def test_computeLineagesAndPrune():
h = hg.HypothesesGraph()
h._graph.add_path([(0, 0), (1, 1), (2, 2)])
h._graph.add_path([(1, 1), (2, 3), (3, 4)])
for n in h._graph.node:
h._graph.node[n]['id'] = n[1]
h._graph.node[n]['traxel'] = pg.Traxel()
h._graph.node[n]['traxel'].Id = n[1]
h._graph.node[n]['traxel'].Timestep = n[0]
solutionDict = {
"detectionResults": [{
"id": 0,
"value": 1
}, {
"id": 1,
"value": 1
}, {
"id": 2,
"value": 1
}, {
"id": 3,
"value": 1
}, {
"id": 4,
"value": 0
}],
"linkingResults": [{
"dest": 1,
"src": 0,
"value": 1
}, {
"dest": 2,
"src": 1,
"value": 1
}, {
"dest": 3,
"src": 1,
"value": 1
}, {
"dest": 4,
"src": 3,
"value": 0
}],
"divisionResults": [{
"id": 1,
"value": True
}, {
"id": 2,
"value": False
}]
}
h.insertSolution(solutionDict)
h.computeLineage()
h.pruneGraphToSolution(0)
h.pruneGraphToSolution(1)
def test_insertEnergies():
skipLinkBias = 20
h = hg.HypothesesGraph()
h._graph.add_path([(0, 1), (1, 1), (2, 1), (3, 1)])
for uuid, i in enumerate([(0, 1), (1, 1), (2, 1), (3, 1)]):
t = Traxel()
t.Timestep = i[0]
t.Id = i[1]
# fill in detProb, divProb, and center of mass
t.Features['detProb'] = [0.2, 0.8]
t.Features['divProb'] = [0.2, 0.8]
t.Features['com'] = [float(i[0]), 0.0]
h._graph.node[i]['traxel'] = t
h._graph.node[i]['id'] = uuid
# set up some dummy functions to compute probabilities from a traxel
def detProbFunc(traxel):
return traxel.Features['detProb']
def divProbFunc(traxel):
return traxel.Features['divProb']
def boundaryCostFunc(traxel, forAppearance):
return 1.0
def transProbFunc(traxelA, traxelB):
dist = np.linalg.norm(
np.array(traxelA.Features['com']) -
np.array(traxelB.Features['com']))
return [1.0 - np.exp(-dist), np.exp(-dist)]
h.insertEnergies(1, detProbFunc, transProbFunc, boundaryCostFunc,
divProbFunc, skipLinkBias)
for n in h.nodeIterator():
assert ('features' in h._graph.node[n])
assert (h._graph.node[n]['features'] == [[1.6094379124341003],
[0.22314355131420971]])
assert ('divisionFeatures' in h._graph.node[n])
assert (h._graph.node[n]['divisionFeatures'] == [[1.6094379124341003],
[0.22314355131420971]
])
assert ('appearanceFeatures' in h._graph.node[n])
assert (h._graph.node[n]['appearanceFeatures'] == [[0.0], [1.0]])
assert ('disappearanceFeatures' in h._graph.node[n])
assert (h._graph.node[n]['disappearanceFeatures'] == [[0.0], [1.0]])
for a in h.arcIterator():
assert ('features' in h._graph.edge[a[0]][a[1]])
srcTraxel = h._graph.node[h.source(a)]['traxel']
destTraxel = h._graph.node[h.target(a)]['traxel']
frame_gap = destTraxel.Timestep - srcTraxel.Timestep
assert (h._graph.edge[a[0]][a[1]]['features'] == [[
0.45867514538708193
], [1.0 + skipLinkBias * (frame_gap - 1)]])
def test_trackletgraph():
h = hg.HypothesesGraph()
h._graph.add_path([(0, 1), (1, 1), (2, 1), (3, 1)])
for i in [(0, 1), (1, 1), (2, 1), (3, 1)]:
t = Traxel()
t.Timestep = i[0]
t.Id = i[1]
h._graph.node[i]['traxel'] = t
t = h.generateTrackletGraph()
assert (t.countArcs() == 1)
assert (t.countNodes() == 2)
assert ('tracklet' in t._graph.node[(0, 1)])
def test_computeLineagesWithMergers():
h = hg.HypothesesGraph()
h._graph.add_path([(0, 0), (1, 1), (2, 2)])
h._graph.add_path([(0, 5), (1, 1), (2, 3), (3, 4)])
