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Commit 64b4ba4d authored by Lionel GUEZ's avatar Lionel GUEZ
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gt_matlab_trajs.py
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#!/usr/bin/env python3
# A script that loads a segmented cf graph in the gt format, iterates on all
# of the edges and cost functions and generates the trajectories as done in
# MATLAB. Segments (nodes) have a new vertex property called "traj" that holds
# the trajectory ID that that segment belongs to. The output is either an
# expanded JSON file and/or an edgelist file with all of the trajectories.
# Inputs:
# orientation
# name and the location of the gt segmented cf graph
# Output:
# trajectories.json that contains all of the trajectories
import graph_tool as gt
from os import path
import json
import csv
import graph_tool.util as ut
orientation = 'anti'
g = gt.Graph()
g.load('segmented_anti_cf.gt')
#g = gt.Graph(directed = True)
# vlist = g.add_vertex(25)
# e1 = g.add_edge(g.vertex(0), g.vertex(1))
# e2 = g.add_edge(g.vertex(1), g.vertex(2))
# e3 = g.add_edge(g.vertex(1), g.vertex(3))
# e4 = g.add_edge(g.vertex(2), g.vertex(4))
# e5 = g.add_edge(g.vertex(3), g.vertex(5))
# e6 = g.add_edge(g.vertex(4), g.vertex(5))
# e7 = g.add_edge(g.vertex(5), g.vertex(6))
# e8 = g.add_edge(g.vertex(6), g.vertex(7))
# e9 = g.add_edge(g.vertex(6), g.vertex(8))
# e10 = g.add_edge(g.vertex(1), g.vertex(10))
# e11 = g.add_edge(g.vertex(10), g.vertex(11))
# e12 = g.add_edge(g.vertex(9), g.vertex(11))
# e13 = g.add_edge(g.vertex(11), g.vertex(12))
# e14 = g.add_edge(g.vertex(12), g.vertex(13))
# e15 = g.add_edge(g.vertex(12), g.vertex(14))
# e16 = g.add_edge(g.vertex(13), g.vertex(15))
# e17 = g.add_edge(g.vertex(14), g.vertex(15))
# e18 = g.add_edge(g.vertex(15), g.vertex(16))
# e19 = g.add_edge(g.vertex(2), g.vertex(17))
# e20 = g.add_edge(g.vertex(17), g.vertex(20))
# e21 = g.add_edge(g.vertex(18), g.vertex(20))
# e22 = g.add_edge(g.vertex(19), g.vertex(20))
# e23 = g.add_edge(g.vertex(20), g.vertex(21))
# e24 = g.add_edge(g.vertex(21), g.vertex(22))
# e25 = g.add_edge(g.vertex(21), g.vertex(23))
# e26 = g.add_edge(g.vertex(23), g.vertex(24))
# nl_cf = g.new_ep('float')
# g.ep['nl_cost_function'] = nl_cf
traj_mark = g.new_vp('int')
g.vp['traj'] = traj_mark
# g.ep.nl_cost_function[e1] = 6
# g.ep.nl_cost_function[e2] = 2
# g.ep.nl_cost_function[e3] = 7
# g.ep.nl_cost_function[e4] = 8
# g.ep.nl_cost_function[e5] = 4
# g.ep.nl_cost_function[e6] = 2
# g.ep.nl_cost_function[e7] = 10
# g.ep.nl_cost_function[e8] = 11
# g.ep.nl_cost_function[e9] = 2
# g.ep.nl_cost_function[e10] = 3
# g.ep.nl_cost_function[e11] = 2
# g.ep.nl_cost_function[e12] = 6
# g.ep.nl_cost_function[e13] = 4
# g.ep.nl_cost_function[e14] = 10
# g.ep.nl_cost_function[e15] = 6
# g.ep.nl_cost_function[e16] = 2
# g.ep.nl_cost_function[e17] = 4
# g.ep.nl_cost_function[e18] = 5
# g.ep.nl_cost_function[e19] = 6
# g.ep.nl_cost_function[e20] = 3
# g.ep.nl_cost_function[e21] = 2
# g.ep.nl_cost_function[e22] = 1
# g.ep.nl_cost_function[e23] = 7
# g.ep.nl_cost_function[e24] = 6
# g.ep.nl_cost_function[e25] = 8
# g.ep.nl_cost_function[e26] = 7
# name = g.new_vp('string')
# g.vp['name'] = name
# for i in range(0, 25):
# g.vp.name[g.vertex(i)] = i
# assign the new vertex property
for node in g.vertices():
g.vp.traj[node] = g.vp.name[node]
##################
# MAIN ALGORITHM #
##################
# iterating on edges:
print('Algorithm starting...')
