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
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)