def test_findPathZero(self):
graphFile = '../data/test_zero.tlp'
graph = tlp.loadGraph(graphFile)
sourceId = 176
targetId = 606
maxNumHops = 1
sourceNode = tp.getNodeById(sourceId, graph)
targetNode = tp.getNodeById(targetId, graph)
finder = tp.PathFinder(graph)
finder.findPaths(sourceNode, targetNode, maxNumHops)
self.assertTrue(len(finder.valid) == 1)
self.assertTrue(finder.valid[0].isSane())
self.assertTrue(len(finder.failed) == 0)
def test_findPathOne(self):
graphFile = '../data/test_one.tlp'
sourceId = 176
targetId = 606
maxNumHops = 4
graph = tlp.loadGraph(graphFile)
sourceNode = tp.getNodeById(sourceId, graph)
targetNode = tp.getNodeById(targetId, graph)
finder = tp.PathFinder(graph)
finder.findPaths(sourceNode, targetNode, maxNumHops)
self.assertTrue(len(finder.valid) == 4)
self.assertTrue(len(finder.failed) == 1)
for path in finder.valid:
self.assertTrue(path.isSane())
def test_basicStatCounting(self):
graphFile = '../data/test_one.tlp'
sourceId = 176
targetId = 606
maxNumHops = 4
graph = tlp.loadGraph(graphFile)
sourceNode = tp.getNodeById(sourceId, graph)
targetNode = tp.getNodeById(targetId, graph)
finder = tp.PathFinder(graph)
finder.findPaths(sourceNode, targetNode, maxNumHops)
stats = tp.PathStats(finder.valid)
# Tests of unique path counting
self.assertTrue(stats.getNumPathsWithLoop() == 2)
self.assertTrue(stats.getNumUniqueTypes() == 4)
self.assertTrue(stats.getNumPaths() == len(finder.valid))
def test_findAllPaths(self):
graphFile = '../data/test_one.tlp'
maxNumHops = 2
sourceId = 176
graph = tlp.loadGraph(graphFile)
sourceNode = tp.getNodeById(sourceId, graph)
finder = tp.PathFinder(graph)
finder.findAllPaths(sourceNode, maxNumHops)
self.assertTrue(len(finder.valid) == 3)
def test_intermediateStatCounting(self):
graphFile = '../data/test_two.tlp'
sourceId = 5860
targetId = 606
maxNumHops = 2
graph = tlp.loadGraph(graphFile)
sourceNode = tp.getNodeById(sourceId, graph)
targetNode = tp.getNodeById(targetId, graph)
finder = tp.PathFinder(graph)
finder.findPaths(sourceNode, targetNode, maxNumHops)
stats = tp.PathStats(finder.valid)
self.assertTrue(stats.getNumPathsWithLoop() == 0)
self.assertTrue(stats.getNumPaths() == len(finder.valid))
self.assertTrue(stats.getNumUniqueTypes() == 2)
unique = stats.getUniqueTypes()
self.assertTrue(unique[0].toStringOfTypes(
) == 'GAC Aii, Gap Junction, CBb3-4i, Ribbon Synapse, GC ON')
self.assertTrue(unique[1].toStringOfTypes() ==
'GAC Aii, Gap Junction, CBb4w, Ribbon Synapse, GC ON')
def setUp(self):
self.graph = tlp.loadGraph('../data/test_one.tlp')
self.startNodeId = 606
self.path = tp.Path(self.graph)
node = tp.getNodeById(self.startNodeId, self.graph)
self.path.addNode(node)
edges = self.graph.getOutEdges(node)
for edge in edges:
self.path.addEdge(edge)
self.lastNode = self.graph.target(edge)
self.path.addNode(self.lastNode)
break
def test_pathTracker(self):
tp.VERBOSE = True
graphFile = '../data/test_one.tlp'
maxNumHops = 2
sourceId = 176
graph = tlp.loadGraph(graphFile)
sourceNode = tp.getNodeById(sourceId, graph)
finder = tp.PathFinder(graph)
finder.findAllPaths(sourceNode, maxNumHops)
tracker = tp.PathTracker()
for path in finder.valid:
tracker.getOrCreatePathTypeID(path)
self.assertTrue(tracker.getNumUniquePathTypes() == 3)
for i in range(0, len(finder.valid)):