for edge in g.edges():
current_cf = g.ep.nl_cost_function[edge]
src = edge.source()
trg = edge.target()
# source is a split
if src.out_degree() > 1:
if current_cf <= min({g.ep.nl_cost_function[e] for e in src.out_edges()}):
# elif target is a merge
if trg.in_degree() > 1:
if current_cf <= min({g.ep.nl_cost_function[e] for e in trg.out_edges()}):
# add trg to src trajectory
g.vp.traj[trg] = g.vp.traj[src]
# else, target is a split or end or continuation
else:
g.vp.traj[trg] = g.vp.traj[src]
# source is a continuation or root with one out
elif (src.in_degree() == 1 and src.out_degree() == 1) or (src.in_degree() == 0 and src.out_degree() == 1) or (src.in_degree() > 1):
if trg.in_degree() > 1:
# if the current cf is the smallest
if current_cf <= min({g.ep.nl_cost_function[e] for e in trg.in_edges()}):
g.vp.traj[trg] = g.vp.traj[src]
else:
g.vp.traj[trg] = g.vp.traj[src]
print('Algorithm done, saving...')
# make a dictionary of trajectories:
trajectories = {}
for node in g.vertices():
if g.vp.traj[node] not in trajectories:
trajectories[g.vp.traj[node]] = []
trajectories[g.vp.traj[node]].append(g.vp.name[node])
else:
trajectories[g.vp.traj[node]].append(g.vp.name[node])
# setup a new trajectory that holds the expanded segments
expanded_trajectories = {}
for trajectory in trajectories.values():
# exp traj of current traj key = []
key = trajectory[0]
for val in trajectory:
node = ut.find_vertex(g, g.vp.name, val)
if len(node) != 1:
print('Something is wrong.')
node = node[0]
seg = g.vp.segment[node]
for s in seg:
if key not in expanded_trajectories:
expanded_trajectories[key] = []
expanded_trajectories[key].append(s)
else:
expanded_trajectories[key].append(s)
# write out the json file
with open("trajectories.json", "w") as outfile:
json.dump(expanded_trajectories, outfile, indent = 4)
print(f'Done saving json: {len(trajectories)} trajectories.')
