segmentation / graph_gui

Commit 25fa0bfee2798ab831c75ced310a05bc1b73b929

Authored by Pavel Govyadinov
1 parent 7c54fa21

Stable, pre-vispy update

Showing 10 changed files with 746 additions and 205 deletions   Show diff stats
Inline Side-by-side
@@ -12,6 +12,7 @@ from vispy import gloo, scene @@ -12,6 +12,7 @@ from vispy import gloo, scene
12 from vispy.gloo import set_viewport, set_state, clear, set_blend_color, context 12 from vispy.gloo import set_viewport, set_state, clear, set_blend_color, context
13 from vispy.util.transforms import perspective, translate, rotate, scale 13 from vispy.util.transforms import perspective, translate, rotate, scale
14 import vispy.gloo.gl as glcore 14 import vispy.gloo.gl as glcore
  15 +from vispy import app
15 16
16 import numpy as np 17 import numpy as np
17 import math 18 import math
@@ -94,7 +95,7 @@ class GraphCanvas(scene.SceneCanvas): @@ -94,7 +95,7 @@ class GraphCanvas(scene.SceneCanvas):
94 n = 10 95 n = 10
95 ne = 10 96 ne = 10
96 #Init dummy structures 97 #Init dummy structures
97 - self.uniforms = [('u_graph_size', np.float32, 3)] 98 + #self.uniforms = [('u_graph_size', np.float32, 3)]
98 self.data = np.zeros(n, dtype=[('a_position', np.float32, 3), 99 self.data = np.zeros(n, dtype=[('a_position', np.float32, 3),
99 ('a_fg_color', np.float32, 4), 100 ('a_fg_color', np.float32, 4),
100 ('a_bg_color', np.float32, 4), 101 ('a_bg_color', np.float32, 4),
@@ -102,13 +103,30 @@ class GraphCanvas(scene.SceneCanvas): @@ -102,13 +103,30 @@ class GraphCanvas(scene.SceneCanvas):
102 ('a_linewidth', np.float32, 1), 103 ('a_linewidth', np.float32, 1),
103 ('a_unique_id', np.float32, 4), 104 ('a_unique_id', np.float32, 4),
104 ]) 105 ])
  106 +
  107 + self.line_data = np.zeros(ne, dtype=[('a_position', np.float32, 3),
  108 + ('a_normal', np.float32, 2),
  109 + ('a_fg_color', np.float32, 4),
  110 + ('a_linewidth', np.float32, 1),
  111 + ])
  112 +
  113 +
  114 + self.clusters = np.zeros(n*4, dtype=[('a_position', np.float32, 3),
  115 + ('a_value', np.float32, 2),
  116 + ('a_bg_color', np.float32, 4),
  117 + ('a_cluster_color', np.float32, 4),
  118 + ('a_arc_length', np.float32, 1),
  119 + ('a_outer_arc_length', np.float32, 4),
  120 + ('a_unique_id', np.float32, 4),
  121 + ])
105 122
106 - self.clusters = np.zeros(n, dtype=[('a_position', np.float32, 3),  
107 - ('a_bg_color', np.float32, 4),  
108 - ('a_value', np.float32, 2),  
109 - ('a_unique_id', np.float32, 4),  
110 - ]) 123 + self.cluster_line_data = np.zeros(ne, dtype=[('a_position', np.float32, 3),
  124 + ('a_normal', np.float32, 2),
  125 + ('a_fg_color', np.float32, 4),
  126 + ('a_linewidth', np.float32, 1),
  127 + ])
111 128
  129 +
112 self.edges = np.random.randint(size=(ne, 2), low=0, 130 self.edges = np.random.randint(size=(ne, 2), low=0,
113 high=n-1).astype(np.uint32) 131 high=n-1).astype(np.uint32)
114 self.edges_s = np.random.randint(size=(ne, 4), low=0, 132 self.edges_s = np.random.randint(size=(ne, 4), low=0,
@@ -134,7 +152,7 @@ class GraphCanvas(scene.SceneCanvas): @@ -134,7 +152,7 @@ class GraphCanvas(scene.SceneCanvas):
134 self.vbo = gloo.VertexBuffer(self.data) 152 self.vbo = gloo.VertexBuffer(self.data)
135 self.vbo_s = gloo.VertexBuffer(self.clusters) 153 self.vbo_s = gloo.VertexBuffer(self.clusters)
136 154
137 - #Need to initialize thick lines. 155 + #Need to initialize thic/k lines.
138 self.index = gloo.IndexBuffer(self.edges) 156 self.index = gloo.IndexBuffer(self.edges)
139 self.index_s = gloo.IndexBuffer(self.edges_s) 157 self.index_s = gloo.IndexBuffer(self.edges_s)
140 158
@@ -151,35 +169,36 @@ class GraphCanvas(scene.SceneCanvas): @@ -151,35 +169,36 @@ class GraphCanvas(scene.SceneCanvas):
151 self.program['u_model'] = self.model 169 self.program['u_model'] = self.model
152 self.program['u_view'] = self.view 170 self.program['u_view'] = self.view
153 self.program['u_projection'] = self.projection 171 self.program['u_projection'] = self.projection
154 - self.program['u_graph_size'] = [1.0, 1.0, 1.0] 172 + #self.program['u_graph_size'] = [1.0, 1.0, 1.0]
155 self.program['u_picking'] = False 173 self.program['u_picking'] = False
156 174
  175 + self.vbo_line = gloo.VertexBuffer(self.line_data)
157 #init shades used for the edges in the graph 176 #init shades used for the edges in the graph
158 self.program_e = gloo.Program(vs, fs) 177 self.program_e = gloo.Program(vs, fs)
159 - self.program_e['u_size'] = 1 178 +# self.program_e['u_size'] = 1
160 self.program_e['u_model'] = self.model 179 self.program_e['u_model'] = self.model
161 self.program_e['u_view'] = self.view 180 self.program_e['u_view'] = self.view
162 self.program_e['u_projection'] = self.projection 181 self.program_e['u_projection'] = self.projection
163 #self.program_e['l_color'] = self.linecolor.astype(np.float32) 182 #self.program_e['l_color'] = self.linecolor.astype(np.float32)
164 - self.program_e.bind(self.vbo)  
165 - 183 + self.program_e.bind(self.vbo_line)
  184 +
166 #init shaders used to the vertices in the subgraph graph. 185 #init shaders used to the vertices in the subgraph graph.
167 self.program_s = gloo.Program(vert_s, frag_s) 186 self.program_s = gloo.Program(vert_s, frag_s)
168 self.program_s.bind(self.vbo_s) 187 self.program_s.bind(self.vbo_s)
169 self.program_s['u_model'] = self.model 188 self.program_s['u_model'] = self.model
170 self.program_s['u_view'] = self.view 189 self.program_s['u_view'] = self.view
171 self.program_s['u_projection'] = self.projection 190 self.program_s['u_projection'] = self.projection
172 - self.program_s['u_graph_size'] = [1.0, 1.0, 1.0] 191 + #self.program_s['u_graph_size'] = [1.0, 1.0, 1.0]
173 self.program_s['u_picking'] = False 192 self.program_s['u_picking'] = False
174 193
175 #init shaders used for the subgraph-edges 194 #init shaders used for the subgraph-edges
176 self.program_e_s = gloo.Program(vs_s, fs_s) 195 self.program_e_s = gloo.Program(vs_s, fs_s)
177 - self.program_e_s['u_size'] = 1  
178 self.program_e_s['u_model'] = self.model 196 self.program_e_s['u_model'] = self.model
179 self.program_e_s['u_view'] = self.view 197 self.program_e_s['u_view'] = self.view
180 self.program_e_s['u_projection'] = self.projection 198 self.program_e_s['u_projection'] = self.projection
181 #self.program_e['l_color'] = self.linecolor.astype(np.float32) 199 #self.program_e['l_color'] = self.linecolor.astype(np.float32)
182 - self.program_e_s.bind(self.vbo_s) 200 + self.vbo_cluster_lines = gloo.VertexBuffer(self.cluster_line_data)
  201 + self.program_e_s.bind(self.vbo_cluster_lines)
183 202
184 203
185 #set up the viewport and the gl state. 204 #set up the viewport and the gl state.
@@ -187,6 +206,86 @@ class GraphCanvas(scene.SceneCanvas): @@ -187,6 +206,86 @@ class GraphCanvas(scene.SceneCanvas):
187 206
188 set_state(clear_color='white', depth_test=True, blend=True, 207 set_state(clear_color='white', depth_test=True, blend=True,
189 blend_func=('src_alpha', 'one_minus_src_alpha'), depth_func = ('lequal')) 208 blend_func=('src_alpha', 'one_minus_src_alpha'), depth_func = ('lequal'))
  209 +
  210 +
  211 + self.timer = app.Timer('auto', connect=self.on_timer, start=False)
  212 +
  213 + def on_timer(self, event):
  214 + #get the temporary positions of the vertices (and edges)
  215 + self.old_pos = np.add(self.old_pos, self.slopes)
  216 + #during each iteration set the new positions in the GPU
  217 + self.data['a_position'] = self.old_pos
  218 + #Adjust the edges
  219 + edges = self.G.get_edges()
  220 + for e in range(edges.shape[0]):
  221 + idx = int(4*edges[e][2])
  222 + p0 = self.old_pos[edges[e][0], :]
  223 + p1 = self.old_pos[edges[e][1], :]
  224 + d = np.subtract(p1, p0)
  225 + #d_norm = np.multiply(d, 1/np.sqrt(np.power(d[0],2) + np.power(d[1],2)))
  226 + d_norm = d[0:2]
  227 + d_norm = d_norm / np.sqrt(np.power(d_norm[0],2) + np.power(d_norm[1],2))
  228 + norm = np.zeros((2,), dtype=np.float32)
  229 + norm[0] = d_norm[1]
  230 + norm[1] = d_norm[0]*-1
  231 +
  232 + self.edge_dict[int(edges[e][0]), int(edges[e][1])] = int(edges[e][2])
  233 + self.line_data['a_position'][idx] = p0
  234 + self.line_data['a_normal'][idx] = norm
  235 +
  236 + self.line_data['a_position'][idx+1] = p1
  237 + self.line_data['a_normal'][idx+1] = norm
  238 +
  239 + self.line_data['a_position'][idx+2] = p0
  240 + self.line_data['a_normal'][idx+2] = -norm
  241 +
  242 + self.line_data['a_position'][idx+3] = p1
  243 + self.line_data['a_normal'][idx+3] = -norm
  244 +
  245 + #send data to GPU renderer
  246 + self.vbo.set_data(self.data)
  247 + self.program.bind(self.vbo)
  248 + self.vbo_line = gloo.VertexBuffer(self.line_data)
  249 + self.program_e.bind(self.vbo_line)
  250 +
  251 +
  252 + self.update_clusters(self.old_pos)
  253 + edges = self.G_cluster.get_edges()
  254 +# #generate the vertex buffer and the connections buffer.
