def testAddEdges(self):
IV = vigraph.INVALID
elist = [[1, 3], [1, 5], [5, 7], [3, 4]]
edges = np.array(elist, dtype=np.uint32)
nodeIds = np.unique(edges.reshape(-1))
g = vigraph.listGraph()
edgeIds = g.addEdges(edges)
assert g.edgeNum == len(elist)
assert g.edgeNum == len(edgeIds)
assert g.nodeNum == len(nodeIds)
assert g.maxNodeId == nodeIds.max()
for ui, vi in elist:
assert g.findEdge(ui, vi) != IV
assert g.findEdge(g.nodeFromId(ui), g.nodeFromId(vi)) != IV
for nId in nodeIds:
nId = int(nId)
assert g.nodeFromId(nId) != IV
for eId in edgeIds:
eId = int(eId)
assert g.edgeFromId(eId) != IV
findEdges = g.findEdges(edges)
assert np.array_equal(findEdges, edgeIds)
def testIters(self):
g = vigraph.listGraph()
nodes = [n for n in g.nodeIter()]
assert len(nodes) == 0
g.addNode(3)
nodes = [n for n in g.nodeIter()]
assert len(nodes) == 1
assert g.id(nodes[0]) == 3
g.addNode(6)
nodes = [n for n in g.nodeIter()]
assert len(nodes) == 2
assert g.id(nodes[0]) == 3
assert g.id(nodes[1]) == 6
g.addNode(2)
nodes = [n for n in g.nodeIter()]
assert len(nodes) == 3
assert g.id(nodes[0]) == 2
assert g.id(nodes[1]) == 3
assert g.id(nodes[2]) == 6
def testIters(self):
g = vigraph.listGraph()
nodes = [n for n in g.nodeIter()]
assert len(nodes)==0
g.addNode(3)
nodes = [n for n in g.nodeIter()]
assert len(nodes)==1
assert g.id(nodes[0]) == 3
g.addNode(6)
nodes = [n for n in g.nodeIter()]
assert len(nodes)==2
assert g.id(nodes[0]) == 3
assert g.id(nodes[1]) == 6
g.addNode(2)
nodes = [n for n in g.nodeIter()]
assert len(nodes)==3
assert g.id(nodes[0]) == 2
assert g.id(nodes[1]) == 3
assert g.id(nodes[2]) == 6
def testAddEdges(self):
IV = vigraph.INVALID
elist = [
[1,3],
[1,5],
[5,7],
[3,4]
]
edges = np.array(elist,dtype=np.uint32)
nodeIds = np.unique(edges.reshape(-1))
g = vigraph.listGraph()
edgeIds = g.addEdges(edges)
assert g.edgeNum == len(elist)
assert g.edgeNum == len(edgeIds)
assert g.nodeNum == len(nodeIds)
assert g.maxNodeId == nodeIds.max()
for ui,vi in elist :
assert g.findEdge(ui,vi)!=IV
assert g.findEdge(g.nodeFromId(ui),g.nodeFromId(vi))!=IV
for nId in nodeIds :
nId = int(nId)
assert g.nodeFromId(nId)!=IV
for eId in edgeIds :
eId = int(eId)
assert g.edgeFromId(eId)!=IV
findEdges = g.findEdges(edges)
assert np.array_equal(findEdges,edgeIds)
from vigra import numpy
from vigra import Timer
iEdgeMap = graphs.implicitMeanEdgeMap
numpy.random.seed(42)
# input
shape = [200, 100, 100]
data = numpy.random.rand(*shape).astype(numpy.float32)
data = vigra.taggedView(data, "xyz")
if False:
labels = numpy.random.randint(5, size=shape[0] * shape[1] * shape[2])
labels = labels.reshape(shape).astype(numpy.uint32)
labels = vigra.analysis.labelVolume(labels)
adjListGraph = graphs.listGraph()
gridGraph = graphs.gridGraph(shape)
rag = graphs.regionAdjacencyGraph(gridGraph, labels)
rag.writeHDF5("bla.h5", "dset")
else:
# load the region adjacency graph
rag = graphs.loadGridRagHDF5("bla.h5", "dset")
print rag.labels.shape, rag.labels.dtype, type(rag.labels)
print "accumulate edge and node features"
edgeCuesMean = rag.accumulateEdgeFeatures(iEdgeMap(rag.baseGraph, data))
edgeCuesMean = numpy.array([edgeCuesMean, edgeCuesMean]).T
def clusteringFeatures(ds,
segId,
extraUV,
edgeIndicator,
liftedNeighborhood,
is_perturb_and_map=False,
with_defects=False):
print "Computing clustering features for lifted neighborhood", liftedNeighborhood
if is_perturb_and_map:
print "For perturb and map"
else:
print "For normal clustering"
uvs_local = modified_adjacency(ds, segId) if (
with_defects and ds.defect_slices) else ds._adjacent_segments(segId)
n_nodes = uvs_local.max() + 1