# Write to an edgelist file if need be to plot the trajectories
# with open('edgelist_60k_trajectories.csv', 'w', newline='') as csvfile:
# spamwriter = csv.writer(csvfile, delimiter=' ', escapechar=' ', quoting=csv.QUOTE_NONE)
# for trajectory in trajectories.values():
# for val in trajectory:
# node = ut.find_vertex(g, g.vp.name, val)
# if len(node) != 1:
# print('Something is wrong...')
# node = node[0]
# seg = g.vp.segment[node]
# for i in range(0, len(seg) - 1):
# spamwriter.writerow([seg[i], seg[i+1]])
# # we wrote the nodes from the segments, now we need to connect the segments
# # they are sequential
# for i in range(0, len(trajectory) - 1):
# src_val = trajectory[i]
# trg_val = trajectory[i+1]
# src = ut.find_vertex(g, g.vp.name, src_val)
# trg = ut.find_vertex(g, g.vp.name, trg_val)
# if len(src) != 1 or len(trg) != 1:
# print('Something is wrong in second loop...')
# src = src[0]
# trg = trg[0]
# seg_1 = g.vp.segment[src]
# seg_2 = g.vp.segment[trg]
# first = seg_1[-1]
# second = seg_2[0]
# spamwriter.writerow([first, second])
\ No newline at end of file
#!/usr/bin/env python3
# A script that loads a segmented cf graph in the gt format, iterates on all
# of the edges and cost functions and generates the trajectories as done in
# MATLAB. Segments (nodes) have a new vertex property called "traj" that holds
# the trajectory ID that that segment belongs to. The output is either an
# expanded JSON file and/or an edgelist file with all of the trajectories.
# Inputs:
# orientation
# name and the location of the gt segmented cf graph
# Output:
# trajectories.json that contains all of the trajectories
import graph_tool as gt
from os import path
import json
import csv
import graph_tool.util as ut
orientation = 'anti'
g = gt.Graph()
g.load('segmented_anti_cf.gt')
#g = gt.Graph(directed = True)
# vlist = g.add_vertex(25)
# e1 = g.add_edge(g.vertex(0), g.vertex(1))
# e2 = g.add_edge(g.vertex(1), g.vertex(2))
# e3 = g.add_edge(g.vertex(1), g.vertex(3))
# e4 = g.add_edge(g.vertex(2), g.vertex(4))
# e5 = g.add_edge(g.vertex(3), g.vertex(5))
# e6 = g.add_edge(g.vertex(4), g.vertex(5))
# e7 = g.add_edge(g.vertex(5), g.vertex(6))
# e8 = g.add_edge(g.vertex(6), g.vertex(7))
# e9 = g.add_edge(g.vertex(6), g.vertex(8))
# e10 = g.add_edge(g.vertex(1), g.vertex(10))
# e11 = g.add_edge(g.vertex(10), g.vertex(11))
# e12 = g.add_edge(g.vertex(9), g.vertex(11))
# e13 = g.add_edge(g.vertex(11), g.vertex(12))
# e14 = g.add_edge(g.vertex(12), g.vertex(13))
# e15 = g.add_edge(g.vertex(12), g.vertex(14))
# e16 = g.add_edge(g.vertex(13), g.vertex(15))
# e17 = g.add_edge(g.vertex(14), g.vertex(15))
# e18 = g.add_edge(g.vertex(15), g.vertex(16))
# e19 = g.add_edge(g.vertex(2), g.vertex(17))
# e20 = g.add_edge(g.vertex(17), g.vertex(20))
# e21 = g.add_edge(g.vertex(18), g.vertex(20))
# e22 = g.add_edge(g.vertex(19), g.vertex(20))
# e23 = g.add_edge(g.vertex(20), g.vertex(21))
# e24 = g.add_edge(g.vertex(21), g.vertex(22))
# e25 = g.add_edge(g.vertex(21), g.vertex(23))
# e26 = g.add_edge(g.vertex(23), g.vertex(24))
# nl_cf = g.new_ep('float')
# g.ep['nl_cost_function'] = nl_cf
traj_mark = g.new_vp('int')
g.vp['traj'] = traj_mark
# g.ep.nl_cost_function[e1] = 6
# g.ep.nl_cost_function[e2] = 2
# g.ep.nl_cost_function[e3] = 7
# g.ep.nl_cost_function[e4] = 8
# g.ep.nl_cost_function[e5] = 4
# g.ep.nl_cost_function[e6] = 2
# g.ep.nl_cost_function[e7] = 10
# g.ep.nl_cost_function[e8] = 11
# g.ep.nl_cost_function[e9] = 2
# g.ep.nl_cost_function[e10] = 3
# g.ep.nl_cost_function[e11] = 2
# g.ep.nl_cost_function[e12] = 6
# g.ep.nl_cost_function[e13] = 4
# g.ep.nl_cost_function[e14] = 10
# g.ep.nl_cost_function[e15] = 6
# g.ep.nl_cost_function[e16] = 2
# g.ep.nl_cost_function[e17] = 4
# g.ep.nl_cost_function[e18] = 5
# g.ep.nl_cost_function[e19] = 6
# g.ep.nl_cost_function[e20] = 3
# g.ep.nl_cost_function[e21] = 2
# g.ep.nl_cost_function[e22] = 1
# g.ep.nl_cost_function[e23] = 7
# g.ep.nl_cost_function[e24] = 6
# g.ep.nl_cost_function[e25] = 8
# g.ep.nl_cost_function[e26] = 7
# name = g.new_vp('string')
# g.vp['name'] = name
# for i in range(0, 25):
# g.vp.name[g.vertex(i)] = i
# assign the new vertex property
for node in g.vertices():
g.vp.traj[node] = g.vp.name[node]
##################
# MAIN ALGORITHM #
##################
# iterating on edges:
print('Algorithm starting...')