  255 + for e in range(edges.shape[0]):
  256 + idx = int(4*edges[e][2])
  257 + p0 = self.cluster_pos[int(edges[e][0])]
  258 + p1 = self.cluster_pos[int(edges[e][1])]
  259 + #p0 = self.G_cluster.vertex_properties["pos"][self.G_cluster.vertex(edges[e][0])]
  260 + #p1 = self.G_cluster.vertex_properties["pos"][self.G_cluster.vertex(edges[e][1])]
  261 + d = np.subtract(p1, p0)
  262 + #d_norm = np.multiply(d, 1/np.sqrt(np.power(d[0],2) + np.power(d[1],2)))
  263 + d_norm = d[0:2]
  264 + d_norm = d_norm / np.sqrt(np.power(d_norm[0],2) + np.power(d_norm[1],2))
  265 + norm = np.zeros((2,), dtype=np.float32)
  266 + norm[0] = d_norm[1]
  267 + norm[1] = d_norm[0]*-1
  268 + #print(np.sqrt(norm[0]*norm[0] + norm[1]*norm[1]))
  269 + #thickness = G.edge_properties["thickness"][e]
  270 + #self.cluster_dict[int(edges[e][0]), int(edges[e][1])] = int(edges[e][2])
  271 + self.cluster_line_data['a_position'][idx] = p0
  272 + self.cluster_line_data['a_normal'][idx] = norm
  273 +
  274 + self.cluster_line_data['a_position'][idx+1] = p1
  275 + self.cluster_line_data['a_normal'][idx+1] = norm
  276 +
  277 + self.cluster_line_data['a_position'][idx+2] = p0
  278 + self.cluster_line_data['a_normal'][idx+2] = -norm
  279 +
  280 + self.cluster_line_data['a_position'][idx+3] = p1
  281 + self.cluster_line_data['a_normal'][idx+3] = -norm
  282 +
  283 + self.vbo_cluster_lines.set_data(self.cluster_line_data)
  284 + self.vbo_s.set_data(self.clusters)
  285 + self.program_s.bind(self.vbo_s)
  286 + self.program_e_s.bind(self.vbo_cluster_lines)
  287 +
  288 + self.update()
190 289
191 """ 290 """
192 Function that recolors vertices based on the selected statistic 291 Function that recolors vertices based on the selected statistic
@@ -377,6 +476,14 @@ class GraphCanvas(scene.SceneCanvas): @@ -377,6 +476,14 @@ class GraphCanvas(scene.SceneCanvas):
377 else: 476 else:
378 G.edge_properties["RGBA"][e] = [0.0, 0.0, 0.0, 0.8] 477 G.edge_properties["RGBA"][e] = [0.0, 0.0, 0.0, 0.8]
379 478
  479 + """
  480 + Test function that only binds the buffer
  481 + """
  482 + def gen_vertex_vbo_minimalist(self):
  483 + self.update()
  484 + self.vbo.set_data(self.data)
  485 + self.program.bind(self.vbo)
  486 + self.update()
380 487
381 """ 488 """
382 Helper function that generates the framebuffer object that stores the vertices 489 Helper function that generates the framebuffer object that stores the vertices
@@ -418,7 +525,7 @@ class GraphCanvas(scene.SceneCanvas): @@ -418,7 +525,7 @@ class GraphCanvas(scene.SceneCanvas):
418 self.data['a_selection'] = G.vertex_properties["selection"].get_array() 525 self.data['a_selection'] = G.vertex_properties["selection"].get_array()
419 #self.data['a_graph_size'] = [bbu-bbl] 526 #self.data['a_graph_size'] = [bbu-bbl]
420 527
421 - self.program['u_graph_size'] = [self.bbu-self.bbl] 528 + #self.program['u_graph_size'] = [self.bbu-self.bbl]
422 529
423 self.vbo = gloo.VertexBuffer(self.data) 530 self.vbo = gloo.VertexBuffer(self.data)
424 self.gen_line_vbo(G) 531 self.gen_line_vbo(G)
@@ -499,7 +606,7 @@ class GraphCanvas(scene.SceneCanvas): @@ -499,7 +606,7 @@ class GraphCanvas(scene.SceneCanvas):
499 #self.program_e['l_color'] = self.linecolor.astype(np.float32) 606 #self.program_e['l_color'] = self.linecolor.astype(np.float32)
500 self.vbo_line = gloo.VertexBuffer(self.line_data) 607 self.vbo_line = gloo.VertexBuffer(self.line_data)
501 self.index = gloo.IndexBuffer(self.edges) 608 self.index = gloo.IndexBuffer(self.edges)
502 - self.program_e['u_size'] = 1 609 +# self.program_e['u_size'] = 1
503 self.program_e['u_model'] = self.model 610 self.program_e['u_model'] = self.model
504 self.program_e['u_view'] = self.view 611 self.program_e['u_view'] = self.view
505 self.program_e['u_projection'] = self.projection 612 self.program_e['u_projection'] = self.projection
@@ -591,7 +698,6 @@ class GraphCanvas(scene.SceneCanvas): @@ -591,7 +698,6 @@ class GraphCanvas(scene.SceneCanvas):
591 self.index_clusters_s = gloo.IndexBuffer(self.cluster_edges) 698 self.index_clusters_s = gloo.IndexBuffer(self.cluster_edges)
592 self.vbo_cluster_lines = gloo.VertexBuffer(self.cluster_line_data) 699 self.vbo_cluster_lines = gloo.VertexBuffer(self.cluster_line_data)
593 700
594 - self.program_e_s['u_size'] = 1  
595 self.program_e_s['u_model'] = self.model 701 self.program_e_s['u_model'] = self.model
596 self.program_e_s['u_view'] = self.view 702 self.program_e_s['u_view'] = self.view
597 self.program_e_s['u_projection'] = self.projection 703 self.program_e_s['u_projection'] = self.projection
@@ -648,8 +754,7 @@ class GraphCanvas(scene.SceneCanvas): @@ -648,8 +754,7 @@ class GraphCanvas(scene.SceneCanvas):
648 self.program_e_s = gloo.Program(vs_s, fs_s) 754 self.program_e_s = gloo.Program(vs_s, fs_s)
649 self.index_clusters_s = gloo.IndexBuffer(self.cluster_edges) 755 self.index_clusters_s = gloo.IndexBuffer(self.cluster_edges)
650 self.vbo_cluster_lines = gloo.VertexBuffer(self.cluster_line_data) 756 self.vbo_cluster_lines = gloo.VertexBuffer(self.cluster_line_data)
651 -  
652 - self.program_e_s['u_size'] = 1 757 +
653 self.program_e_s['u_model'] = self.model 758 self.program_e_s['u_model'] = self.model
654 self.program_e_s['u_view'] = self.view 759 self.program_e_s['u_view'] = self.view
655 self.program_e_s['u_projection'] = self.projection 760 self.program_e_s['u_projection'] = self.projection
@@ -721,78 +826,99 @@ class GraphCanvas(scene.SceneCanvas): @@ -721,78 +826,99 @@ class GraphCanvas(scene.SceneCanvas):
721 def expand_based_on_clusters(self, G, n): 826 def expand_based_on_clusters(self, G, n):
722 pos = G.vertex_properties["pos"].get_2d_array(range(3)).T 827 pos = G.vertex_properties["pos"].get_2d_array(range(3)).T
723 for p in range(pos.shape[0]): 828 for p in range(pos.shape[0]):
724 - pos[p][0] = pos[p][0] + self.clusters["a_position"][G.vertex_properties["clusters"][G.vertex(p)]][0]  
725 - pos[p][1] = pos[p][1] + self.clusters["a_position"][G.vertex_properties["clusters"][G.vertex(p)]][1]  
726 - pos[p][2] = pos[p][2] + self.clusters["a_position"][G.vertex_properties["clusters"][G.vertex(p)]][2] 829 + pos[p][0] = pos[p][0] - self.clusters["a_position"][G.vertex_properties["clusters"][G.vertex(p)]][0]
  830 + pos[p][1] = pos[p][1] - self.clusters["a_position"][G.vertex_properties["clusters"][G.vertex(p)]][1]
  831 + pos[p][2] = pos[p][2] - self.clusters["a_position"][G.vertex_properties["clusters"][G.vertex(p)]][2]
727 G.vertex_properties["pos"] = G.new_vertex_property("vector<double>", vals = pos) 832 G.vertex_properties["pos"] = G.new_vertex_property("vector<double>", vals = pos)
728 - for i in range(n):  
729 - index = 4*i  
730 - #generate the vertex filter for this cluster  
731 - num_v_in_cluster = len(np.argwhere(self.labels == i))  
732 - vfilt = np.zeros([G.num_vertices(), 1], dtype="bool")  
733 - vfilt[np.argwhere(self.labels == i)] = 1  
734 - vfilt_prop = G.new_vertex_property("bool", vals = vfilt)  
735 - G.set_vertex_filter(vfilt_prop) 833 +# for i in range(n):
  834 +# index = 4*i
  835 +# #generate the vertex filter for this cluster
  836 +# num_v_in_cluster = len(np.argwhere(self.labels == i))
  837 +# vfilt = np.zeros([G.num_vertices(), 1], dtype="bool")
  838 +# vfilt[np.argwhere(self.labels == i)] = 1
  839 +# vfilt_prop = G.new_vertex_property("bool", vals = vfilt)
  840 +# G.set_vertex_filter(vfilt_prop)
  841 +#
  842 +# #get the filtered properties
  843 +# g = nwt.gt.Graph(G, prune=True, directed=False)
  844 +# positions = g.vertex_properties["pos"].get_2d_array(range(3)).T
  845 +# position = np.sum(positions, 0)/num_v_in_cluster
  846 +# p, v = self.gen_cluster_coords(position, np.sum(g.vertex_properties['degree'].get_array()))
  847 +# self.clusters['a_position'][index:index+4] = np.asarray(p, dtype=np.float32)
  848 +# self.clusters['a_value'][index:index+4] = np.asarray(v, dtype=np.float32)
  849 +# G.clear_filters()
  850 +# self.cluster_pos[i] = position
  851 +# color = G.vertex_properties["RGBA"].get_2d_array(range(4)).T
  852 +# size = nwt.Network.map_vertices_to_range(G, [30*self.pixel_scale, 8*self.pixel_scale], 'degree').get_array()
  853 +#
  854 +# position = G.vertex_properties["pos"].get_2d_array(range(3)).T
  855 +# #for p in range(position.shape[0]):
  856 +# # position[p][0] = position[p][0] + self.clusters["a_position"][G.vertex_properties["clusters"][G.vertex(p)]][0]
  857 +# # position[p][1] = position[p][1] + self.clusters["a_position"][G.vertex_properties["clusters"][G.vertex(p)]][1]
  858 +# # position[p][2] = position[p][2] + self.clusters["a_position"][G.vertex_properties["clusters"][G.vertex(p)]][2]
  859 +# #G.vertex_properties["pos"] = G.new_vertex_property("vector<double>", vals = position)
  860 +#
  861 +#
  862 +# edges = G.get_edges();
  863 +# edges = edges[:, 0:2]
  864 +# #width = nwt.Network.map_edges_to_range(G, [1*self.pixel_scale, 5*self.pixel_scale], 'volume').get_array()
  865 +# #ecolor = G.edge_properties["RGBA"].get_2d_array(range(4)).T
  866 +#
  867 +# self.data = np.zeros(G.num_vertices(), dtype=[('a_position', np.float32, 3),
  868 +# ('a_fg_color', np.float32, 4),
  869 +# ('a_bg_color', np.float32, 4),
  870 +# ('a_size', np.float32, 1),
  871 +# ('a_linewidth', np.float32, 1),
  872 +# ('a_unique_id', np.float32, 4),
  873 +# ('a_selection', np.float32, 1),
  874 +# ])
  875 +#
  876 +# #self.edges = edges.astype(np.uint32)
  877 +# self.data['a_position'] = position
  878 +# #fg color is the color of the ring
  879 +# self.data['a_fg_color'] = 0, 0, 0, 1
  880 +# self.data['a_bg_color'] = color
  881 +# self.data['a_size'] = size
  882 +# self.data['a_linewidth'] = 4.*self.pixel_scale
  883 +# self.data['a_unique_id'] = self.gen_vertex_id(G)
  884 +# self.data['a_selection'] = G.vertex_properties["selection"].get_array()
  885 +# #self.data['a_graph_size'] = [bbu-bbl]
  886 +#
  887 +# self.program['u_graph_size'] = [self.bbu-self.bbl]
  888 +# self.vbo = gloo.VertexBuffer(self.data)
  889 +# self.gen_line_vbo(G)
  890 +# if(self.subgraphs):
  891 +# self.vbo_s = gloo.VertexBuffer(self.clusters)
  892 +# self.index_s = gloo.IndexBuffer(self.edges_s)
  893 +# #self.index = gloo.IndexBuffer(self.edges)
  894 +# self.program_e.bind(self.vbo_line)
  895 +# self.program.bind(self.vbo)
  896 +# if(self.subgraphs):
  897 +# #self.program_e_s.bind(self.vbo_s)
  898 +# self.program_s.bind(self.vbo_s)
  899 +# if DEBUG:
  900 +# print(self.view)
  901 +# self.update()
736 902
737 - #get the filtered properties  
738 - g = nwt.gt.Graph(G, prune=True, directed=False)  
739 - positions = g.vertex_properties["pos"].get_2d_array(range(3)).T  
740 - position = np.sum(positions, 0)/num_v_in_cluster  
741 - p, v = self.gen_cluster_coords(position, np.sum(g.vertex_properties['degree'].get_array())) 903 +
  904 + """
  905 + Function that updates the cluster positions based on new vertex positions
  906 + in the graph. Primarity used for animation.