# if we have a segmentation mask, remove all the uv ids that link to the ignore segment (==0)
if ds.has_seg_mask:
where_uv_local = (uvs_local != ds.ignore_seg_value).all(axis=1)
uvs_local = uvs_local[where_uv_local]
edgeIndicator = edgeIndicator[where_uv_local]
assert numpy.sum((extraUV == ds.ignore_seg_value).any(axis=1)) == 0
assert edgeIndicator.shape[0] == uvs_local.shape[0]
originalGraph = vgraph.listGraph(n_nodes)
originalGraph.addEdges(uvs_local)
extraUV = numpy.require(extraUV, dtype='uint32')
uvOriginal = originalGraph.uvIds()
liftedGraph = vgraph.listGraph(originalGraph.nodeNum)
liftedGraph.addEdges(uvOriginal)
liftedGraph.addEdges(extraUV)
uvLifted = liftedGraph.uvIds()
foundEdges = originalGraph.findEdges(uvLifted)
foundEdges[foundEdges >= 0] = 0
foundEdges *= -1
nAdditionalEdges = liftedGraph.edgeNum - originalGraph.edgeNum
whereLifted = numpy.where(foundEdges == 1)[0].astype('uint32')
assert len(whereLifted) == nAdditionalEdges
assert foundEdges.sum() == nAdditionalEdges
eLen = vgraph.getEdgeLengths(originalGraph)
nodeSizes_ = vgraph.getNodeSizes(originalGraph)
# FIXME GIL is not lifted for vigra function (probably cluster)
def cluster(wardness):
edgeLengthsNew = numpy.concatenate(
[eLen, numpy.zeros(nAdditionalEdges)]).astype('float32')
edgeIndicatorNew = numpy.concatenate(
[edgeIndicator, numpy.zeros(nAdditionalEdges)]).astype('float32')
nodeSizes = nodeSizes_.copy()
nodeLabels = vgraph.graphMap(originalGraph, 'node', dtype='uint32')
nodeFeatures = vgraph.graphMap(liftedGraph, 'node', addChannelDim=True)
nodeFeatures[:] = 0
outWeight = vgraph.graphMap(liftedGraph,
item='edge',
dtype=numpy.float32)
mg = vgraph.mergeGraph(liftedGraph)
clusterOp = vgraph.minEdgeWeightNodeDist(mg,
edgeWeights=edgeIndicatorNew,
edgeLengths=edgeLengthsNew,
nodeFeatures=nodeFeatures,
nodeSizes=nodeSizes,
nodeLabels=nodeLabels,
beta=0.5,
metric='l1',
wardness=wardness,
outWeight=outWeight)
clusterOp.setLiftedEdges(whereLifted)
hc = vgraph.hierarchicalClustering(clusterOp,
nodeNumStopCond=1,
buildMergeTreeEncoding=False)
hc.cluster()
assert mg.edgeNum == 0, str(mg.edgeNum)
# FIXME I am disabling these checks for now, but will need to investigate this further
# They can fail because with defects and seg mask we can get unconnected pieces in the graph
# if we have completely defected slcies, we get a non-connected merge graph
# TODO I don't know if this is a problem, if it is, we could first remove them
# and then add dummy values later
#if not with_defects:
# assert mg.nodeNum == 1, str(mg.nodeNum)
#else:
# # TODO test hypothesis
# assert mg.nodeNum == len(ds.defect_slice_list) + 1, "%i, %i" % (mg.nodeNum, len(ds.defect_slice_list) + 1)
tweight = edgeIndicatorNew.copy()
hc.ucmTransform(tweight)
whereInLifted = liftedGraph.findEdges(extraUV)
assert whereInLifted.min() >= 0
feat = tweight[whereInLifted]
assert feat.shape[0] == extraUV.shape[0]
return feat[:, None]
wardness_vals = [0.01, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7]
# TODO set from ppl parameter
with futures.ThreadPoolExecutor(max_workers=8) as executor:
tasks = [executor.submit(cluster, w) for w in wardness_vals]
allFeat = [t.result() for t in tasks]
weights = numpy.concatenate(allFeat, axis=1)
mean = numpy.mean(weights, axis=1)[:, None]
stddev = numpy.std(weights, axis=1)[:, None]
allFeat = numpy.nan_to_num(
numpy.concatenate([weights, mean, stddev], axis=1))
allFeat = numpy.require(allFeat, dtype='float32')
assert allFeat.shape[0] == extraUV.shape[0]
return allFeat
numpy.random.seed(42)
# input
shape = [200, 100, 100]
data = numpy.random.rand(*shape).astype(numpy.float32)
