def _runAll(self):
for runNr in range(20):
model = self._buildModel()
averaged = self.optimizeModel(model)
c = self.updatePExperts(averaged)
if c < 0.00001:
break
vigra.segShow(imgRgb, self.lastNodeLabels + 1)
vigra.show()
def allPairsOfShortestPath(graph, weights):
pathFinder = vigra.graphs.ShortestPathPathDijkstra(graph)
distances = numpy.zeros([graph.nodeNum] * 2)
for ni, node in enumerate(graph.nodeIter()):
pathFinder.run(weights**1, node)
d = pathFinder.distances()**1
distances[ni, :] = d[:]
ggf = graph.projectNodeFeaturesToGridGraph(d)
ggf = vigra.taggedView(ggf, 'xy')
if ni < 1:
vigra.imshow(ggf)
vigra.show()
print distances.min(), distances.max()
return distances
def makeRag(raw, showSeg=False):
# raw = vigra.gaussianSmoothing(raw,1.0)
ew = vigra.filters.hessianOfGaussianEigenvalues(-1.0 * raw, 2.3)[:, :, 0]
seg, nseg = vigra.analysis.watershedsNew(ew)
# seg, nseg = vigra.analysis.slicSuperpixels(raw,intensityScaling=4.5, seedDistance=20)
seg = seg.squeeze()
if showSeg:
vigra.segShow(raw, seg)
vigra.show()
# get the rag
seg -= 1
assert seg.min() == 0
assert seg.max() == nseg - 1
return nifty.graph.rag.gridRag(seg)
def makeRag(raw, showSeg=False):
#raw = vigra.gaussianSmoothing(raw,1.0)
ew = vigra.filters.hessianOfGaussianEigenvalues(-1.0 * raw, 2.3)[:, :, 0]
seg, nseg = vigra.analysis.watershedsNew(ew)
#seg, nseg = vigra.analysis.slicSuperpixels(raw,intensityScaling=4.5, seedDistance=20)
seg = seg.squeeze()
if showSeg:
vigra.segShow(raw, seg)
vigra.show()
# get the rag
seg -= 1
assert seg.min() == 0
assert seg.max() == nseg - 1
return nifty.graph.rag.gridRag(seg)
def optimizeModel(self, model):
if self.gtAsCut is None:
# generate external proposals
# ( we should do this only once)
self.gtAsCut = []
for gti in range(self.nExperts):
gt2d = self.gts[:, :, gti].astype('uint64')
#print gt2d.shape
gt1d = model.flattenLabels(gt2d)
#print gt1d
edgeGt = model.nodeLabelsToEdgeLabels(gt1d)
self.gtAsCut.append(edgeGt)
# settings for proposal generator
settingsProposalGen = agraph.settingsProposalsFusionMovesSubgraphProposals(
model)
settingsProposalGen.subgraphRadius = 20
# settings for solver itself
settings = agraph.settingsFusionMoves(settingsProposalGen)
settings.maxNumberOfIterations = 4
settings.nParallelProposals = 50
settings.reduceIterations = 0
settings.seed = 42
for ep in self.gtAsCut:
settings.addPropoal(ep)
# solver
solver = agraph.fusionMoves(model, settings)
# solve the damn thing
out = solver.run()
nodeLabels = model.edgeLabelsToNodeLabels(out)
nodeLabels = nodeLabels.astype('uint32')
nodeLabels = nodeLabels.reshape(shape, order='F')
nodeLabels = vigra.taggedView(nodeLabels, 'xy')
self.lastNodeLabels = nodeLabels
vigra.segShow(imgRgb, nodeLabels + 1)
vigra.show()
return out
partial(vigra.filters.gaussianGradientMagnitude, sigma=1.0),
partial(vigra.filters.gaussianGradientMagnitude, sigma=2.0),
]
dataset, test_set = secondOrderImageDataset(imgs=imgs,
gts=gt,
numberOfLabels=2,
fUnary=fUnary,
fBinary=fBinary,
addConstFeature=False)
learner = learning.subgradientSSVM(dataset,
learningRate=0.1,
C=100,
learningMode='batch',
maxIterations=10)
learner.learn(infCls=opengm.inference.QpboExternal,
parameter=opengm.InfParam())
# predict on test test
for (rgbImg, gtImg, gm) in test_set:
# infer for test image
inf = opengm.inference.QpboExternal(gm)
inf.infer()
arg = inf.arg()