  907 + """
  908 + def update_clusters(self, new_pos):
  909 + clusters = self.G.vertex_properties["clusters"].get_array().T
  910 + for i in range(self.n_c):
  911 + idx = np.argwhere(clusters == i)
  912 + pos = np.sum(new_pos[idx], 0)/len(idx)
  913 + self.cluster_pos[i] = pos.reshape(3)
  914 + index = i*4
  915 + p, v = self.gen_cluster_coords(self.cluster_pos[i], self.cluster_size[i])
742 self.clusters['a_position'][index:index+4] = np.asarray(p, dtype=np.float32) 916 self.clusters['a_position'][index:index+4] = np.asarray(p, dtype=np.float32)
743 self.clusters['a_value'][index:index+4] = np.asarray(v, dtype=np.float32) 917 self.clusters['a_value'][index:index+4] = np.asarray(v, dtype=np.float32)
744 - G.clear_filters()  
745 - self.cluster_pos[i] = position  
746 - color = G.vertex_properties["RGBA"].get_2d_array(range(4)).T  
747 - size = nwt.Network.map_vertices_to_range(G, [30*self.pixel_scale, 8*self.pixel_scale], 'degree').get_array()  
748 -  
749 - position = G.vertex_properties["pos"].get_2d_array(range(3)).T  
750 - #for p in range(position.shape[0]):  
751 - # position[p][0] = position[p][0] + self.clusters["a_position"][G.vertex_properties["clusters"][G.vertex(p)]][0]  
752 - # position[p][1] = position[p][1] + self.clusters["a_position"][G.vertex_properties["clusters"][G.vertex(p)]][1]  
753 - # position[p][2] = position[p][2] + self.clusters["a_position"][G.vertex_properties["clusters"][G.vertex(p)]][2]  
754 - #G.vertex_properties["pos"] = G.new_vertex_property("vector<double>", vals = position)  
755 - edges = G.get_edges();  
756 - edges = edges[:, 0:2]  
757 - #width = nwt.Network.map_edges_to_range(G, [1*self.pixel_scale, 5*self.pixel_scale], 'volume').get_array()  
758 - #ecolor = G.edge_properties["RGBA"].get_2d_array(range(4)).T  
759 -  
760 - self.data = np.zeros(G.num_vertices(), dtype=[('a_position', np.float32, 3),  
761 - ('a_fg_color', np.float32, 4),  
762 - ('a_bg_color', np.float32, 4),  
763 - ('a_size', np.float32, 1),  
764 - ('a_linewidth', np.float32, 1),  
765 - ('a_unique_id', np.float32, 4),  
766 - ('a_selection', np.float32, 1),  
767 - ])  
768 -  
769 - #self.edges = edges.astype(np.uint32)  
770 - self.data['a_position'] = position  
771 - #fg color is the color of the ring  
772 - self.data['a_fg_color'] = 0, 0, 0, 1  
773 - self.data['a_bg_color'] = color  
774 - self.data['a_size'] = size  
775 - self.data['a_linewidth'] = 4.*self.pixel_scale  
776 - self.data['a_unique_id'] = self.gen_vertex_id(G)  
777 - self.data['a_selection'] = G.vertex_properties["selection"].get_array()  
778 - #self.data['a_graph_size'] = [bbu-bbl]  
779 -  
780 - self.program['u_graph_size'] = [bbu-bbl]  
781 - self.vbo = gloo.VertexBuffer(self.data)  
782 - self.gen_line_vbo(G)  
783 - if(self.subgraphs):  
784 - self.vbo_s = gloo.VertexBuffer(self.clusters)  
785 - self.index_s = gloo.IndexBuffer(self.edges_s)  
786 - #self.index = gloo.IndexBuffer(self.edges)  
787 - self.program_e.bind(self.vbo_line)  
788 - self.program.bind(self.vbo)  
789 - if(self.subgraphs):  
790 - #self.program_e_s.bind(self.vbo_s)  
791 - self.program_s.bind(self.vbo_s)  
792 - if DEBUG:  
793 - print(self.view)  
794 - self.update()  
795 - 918 + self.G_cluster.vertex_properties["pos"][self.G_cluster.vertex(i)] = self.cluster_pos[i]
  919 +
  920 +
  921 +
796 922
797 """ 923 """
798 Function that generates the clusters for an unclustered graph 924 Function that generates the clusters for an unclustered graph
@@ -827,7 +953,7 @@ class GraphCanvas(scene.SceneCanvas): @@ -827,7 +953,7 @@ class GraphCanvas(scene.SceneCanvas):
827 #self.clusters['a_fg_color'] = 1., 1., 1., 0.0 953 #self.clusters['a_fg_color'] = 1., 1., 1., 0.0
828 #self.clusters['a_linewidth'] = 4.*self.pixel_scale 954 #self.clusters['a_linewidth'] = 4.*self.pixel_scale
829 955
830 - G.vertex_properties["pos"] = nwt.gt.sfdp_layout(G, groups = G.vertex_properties["clusters"], pos = G.vertex_properties["pos"]) 956 + G.vertex_properties["pos"] = nwt.gt.sfdp_layout(G, groups = G.vertex_properties["clusters"], pos = G.vertex_properties["pos"], C = 1.0, K = 10)
831 temp = [] 957 temp = []
832 temp_pos = [] 958 temp_pos = []
833 #Find the global total of the metric. 959 #Find the global total of the metric.
@@ -897,14 +1023,11 @@ class GraphCanvas(scene.SceneCanvas): @@ -897,14 +1023,11 @@ class GraphCanvas(scene.SceneCanvas):
897 print(self.clusters['a_outer_arc_length']) 1023 print(self.clusters['a_outer_arc_length'])
898 maximum = max(temp) 1024 maximum = max(temp)
899 minimum = min(temp) 1025 minimum = min(temp)
900 - if len(temp) > 1:  
901 - temp = ((temp-minimum)/(maximum-minimum)*(60*self.pixel_scale)+20*self.pixel_scale)  
902 - else:  
903 - temp = [60*self.pixel_scale] 1026 + temp = ((temp-minimum)/(maximum-minimum)*(60*self.pixel_scale)+20*self.pixel_scale)*2.0
904 for i in range(num_clusters): 1027 for i in range(num_clusters):
905 index = i*4 1028 index = i*4
906 index_t = i*2 1029 index_t = i*2
907 - p, v = self.gen_cluster_coords(temp_pos[i], temp[i]*2.0) 1030 + p, v = self.gen_cluster_coords(temp_pos[i], temp[i])
908 self.clusters['a_position'][index:index+4] = np.asarray(p, dtype=np.float32) 1031 self.clusters['a_position'][index:index+4] = np.asarray(p, dtype=np.float32)
909 self.clusters['a_value'][index:index+4] = np.asarray(v, dtype=np.float32) 1032 self.clusters['a_value'][index:index+4] = np.asarray(v, dtype=np.float32)
910 1033
@@ -913,6 +1036,7 @@ class GraphCanvas(scene.SceneCanvas): @@ -913,6 +1036,7 @@ class GraphCanvas(scene.SceneCanvas):
913 #self.edges_s[i][0:4] = np.asarray(range(index, index+4), dtype=np.uint32) 1036 #self.edges_s[i][0:4] = np.asarray(range(index, index+4), dtype=np.uint32)
914 #self.edges_s[i] 1037 #self.edges_s[i]
915 self.cluster_pos = temp_pos 1038 self.cluster_pos = temp_pos
  1039 + self.cluster_size = temp
916 #self.expand_based_on_clusters(G, self.n_c) 1040 #self.expand_based_on_clusters(G, self.n_c)
917 G.clear_filters() 1041 G.clear_filters()
918 # self.edges_s[1][0:4] = np.asarray(range(0, 0+4), dtype=np.uint32) 1042 # self.edges_s[1][0:4] = np.asarray(range(0, 0+4), dtype=np.uint32)
@@ -924,7 +1048,7 @@ class GraphCanvas(scene.SceneCanvas): @@ -924,7 +1048,7 @@ class GraphCanvas(scene.SceneCanvas):
924 # self.edges_s[0][5] = index+2 1048 # self.edges_s[0][5] = index+2
925 #self.clusters['a_size'] = temp 1049 #self.clusters['a_size'] = temp
926 self.gen_cluster_line_vbo(G) 1050 self.gen_cluster_line_vbo(G)
927 - self.program_s['u_graph_size'] = [bbu-bbl] 1051 + #self.program_s['u_graph_size'] = [bbu-bbl]
928 #if len(temp_e) > 0: 1052 #if len(temp_e) > 0:
929 # self.edges_s = np.unique(np.asarray(temp_e, np.uint32), axis=0) 1053 # self.edges_s = np.unique(np.asarray(temp_e, np.uint32), axis=0)
930 #else: 1054 #else:
@@ -1003,7 +1127,7 @@ class GraphCanvas(scene.SceneCanvas): @@ -1003,7 +1127,7 @@ class GraphCanvas(scene.SceneCanvas):
1003 self.data['a_selection'] = G.vertex_properties["selection"].get_array() 1127 self.data['a_selection'] = G.vertex_properties["selection"].get_array()
1004 #self.data['a_graph_size'] = [bbu-bbl] 1128 #self.data['a_graph_size'] = [bbu-bbl]
1005 1129
1006 - self.program['u_graph_size'] = [bbu-bbl] 1130 + #self.program['u_graph_size'] = [bbu-bbl]
1007 1131
1008 self.vbo = gloo.VertexBuffer(self.data) 1132 self.vbo = gloo.VertexBuffer(self.data)
1009 self.gen_line_vbo(G) 1133 self.gen_line_vbo(G)
@@ -1033,6 +1157,7 @@ class GraphCanvas(scene.SceneCanvas): @@ -1033,6 +1157,7 @@ class GraphCanvas(scene.SceneCanvas):
1033 Overloaded function that is called during every self.update() call 1157 Overloaded function that is called during every self.update() call
1034 """ 1158 """
1035 def on_draw(self, event): 1159 def on_draw(self, event):
  1160 + gloo.clear()
1036 clear(color='white', depth=True) 1161 clear(color='white', depth=True)
1037 self.program_e.draw('triangles', indices=self.index) 1162 self.program_e.draw('triangles', indices=self.index)
1038 self.program.draw('points') 1163 self.program.draw('points')
@@ -1041,6 +1166,49 @@ class GraphCanvas(scene.SceneCanvas): @@ -1041,6 +1166,49 @@ class GraphCanvas(scene.SceneCanvas):
1041 self.program_e_s.draw('triangles', indices=self.index_clusters_s) 1166 self.program_e_s.draw('triangles', indices=self.index_clusters_s)
1042 self.program_s.draw('triangles', indices=self.index_s) 1167 self.program_s.draw('triangles', indices=self.index_s)
1043 1168
  1169 +
  1170 +# """
  1171 +# A function to animate from one layout to another layout given a new G.
  1172 +# """
  1173 + def animate(self, old_pos, new_pos):
  1174 +
  1175 +# old_pos = self.G.vertex_properties["pos"].get_2d_array(range(3)).T
  1176 +# new_pos = new_G.vertex_properties["pos"].get_2d_array(range(3)).T
  1177 + #we want to animate the move over 2 seconds. At 60 frames per second
  1178 + #we'd get 120 different positions along the transitional distance.
  1179 + self.new_pos = new_pos
  1180 + self.old_pos = old_pos
  1181 + self.slopes = np.zeros(old_pos.shape)
  1182 + for i in range(old_pos.shape[0]):
  1183 + self.slopes[i, 0] = (new_pos[i, 0] - old_pos[i, 0])/120.0
  1184 + self.slopes[i, 1] = (new_pos[i, 1] - old_pos[i, 1])/120.0
  1185 +
  1186 + #self.timer.start()
  1187 + #for i in range(120):
  1188 + #self.old_pos = np.add(old_pos, self.slopes)
  1189 + self.timer.start(iterations=120)
  1190 + #self.data['a_position'] = old_pos
  1191 + #self.gen_vertex_vbo_minimalist()
  1192 + #self.update()
  1193 +## self.gen_line_vbo(self.G)
  1194 +## self.program_e.bind(self.vbo_line)
  1195 +## self.program.bind(self.vbo)
  1196 +# self.update()
  1197 +# #self.program_e.draw('lines')
  1198 +# print(i)
  1199 + #self.timer.stop()
  1200 +
  1201 + #self.G = new_G
  1202 + #self.gen_vertex_vbo(self.G)
  1203 + #self.update()
  1204 +
  1205 +# def on_timer(self, event):
  1206 +# self.vbo = gloo.VertexBuffer(self.data)
  1207 +# #self.gen_line_vbo(self.G)
  1208 +# #self.program_e.bind(self.vbo_line)
  1209 +# self.program.bind(self.vbo)
  1210 +# self.update()
  1211 +# gloo.wrappers.flush()
1044 """ 1212 """
1045 Function performed during a mouse click (either right or left) 1213 Function performed during a mouse click (either right or left)
1046 gets the unique id of the object drawn underneath the cursor 1214 gets the unique id of the object drawn underneath the cursor
@@ -1356,7 +1524,7 @@ class GraphCanvas(scene.SceneCanvas): @@ -1356,7 +1524,7 @@ class GraphCanvas(scene.SceneCanvas):
1356 1524
1357 #get the filtered properties 1525 #get the filtered properties
1358 g = nwt.gt.Graph(G, prune=True, directed=False) 1526 g = nwt.gt.Graph(G, prune=True, directed=False)
1359 - p, v = self.gen_cluster_coords(pos, np.sum(g.vertex_properties['degree'].get_array())) 1527 + p, v = self.gen_cluster_coords(pos, self.cluster_size[c_id])
1360 self.clusters['a_position'][index:index+4] = np.asarray(p, dtype=np.float32) 1528 self.clusters['a_position'][index:index+4] = np.asarray(p, dtype=np.float32)
1361 self.clusters['a_value'][index:index+4] = np.asarray(v, dtype=np.float32) 1529 self.clusters['a_value'][index:index+4] = np.asarray(v, dtype=np.float32)
1362 G.clear_filters() 1530 G.clear_filters()
@@ -10,6 +10,8 @@ from GraphCanvas import GraphCanvas @@ -10,6 +10,8 @@ from GraphCanvas import GraphCanvas
10 from pyqtgraph.Qt import QtCore, QtGui, QtWidgets 10 from pyqtgraph.Qt import QtCore, QtGui, QtWidgets
11 import network_dep as nwt 11 import network_dep as nwt
12 12
  13 +import numpy as np
  14 +
13 DEBUG = False 15 DEBUG = False
14 16
15 """ 17 """
@@ -69,6 +71,9 @@ class GraphWidget(QtGui.QWidget): @@ -69,6 +71,9 @@ class GraphWidget(QtGui.QWidget):