data = vigra.taggedView(data,"xyz")
if False:
labels = numpy.random.randint(5, size=shape[0]*shape[1]*shape[2])
labels = labels.reshape(shape).astype(numpy.uint32)
labels = vigra.analysis.labelVolume(labels)
adjListGraph = graphs.listGraph()
gridGraph = graphs.gridGraph(shape)
rag = graphs.regionAdjacencyGraph(gridGraph, labels)
rag.writeHDF5("bla.h5", "dset")
else :
# load the region adjacency graph
rag = graphs.loadGridRagHDF5("bla.h5","dset")
print rag.labels.shape, rag.labels.dtype ,type(rag.labels)
print "accumulate edge and node features"
def testAddNodesWithIds(self):
IV = vigraph.INVALID
g = vigraph.listGraph()
assert g.nodeNum == 0
assert g.edgeNum == 0
assert g.nodeFromId(0) == IV
assert g.nodeFromId(1) == IV
assert g.nodeFromId(2) == IV
assert g.nodeFromId(3) == IV
assert g.nodeFromId(4) == IV
assert g.nodeFromId(5) == IV
assert g.nodeFromId(6) == IV
assert g.nodeFromId(7) == IV
n5 = g.addNode(5)
assert g.id(n5) == 5
assert n5 != IV
assert g.nodeNum == 1
assert g.edgeNum == 0
assert g.nodeFromId(0) == IV
assert g.nodeFromId(1) == IV
assert g.nodeFromId(2) == IV
assert g.nodeFromId(3) == IV
assert g.nodeFromId(4) == IV
assert g.nodeFromId(5) != IV
assert g.nodeFromId(6) == IV
assert g.nodeFromId(7) == IV
n2 = g.addNode(2)
assert n2 != IV
assert g.nodeNum == 2
assert g.nodeFromId(0) == IV
assert g.nodeFromId(1) == IV
assert g.nodeFromId(2) != IV
assert g.nodeFromId(3) == IV
assert g.nodeFromId(4) == IV
assert g.nodeFromId(5) != IV
assert g.nodeFromId(6) == IV
assert g.nodeFromId(7) == IV
n6 = g.addNode(6)
assert n6 != IV
assert g.nodeNum == 3
assert g.nodeFromId(0) == IV
assert g.nodeFromId(1) == IV
assert g.nodeFromId(2) != IV
assert g.nodeFromId(3) == IV
assert g.nodeFromId(4) == IV
assert g.nodeFromId(5) != IV
assert g.nodeFromId(6) != IV
assert g.nodeFromId(7) == IV
n6 = g.addNode(5)
n2 = g.addNode(2)
n6 = g.addNode(6)
assert g.nodeNum == 3
assert g.nodeFromId(0) == IV
assert g.nodeFromId(1) == IV
assert g.nodeFromId(2) != IV
assert g.nodeFromId(3) == IV
assert g.nodeFromId(4) == IV
assert g.nodeFromId(5) != IV
assert g.nodeFromId(6) != IV
assert g.nodeFromId(7) == IV
def testAddNodesWithIds(self):
IV = vigraph.INVALID
g = vigraph.listGraph()
assert g.nodeNum == 0
assert g.edgeNum == 0
assert g.nodeFromId(0)==IV
assert g.nodeFromId(1)==IV
assert g.nodeFromId(2)==IV
assert g.nodeFromId(3)==IV
assert g.nodeFromId(4)==IV
assert g.nodeFromId(5)==IV
assert g.nodeFromId(6)==IV
assert g.nodeFromId(7)==IV
n5 =g.addNode(5)
assert g.id(n5)==5
assert n5!=IV
assert g.nodeNum == 1
assert g.edgeNum == 0
assert g.nodeFromId(0)==IV
assert g.nodeFromId(1)==IV
assert g.nodeFromId(2)==IV
assert g.nodeFromId(3)==IV
assert g.nodeFromId(4)==IV
assert g.nodeFromId(5)!=IV
assert g.nodeFromId(6)==IV
assert g.nodeFromId(7)==IV
n2=g.addNode(2)
assert n2!=IV
assert g.nodeNum == 2
assert g.nodeFromId(0)==IV
assert g.nodeFromId(1)==IV
assert g.nodeFromId(2)!=IV
assert g.nodeFromId(3)==IV
assert g.nodeFromId(4)==IV
assert g.nodeFromId(5)!=IV
assert g.nodeFromId(6)==IV
assert g.nodeFromId(7)==IV
n6=g.addNode(6)
assert n6!=IV
assert g.nodeNum == 3
assert g.nodeFromId(0)==IV
assert g.nodeFromId(1)==IV
assert g.nodeFromId(2)!=IV
assert g.nodeFromId(3)==IV
assert g.nodeFromId(4)==IV
assert g.nodeFromId(5)!=IV
assert g.nodeFromId(6)!=IV
assert g.nodeFromId(7)==IV
n6=g.addNode(5)
n2=g.addNode(2)
n6=g.addNode(6)
assert g.nodeNum == 3
assert g.nodeFromId(0)==IV
assert g.nodeFromId(1)==IV
assert g.nodeFromId(2)!=IV
assert g.nodeFromId(3)==IV
assert g.nodeFromId(4)==IV
assert g.nodeFromId(5)!=IV
assert g.nodeFromId(6)!=IV
assert g.nodeFromId(7)==IV
