(self, d_thr=2.0):
from VascGraph.GraphIO import ReadPajek
try:
g = ReadPajek(self.g_path).GetOutput()
if self.fix_rad:
self.g = self.fixRad(g)
else:
self.g = g
self.gtrue = ReadPajek(self.gtrue_path).GetOutput()
except:
g = ReadPajek(os.getcwd() + '/' + self.g_path).GetOutput()
self.g = self.fixRad(g)
self.gtrue = ReadPajek(os.getcwd() + '/' +
self.gtrue_path).GetOutput()
self.g_path = os.getcwd() + '/' + self.g_path
self.gtrue_path = os.getcwd() + '/' + self.gtrue_path
nodes_exp = np.array(self.g.GetNodesPos())
nodes_real = np.array(self.gtrue.GetNodesPos())
radius_exp = np.array(self.g.GetRadii())[:, None]
radius_real = np.array(self.gtrue.GetRadii())[:, None]
dist1 = []
for idx, i in enumerate(nodes_real):
dist1.append(np.sum((i - nodes_exp)**2, axis=1))
#real nodes with the corresponding exp. ones
idx1 = np.argmin(dist1, axis=1)
d1 = np.array([i[idx1[j]]**.5 for j, i in enumerate(dist1)])
radius_exp_m = radius_exp[idx1]
self.rad_real = radius_real[d1 < d_thr]
self.rad_exp_m = radius_exp_m[d1 < d_thr]
dist2 = []
for idx, i in enumerate(nodes_exp):
dist2.append(np.sum((i - nodes_real)**2, axis=1))
#exp nodes with the corresponding real. ones
idx2 = np.argmin(dist2, axis=1)
d2 = np.array([i[idx2[j]]**.5 for j, i in enumerate(dist2)])
radius_real_m = radius_real[idx2]
self.rad_exp = radius_exp[d2 < d_thr]
self.rad_real_m = radius_real_m[d2 < d_thr]
def fixRad(self, g):
'''
fix radius values across graph branches
'''
from VascGraph.GeomGraph import GraphObject
obj = GraphObject(g)
obj.InitGraph()
obj.UpdateReducedGraph()
obj.UpdateDictBranches()
red = obj.GetDictBranches()
b = []
for i in red.keys():
for j in red[i]:
b.append(j)
for i in b:
r = np.array([g.node[k]['r'] for k in i])
if self.mode == 'mean':
r = np.mean(r)
elif self.mode == 'max':
r = np.max(r)
else:
r = np.median(r)
for k in i:
g.node[k]['r'] = r
return g
def Normalize(self, x):
return (x - x.min()) / (x.max() - x.min())
def MSEerror(self, x, y):
e = (x - y)**2
e = np.mean(e, axis=0)
return e[0]
def MPEerror(self, y_pred, y_true):
m = y_true.min()
if m < 1.0:
y_pred = y_pred + (1 - m)
y_true = y_true + (1 - m)
return np.mean(np.abs((y_true - y_pred) / y_true)) * 100
def KSerror(self, x, y):
e = kstest(x, y)
return e[0]
def GetScores(self, d_thr=10.0):
'''
Compute errors between radius values in the expiremental graph the true one
Output:
- mse: minimum mean square error
- mpe: mean percentage error
- kse: kolomogorov smirnove measure
'''
self.__init(
d_thr=d_thr
) # threshold of maximum distance when matching the two graphs
self.rad_exp = self.Normalize(self.rad_exp)
self.rad_real_m = self.Normalize(self.rad_real_m)
mse = self.MSEerror(self.rad_exp, self.rad_real_m)
mpe = self.MPEerror(self.rad_exp, self.rad_real_m)
kse = self.KSerror(self.rad_exp[:, 0], self.rad_real_m[:, 0])
return mse, mpe, kse
if len(check_result)==0:
print('Item not found!!!')
lines_=[]
ind=[]
for idx, l in enumerate(lines):
if l.find('(')!=-1:
lines_.append(l)
ind.append(idx)
attr=file.attr
'''
# read/write
from VascGraph.GraphIO import WritePajek, ReadPajek
namepajek = ''.join(attr_filename.split('.')[:-1]) + '.pajek'
WritePajek('', namepajek, g)
g = ReadPajek(namepajek, mode='di').GetOutput()
from OxyGraph import OxyGraph
og = OxyGraph(g)
og.AddType()
og.AddVelocityFromFlow()
og.AddSo2FromPo2()
og.BuildDirectionsGraph()
g = og.g
gplot = GraphPlot(new_engine=True)
gplot.Update(g)
gplot.SetTubeRadius(3)
gplot.SetTubeRadiusByScale(True)
gplot.SetTubeRadiusByColor(True)
degree_threshold=degree_threshold,
clustering_resolution=clustering_r,
stop_param=stop_param,
n_free_iteration=n_free_iteration,
area_param=area_param,
poly_param=poly_param)
sk.UpdateWithStitching(size=size,
niter1=niter1,
niter2=niter2,
is_parallel=is_parallel,
n_parallel=n_parallel)
fullgraph = sk.GetOutput()
# save graph
WritePajek(path='', name='mygraph.pajek', graph=fixG(fullgraph))
#load graph
loaded_g = ReadPajek('mygraph.pajek').GetOutput()
print('--Visualize final skeleton ...')
splot = StackPlot(new_engine=True)
splot.Update((s > 0).astype(int))
gplot = GraphPlot()
gplot.Update(loaded_g)
gplot.SetTubeRadiusByScale(True)
gplot.SetTubeRadiusByColor(True)
gplot.SetTubeRadius(3)