arg = arg.reshape(numpy.squeeze(gtImg.shape))
vigra.segShow(rgbImg, arg + 2)
vigra.show()
nodeFeatures = rag.accumulateNodeFeatures(imgLab)
# do agglomerativeClustering
labels = graphs.agglomerativeClustering(graph=rag, edgeWeights=edgeWeights,
beta=beta, nodeFeatures=nodeFeatures,
nodeNumStop=nodeNumStop)
# show result
f = pylab.figure()
ax1 = f.add_subplot(2, 2, 1)
vigra.imshow(gradMag,show=False)
ax1.set_title("Input Image")
pylab.axis('off')
ax2 = f.add_subplot(2, 2, 2)
rag.show(img)
ax2.set_title("Over-Segmentation")
pylab.axis('off')
ax3 = f.add_subplot(2, 2, 3)
rag.show(img, labels)
ax3.set_title("Result-Segmentation")
pylab.axis('off')
ax4 = f.add_subplot(2, 2, 4)
rag.showNested(img, labels)
ax4.set_title("Result-Segmentation")
pylab.axis('off')
vigra.show()
def __init__(self, raw, seg, gt=None, patchSize=[100, 100], **kwargs):
#raw input data
self.raw = numpy.squeeze(raw)
self.seg = numpy.squeeze(seg)
self.gt = numpy.squeeze(gt)
# shorthands
self.shape = self.raw.shape
# settings
self.patchSize = patchSize
# apply paddings
ps = self.patchSize
padding = ((ps[0], ps[0]), (ps[1], ps[1]))
pad = partial(numpy.pad, pad_width=padding)
self.paddingMask = pad(numpy.zeros(self.shape),
mode='constant',
constant_values=1)
self.paddedRaw = pad(self.raw, mode='reflect')
self.paddedSeg = vigra.analysis.labelImage(
pad(self.seg, mode='reflect')).squeeze()
self.paddedGt = None
if self.gt is not None:
self.paddedGt = vigra.analysis.labelImage(
pad(self.gt, mode='reflect')).squeeze()
#self.paddedGt = pad(self.gt + 1, mode='constant', constant_values=0)
# compute cgp
self.tGrid = ncgp.TopologicalGrid2D(self.paddedSeg)
self.tShape = self.tGrid.topologicalGridShape
self.numberOfCells = self.tGrid.numberOfCells
self.fGrid = ncgp.FilledTopologicalGrid2D(self.tGrid)
self.cellGrids = [
self.fGrid.cellMask([1, 0, 0]),
self.fGrid.cellMask([0, 1, 0]), None
]
self.cellGrids[0][
self.cellGrids[0] != 0] -= self.fGrid.cellTypeOffset[0]
self.cellGrids[1][
self.cellGrids[1] != 0] -= self.fGrid.cellTypeOffset[1]
self.cellMasks = [numpy.clip(x, 0, 1)
for x in self.cellGrids[0:2]] + [None]
rawT = vigra.sampling.resize(self.paddedRaw, self.tShape)
#rawT[self.cellMasks[1]!=0] = 0
self.cellsBounds = self.tGrid.extractCellsBounds()
self.cellsGeometry = self.tGrid.extractCellsGeometry(fill=True)
self.cells1Bounds = self.cellsBounds[1]
self.cells1Geometry = self.cellsGeometry[1]
# center of mass
self.cell1CentersOfMass = self.cells1Geometry.centersOfMass()
print(self.cell1CentersOfMass)
# compute gt
ol = Overlap(self.numberOfCells[2], self.paddedSeg, self.paddedGt)
cell1Probs = ol.differentOverlaps(numpy.array(self.cells1Bounds))
with nifty.Timer("makeCellImage"):
probImg = ncgp.makeCellImage(rawT, self.cellGrids[1],
cell1Probs * 255.0)
vigra.imshow(probImg.astype('uint8'), cmap='gist_heat')
vigra.show()
if False:
vigra.imshow(self.paddingMask)
vigra.show()
vigra.imshow(self.paddedRaw)
vigra.show()
vigra.segShow(self.paddedRaw, self.paddedSeg)
vigra.show()
vigra.segShow(self.paddedRaw, self.paddedGt)
vigra.show()
def runLiftedMc(dataDict, settings):
rawData = dataDict['raw']
outDir = dataDict['outDir']
localRfPredictDir = os.path.join(outDir, 'localClfProbs')
ragsAndSuperpixels = getRagsAndSuperpixels(dataDict, settings)
liftedFeaturesDir = os.path.join(outDir, 'liftedFeatures')
liftedProbsDir = os.path.join(outDir, 'liftedProbs')