for n in h._graph.node:
h._graph.node[n]['id'] = n[1]
h._graph.node[n]['traxel'] = pg.Traxel()
h._graph.node[n]['traxel'].Id = n[1]
h._graph.node[n]['traxel'].Timestep = n[0]
solutionDict = {
"detectionResults": [{
"id": 0,
"value": 1
}, {
"id": 1,
"value": 2
}, {
"id": 2,
"value": 1
}, {
"id": 3,
"value": 1
}, {
"id": 4,
"value": 1
}, {
"id": 5,
"value": 1
}],
"linkingResults": [{
"dest": 1,
"src": 0,
"value": 1
}, {
"dest": 1,
"src": 5,
"value": 1
}, {
"dest": 2,
"src": 1,
"value": 1
}, {
"dest": 3,
"src": 1,
"value": 1
}, {
"dest": 4,
"src": 3,
"value": 1
}],
"divisionResults": [{
"id": 1,
"value": False
}, {
"id": 2,
"value": False
}]
}
h.insertSolution(solutionDict)
h.computeLineage()
assert (h._graph.node[(0, 0)]['lineageId'] == 2)
assert (h._graph.node[(0, 5)]['lineageId'] == 3)
assert (h._graph.node[(1, 1)]['lineageId'] == 3)
assert (h._graph.node[(1, 1)]['lineageId'] == 3)
assert (h._graph.node[(2, 3)]['lineageId'] == 3)
assert (h._graph.node[(3, 4)]['lineageId'] == 3)
def test_insertAndExtractSolution():
h = hg.HypothesesGraph()
h._graph.add_path([(0, 0), (1, 1), (2, 2)])
h._graph.add_path([(1, 1), (2, 3), (3, 4)])
for n in h._graph.node:
h._graph.node[n]['id'] = n[1]
h._graph.node[n]['traxel'] = pg.Traxel()
h._graph.node[n]['traxel'].Id = n[1]
h._graph.node[n]['traxel'].Timestep = n[0]
solutionDict = {
"detectionResults": [{
"id": 0,
"value": 1
}, {
"id": 1,
"value": 1
}, {
"id": 2,
"value": 1
}, {
"id": 3,
"value": 1
}, {
"id": 4,
"value": 0
}],
"linkingResults": [{
"dest": 1,
"src": 0,
"value": 1
}, {
"dest": 2,
"src": 1,
"value": 1
}, {
"dest": 3,
"src": 1,
"value": 1
}, {
"dest": 4,
"src": 3,
"value": 0
}],
"divisionResults": [{
"id": 1,
"value": True
}, {
"id": 2,
"value": False
}]
}
h.insertSolution(solutionDict)
outSolutionDict = h.getSolutionDictionary()
# from solution to outSolution
for group in (["detectionResults", "divisionResults"]):
for entry in solutionDict[group]:
ref = [m for m in outSolutionDict[group] if m['id'] == entry['id']]
assert (len(ref) <= 1)
if len(ref) == 1:
for k, v in ref[0].items():
assert (v == entry[k])
else:
assert (entry['value'] == 0)
# from outSolution to Solution
for group in (["detectionResults", "divisionResults"]):
for entry in outSolutionDict[group]:
ref = [m for m in solutionDict[group] if m['id'] == entry['id']]
assert (len(ref) <= 1)
if len(ref) == 1:
for k, v in ref[0].items():
assert (v == entry[k])
else:
assert (entry['value'] == 0)
assert (h._graph.node[(1, 1)]["divisionValue"] == 1)
assert (h._graph.node[(2, 2)]["divisionValue"] == 0)
assert (h._graph.node[(0, 0)]["value"] == 1)
assert (h._graph.node[(1, 1)]["value"] == 1)
assert (h._graph.node[(2, 2)]["value"] == 1)
assert (h._graph.node[(2, 3)]["value"] == 1)
assert (h._graph.node[(3, 4)]["value"] == 0)
assert (h._graph.edge[(0, 0)][(1, 1)]["value"] == 1)
assert (h._graph.edge[(1, 1)][(2, 2)]["value"] == 1)
assert (h._graph.edge[(1, 1)][(2, 3)]["value"] == 1)
assert (h._graph.edge[(2, 3)][(3, 4)]["value"] == 0)
h.computeLineage()
assert (set(h._graph.node[(1, 1)]["children"]) == set([(2, 2), (2, 3)]))
assert (h._graph.node[(2, 2)]["parent"] == (1, 1))
assert (h._graph.node[(2, 3)]["parent"] == (1, 1))