def load_timeseries_graph(dir_):
from pymira import spatialgraph
graph = []
time = []
for file in os.listdir(dir_):
if file.endswith('.am'):
#print(os.path.join("/mydir", file))
g = spatialgraph.SpatialGraph()
try:
g.read(os.path.join(dir_, file))
graph.append(g)
t = np.float(g.get_parameter_value('Time'))
time.append(t)
except Exception as e:
print(e)
time = np.asarray(time)
graph = np.asarray(graph)
srtInds = time.argsort()
time = time[srtInds]
graph = graph[srtInds]
return graph, time
def main():
#dir_ = 'C:\\Users\\simon\\Dropbox\\Mesentery\\'
#f = dir_ + 'Flow2AmiraPressure.am'
# dir_ = 'C:\\Users\\simon\\Dropbox\\160113_paul_simulation_results\\LS147T\\1\\'
# #dir_ = 'C:\\Users\\simon\\Dropbox\\160113_paul_simulation_results\\LS147T - Post-VDA\\1\\'
# #dir_ = 'C:\\Users\\simon\\Dropbox\\160113_paul_simulation_results\\SW1222\\1\\'
# #dir_ = 'C:\\Users\\simon\\Dropbox\\160113_paul_simulation_results\\SW1222\\1\\'
# #f = dir_+'spatialGraph_RIN.am'
#dir_ = r"C:\Users\simon\Dropbox\VDA_1_lectin\Control\SW#1"
#f = dir_+r'\SW1_spatialGraph_scaled.am'
# pixsize = 6.98
# dir_ = r"G:\OPT\2015.11.VDA_1 study\VDA Colorectal cancer\Control\LS\LS#2"
# f = dir_+r'\LS2_bg_removed_frangi_response_skeletonised_with_radius.SptGraph.am'
# pixsize = 8.21
# #dir_ = r"G:\OPT\2015.11.VDA_1 study\VDA Colorectal cancer\Control\LS\LS#4"
# #pixsize = 8.21
#dirs = [r"C:\Users\simon\Dropbox\VDA_1_lectin\Control\SW#2",
# r"C:\Users\simon\Dropbox\VDA_1_lectin\Control\SW#3"]
#fs = [r'\SW2_spatialGraph_scaled.am',
# r'\SW3_spatialGraph_scaled.am']
dirs = [r'C:\Users\simon\Dropbox\VDA_1_lectin\Treated\LS#1']
fs = [r'\LS1t_vessel_seg_frangi_response_skel_with_radius.am']
pixsize = [4.78]
for i,dir_ in enumerate(dirs):
f = fs[i]
pix = pixsize[i]
from pymira import spatialgraph
graph = spatialgraph.SpatialGraph()
print('Reading graph...')
graph.read(dir_+f)
print('Graph read')
if pix is not None:
ofile = dir_+'\spatialGraph_scaled.am'
graph.rescale_coordinates(pix,pix,pix)
graph.rescale_radius(pix,ofile=ofile)
stats = Statistics(graph,path=dir_)
stats.do_stats(path=dir_)
# -*- coding: utf-8 -*-
"""
Created on Wed May 31 14:42:15 2017
@author: simon
"""
from pymira import spatialgraph
import os
dir_ = r'C:\Users\simon\Dropbox\Ben Vessel Networks'
f = os.path.join(dir_, 'C2M3_vessels.am')
print 'Reading graph: {}'.format(f)
graph = spatialgraph.SpatialGraph()
graph.read(f)
print 'Graph read'
editor = spatialgraph.Editor()
graph = editor.largest_graph(graph)
ofile = os.path.join(dir_, 'C2M3_vessels_largest_network.am')
graph.write(ofile)
def main():
plt.close('all')
from pymira import spatialgraph
dir_ = 'C:\\Users\\simon\\Dropbox\\Mesentery\\'
f = dir_ + 'ct_output.am'
graph = spatialgraph.SpatialGraph()
print('Reading graph...')
graph.read(f)
print('Graph read')
points = graph.get_data('EdgePointCoordinates')
npoints = points.shape[0]
nEdgePoint = graph.get_data('NumEdgePoints')
edgePointIndex = np.zeros(npoints, dtype='int')
offset = 0
edgeCount = 0
for npCur in nEdgePoint:
edgePointIndex[offset:offset + npCur] = edgeCount
edgeCount += 1
offset += npCur
assert offset == npoints
concFieldInds = [
i for i, x in enumerate(graph.fieldNames) if 'Concentration' in x
]
concFields = [graph.fieldNames[i] for i in concFieldInds]
time = np.asarray(
[float(x.replace('Concentration_', '')) for x in concFields])
nt = len(time)
npoint = points.shape[0]
conc = np.zeros((nt, npoint), dtype='float')
for ci, concField in enumerate(concFieldInds):
field = graph.fields[concField]
if 'data' in field:
conc[ci, :] = field['data']
else:
conc[ci, :] = conc[ci - 1, :]
print(('Data missing: {}'.format(concFields[ci])))
#nodes = [[10.,10.,10.],
# [10.,20.,10.],
# [30.,30.,10.]]
#import pdb
#pdb.set_trace()
jump = 1
lim = -1 #jump*50
time = time[0:lim:jump]
conc = conc[0:lim:jump, :]
#conc = conc[:,0:100]
#points = points[0:100,:]
#edgePointIndex = edgePointIndex[0:100]
inter = Interstitium()
try:
inter.interstitial_diffusion(points, edgePointIndex, conc, time)
except KeyboardInterrupt:
print('Keyboard interrupt')
#inter.normalise()
#pass
#import pdb
#pdb.set_trace()
#inter.display_grid(last=False)
inter.save_grid(dir_)
nodes[1],
nodes[2],
nodes[2],
nodes[3],
nodes[2],
nodes[4]
]
edgePoints = np.asarray(edgePoints,dtype='float')
radii = np.zeros(edgePoints.shape[0]) + 0.05
nedgepoints = [6,
2,
2,
2]
nedgepoints = np.asarray(nedgepoints,dtype='int')
graph = spatialgraph.SpatialGraph(initialise=True,scalars=['Radii'])
graph.set_definition_size('VERTEX',nodes.shape[0])
graph.set_definition_size('EDGE',edgeConn.shape[0])
graph.set_definition_size('POINT',edgePoints.shape[0])
graph.set_data(nodes,name='VertexCoordinates')
graph.set_data(edgeConn,name='EdgeConnectivity')
graph.set_data(nedgepoints,name='NumEdgePoints')
graph.set_data(edgePoints,name='EdgePointCoordinates')
graph.set_data(radii,name='Radii')
ofile = 'C:\\Anaconda2\\Lib\\site-packages\\pymira\\test_graph.am'
graph.write(ofile)