def color_map(alpha=True, as_int=False, int_type='uint8'):
"""Generates a color map from color ids to rgb
Arguments
---------
alpha : bool
If True return a color map with alpha values.
Returns
-------
color_map : array
An array of rgb colors for each label.
"""
cm = annotation.colors_rgb
return col.color(cm, alpha=alpha, as_int=as_int, int_type=int_type)
def label_to_color(self,
label,
key='order',
level=None,
alpha=True,
as_int=False,
int_type='uint8'):
cm = self.colors_rgb
cm = col.color(cm, alpha=alpha, as_int=as_int, int_type=int_type)
if key != 'order' or level is not None:
label = self.convert_label(label,
key=key,
value='order',
level=level)
return cm[label]
def set_background(view, color):
"""Set the background color of the view.
Arguments
---------
view : view
The vispy window.
color : color specification
The color for the background.
Returns
-------
view : view
The vispy view of the plot.
"""
view = get_view(view)
view.canvas.bgcolor = col.color(color, alpha=True, as_int=False)
return view
def color(self, *args, **kwargs):
return col.color(self.data['rgb'], **kwargs)
def _test():
import numpy as np
import ClearMap.Tests.Files as tf
import ClearMap.Analysis.Graphs.GraphProcessing as gp
#reload(gp)
skeleton = tf.source('skeleton');
#import ClearMap.Visualization.Plot3d as p3d
#p3d.plot(skeleton)
#reload(gp)
g = gp.graph_from_skeleton(skeleton)
g.vertex_coordinates()
s = gp.graph_to_skeleton(g)
assert np.all(s==skeleton)
gc = gp.clean_graph(g, verbose=True)
gr = gp.reduce_graph(gc, verbose=True)
gr2 = gr.copy();
gr2.set_edge_geometry_type('edge')
l = gr.edge_geometry_lengths();
print(l)
g = gp.ggt.Graph(n_vertices=10);
g.add_edge(np.array([[7,8],[7,9],[1,2],[2,3],[3,1],[1,4],[4,5],[2,6],[6,7]]));
g.set_vertex_coordinates(np.array([[10,10,10],[0,0,0],[1,1,1],[1,1,0],[5,0,0],[8,0,1],[0,7,1],[0,10,2],[0,12,3],[3,7,7]], dtype=float));
import ClearMap.Visualization.Plot3d as p3d
p3d.plot_graph_line(g)
gc = gp.clean_graph(g, verbose=True);
p3d.plot_graph_line(gc)
gr = gp.reduce_graph(gc, edge_geometry=True, verbose=True)
#gr.set_edge_geometry(0.1*np.ones(gr.edge_geometry(as_list=False).shape[0]), 'radii')
import ClearMap.Visualization.Plot3d as p3d
vertex_colors = np.random.rand(g.n_vertices, 4);
vertex_colors[:,3] = 1;
p3d.plot_graph_mesh(gr, default_radius=1, vertex_colors=vertex_colors)
eg = gr.edge_geometry(as_list=False);
egs = 0.5 * eg;
gr.set_edge_geometry(name='coordinates', values=egs)
#tracing
import numpy as np
import ClearMap.Visualization.Plot3d as p3d
import ClearMap.Analysis.Graphs.GraphProcessing as gp
g = gp.ggt.Graph(n_vertices=10);
g.add_edge(np.array([[0,1],[1,2],[2,3],[3,4],[4,0],[0,5],[5,6],[6,7],[0,8],[8,9],[9,0]]));
g.set_vertex_coordinates(np.array([[0,0,0],[1,0,0],[2,0,0],[2,2,0],[0,1,0],[0,0,1],[0,0,2],[0,0,3],[0,-1,0],[0,-1,-1]], dtype=float));
g.set_vertex_radii(np.array([10,6,4,6,7,4,2,2,5,5]) * 0.02)
vertex_colors = np.array([g.vertex_radii()]*4).T; vertex_colors = vertex_colors / vertex_colors.max(); vertex_colors[:,3] = 1;
p3d.plot_graph_mesh(g, default_radius=1, vertex_colors=vertex_colors)
def condition(graph, vertex):
r = graph.vertex_radii(vertex=vertex);
print('condition, vertex=%d, radius=%r' % (vertex,r))
return r >= 5 * 0.02;
label = np.zeros(g.n_vertices, dtype=bool);
label[0] = True;
traced = gp.trace_vertex_label(g, label, condition=condition, steps=1)
print(traced)
vertex_colors = np.array([[1,0,0,1],[1,1,1,1]])[np.asarray(traced, dtype=int)]
p3d.plot_graph_mesh(g, default_radius=1, vertex_colors=vertex_colors)
from importlib import reload;
reload(gp)
# edge tracing
import ClearMap.Analysis.Graphs.GraphGt as ggt
edges = [[0,1],[1,2],[2,3],[4,5],[5,6],[1,7]];
g = ggt.Graph(edges=edges)
l,m = g.edge_graph(return_edge_map=True);
import numpy as np
label = np.zeros(len(edges), dtype=bool);
label[1] = True;
import ClearMap.Analysis.Graphs.GraphProcessing as gp
def condition(graph, edge):
print('condition, edge=%d' % (edge,))
return True;
traced = gp.trace_edge_label(g, label, condition=condition);
print(traced)
# expansion of edge lengths
import numpy as np
import ClearMap.Tests.Files as tf
import ClearMap.Analysis.Graphs.GraphProcessing as gp
graph = gp.ggt.Graph(n_vertices=5);
graph.add_edge([[0,1],[0,2],[0,3],[2,3],[2,1],[0,4]]);
graph.add_edge_property('length', np.array([0,1,2,3,4,5])+2);
e, m = gp.expand_graph_length(graph, 'length', True)
import graph_tool.draw as gd
pos = gp.ggt.vertex_property_map_to_python(gd.sfdp_layout(e.base))
import matplotlib.pyplot as plt
plt.figure(1); plt.clf();
import matplotlib.collections as mc
import ClearMap.Visualization.Color as col
colors = np.array([col.color(c) for c in ['red', 'blue', 'green', 'black', 'purple', 'orange']])
ec = e.edge_connectivity();
lines = pos[ec];
cols = colors[m];
lc = mc.LineCollection(lines, linewidths=1, color=cols);
ax = plt.gca();
ax.add_collection(lc)
ax.autoscale()
ax.margins(0.1)
plt.scatter(pos[:,0], pos[:,1])
p =pos[:graph.n_vertices]
plt.scatter(p[:,0],p[:,1], color='red')