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TrakEM2 Scripting

986 bytes added, 08:41, 16 October 2010
Compute the betweenness centrality of every node
# Print the value for each node
for e in bc.entrySet(): print e.getKey(), "=>", e.getValue()
We may then use the centrality to colorize the tree with a heat map: the higher the centrality value, the more intense the yellow color; the lower, the more intense the blue color:
<source lang="python">
from ini.trakem2.display import Display
from java.awt import Color
def computeColor(centrality, highest):
red = centrality / float(highest)
blue = 1 - red
return Color(red, red, blue)
# Obtain the currently selected Tree in the canvas:
tree = Display.getFront().getActive()
# Compute betweenness centrality
bc = tree.computeCentrality() # a java.util.Map
# Find out the maximum centrality value, to scale:
maximum = reduce(max, bc.values())
# Colorize each node according to its centrality
for e in bc.entrySet():
node = e.getKey()
centrality = e.getValue()
node.setColor(computeColor(centrality, maximum))
# Update display
# Show the tree in the 3D Viewer
== Find branch nodes or end nodes ==
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