69 #EXP = menu.addAction('Export VTK') 71 #EXP = menu.addAction('Export VTK')
70 #EXP_adv = menu.addAction('Export VTK Advanced') 72 #EXP_adv = menu.addAction('Export VTK Advanced')
71 NL = menu.addAction('New Layout') 73 NL = menu.addAction('New Layout')
  74 + NSL = menu.addAction('New Spring-Onion Layout (sum)')
  75 + NSLMI = menu.addAction('New Spring-Onion Layout(max)')
  76 + EXPAND = menu.addAction('Expand')
72 action = menu.exec_(event.native.globalPos()) 77 action = menu.exec_(event.native.globalPos())
73 if DEBUG: 78 if DEBUG:
74 print(action) 79 print(action)
@@ -108,11 +113,43 @@ class GraphWidget(QtGui.QWidget): @@ -108,11 +113,43 @@ class GraphWidget(QtGui.QWidget):
108 #self.cb.currentIndexChanged.connect(self.selection_change) 113 #self.cb.currentIndexChanged.connect(self.selection_change)
109 #self.cb.show() 114 #self.cb.show()
110 if action == NL: 115 if action == NL:
111 - self.canvas.G = nwt.Network.gen_new_fd_layout(self.canvas.G)  
112 - self.canvas.gen_vertex_vbo(self.canvas.G) 116 + old_pos = self.canvas.G.vertex_properties["pos"].get_2d_array(range(3)).T
  117 + nG = nwt.Network.gen_new_fd_layout(self.canvas.G)
  118 + new_pos = nG.vertex_properties["pos"].get_2d_array(range(3)).T
  119 + self.canvas.animate(old_pos, new_pos)
  120 +
  121 + #self.canvas.gen_vertex_vbo(self.canvas.G)
113 #self.canvas.set_data(self.canvas.G, self.canvas.bbl, self.canvas.bbu) 122 #self.canvas.set_data(self.canvas.G, self.canvas.bbl, self.canvas.bbu)
  123 + #self.canvas.expand_clusters(self.canvas.G, self.canvas.n_c)
  124 + if action == NSL:
  125 + old_pos = self.canvas.G.vertex_properties["pos"].get_2d_array(range(3)).T
  126 + nG = nwt.Network.gen_spring_onion_layout(self.canvas.G, 'degree', 1.0, 1000, 0.01, 1.0)
  127 + new_pos = nG.vertex_properties["pos"].get_2d_array(range(3)).T
  128 +
  129 + self.canvas.animate(old_pos, new_pos)
  130 + #self.canvas.set_data(nG, self.canvas.bbl, self.canvas.bbu)
  131 +
  132 + #self.canvas.gen_vertex_vbo(self.canvas.G)
  133 + #self.canvas.expand_clusters(self.canvas.G, self.canvas.n_c)
  134 + if action == NSLMI:
  135 + old_pos = self.canvas.G.vertex_properties["pos"].get_2d_array(range(3)).T
  136 + nG = nwt.Network.gen_spring_onion_layout(self.canvas.G, 'degree', 1.0, 1000, 0.01, 1.0, False)
  137 + new_pos = nG.vertex_properties["pos"].get_2d_array(range(3)).T
  138 +
  139 + self.canvas.animate(old_pos, new_pos)
  140 + #self.canvas.set_data(nG, self.canvas.bbl, self.canvas.bbu)
  141 + #self.canvas.expand_clusters(self.canvas.G, self.canvas.n_c)
  142 +
  143 + #self.canvas.gen_vertex_vbo(self.canvas.G)
  144 +
  145 + if action == EXPAND:
  146 + #self.canvas.gen_vertex_vbo(self.canvas.G)
  147 + old_pos = self.canvas.G.vertex_properties["pos"].get_2d_array(range(3)).T
114 self.canvas.expand_clusters(self.canvas.G, self.canvas.n_c) 148 self.canvas.expand_clusters(self.canvas.G, self.canvas.n_c)
115 - 149 + new_pos = self.canvas.G.vertex_properties["pos"].get_2d_array(range(3)).T
  150 + #self.canvas.expand_clusters(self.canvas.G, self.canvas.n_c)
  151 +
  152 + self.canvas.animate(old_pos, new_pos)
116 #self.canvas.size_vertices(self.canvas.G, 'degree_volume') 153 #self.canvas.size_vertices(self.canvas.G, 'degree_volume')
117 else: 154 else:
118 if self.canvas.view[0][0] >= 0.0010: 155 if self.canvas.view[0][0] >= 0.0010:
@@ -144,6 +181,12 @@ class GraphWidget(QtGui.QWidget): @@ -144,6 +181,12 @@ class GraphWidget(QtGui.QWidget):
144 def on_mouse_double_click(self, event): 181 def on_mouse_double_click(self, event):
145 self.canvas.update_path(event) 182 self.canvas.update_path(event)
146 self.select.emit(self.canvas.get_path()) 183 self.select.emit(self.canvas.get_path())
  184 + old_pos = self.canvas.G.vertex_properties["pos"].get_2d_array(range(3)).T
  185 + nG = nwt.Network.gen_new_fd_layout(self.canvas.G)
  186 + # def animate(self, new_G):
  187 +#
  188 + new_pos = nG.vertex_properties["pos"].get_2d_array(range(3)).T
  189 + self.canvas.animate(old_pos, new_pos)
147 190
148 """ 191 """
149 Handles the mouse release event. 192 Handles the mouse release event.
@@ -39,7 +39,6 @@ top = QtGui.QWidget() @@ -39,7 +39,6 @@ top = QtGui.QWidget()
39 top.resize(900, 900) 39 top.resize(900, 900)
40 40
41 41
42 -hist = pg.PlotWidget()  
43 #fibers = FiberView() 42 #fibers = FiberView()
44 fibers = TubeWidget() 43 fibers = TubeWidget()
45 fibers.canvas.create_native() 44 fibers.canvas.create_native()
@@ -66,15 +65,16 @@ top.setLayout(layout) @@ -66,15 +65,16 @@ top.setLayout(layout)
66 top.show() 65 top.show()
67 66
68 67
69 -def draw_histogram(G, value):  
70 - vals = G.edge_properties[value].get_array()  
71 - y, x = np.histogram(vals,40)  
72 - hist.plot(x,y, stepMode=True, fillLevel=0, brush=(0,0,255,150)) 68 +#def draw_histogram(G, value):
  69 +# vals = G.edge_properties[value].get_array()
  70 +# y, x = np.histogram(vals,40)
  71 +# hist.plot(x,y, stepMode=True, fillLevel=0, brush=(0,0,255,150))
73 72
74 def load_nwt(filepath): 73 def load_nwt(filepath):
75 net = nwt.Network(filepath) 74 net = nwt.Network(filepath)
76 G = net.createFullGraph_gt() 75 G = net.createFullGraph_gt()
77 G = net.filterDisconnected(G) 76 G = net.filterDisconnected(G)
  77 + #G = net.gen_spring_onion_layout(G, 'degree', 1.0, 1000, 0.01, 1.0)
78 #G = net.filterFullGraph_gt(G, erode=True) 78 #G = net.filterFullGraph_gt(G, erode=True)
79 #G = net.filterFullGraph_gt(G, erode=True) 79 #G = net.filterFullGraph_gt(G, erode=True)
80 #G = net.gen_new_fd_layout(G) 80 #G = net.gen_new_fd_layout(G)
@@ -104,7 +104,7 @@ center = (bbu-bbl)/2.0 @@ -104,7 +104,7 @@ center = (bbu-bbl)/2.0
104 #fibers.opts['distance'] = 5 104 #fibers.opts['distance'] = 5
105 # item = NodeItem(G) 105 # item = NodeItem(G)
106 # graph.addItem(item) 106 # graph.addItem(item)
107 -draw_histogram(G, "length") 107 +#draw_histogram(G, "length")
108 graph.canvas.set_data(G, bbl, bbu) 108 graph.canvas.set_data(G, bbl, bbu)
109 fibers.canvas.set_data(G, bbl, bbu, 16) 109 fibers.canvas.set_data(G, bbl, bbu, 16)
110 #fibers.draw_all(G, center, fibers, graph, node_tex) 110 #fibers.draw_all(G, center, fibers, graph, node_tex)
@@ -68,7 +68,7 @@ class TubeDraw(scene.SceneCanvas): @@ -68,7 +68,7 @@ class TubeDraw(scene.SceneCanvas):
68 blend_func=('src_alpha', 'one_minus_src_alpha'), depth_func = ('lequal')) 68 blend_func=('src_alpha', 'one_minus_src_alpha'), depth_func = ('lequal'))
69 #set_blend_color(color='black') 69 #set_blend_color(color='black')
70 #set_state('translucent') 70 #set_state('translucent')
71 - self.program['u_LightPos'] = [0., 0., -1000.] 71 + #self.program['u_LightPos'] = [0., 0., -1000.]
72 #self.camera = self.central_widget.add_view() 72 #self.camera = self.central_widget.add_view()
73 #self.camera.camera = 'turntable' 73 #self.camera.camera = 'turntable'
74 self.down = False 74 self.down = False
@@ -107,7 +107,7 @@ class TubeDraw(scene.SceneCanvas): @@ -107,7 +107,7 @@ class TubeDraw(scene.SceneCanvas):
107 self.projection = perspective(90.0, self.physical_size[0]/self.physical_size[1], 1.0, 1000.0) 107 self.projection = perspective(90.0, self.physical_size[0]/self.physical_size[1], 1.0, 1000.0)
108 #self.projection = perspective(90.0, 1.0, -1.0, 1.0) 108 #self.projection = perspective(90.0, 1.0, -1.0, 1.0)
109 self.program['u_model'] = self.model 109 self.program['u_model'] = self.model
110 - self.program['u_LightPos'] = [0., 0., 1000.] 110 + #self.program['u_LightPos'] = [0., 0., 1000.]
111 #self.program['u_view'] = self.view 111 #self.program['u_view'] = self.view
112 self.program['u_projection'] = self.projection 112 self.program['u_projection'] = self.projection
113 self.program.bind(self.vbo) 113 self.program.bind(self.vbo)
@@ -481,8 +481,8 @@ class TubeDraw(scene.SceneCanvas): @@ -481,8 +481,8 @@ class TubeDraw(scene.SceneCanvas):
481 #coord[1] = 0 481 #coord[1] = 0
482 #coord2[1] = 0 482 #coord2[1] = 0
483 483
484 - theta = (coord[0]-coord2[0])*360.0/2.0/np.pi  
485 - phi = (coord[1]-coord2[1])*360.0/2.0/np.pi 484 + phi = (coord[0]-coord2[0])*360.0/2.0/np.pi
  485 + theta = (coord[1]-coord2[1])*360.0/2.0/np.pi
486 if DEBUG: 486 if DEBUG:
487 print(theta*360.0/2.0/np.pi, -phi*360.0/2.0/np.pi) 487 print(theta*360.0/2.0/np.pi, -phi*360.0/2.0/np.pi)
488 self.camera = self.camera - self.translate 488 self.camera = self.camera - self.translate
@@ -533,7 +533,7 @@ class TubeDraw(scene.SceneCanvas): @@ -533,7 +533,7 @@ class TubeDraw(scene.SceneCanvas):
533 print("current position ", self.camera, " and up vector ", self.up) 533 print("current position ", self.camera, " and up vector ", self.up)
534 self.program['u_eye'] = self.camera 534 self.program['u_eye'] = self.camera
535 self.program['u_up'] = self.up 535 self.program['u_up'] = self.up
536 - self.program['u_LightPos'] = [self.camera[0], self.camera[1], self.camera[2]] 536 + #self.program['u_LightPos'] = [self.camera[0], self.camera[1], self.camera[2]]
537 self.update() 537 self.update()
538 538
539 #reverts the mouse state during release. 539 #reverts the mouse state during release.
@@ -14,7 +14,7 @@ Created on Mon Aug 5 15:53:16 2019 @@ -14,7 +14,7 @@ Created on Mon Aug 5 15:53:16 2019
14 from pyqtgraph.Qt import QtCore, QtGui, QtWidgets 14 from pyqtgraph.Qt import QtCore, QtGui, QtWidgets
15 from TubeCanvas import TubeDraw 15 from TubeCanvas import TubeDraw
16 import numpy as np 16 import numpy as np
17 -import trimesh as tm 17 +#import trimesh as tm
18 18
19 DEBUG = False 19 DEBUG = False
20 20
@@ -14,14 +14,14 @@ vert = &quot;&quot;&quot; @@ -14,14 +14,14 @@ vert = &quot;&quot;&quot;
14 #version 120 14 #version 120
15 // Uniforms 15 // Uniforms
16 // ------------------------------------ 16 // ------------------------------------
  17 +uniform float u_size;
  18 +uniform float u_antialias;
17 uniform mat4 u_model; 19 uniform mat4 u_model;
18 uniform mat4 u_view; 20 uniform mat4 u_view;
19 uniform mat4 u_projection; 21 uniform mat4 u_projection;
20 -uniform float u_antialias;  
21 -uniform float u_size; 22 +//uniform vec3 u_graph_size;
22 uniform bool u_picking; 23 uniform bool u_picking;
23 24
24 -uniform vec3 u_graph_size;  
25 // Attributes 25 // Attributes
26 // ------------------------------------ 26 // ------------------------------------
27 attribute vec3 a_position; 27 attribute vec3 a_position;
@@ -65,7 +65,6 @@ uniform mat4 u_model; @@ -65,7 +65,6 @@ uniform mat4 u_model;
65 uniform mat4 u_view; 65 uniform mat4 u_view;
66 uniform mat4 u_projection; 66 uniform mat4 u_projection;
67 uniform float u_antialias; 67 uniform float u_antialias;
68 -uniform float u_size;  
69 uniform bool u_picking; 68 uniform bool u_picking;
70 69
71 // Varyings 70 // Varyings
@@ -192,8 +191,6 @@ attribute vec3 a_position; @@ -192,8 +191,6 @@ attribute vec3 a_position;
192 attribute vec2 a_normal; 191 attribute vec2 a_normal;
193 attribute vec4 a_fg_color; 192 attribute vec4 a_fg_color;
194 attribute float a_linewidth; 193 attribute float a_linewidth;
195 -//attribute vec4 a_unique_id;  
196 -//attribute vec4 l_color;  
197 194
198 // Varyings 195 // Varyings
199 // ------------------------------------ 196 // ------------------------------------
@@ -253,4 +250,4 @@ float new_alpha(float zoom_level) @@ -253,4 +250,4 @@ float new_alpha(float zoom_level)
253 return val; 250 return val;
254 251
255 } 252 }
256 -"""  
257 \ No newline at end of file 253 \ No newline at end of file
  254 +"""
@@ -1115,9 +1115,163 @@ class Network: @@ -1115,9 +1115,163 @@ class Network:
1115 G_0.clear_filters() 1115 G_0.clear_filters()
1116 1116
1117 return graph 1117 return graph
  1118 +
  1119 + '''
  1120 + Generates a layout based a 3 neighbors spring system.