ragsAndSuperpixels = getRagsAndSuperpixels(dataDict, settings)
for sliceIndex in range(rawData.shape[0]):
# local probs
predictionFile = os.path.join(
localRfPredictDir, 'rag_pred_clf%s_%d.h5' % ('0', sliceIndex))
localProbs = h5Read(predictionFile)[:, 1]
# lifted probs
liftedProbsFile = os.path.join(liftedProbsDir,
'lifted_probs_%d.h5' % (sliceIndex))
liftedProbs = h5Read(liftedProbsFile)
# set up the lifted objective
rag, sp = ragsAndSuperpixels[sliceIndex]
obj = nifty.graph.lifted_multicut.liftedMulticutObjective(rag)
liftedGraph = obj.liftedGraph
distance = obj.insertLiftedEdgesBfs(
5, returnDistance=True).astype('float32')
liftedUvIds = obj.liftedUvIds()
# numeric factor to not get to small weights
# might not be necessary
C = 100.0
# local weights
eps = 0.0001
clipped = numpy.clip(localProbs, eps, 1.0 - eps)
beta = settings['betaLocal']
wLocal = numpy.log((1.0 - clipped) / (clipped)) + numpy.log(
(1.0 - beta) / (beta))
# normalize by number of local edges length
wLocal *= C / len(wLocal)
wLocal *= settings['gamma']
# non local weights
eps = 0.0001
clipped = numpy.clip(liftedProbs, eps, 1.0 - eps)
beta = settings['betaLifted']
wLifted = numpy.log((1.0 - clipped) / (clipped)) + numpy.log(
(1.0 - beta) / (beta))
# normalize by the distance (give close one more weight)
distanceWeight = 1.0 / (distance - 1.0)
#wLifted *= C/distanceWeight.sum()
wLifted *= C / len(wLifted)
print numpy.abs(wLocal).sum(), numpy.abs(wLifted).sum()
# write the weighs into the objective
obj.setLiftedEdgesCosts(wLifted, overwrite=True)
obj.setGraphEdgesCosts(wLocal, overwrite=True)
# warm start with normal multicut
mcObj = nifty.graph.multicut.multicutObjective(rag, wLocal)
solverFactory = mcObj.multicutIlpCplexFactory()
solver = solverFactory.create(mcObj)
visitor = mcObj.multicutVerboseVisitor()
argMc = solver.optimize(visitor)
emc = obj.evalNodeLabels(argMc)
# finaly optimize it
solverFactory = obj.liftedMulticutAndresGreedyAdditiveFactory()
solver = solverFactory.create(obj)
visitor = obj.verboseVisitor()
arg = solver.optimize(visitor)
eg = obj.evalNodeLabels(arg)
solverFactory = obj.liftedMulticutAndresKernighanLinFactory()
solver = solverFactory.create(obj)
visitor = obj.verboseVisitor()
arg = solver.optimize(visitor, arg.copy())
ekl = obj.evalNodeLabels(arg)
print "e", emc, eg, ekl
#projectToPixels
pixelData = nifty.graph.rag.projectScalarNodeDataToPixels(
rag, arg.astype('uint32'))
vigra.segShow(rawData[sliceIndex, :, :], pixelData)
vigra.show()
def runLiftedMc(dataDict, settings):
rawData = dataDict['raw']
outDir = dataDict['outDir']
localRfPredictDir = os.path.join(outDir,'localClfProbs')
ragsAndSuperpixels = getRagsAndSuperpixels(dataDict, settings)
liftedFeaturesDir = os.path.join(outDir,'liftedFeatures')
liftedProbsDir = os.path.join(outDir,'liftedProbs')
ragsAndSuperpixels = getRagsAndSuperpixels(dataDict, settings)
for sliceIndex in range(rawData.shape[0]):
# local probs
predictionFile = os.path.join(localRfPredictDir,'rag_pred_clf%s_%d.h5'%('0', sliceIndex))
localProbs = h5Read(predictionFile)[:,1]
# lifted probs
liftedProbsFile = os.path.join(liftedProbsDir,'lifted_probs_%d.h5'%(sliceIndex))
liftedProbs = h5Read(liftedProbsFile)
# set up the lifted objective
rag, sp = ragsAndSuperpixels[sliceIndex]
obj = nifty.graph.lifted_multicut.liftedMulticutObjective(rag)