self.assertTrue(tracker.getOrCreatePathTypeID(finder.valid[i]) == i)
""" Example of finding paths and visualizing them for debugging. """
from tulip import *
from tulipgui import *
import tulippaths as tp
# Path parameters
graphFile = '../data/test_one.tlp'
sourceNodeId = 176
maxNumHops = 2
# Load the graph
graph = tlp.loadGraph(graphFile)
# Find start and end nodes
source = tp.getNodeById(sourceNodeId, graph)
# Find paths
finder = tp.PathFinder(graph)
results = finder.findAllPaths(source, maxNumHops)
print('The valid paths are:')
for path in finder.valid:
print((' ' + path.toString()))
print((' ' + path.toStringOfTypes()))
print((' ' + path.toStringOfIds()))
# Make all edges and nodes transparent
transparentGrey = tlp.Color(50, 50, 50, 50)
tp.setEdgeColor(transparentGrey, graph)
tp.setNodeColor(transparentGrey, graph)
""" Example of finding paths and unique types using PathStats """
from tulip import *
from tulipgui import *
import tulippaths as tp
# Path parameters
graphFile = '../data/514_4hops.tlp'
sourceNodeId = 593
targetNodeId = 514
maxNumHops = 5
graph = tlp.loadGraph(graphFile)
# Find start and end nodes
source = tp.getNodeById(sourceNodeId, graph)
target = tp.getNodeById(targetNodeId, graph)
finder = tp.PathFinder(graph)
print 'hops, total, valid, unique, num w\ loop'
for i in range(0, maxNumHops):
finder.reset()
finder.findPaths(source, target, i)
stats = tp.PathStats(finder.valid)
print str(i) + ', ' + str(len(finder.valid) + len(finder.failed)) + ', ' + str(len(finder.valid)) + ', ' + \
str(stats.getNumUniqueTypes()) + ', ' + str(stats.getNumPathsWithLoop())
# Render the graph in a node-link diagram.
nodeLinkView = tlpgui.createNodeLinkDiagramView(graph)
""" Example of messing with node color
This will turn all nodes black, then set the start node and end node to green and red repsectively.
"""
from tulip import *
from tulipgui import *
import tulippaths as tp
graph = tlp.loadGraph("../data/test_one.tlp")
viewColor = graph.getColorProperty("viewColor")
source = tp.getNodeById(176, graph)
target = tp.getNodeById(606, graph)
# Make all nodes black
for node in graph.getNodes():
viewColor[node] = tlp.Color.Black
# Make start node green and end node red.
viewColor[source] = tlp.Color(0, 255, 0)
viewColor[target] = tlp.Color(255, 0, 0)
# Render the graph in a node-link diagram.
nodeLinkView = tlpgui.createNodeLinkDiagramView(graph)
renderingParameters = nodeLinkView.getRenderingParameters()
""" Example of finding paths and unique types using PathStats """
from tulip import *
from tulipgui import *
import tulippaths as tp
# Path parameters
graphFile = '../data/514_4hops.tlp'
sourceNodeId = 593
targetNodeId = 514
maxNumHops = 5
graph = tlp.loadGraph(graphFile)
# Find start and end nodes
source = tp.getNodeById(sourceNodeId, graph)
target = tp.getNodeById(targetNodeId, graph)
finder = tp.PathFinder(graph)
print('hops, total, valid, unique, num w\ loop')
for i in range(0, maxNumHops):
finder.reset()
finder.findPaths(source, target, i)
stats = tp.PathStats(finder.valid)
print((str(i) + ', ' + str(len(finder.valid) + len(finder.failed)) + ', ' + str(len(finder.valid)) + ', ' + \
str(stats.getNumUniqueTypes()) + ', ' + str(stats.getNumPathsWithLoop())))
# Render the graph in a node-link diagram.
nodeLinkView = tlpgui.createNodeLinkDiagramView(graph)