diff --git a/gt_matlab_trajs.py b/gt_matlab_trajs.py
index 5d165c50c40c4fda12f8d4f405ad4134f16a36f8..fc747c6054ae6a27d4d0f678fd5fb697b378774a 100644
--- a/gt_matlab_trajs.py
+++ b/gt_matlab_trajs.py
@@ -1,212 +1,212 @@
-#!/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])