  1121 + Vertices within 1 edge, 2 edges and 3 edges act upon one another based on
  1122 + Hooke's law. 1e springs are the stronges and strength decreases as edges get further away
  1123 +
  1124 + '''
  1125 + def gen_spring_onion_layout(G, v_property, k, n_steps, time_step, min_distance, Sum=True):
  1126 + start = time.time()
  1127 +
  1128 + one_neighbors = G.new_vertex_property("vector<int>")
  1129 + o1_n = []
  1130 + two_neighbors = G.new_vertex_property("vector<int>")
  1131 + o2_n = []
  1132 + three_neighbors = G.new_vertex_property("vector<int>")
  1133 + o3_n = []
  1134 + #generate the map of 1, 2 and 3 neighborhood vertices.
  1135 + for v in G.vertices():
  1136 + one_n = []
  1137 + two_n = []
  1138 + three_n = []
  1139 + #find all 1 neighbors
  1140 + for i in v.all_neighbors():
  1141 + one_n.append(int(i))
  1142 + if(len(one_n) == 0):
  1143 + print("WTF")
  1144 + #find all 2 neighbors
  1145 + for i in one_n:
  1146 + for j in G.vertex(i).all_neighbors():
  1147 + if(int(j) not in one_n):
  1148 + two_n.append(int(j))
  1149 +
  1150 + #find all 3 neighbors
  1151 + for i in two_n:
  1152 + for j in G.vertex(i).all_neighbors():
  1153 + if(int(j) not in one_n and int(j) not in two_n):
  1154 + three_n.append(int(j))
1118 1155
  1156 + #we do not keep ones that have already counted, i.e. a vertex
  1157 + #appears in all 3 arrays only once.
  1158 + #it's ok to add self to any array because the distance -k(x=0) = 0
  1159 + one_neighbors[v] = np.asarray(one_n)
  1160 + o1_n.append(np.asarray(one_n))
  1161 + two_neighbors[v] = np.asarray(two_n)
  1162 + o2_n.append(np.asarray(two_n))
  1163 + three_neighbors[v] = np.asarray(three_n)
  1164 + o3_n.append(np.asarray(three_n))
1119 1165
1120 - 1166 + print("generating neighborhoods: ", time.time() - start)
  1167 + start = time.time()
  1168 + G.vertex_properties["1_neighbor"] = one_neighbors
  1169 + G.vertex_properties["2_neighbor"] = two_neighbors
  1170 + G.vertex_properties["3_neighbor"] = three_neighbors
  1171 +
  1172 + cooling = 1.0
  1173 + cooling_step = cooling/n_steps
  1174 +
  1175 +
  1176 +# #get points of the centers of every cluster
  1177 +# #generate voronoi region and plot it.
  1178 +# fig, ax = plt.subplots(2, 1, sharex='col', sharey='row')
  1179 +# fig.tight_layout()
  1180 +# grid = plt.GridSpec(2,1)
  1181 +# grid.update(wspace=0.025, hspace=0.2)
  1182 +# ax[0].axis('off')
  1183 +# ax[1].axis('off')
  1184 +#
  1185 +#
  1186 +# before = fig.add_subplot(grid[0])
  1187 +# after = fig.add_subplot(grid[1])
  1188 +# pts = G.vertex_properties["pos"].get_2d_array(range(2)).T
  1189 +# before.scatter(pts[:,0], pts[:, 1], marker="*")
  1190 +#
  1191 +# #plot the connections of the top level graph
  1192 +# for e in G.edges():
  1193 +# coord = G.vertex_properties["pos"][e.source()]
  1194 +# coord2 = G.vertex_properties["pos"][e.target()]
  1195 +# x = [coord[0], coord2[0]]
  1196 +# y = [coord[1], coord2[1]]
  1197 +# before.plot(x, y, 'go--', linewidth=1, markersize=1)
  1198 +#
  1199 +# #plot the connections of the top level graph
  1200 +# for e in G.edges():
  1201 +# coord = G.vertex_properties["pos"][e.source()]
  1202 +# coord2 = G.vertex_properties["pos"][e.target()]
  1203 +# x = [coord[0], coord2[0]]
  1204 +# y = [coord[1], coord2[1]]
  1205 +# before.plot(x, y, 'go--', linewidth=1, markersize=1)
  1206 +
  1207 + velocities = np.zeros([G.num_vertices(), 3])
  1208 + print("setting neighborhoods: ", time.time() - start)
  1209 + start = time.time()
  1210 +
  1211 + pos = G.vertex_properties["pos"].get_2d_array(range(3)).T
  1212 + weight = G.vertex_properties[v_property].get_array().T
  1213 +
  1214 + for n in range(n_steps+1):
  1215 + forces = np.zeros([G.num_vertices(), 3])
  1216 + #pos = G.vertex_properties["pos"].get_2d_array(range(2)).T
  1217 + if Sum:
  1218 + for v in G.vertices():
  1219 + for i in o1_n[int(v)]:
  1220 + x = pos[int(i), :] - pos[int(v), :]
  1221 + forces[int(v), 0] += -k*(x[0])
  1222 + forces[int(v), 1] += -k*(x[1])
  1223 + for i in o2_n[int(v)]:
  1224 + x = pos[int(i)] - pos[int(v)]
  1225 + forces[int(v), 0] += -k*(x[0])/2.0
  1226 + forces[int(v), 1] += -k*(x[1])/2.0
  1227 + for i in o3_n[int(v)]:
  1228 + x = pos[int(i)] - pos[int(v)]
  1229 + forces[int(v), 0] += -k*(x[0])/4.0
  1230 + forces[int(v), 1] += -k*(x[1])/4.0
  1231 + else:
  1232 + for v in G.vertices():
  1233 + for i in o3_n[int(v)]:
  1234 + x = pos[int(i)] - pos[int(v)]
  1235 + forces[int(v), 0] = -k*(x[0])/4.0
  1236 + forces[int(v), 1] = -k*(x[1])/4.0
  1237 +
  1238 + forces[:, 0] = forces[:, 0]/weight[:]
  1239 + forces[:, 1] = forces[:, 1]/weight[:]
  1240 +# if n < 1:
  1241 +# velocities = forces * time_step*G.num_vertices()
  1242 +# else:
  1243 +# pos += velocities * time_step
  1244 +# velocities = forces * time_step * cooling
  1245 +# cooling -= cooling_step
  1246 +#
  1247 +
  1248 + for v in G.vertices():
  1249 + if n < 1:
  1250 + velocities = forces * time_step
  1251 + #G.vertex_properties["pos"][v] = pos[int(v), :] + forces[int(v), :] * time_step
  1252 + else:
  1253 + pos[int(v), :] = pos[int(v), :] + velocities[int(v), :] * time_step
  1254 + velocities = forces * time_step * cooling
  1255 + cooling -= cooling_step
  1256 +
  1257 + G.vertex_properties["pos"] = G.new_vertex_property("vector<double>", vals = pos)
  1258 + print("calculating new positions: ", time.time() - start)
  1259 +# pts = G.vertex_properties["pos"].get_2d_array(range(2)).T
  1260 +# after.scatter(pts[:,0], pts[:, 1], marker="*")
  1261 +#
  1262 +# #plot the connections of the top level graph
  1263 +# for e in G.edges():
  1264 +# coord = G.vertex_properties["pos"][e.source()]
  1265 +# coord2 = G.vertex_properties["pos"][e.target()]
  1266 +# x = [coord[0], coord2[0]]
  1267 +# y = [coord[1], coord2[1]]
  1268 +# after.plot(x, y, 'go--', linewidth=1, markersize=1)
  1269 +#
  1270 +# plt.show()
  1271 + return G
  1272 +
  1273 +
  1274 +
1121 1275
1122 ''' 1276 '''
1123 Creates a graph from a list of nodes and a list of edges 1277 Creates a graph from a list of nodes and a list of edges
@@ -1537,8 +1691,9 @@ class Network: @@ -1537,8 +1691,9 @@ class Network:
1537 1691
1538 1692
1539 def gen_new_fd_layout(G): 1693 def gen_new_fd_layout(G):
1540 - pos = gt.sfdp_layout(G, C = 1.0, K = 10)  
1541 - G.vertex_properties["pos"] = pos 1694 + G.vertex_properties["pos"] = gt.sfdp_layout(G, groups = G.vertex_properties["clusters"], pos = G.vertex_properties["pos"], C = 1.0, K = 10)
  1695 + #pos = gt.sfdp_layout(G, C = 1.0, K = 10)
  1696 + #G.vertex_properties["pos"] = pos
1542 return G 1697 return G
1543 1698
1544 def map_edges_to_range(G, rng, propertymap): 1699 def map_edges_to_range(G, rng, propertymap):
@@ -1668,7 +1823,7 @@ class Network: @@ -1668,7 +1823,7 @@ class Network:
1668 G.vertex_properties["partition"] = G.new_vertex_property("vector<boolean>", array_cluster_bel) 1823 G.vertex_properties["partition"] = G.new_vertex_property("vector<boolean>", array_cluster_bel)
1669 G.edge_properties["partition"] = G.new_edge_property("vector<boolean>", array_ecluster_bel) 1824 G.edge_properties["partition"] = G.new_edge_property("vector<boolean>", array_ecluster_bel)
1670 j = 0 1825 j = 0
1671 - gt.graph_draw(G, pos = gt.sfdp_layout(G), output="Graph_full.pdf") 1826 + #gt.graph_draw(G, pos = gt.sfdp_layout(G), output="Graph_full.pdf")
1672 for i in range(c): 1827 for i in range(c):
1673 TFv = G.new_vertex_property("bool", vals=array_cluster_bel[i,:]) 1828 TFv = G.new_vertex_property("bool", vals=array_cluster_bel[i,:])
1674 TFe = G.new_edge_property("bool", vals=array_ecluster_bel[i,:]) 1829 TFe = G.new_edge_property("bool", vals=array_ecluster_bel[i,:])
subgraph_shaders.py
  Show/Hide comments   View file @25fa0bf
@@ -14,7 +14,7 @@ vert_s = &quot;&quot;&quot; @@ -14,7 +14,7 @@ vert_s = &quot;&quot;&quot;
14 uniform mat4 u_model; 14 uniform mat4 u_model;
15 uniform mat4 u_view; 15 uniform mat4 u_view;
16 uniform mat4 u_projection; 16 uniform mat4 u_projection;
17 -uniform vec3 u_graph_size; 17 +//uniform vec3 u_graph_size;
18 uniform bool u_picking; 18 uniform bool u_picking;
19 // Attributes 19 // Attributes
20 // ------------------------------------ 20 // ------------------------------------
@@ -214,8 +214,6 @@ attribute vec3 a_position; @@ -214,8 +214,6 @@ attribute vec3 a_position;
214 attribute vec2 a_normal; 214 attribute vec2 a_normal;
215 attribute vec4 a_fg_color; 215 attribute vec4 a_fg_color;
216 attribute float a_linewidth; 216 attribute float a_linewidth;
217 -//attribute vec4 a_unique_id;  
218 -//attribute vec4 l_color;  
219 217
220 // Varyings 218 // Varyings
221 // ------------------------------------ 219 // ------------------------------------
@@ -273,4 +271,4 @@ float new_alpha(float zoom_level) @@ -273,4 +271,4 @@ float new_alpha(float zoom_level)
273 } 271 }
274 return val; 272 return val;
275 } 273 }
276 -"""  
277 \ No newline at end of file 274 \ No newline at end of file
  275 +"""
@@ -11,7 +11,6 @@ VERT_SHADER = &quot;&quot;&quot; @@ -11,7 +11,6 @@ VERT_SHADER = &quot;&quot;&quot;
11 // Uniforms 11 // Uniforms
12 // ------------------------------------ 12 // ------------------------------------
13 uniform vec4 u_bb[26]; 13 uniform vec4 u_bb[26];
14 -uniform vec3 u_LightPost;  
15 uniform mat4 u_model; 14 uniform mat4 u_model;
16 //uniform mat4 u_view; 15 //uniform mat4 u_view;
17 uniform mat4 u_projection; 16 uniform mat4 u_projection;
@@ -53,8 +52,8 @@ void main (void) { @@ -53,8 +52,8 @@ void main (void) {
53 v_position = vec3(MV*vec4(a_position, 1.0)); 52 v_position = vec3(MV*vec4(a_position, 1.0));
54 vt_position = vec3(a_position); 53 vt_position = vec3(a_position);
55 v_fg_color = a_fg_color; 54 v_fg_color = a_fg_color;
56 - v_selection = a_selection;  
57 gl_Position = MVP * vec4(a_position, 1.0); 55 gl_Position = MVP * vec4(a_position, 1.0);
  56 + v_selection = a_selection;
58 } 57 }
59 58