liftedGraph = obj.liftedGraph
distance = obj.insertLiftedEdgesBfs(5, returnDistance=True).astype('float32')
liftedUvIds = obj.liftedUvIds()
# numeric factor to not get to small weights
# might not be necessary
C = 100.0
# local weights
eps = 0.0001
clipped = numpy.clip(localProbs, eps, 1.0-eps)
beta = settings['betaLocal']
wLocal = numpy.log((1.0-clipped)/(clipped)) + numpy.log((1.0-beta)/(beta))
# normalize by number of local edges length
wLocal *= C/len(wLocal)
wLocal *= settings['gamma']
# non local weights
eps = 0.0001
clipped = numpy.clip(liftedProbs, eps, 1.0-eps)
beta = settings['betaLifted']
wLifted = numpy.log((1.0-clipped)/(clipped)) + numpy.log((1.0-beta)/(beta))
# normalize by the distance (give close one more weight)
distanceWeight = 1.0 / (distance-1.0)
#wLifted *= C/distanceWeight.sum()
wLifted *= C/len(wLifted)
print numpy.abs(wLocal).sum(), numpy.abs(wLifted).sum()
# write the weighs into the objective
obj.setLiftedEdgesCosts(wLifted, overwrite=True)
obj.setGraphEdgesCosts(wLocal, overwrite=True)
# warm start with normal multicut
mcObj = nifty.graph.multicut.multicutObjective(rag, wLocal)
solverFactory = mcObj.multicutIlpCplexFactory()
solver = solverFactory.create(mcObj)
visitor = mcObj.multicutVerboseVisitor()
argMc = solver.optimize(visitor)
emc = obj.evalNodeLabels(argMc)
# finaly optimize it
solverFactory = obj.liftedMulticutAndresGreedyAdditiveFactory()
solver = solverFactory.create(obj)
visitor = obj.verboseVisitor()
arg = solver.optimize(visitor)
eg = obj.evalNodeLabels(arg)
solverFactory = obj.liftedMulticutAndresKernighanLinFactory()
solver = solverFactory.create(obj)
visitor = obj.verboseVisitor()
arg = solver.optimize(visitor, arg.copy())
ekl = obj.evalNodeLabels(arg)
print "e",emc,eg,ekl
#projectToPixels
pixelData = nifty.graph.rag.projectScalarNodeDataToPixels(rag, arg.astype('uint32'))
vigra.segShow(rawData[sliceIndex,:,:], pixelData)
vigra.show()
def test_mcgala():
# get the dataset
imgs, gts = make_dataset(10, noise=4.5, shape=(200, 200))
Obj = G.MulticutObjective
CG = G.EdgeContractionGraph
CGObj = CG.MulticutObjective
greedyFactory = Obj.greedyAdditiveFactory()
ilpFactory = Obj.multicutIlpFactory(
ilpSolver="cplex",
addThreeCyclesConstraints=False,
addOnlyViolatedThreeCyclesConstraints=False
# memLimit= 0.01
)
fmFactoryA = CGObj.fusionMoveBasedFactory(
# fusionMove=CGObj.fusionMoveSettings(mcFactory=greedyFactory),
fusionMove=CGObj.fusionMoveSettings(mcFactory=ilpFactory),
# proposalGen=nifty.greedyAdditiveProposals(sigma=30,nodeNumStopCond=-1,weightStopCond=0.0),
proposalGen=CGObj.watershedProposals(sigma=1, seedFraction=0.1),
numberOfIterations=10,
numberOfParallelProposals=40, # no effect if nThreads equals 0 or 1
numberOfThreads=40,
stopIfNoImprovement=2,
fuseN=2,
)
ragTrain = makeRag(imgs[0], showSeg=True)
fOpTrain, minVal, maxVal = makeFeatureOp(ragTrain, imgs[0])
edgeGt = makeEdgeGt(ragTrain, gts[0])
cOrderSettigns = G.galaContractionOrderSettings(mcMapFactory=fmFactoryA, runMcMapEachNthTime=10)
# gala class
settings = G.galaSettings(
threshold0=0.1,
threshold1=0.9,
thresholdU=0.1,
numberOfEpochs=1,
numberOfTrees=200,
contractionOrderSettings=cOrderSettigns
# mapFactory=fmFactoryA,
# perturbAndMapFactory=fmFactoryB
)
gala = G.gala(settings)
trainingInstance = ngala.galaTrainingInstance(ragTrain, fOpTrain, edgeGt)
gala.addTrainingInstance(trainingInstance)