for edge in g.edges():
current_cf = g.ep.nl_cost_function[edge]
src = edge.source()
trg = edge.target()
# source is a split
if src.out_degree() > 1:
if current_cf <= min({g.ep.nl_cost_function[e] for e in src.out_edges()}):
# elif target is a merge
if trg.in_degree() > 1:
if current_cf <= min({g.ep.nl_cost_function[e] for e in trg.out_edges()}):
# add trg to src trajectory
g.vp.traj[trg] = g.vp.traj[src]
# else, target is a split or end or continuation
else:
g.vp.traj[trg] = g.vp.traj[src]
# source is a continuation or root with one out
elif (src.in_degree() == 1 and src.out_degree() == 1) or (src.in_degree() == 0 and src.out_degree() == 1) or (src.in_degree() > 1):
if trg.in_degree() > 1:
# if the current cf is the smallest
if current_cf <= min({g.ep.nl_cost_function[e] for e in trg.in_edges()}):
g.vp.traj[trg] = g.vp.traj[src]
else:
g.vp.traj[trg] = g.vp.traj[src]
print('Algorithm done, saving...')
# make a dictionary of trajectories:
trajectories = {}
for node in g.vertices():
if g.vp.traj[node] not in trajectories:
trajectories[g.vp.traj[node]] = []
trajectories[g.vp.traj[node]].append(g.vp.name[node])
else:
trajectories[g.vp.traj[node]].append(g.vp.name[node])
# setup a new trajectory that holds the expanded segments
expanded_trajectories = {}
for trajectory in trajectories.values():
# exp traj of current traj key = []
key = trajectory[0]
for val in trajectory:
node = ut.find_vertex(g, g.vp.name, val)
if len(node) != 1:
print('Something is wrong.')
node = node[0]
seg = g.vp.segment[node]
for s in seg:
if key not in expanded_trajectories:
expanded_trajectories[key] = []
expanded_trajectories[key].append(s)
else:
expanded_trajectories[key].append(s)
# write out the json file
with open("trajectories.json", "w") as outfile:
json.dump(expanded_trajectories, outfile, indent = 4)
print(f'Done saving json: {len(trajectories)} trajectories.')
# Write to an edgelist file if need be to plot the trajectories
# with open('edgelist_60k_trajectories.csv', 'w', newline='') as csvfile:
# spamwriter = csv.writer(csvfile, delimiter=' ', escapechar=' ', quoting=csv.QUOTE_NONE)
# for trajectory in trajectories.values():
# for val in trajectory:
# node = ut.find_vertex(g, g.vp.name, val)
# if len(node) != 1:
# print('Something is wrong...')
# node = node[0]
# seg = g.vp.segment[node]
# for i in range(0, len(seg) - 1):
# spamwriter.writerow([seg[i], seg[i+1]])
# # we wrote the nodes from the segments, now we need to connect the segments
# # they are sequential
# for i in range(0, len(trajectory) - 1):
# src_val = trajectory[i]
# trg_val = trajectory[i+1]
# src = ut.find_vertex(g, g.vp.name, src_val)
# trg = ut.find_vertex(g, g.vp.name, trg_val)
# if len(src) != 1 or len(trg) != 1:
# print('Something is wrong in second loop...')
# src = src[0]
# trg = trg[0]
# seg_1 = g.vp.segment[src]
# seg_2 = g.vp.segment[trg]
# first = seg_1[-1]
# second = seg_2[0]
# spamwriter.writerow([first, second])
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