60 mat4 make_view(vec3 eye, vec3 target, vec3 up) 59 mat4 make_view(vec3 eye, vec3 target, vec3 up)
@@ -87,7 +86,6 @@ FRAG_SHADER = &quot;&quot;&quot; @@ -87,7 +86,6 @@ FRAG_SHADER = &quot;&quot;&quot;
87 // Uniforms 86 // Uniforms
88 // ------------------------------------ 87 // ------------------------------------
89 uniform vec3 u_bb[26]; 88 uniform vec3 u_bb[26];
90 -uniform vec3 u_LightPos;  
91 uniform mat4 u_model; 89 uniform mat4 u_model;
92 //uniform mat4 u_view; 90 //uniform mat4 u_view;
93 uniform mat4 u_projection; 91 uniform mat4 u_projection;
@@ -198,7 +196,7 @@ float new_alpha() @@ -198,7 +196,7 @@ float new_alpha()
198 float bin_alpha(float alpha) 196 float bin_alpha(float alpha)
199 { 197 {
200 198
201 - 199 +
202 if(alpha > 0.8) 200 if(alpha > 0.8)
203 return 0.0; 201 return 0.0;
204 else if(alpha > 0.6) 202 else if(alpha > 0.6)
@@ -211,7 +209,7 @@ float bin_alpha(float alpha) @@ -211,7 +209,7 @@ float bin_alpha(float alpha)
211 return 1.0; 209 return 1.0;
212 else 210 else
213 return 1.0; 211 return 1.0;
214 - 212 +
215 // if(alpha > 0.9) 213 // if(alpha > 0.9)
216 // return 0.0; 214 // return 0.0;
217 // else if(alpha > 0.8) 215 // else if(alpha > 0.8)
@@ -31,32 +31,50 @@ import network_dep as nwt @@ -31,32 +31,50 @@ import network_dep as nwt
31 class Polygon_mass: 31 class Polygon_mass:
32 def __init__(self, G): 32 def __init__(self, G):
33 self.G = G 33 self.G = G
  34 + print(nwt.gt.graph_tool.topology.is_planar(G))
34 self.get_aabb() 35 self.get_aabb()
35 self.gen_polygon() 36 self.gen_polygon()
36 self.torque = [] 37 self.torque = []
  38 + self.forces_r = np.zeros(2)
  39 + self.forces_a = np.zeros(2)
37 self.vel = 0.0 40 self.vel = 0.0
38 self.aa = 0.0 41 self.aa = 0.0
  42 + self.degree = 0
39 43
40 44
41 def clear_torques(self): 45 def clear_torques(self):
42 self.torque = [] 46 self.torque = []
43 47
  48 + def clear_forces(self):
  49 + self.forces_r = np.zeros(2)
  50 + self.forces_a = np.zeros(2)
  51 +
  52 + def set_degree(self, degree):
  53 + self.degree = degree
  54 +
44 def add_torque(self, p, f): 55 def add_torque(self, p, f):
45 #direction of the torque = cross of (r, f) 56 #direction of the torque = cross of (r, f)
46 #magnitude = ||r||*||f||*sin(theta) 57 #magnitude = ||r||*||f||*sin(theta)
47 #r = level arm vector 58 #r = level arm vector
48 d = self.CoM - p 59 d = self.CoM - p
49 - r = np.linalg.norm(self.CoM - p)  
50 - theta = math.acos(np.dot(d, f)/np.dot(d, d)/np.dot(f, f))  
51 - torque = math.sin(theta) * np.sqrt(f[0]*f[0]+f[1]*f[1]) * np.sqrt(r[0]*r[0]+r[1]*r[1]) 60 + #r = np.linalg.norm(self.CoM - p)
  61 + value = np.dot(d, f)/np.dot(d, d)/np.dot(f, f)
  62 + if value < 1.0 and value > -1.0:
  63 + theta = math.acos(value)
  64 + torque = math.sin(theta) * np.sqrt(f[0]*f[0]+f[1]*f[1]) * np.sqrt(d[0]*d[0]+d[1]*d[1])
  65 + else:
  66 + #print("value = ", value)
  67 + torque = 0.0
  68 +
52 #if < 0 then clockwise, else counter 69 #if < 0 then clockwise, else counter
53 - direction = np.cross(r, f) 70 + direction = np.cross(d, f)
54 if direction < 0: 71 if direction < 0:
55 - self.torque.append([torque, "clockwise"]) 72 + self.torque.append([torque, f, p, "counterclock"])
56 else: 73 else:
57 - self.torque.append([torque, "counterclock"]) 74 + self.torque.append([torque, f, p, "clockwise"])
  75 +
58 76
59 - def calculate_moment(self): 77 + def calculate_moment(self, use_graph=False):
60 78
61 #returns the area of a triangle defined by two points 79 #returns the area of a triangle defined by two points
62 def area(t): 80 def area(t):
@@ -65,6 +83,7 @@ class Polygon_mass: @@ -65,6 +83,7 @@ class Polygon_mass:
65 83
66 def center(t): 84 def center(t):
67 output = np.asarray([(t[0,0]+t[1,0]+t[2,0])/3.0, (t[0,1]+t[1,1]+t[2,1])/3.0]) 85 output = np.asarray([(t[0,0]+t[1,0]+t[2,0])/3.0, (t[0,1]+t[1,1]+t[2,1])/3.0])
  86 + return output
68 87
69 segs = [] 88 segs = []
70 pts = np.asarray(self.polygon.exterior.xy).T 89 pts = np.asarray(self.polygon.exterior.xy).T
@@ -72,9 +91,19 @@ class Polygon_mass: @@ -72,9 +91,19 @@ class Polygon_mass:
72 for k in range(pts.shape[0]-1): 91 for k in range(pts.shape[0]-1):
73 segs.append([k, k+1]) 92 segs.append([k, k+1])
74 segs.append([pts.shape[0]-1, 0]) 93 segs.append([pts.shape[0]-1, 0])
  94 + if use_graph:
  95 + points = self.G.vertex_properties["pos"].get_2d_array(range(2)).T
  96 + segs2 = []
  97 + n_pts = pts.shape[0]
  98 + for e in self.G.edges():
  99 + segs2.append([int(e.source())+n_pts, int(e.target())+n_pts])
  100 + pts = np.concatenate((pts, points))
  101 + segs = segs + segs2
75 mesh = dict(vertices=pts, segments=segs) 102 mesh = dict(vertices=pts, segments=segs)
76 #print(self.polygon.area()) 103 #print(self.polygon.area())
77 - tri = triangulate(mesh, 'pq20D') 104 + tri = triangulate(mesh, 'pq20Ds')
  105 + self.mesh = mesh
  106 + self.tri = tri
78 moment = 0.0 107 moment = 0.0
79 #NEED TO ADD MASS maybe? 108 #NEED TO ADD MASS maybe?
80 for i in range(tri['triangles'].shape[0]): 109 for i in range(tri['triangles'].shape[0]):
@@ -84,59 +113,75 @@ class Polygon_mass: @@ -84,59 +113,75 @@ class Polygon_mass:
84 Moi = A+A*np.linalg.norm(C-self.CoM)**2 113 Moi = A+A*np.linalg.norm(C-self.CoM)**2
85 moment += Moi 114 moment += Moi
86 115
87 - self.MoI = moment 116 + self.MoI = abs(math.log(moment))
  117 + #self.MoI = 10
  118 + print(self.MoI)
88 # triangle_plot(plt.gca(), **tri) 119 # triangle_plot(plt.gca(), **tri)
89 # plt.gca().set_title(str(self.polygon.area)) 120 # plt.gca().set_title(str(self.polygon.area))
90 - 121 +
  122 + def translate(self, step):
  123 + d = self.forces_a + self.forces_r
  124 + #print(self.forces_a, self.forces_r)
  125 + d0 = step*d
  126 + self.CoM = self.CoM + d0
  127 + pos = self.G.vertex_properties["pos"].get_2d_array(range(2)).T
  128 + pos = pos + d0
  129 + self.G.vertex_properties["pos"] = self.G.new_vertex_property("vector<double>", vals = pos)
  130 +
91 def rotate(self, phi, direction = "counterclock"): 131 def rotate(self, phi, direction = "counterclock"):
92 if("counterclock"): 132 if("counterclock"):
93 - for v in self.G.vertices:  
94 - p = self.G.vertex_properties["pos"][v]  
95 - p[0] = self.CoM[0] + math.cos(phi) * (self.CoM[0] - p[0]) - math.sin(phi) * (p[1] - self.CoM[1])  
96 - p[1] = self.CoM[1] + math.sin(phi) * (self.CoM[0] - p[0]) + math.cos(phi) * (p[1] - self.CoM[1])  
97 - self.G.vertex_properties["pos"][v] = p 133 + for v in self.G.vertices():
  134 + p_prime = copy.deepcopy(self.G.vertex_properties["pos"][v])
  135 + p = copy.deepcopy(self.G.vertex_properties["pos"][v])
  136 + p_prime[0] = self.CoM[0] + math.cos(phi) * (p[0] - self.CoM[0]) - math.sin(phi) * (p[1] - self.CoM[1])
  137 + p_prime[1] = self.CoM[1] + math.sin(phi) * (p[0] - self.CoM[0]) + math.cos(phi) * (p[1] - self.CoM[1])
  138 + self.G.vertex_properties["pos"][v] = p_prime
  139 + #rotate points in mesh
  140 + points = copy.deepcopy(self.mesh['vertices'])
  141 + for v in range(points.shape[0]):
  142 + points[v][0] = self.CoM[0] + math.cos(phi) * (self.mesh['vertices'][v][0] - self.CoM[0]) - math.sin(phi) * (self.mesh['vertices'][v][1] - self.CoM[1])
  143 + points[v][1] = self.CoM[1] + math.sin(phi) * (self.mesh['vertices'][v][0] - self.CoM[0]) + math.cos(phi) * (self.mesh['vertices'][v][1] - self.CoM[1])
  144 + self.mesh['vertices'] = points
98 else: 145 else:
99 - for v in self.G.vertices:  
100 - p = self.G.vertex_properties["pos"][v]  
101 - p[0] = self.CoM[0] + math.cos(phi) * (self.CoM[0] + p[0]) + math.sin(phi) * (p[1] - self.CoM[1])  
102 - p[1] = self.CoM[1] + math.sin(phi) * (self.CoM[0] + p[0]) - math.cos(phi) * (p[1] - self.CoM[1])  
103 - self.G.vertex_properties["pos"][v] = p 146 + for v in self.G.vertices():
  147 + p_prime = copy.deepcopy(self.G.vertex_properties["pos"][v])
  148 + p = copy.deepcopy(self.G.vertex_properties["pos"][v])
  149 + p_prime[0] = self.CoM[0] + math.cos(phi) * (p[0] - self.CoM[0]) + math.sin(phi) * (p[1] - self.CoM[1])
  150 + p_prime[1] = self.CoM[1] - math.sin(phi) * (p[0] - self.CoM[0]) + math.cos(phi) * (p[1] - self.CoM[1])
  151 + self.G.vertex_properties["pos"][v] = p_prime
  152 + #rotate points in mesh
  153 + points = copy.deepcopy(self.mesh['vertices'])
  154 + for v in range(points.shape[0]):
  155 + points[v][0] = self.CoM[0] + math.cos(phi) * (self.mesh['vertices'][v][0] - self.CoM[0]) + math.sin(phi) * (self.mesh['vertices'][v][1] - self.CoM[1])
  156 + points[v][1] = self.CoM[1] - math.sin(phi) * (self.mesh['vertices'][v][0] - self.CoM[0]) + math.cos(phi) * (self.mesh['vertices'][v][1] - self.CoM[1])
  157 + self.mesh['vertices'] = points
104 158
  159 +
105 160
106 161
107 def plot_graph(self, D, x, y): 162 def plot_graph(self, D, x, y):
108 plt.figure() 163 plt.figure()
109 ext = [self.a[0], self.b[0], self.a[1], self.b[1]] 164 ext = [self.a[0], self.b[0], self.a[1], self.b[1]]
110 - plt.imshow(D, origin = 'lower', extent=ext) 165 + #plt.imshow(D, origin = 'lower', extent=ext)
111 p = self.G.vertex_properties["pos"].get_2d_array(range(2)).T 166 p = self.G.vertex_properties["pos"].get_2d_array(range(2)).T
112 plt.scatter(p[:,0], p[:,1], color='r') 167 plt.scatter(p[:,0], p[:,1], color='r')
113 plt.scatter(self.CoM[0], self.CoM[1], marker='*') 168 plt.scatter(self.CoM[0], self.CoM[1], marker='*')
114 169
  170 + #mesh = dict(vertices=pts, segments=segs)
  171 + #print(self.polygon.area())
  172 + #tri = triangulate(mesh, 'pq20Ds')
  173 + triangle_plot(plt.gca(), **self.mesh)
115 174
116 - segs = []  
117 - pts = np.asarray(self.polygon.exterior.xy).T  
118 - pts = pts[:-1, :]  
119 - for k in range(pts.shape[0]-1):  
120 - segs.append([k, k+1])  
121 - segs.append([pts.shape[0]-1, 0])  
122 - points = self.G.vertex_properties["pos"].get_2d_array(range(2)).T  
123 - segs2 = []  
124 - n_pts = pts.shape[0]  
125 - for e in self.G.edges():  
126 - segs2.append([int(e.source())+n_pts, int(e.target())+n_pts])  
127 - 175 + #plot polygon
  176 + #plt.plot(*self.polygon.exterior.xy, color = 'r')
128 177
129 178
130 - pts = np.concatenate((pts, points))  
131 - segs = segs + segs2  
132 - mesh = dict(vertices=pts, segments=segs)  
133 - #print(self.polygon.area())  
134 - # tri = triangulate(mesh, 'pq20D')  
135 - triangle_plot(plt.gca(), **mesh)  
136 - for i in range(len(segs)):  
137 - plt.plot((pts[segs[i][0]][0], pts[segs[i][0]][1]), (pts[segs[i][1]][0], pts[segs[i][1]][1]), color='b') 179 +# for i in range(len(segs)):
  180 +# plt.plot((pts[segs[i][0]][0], pts[segs[i][1]][0]), (pts[segs[i][0]][1], pts[segs[i][1]][1]), color='b')
138 plt.gca().set_title(str(self.polygon.area)) 181 plt.gca().set_title(str(self.polygon.area))
139 182
  183 + for e in self.torque:
  184 + plt.quiver(e[2][0], e[2][1], e[1][0], e[1][1], color='r')
140 #tri = Delaunay(np.asarray(self.polygon.exterior.coords.xy).T) 185 #tri = Delaunay(np.asarray(self.polygon.exterior.coords.xy).T)
141 #tri = triangulate(mesh, 'pq20a' + str(self.polygon.area/100.0)+'D') 186 #tri = triangulate(mesh, 'pq20a' + str(self.polygon.area/100.0)+'D')
142 #delaunay_plot_2d(tri) 187 #delaunay_plot_2d(tri)
@@ -159,8 +204,7 @@ class Polygon_mass: @@ -159,8 +204,7 @@ class Polygon_mass:
159 # Y = [coord[1], coord2[1]] 204 # Y = [coord[1], coord2[1]]
160 # #all_plots.plot(x, y, 'go--', linewidth=1, markersize=1) 205 # #all_plots.plot(x, y, 'go--', linewidth=1, markersize=1)
161 # plt.plot(X, Y, 'go--', linewidth=1, markersize=1) 206 # plt.plot(X, Y, 'go--', linewidth=1, markersize=1)
162 -#  
163 - plt.plot(*self.polygon.exterior.xy, color = 'r') 207 +#
164 plt.show() 208 plt.show()
165 209
166 def get_aabb(self): 210 def get_aabb(self):
@@ -200,7 +244,7 @@ class Polygon_mass: @@ -200,7 +244,7 @@ class Polygon_mass:
200 contour[: ,1] = Y(cn[0][:, 0]) 244 contour[: ,1] = Y(cn[0][:, 0])
201 self.polygon = Polygon(contour) 245 self.polygon = Polygon(contour)
202 self.CoM = self.centroid_com(contour) 246 self.CoM = self.centroid_com(contour)
203 - 247 + self.calculate_moment(True)
204 #cn = plt.contour(x, y, D, levels = [level]) 248 #cn = plt.contour(x, y, D, levels = [level])
205 #cn = plt.contour(x, y, D, levels = [level]) 249 #cn = plt.contour(x, y, D, levels = [level])
206 # plt.close() 250 # plt.close()
@@ -215,12 +259,11 @@ class Polygon_mass: @@ -215,12 +259,11 @@ class Polygon_mass:
215 # #nlist = c.trace(level, level, 0) 259 # #nlist = c.trace(level, level, 0)
216 # #segs = nlist[:len(nlist)//2] 260 # #segs = nlist[:len(nlist)//2]
217 #self.polygon = Polygon(pts) 261 #self.polygon = Polygon(pts)
218 - self.plot_graph(D, x, y) 262 + #self.plot_graph(D, x, y)
219 263
220 264
221 265
222 def distancefield(self): 266 def distancefield(self):
223 -  
224 #generate a meshgrid of the appropriate size and resolution to surround the network 267 #generate a meshgrid of the appropriate size and resolution to surround the network
225 #get the space occupied by the network 268 #get the space occupied by the network
226 lower = self.a 269 lower = self.a
@@ -271,6 +314,9 @@ class Polygon_mass: @@ -271,6 +314,9 @@ class Polygon_mass:
271 # R = (200, 200, 200) 314 # R = (200, 200, 200)
272 315
273 D, I = tree.query(Q) 316 D, I = tree.query(Q)
  317 + self.D = D
  318 + self.x = x
  319 + self.y = y
274 320
275 return D, x, y 321 return D, x, y
276 322
@@ -301,23 +347,66 @@ def get_torques(G, masses): @@ -301,23 +347,66 @@ def get_torques(G, masses):
301 #if the source and target cluster is not equal to each other 347 #if the source and target cluster is not equal to each other
302 #add an inter subgraph edge. 348 #add an inter subgraph edge.
303 if(G.vertex_properties["clusters"][e.source()] != G.vertex_properties["clusters"][e.target()]): 349 if(G.vertex_properties["clusters"][e.source()] != G.vertex_properties["clusters"][e.target()]):
304 - pf0 = G.vertex_properties["pos"][e.target()].get_2D_array(range(2))  
305 - pf1 = G.vertex_properties["pos"][e.source()].get_2D_array(range(2)) 350 + #index of the cluster
  351 + t0 = G.vertex_properties["clusters"][e.target()]
  352 + t1 = G.vertex_properties["clusters"][e.source()]
  353 + #index of the vertex outside of the subgraph
  354 + v0_index = G.vertex_properties["idx"][e.target()]
  355 + v1_index = G.vertex_properties["idx"][e.source()]
  356 + #location of torque arm in the subgraph
  357 + p0 = masses[t0].G.vertex_properties["pos"][np.argwhere(masses[t0].G.vertex_properties["idx"].get_array() == v0_index)]
  358 + p1 = masses[t1].G.vertex_properties["pos"][np.argwhere(masses[t1].G.vertex_properties["idx"].get_array() == v1_index)]
306 359
307 - t0 = G.vertex_properties["clusters"][e.source()]  
308 - t1 = G.vertex_properties["clusters"][e.target()] 360 + f0 = np.subtract(p0, p1)
  361 + f1 = np.subtract(p1, p0)
  362 + masses[t0].add_torque(p0, f1)
  363 + masses[t1].add_torque(p1, f0)
  364 +'''
  365 + c1 scales the attractive force before log.
  366 + c2 scales the attractive force inside log.
  367 + c3 scales the repulsive force.
  368 +'''
  369 +def get_forces(G, masses, c1 = 50.0, c2 = 1.0, c3 = 1.0):
  370 + for i in range(len(masses)):
  371 + masses[i].clear_forces()
  372 + f_total = np.zeros(2)
  373 + for j in range(len(masses)):
  374 + if i != j:
  375 + f0 = np.subtract(masses[i].CoM, masses[j].CoM)
  376 + f1 = np.power(f0, 3.0)
  377 + f1[0] = c3/f1[0]*np.sign(f0[0])
  378 + f1[1] = c3/f1[1]*np.sign(f0[1])
  379 + f_total = np.add(f_total, f1)
  380 + masses[i].forces_r = f_total
309 381
310 - v0_index = G.vertex_properties["idx"][e.source()]  
311 - v1_index = G.vertex_properties["idx"][e.target()] 382 + for e in G.edges():
  383 + #if the source and target cluster is not equal to each other
  384 + #add an inter subgraph edge.
  385 + if(G.vertex_properties["clusters"][e.source()] != G.vertex_properties["clusters"][e.target()]):
  386 + #index of the cluster
  387 + t0 = G.vertex_properties["clusters"][e.target()]
  388 + t1 = G.vertex_properties["clusters"][e.source()]
  389 + #index of the vertex outside of the subgraph
  390 + v0_index = G.vertex_properties["idx"][e.target()]
  391 + v1_index = G.vertex_properties["idx"][e.source()]
  392 + #location of torque arm in the subgraph
  393 + p0 = masses[t0].G.vertex_properties["pos"][np.argwhere(masses[t0].G.vertex_properties["idx"].get_array() == v0_index)]
  394 + p1 = masses[t1].G.vertex_properties["pos"][np.argwhere(masses[t1].G.vertex_properties["idx"].get_array() == v1_index)]
312 395
313 - p0 = masses[t0].G.vertex_properties["pos"][masses[t0].G.vertex(v0_index)].get_2D_array(range(2))  
314 - p1 = masses[t1].G.vertex_properties["pos"][masses[t1].G.vertex(v1_index)].get_2D_array(range(2)) 396 + f0 = np.subtract(p1, p0)
  397 + f0_1 = abs(f0)
  398 + f0_1 = c1*np.log(f0_1/c2)/masses[t0].degree
  399 + f0_1 = f0_1*np.sign(f0)
  400 + f1 = np.subtract(p0, p1)
  401 + f1_1 = abs(f1)
  402 + f1_1 = c1*np.log(f1_1/c2)/masses[t1].degree
  403 + f1_1 = f1_1*np.sign(f1)
  404 + masses[t0].forces_a = np.add(masses[t0].forces_a, f1_1)
  405 + masses[t1].forces_a = np.add(masses[t1].forces_a, f0_1)
315 406
316 - f0 = pf0-p1  
317 - f1 = pf1-p0  
318 - masses[t0].add_torque(p0, f0)  
319 - masses[t1].add_torque(p1, f1)  
320 - 407 +
  408 +
  409 +
321 410
322 def voronoi_polygons(voronoi, diameter): 411 def voronoi_polygons(voronoi, diameter):
323 """Generate shapely.geometry.Polygon objects corresponding to the 412 """Generate shapely.geometry.Polygon objects corresponding to the
@@ -446,7 +535,7 @@ def gen_cluster_graph(G, num_clusters, cluster_pos): @@ -446,7 +535,7 @@ def gen_cluster_graph(G, num_clusters, cluster_pos):
446 G_cluster.vertex_properties["bc"] = vbetweeness_centrality 535 G_cluster.vertex_properties["bc"] = vbetweeness_centrality
447 G_cluster.edge_properties["bc"] = ebetweeness_centrality 536 G_cluster.edge_properties["bc"] = ebetweeness_centrality
448 G_cluster.edge_properties["bc_scaled"] = G_cluster.new_edge_property("double", vals=ebc) 537 G_cluster.edge_properties["bc_scaled"] = G_cluster.new_edge_property("double", vals=ebc)
449 - 538 + G_cluster.edge_properties["log"] = G_cluster.new_edge_property("double", vals=abs(np.log(G_cluster.edge_properties["volume"].get_array())))
450 dg = G_cluster.vertex_properties["degree"].get_array() 539 dg = G_cluster.vertex_properties["degree"].get_array()
451 dg = 2*max(dg) - dg 540 dg = 2*max(dg) - dg
452 d = G_cluster.new_vertex_property("int", vals=dg) 541 d = G_cluster.new_vertex_property("int", vals=dg)
@@ -570,7 +659,35 @@ def centroid_region(vertices): @@ -570,7 +659,35 @@ def centroid_region(vertices):
570 C_y = (1.0 / (6.0 * A)) * C_y 659 C_y = (1.0 / (6.0 * A)) * C_y
571 660
572 return np.array([C_x, C_y]) 661 return np.array([C_x, C_y])
573 - 662 +
  663 +def find_equlibrium(masses, t = 0.01):
  664 + for m in masses:
  665 + sum_torque = 0
  666 + for torque in m.torque:
  667 + if torque[3] == "clockwise":
  668 + sum_torque -= torque[0]
  669 + else:
  670 + sum_torque += torque[0]
  671 + m.vel = m.aa * t + m.vel
  672 + m.aa = sum_torque/m.MoI
  673 + #print(m.G.vertex_properties["clusters"][0], m.vel)
  674 + if m.vel != 0.0:
  675 + if m.vel < 0.0:
  676 + m.rotate(abs(m.vel * t),"counterclock")
  677 + else:
  678 + m.rotate(abs(m.vel * t), "clockwise")
  679 +
  680 +
  681 +def gen_Eades(G, masses, M = 10):
  682 + for i in range(M):
  683 + get_forces(G, masses)
  684 + for j in masses:
  685 + j.translate(0.001)
  686 +
  687 +def onion_springs(G, masses, min_length):
  688 + for v in G.vertices():
  689 +
  690 +
574 691
575 def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False): 692 def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False):
576 #def gen_image(G, G_c, vor, vor_filtered): 693 #def gen_image(G, G_c, vor, vor_filtered):
@@ -580,18 +697,24 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False): @@ -580,18 +697,24 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False):
580 697
581 #get points of the centers of every cluster 698 #get points of the centers of every cluster
582 #generate voronoi region and plot it. 699 #generate voronoi region and plot it.
583 - fig, ax = plt.subplots(3, 1, sharex='col', sharey='row') 700 + fig, ax = plt.subplots(4, 1, sharex='col', sharey='row')
584 fig.tight_layout() 701 fig.tight_layout()
585 - grid = plt.GridSpec(3,1) 702 + grid = plt.GridSpec(4,1)
586 grid.update(wspace=0.025, hspace=0.2) 703 grid.update(wspace=0.025, hspace=0.2)
587 ax[0].axis('off') 704 ax[0].axis('off')
588 ax[1].axis('off') 705 ax[1].axis('off')
589 ax[2].axis('off') 706 ax[2].axis('off')
  707 + ax[3].axis('off')
  708 +
590 709
  710 + #Add plots to the axes and get their handles
591 all_plots = fig.add_subplot(grid[0]) 711 all_plots = fig.add_subplot(grid[0])
592 ax[0].set_title(itr) 712 ax[0].set_title(itr)
593 no_links = fig.add_subplot(grid[1], sharey=all_plots, sharex=all_plots) 713 no_links = fig.add_subplot(grid[1], sharey=all_plots, sharex=all_plots)
594 voronoi = fig.add_subplot(grid[2], sharey=all_plots, sharex=all_plots) 714 voronoi = fig.add_subplot(grid[2], sharey=all_plots, sharex=all_plots)
  715 + rotated = fig.add_subplot(grid[3], sharey=all_plots, sharex=all_plots)
  716 +
  717 + #Get the points and generate the voronoi region
595 pts = G_c.vertex_properties["pos"].get_2d_array(range(2)).T 718 pts = G_c.vertex_properties["pos"].get_2d_array(range(2)).T
596 if bb_flag == False: 719 if bb_flag == False:
597 vor = Voronoi(pts) 720 vor = Voronoi(pts)
@@ -601,16 +724,20 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False): @@ -601,16 +724,20 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False):
601 a = voronoi.get_ylim() 724 a = voronoi.get_ylim()
602 b = voronoi.get_xlim() 725 b = voronoi.get_xlim()
603 bb = np.array([b[0], b[1], a[0], a[1]]) 726 bb = np.array([b[0], b[1], a[0], a[1]])
  727 +
  728 + #generate the polygons based on the voronoi regions
604 G_c, regions, vor = gen_polygons(G_c, bb) 729 G_c, regions, vor = gen_polygons(G_c, bb)
605 if bb_flag == True: 730 if bb_flag == True:
606 voronoi_plot_2d(vor, all_plots) 731 voronoi_plot_2d(vor, all_plots)
607 voronoi_plot_2d(vor, no_links) 732 voronoi_plot_2d(vor, no_links)
608 voronoi_plot_2d(vor, voronoi) 733 voronoi_plot_2d(vor, voronoi)
  734 +
609 #plot the top-level graph 735 #plot the top-level graph
610 pts = G_c.vertex_properties["pos"].get_2d_array(range(2)).T 736 pts = G_c.vertex_properties["pos"].get_2d_array(range(2)).T
611 all_plots.scatter(pts[:,0], pts[:, 1], s=20*G_c.vertex_properties["degree"].get_array(), marker="*") 737 all_plots.scatter(pts[:,0], pts[:, 1], s=20*G_c.vertex_properties["degree"].get_array(), marker="*")
612 no_links.scatter(pts[:,0], pts[:, 1], s=20*G_c.vertex_properties["degree"].get_array(), marker="*") 738 no_links.scatter(pts[:,0], pts[:, 1], s=20*G_c.vertex_properties["degree"].get_array(), marker="*")
613 voronoi.scatter(pts[:,0], pts[:, 1], s=20*G_c.vertex_properties["degree"].get_array(), marker="*") 739 voronoi.scatter(pts[:,0], pts[:, 1], s=20*G_c.vertex_properties["degree"].get_array(), marker="*")
  740 +
614 #plot the connections of the top level graph 741 #plot the connections of the top level graph
615 for e in G_c.edges(): 742 for e in G_c.edges():
616 coord = G_c.vertex_properties["pos"][e.source()] 743 coord = G_c.vertex_properties["pos"][e.source()]
@@ -621,18 +748,25 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False): @@ -621,18 +748,25 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False):
621 no_links.plot(x, y, 'go--', linewidth=1, markersize=1) 748 no_links.plot(x, y, 'go--', linewidth=1, markersize=1)
622 voronoi.plot(x, y, 'go--', linewidth=1, markersize=1) 749 voronoi.plot(x, y, 'go--', linewidth=1, markersize=1)
623 750
624 - #for every subgraph generate a layout and plot the resulting Polygon_mass 751 + #For every subgraph generate a layout and plot the resulting Polygon_mass
  752 + #These polygons are not the same as the voronoi polygons and instead surround
  753 + #graph.
625 masses = [] 754 masses = []
626 for i in range(num_clusters): 755 for i in range(num_clusters):
627 g, center = gen_subclusters(G, G_c, i, reposition) 756 g, center = gen_subclusters(G, G_c, i, reposition)
628 d = G_c.vertex_properties["pos"][i] - center 757 d = G_c.vertex_properties["pos"][i] - center
629 - t = Polygon_mass(g)  
630 - masses.append(g)  
631 - #t.distancefield()  
632 for v in g.vertices(): 758 for v in g.vertices():
633 G.vertex_properties["pos"][g.vertex_properties["idx"][v]] = g.vertex_properties["pos"][v] + d 759 G.vertex_properties["pos"][g.vertex_properties["idx"][v]] = g.vertex_properties["pos"][v] + d
  760 + g.vertex_properties["pos"][v] = g.vertex_properties["pos"][v] + d
  761 + t = Polygon_mass(g)
  762 + t.set_degree(G_c.vertex_properties["degree"][i])
  763 + masses.append(t)
  764 + #t.distancefield()
634 765
635 - 766 + #get the torques generated by the positioning of the graphs.
  767 + get_torques(G, masses)
  768 +# for i in masses:
  769 +# i.plot_graph(i.D, i.x, i.y)
636 #g.vertex_properties["pos"][g.vertex_properties["idx"][v]] = g.vertex_properties["pos"][v] + d 770 #g.vertex_properties["pos"][g.vertex_properties["idx"][v]] = g.vertex_properties["pos"][v] + d
637 #sub_pts = g.vertex_properties["pos"].get_2d_array(range(2)).T 771 #sub_pts = g.vertex_properties["pos"].get_2d_array(range(2)).T
638 #all_plots.scatter(pts[:,0], pts[:, 1], marker="*") 772 #all_plots.scatter(pts[:,0], pts[:, 1], marker="*")
@@ -642,7 +776,9 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False): @@ -642,7 +776,9 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False):
642 # x = [coord[0], coord2[0]] 776 # x = [coord[0], coord2[0]]
643 # y = [coord[1], coord2[1]] 777 # y = [coord[1], coord2[1]]
644 # plt.plot(x, y, 'ro--', linewidth=1, markersize=1) 778 # plt.plot(x, y, 'ro--', linewidth=1, markersize=1)
645 - 779 +
  780 +
  781 + #Plot the cluster level connections and the vertex level connections.
646 for e in G.edges(): 782 for e in G.edges():
647 coord = G.vertex_properties["pos"][e.source()] 783 coord = G.vertex_properties["pos"][e.source()]
648 coord2 = G.vertex_properties["pos"][e.target()] 784 coord2 = G.vertex_properties["pos"][e.target()]
@@ -653,7 +789,8 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False): @@ -653,7 +789,8 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False):
653 no_links.plot(x, y, 'ro--', linewidth=1, markersize=1) 789 no_links.plot(x, y, 'ro--', linewidth=1, markersize=1)
654 else: 790 else:
655 all_plots.plot(x, y, 'bo--', linewidth=1, markersize=1) 791 all_plots.plot(x, y, 'bo--', linewidth=1, markersize=1)
656 - 792 +
  793 + #Update the centroids based on the voronoi polygons
657 no_links.xaxis.set_visible(False) 794 no_links.xaxis.set_visible(False)
658 all_plots.xaxis.set_visible(False) 795 all_plots.xaxis.set_visible(False)
659 for v in G_c.vertices(): 796 for v in G_c.vertices():
@@ -661,11 +798,16 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False): @@ -661,11 +798,16 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False):
661 centroid = centroid_region(region[0]) 798 centroid = centroid_region(region[0])
662 G_c.vertex_properties["pos"][v] = centroid 799 G_c.vertex_properties["pos"][v] = centroid
663 800
  801 +
  802 + print(G_c.num_vertices(), G_c.num_edges())
  803 +
  804 + #Plots the vertices of the subgraphs
664 pts_temp = G_c.vertex_properties["pos"].get_2d_array(range(2)).T 805 pts_temp = G_c.vertex_properties["pos"].get_2d_array(range(2)).T
665 all_plots.scatter(pts_temp[:,0], pts_temp[:, 1], marker='.', color='r') 806 all_plots.scatter(pts_temp[:,0], pts_temp[:, 1], marker='.', color='r')
666 no_links.scatter(pts_temp[:,0], pts_temp[:, 1], marker='.', color='r') 807 no_links.scatter(pts_temp[:,0], pts_temp[:, 1], marker='.', color='r')
667 voronoi.scatter(pts_temp[:,0], pts_temp[:, 1], marker='.', color='r') 808 voronoi.scatter(pts_temp[:,0], pts_temp[:, 1], marker='.', color='r')
668 809
  810 + #set the limits of the plots.
669 all_plots.set_xlim([bb[0], bb[1]]) 811 all_plots.set_xlim([bb[0], bb[1]])
670 all_plots.set_ylim([bb[2], bb[3]]) 812 all_plots.set_ylim([bb[2], bb[3]])
671 813
@@ -675,10 +817,44 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False): @@ -675,10 +817,44 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False):
675 voronoi.set_xlim([bb[0], bb[1]]) 817 voronoi.set_xlim([bb[0], bb[1]])
676 voronoi.set_ylim([bb[2], bb[3]]) 818 voronoi.set_ylim([bb[2], bb[3]])
677 819
  820 + #show the plots.
678 plt.show() 821 plt.show()
679 822
  823 +# for j in [7, 10, 15]:
  824 +# masses[j].plot_graph(masses[j].D, masses[j].x, masses[j].y)
  825 +
  826 + for j in range(10):
  827 + for i in range(100):
  828 + get_torques(G, masses)
  829 + find_equlibrium(masses)
  830 + gen_Eades(G, masses)
  831 +# for j in [7, 10]:
  832 +# masses[j].plot_graph(masses[j].D, masses[j].x, masses[j].y)
  833 +# for j in [7, 10, 15]:
  834 +# masses[j].plot_graph(masses[j].D, masses[j].x, masses[j].y)
  835 +
  836 + for i in masses:
  837 + for v in i.G.vertices():
  838 + G.vertex_properties["pos"][i.G.vertex_properties["idx"][v]] = i.G.vertex_properties["pos"][v]
  839 +
  840 +
  841 + #Plot the cluster level connections and the vertex level connections.
  842 + for e in G.edges():
  843 + coord = G.vertex_properties["pos"][e.source()]
  844 + coord2 = G.vertex_properties["pos"][e.target()]
  845 + x = [coord[0], coord2[0]]
  846 + y = [coord[1], coord2[1]]
  847 + if (G.vertex_properties["clusters"][e.source()] == G.vertex_properties["clusters"][e.target()]):
  848 + rotated.plot(x, y, 'ro--', linewidth=1, markersize=1)
  849 + else:
  850 + rotated.plot(x, y, 'bo--', linewidth=1, markersize=1)
  851 +
  852 + pts_temp = G.vertex_properties["pos"].get_2d_array(range(2)).T
  853 + rotated.scatter(pts_temp[:,0], pts_temp[:, 1], marker='.', color='r')
  854 +
  855 +
680 856
681 - return G, G_c, bb 857 + return G, G_c, bb, masses
682 858
683 859
684 860
@@ -691,19 +867,25 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False): @@ -691,19 +867,25 @@ def gen_image(G, G_c, itr, bb_flag = False, bb = None, reposition = False):
691 867
692 G, bbl, bbu = load_nwt("/home/pavel/Documents/Python/GraphGuiQt/network_4.nwt") 868 G, bbl, bbu = load_nwt("/home/pavel/Documents/Python/GraphGuiQt/network_4.nwt")
693 G_c, G = gen_clusters(G, bbl, bbu) 869 G_c, G = gen_clusters(G, bbl, bbu)
  870 +
694 num_clusters = 20 871 num_clusters = 20
695 872
696 #G_c.vertex_properties["pos"] = nwt.gt.radial_tree_layout(G_c, root=np.argwhere(G_c.vertex_properties["degree"].get_array() == max(G_c.vertex_properties["degree"].get_array())), node_weight = G_c.vertex_properties["10-degree"], r= 2.0) 873 #G_c.vertex_properties["pos"] = nwt.gt.radial_tree_layout(G_c, root=np.argwhere(G_c.vertex_properties["degree"].get_array() == max(G_c.vertex_properties["degree"].get_array())), node_weight = G_c.vertex_properties["10-degree"], r= 2.0)
697 G_c.vertex_properties["pos"] = nwt.gt.sfdp_layout(G_c, eweight=G_c.edge_properties["volume"], vweight=G_c.vertex_properties["degree"], C = 1.0, K = 10) 874 G_c.vertex_properties["pos"] = nwt.gt.sfdp_layout(G_c, eweight=G_c.edge_properties["volume"], vweight=G_c.vertex_properties["degree"], C = 1.0, K = 10)
698 875
699 -G, G_c, bb = gen_image(G, G_c, "base", reposition = True) 876 +
  877 +
  878 +G, G_c, bb, masses = gen_image(G, G_c, "base", reposition = True)
  879 +
  880 +print("Planarity test: G_c, G = " , nwt.gt.graph_tool.topology.is_planar(G_c), nwt.gt.graph_tool.topology.is_planar(G))
  881 +
700 itr = 0 882 itr = 0
701 883
702 #for itr in range(5): 884 #for itr in range(5):
703 -# G, G_c, bb = gen_image(G, G_c, itr, True, bb) 885 +# G, G_c, bb, masses = gen_image(G, G_c, itr, True, bb)
704 # itr+=1 886 # itr+=1
705 887
706 -g, center = gen_subclusters(G, G_c) 888 +#g, center = gen_subclusters(G, G_c)
707 #d = G_c.vertex_properties["pos"][0] - center 889 #d = G_c.vertex_properties["pos"][0] - center
708 #for v in g.vertices(): 890 #for v in g.vertices():
709 # g.vertex_properties["pos"][v] = g.vertex_properties["pos"][v] + d 891 # g.vertex_properties["pos"][v] = g.vertex_properties["pos"][v] + d