gala.train()
for x in range(3, 10):
ragTest = makeRag(imgs[x], showSeg=False)
fOpTest, minVal, maxVal = makeFeatureOp(ragTest, imgs[x], minVal, maxVal)
instance = ngala.galaInstance(ragTest, fOpTest)
edgeGt = makeEdgeGt(ragTest, gts[x])
nodeRes = gala.predict(instance)
pixelNodeRes = nrag.projectScalarNodeDataToPixels(ragTest, nodeRes, -1)
vigra.segShow(imgs[x], pixelNodeRes)
vigra.show()
def makeFeat(rag, raw, labels, show=True):
featureExtractor = graphs.gridRagFeatureExtractor(rag, labels)
featureExtractor.labels = labels
featureExtractor.graph = rag
geoFeat = featureExtractor.geometricFeatures()
topoFeat = featureExtractor.topologicalFeatures()
features = [geoFeat, topoFeat]
# ward facs
wardness = numpy.array([0.0, 0.1, 0.15, 0.25, 0.5, 1.0], dtype="float32")
accFeat = featureExtractor.accumulatedFeatures(raw)
features.append(accFeat)
for s in [2.0, 3.0, 4.0]:
res = vigra.filters.gaussianGradientMagnitude(raw, s)
accFeat = featureExtractor.accumulatedFeatures(res)
features.append(accFeat)
for s in [2.0, 3.0, 4.0]:
res = vigra.filters.laplacianOfGaussian(raw, s)
accFeat = featureExtractor.accumulatedFeatures(res)
features.append(accFeat)
for s in [2.0, 3.0, 4.0]:
res = vigra.gaussianSmoothing(raw, s)
accFeat = featureExtractor.accumulatedFeatures(res)
features.append(accFeat)
# st ev
for s in [2.0, 3.0, 4.0]:
res = stEv(raw, s)
accFeat = featureExtractor.accumulatedFeatures(res)
mean = accFeat[:, 0]
ucm = featureExtractor.ucmTransformFeatures(mean[:, None], wardness)
features.extend([accFeat, ucm])
if False:
for x in range(ucm.shape[1]):
rag.showEdgeFeature(raw, ucm[:, x])
vigra.show()
# hessian ev
for s in [1.0, 3.0, 4.0, 6.0, 8.0]:
img = hessianEv2(raw, s, 2.0)
# vigra.imshow(img)
# vigra.show()
accFeat = featureExtractor.accumulatedFeatures(img)
mean = accFeat[:, 0]
ucm = featureExtractor.ucmTransformFeatures(mean[:, None], wardness)
features.extend([accFeat, ucm])
if False:
for x in range(ucm.shape[1]):
print "x", x
rag.showEdgeFeature(raw, ucm[:, x])
vigra.show()
# break
#
features = numpy.concatenate(features, axis=1)
return features
def test_mcgala():
# get the dataset
imgs, gts = make_dataset(10, noise=4.5, shape=(200, 200))
Obj = G.MulticutObjective
CG = G.EdgeContractionGraph
CGObj = CG.MulticutObjective
greedyFactory = Obj.greedyAdditiveFactory()
ilpFactory = Obj.multicutIlpFactory(
ilpSolver='cplex',
addThreeCyclesConstraints=False,
addOnlyViolatedThreeCyclesConstraints=False
#memLimit= 0.01
)
fmFactoryA = CGObj.fusionMoveBasedFactory(
#fusionMove=CGObj.fusionMoveSettings(mcFactory=greedyFactory),
fusionMove=CGObj.fusionMoveSettings(mcFactory=ilpFactory),
#proposalGen=nifty.greedyAdditiveProposals(sigma=30,nodeNumStopCond=-1,weightStopCond=0.0),
proposalGen=CGObj.watershedProposals(sigma=1, seedFraction=0.1),
numberOfIterations=10,
numberOfParallelProposals=40, # no effect if nThreads equals 0 or 1
numberOfThreads=40,
stopIfNoImprovement=2,
fuseN=2,
)
ragTrain = makeRag(imgs[0], showSeg=True)
fOpTrain, minVal, maxVal = makeFeatureOp(ragTrain, imgs[0])
edgeGt = makeEdgeGt(ragTrain, gts[0])
cOrderSettigns = G.galaContractionOrderSettings(mcMapFactory=fmFactoryA,
runMcMapEachNthTime=10)
# gala class
settings = G.galaSettings(
threshold0=0.1,
threshold1=0.9,
thresholdU=0.1,
numberOfEpochs=1,
numberOfTrees=200,
contractionOrderSettings=cOrderSettigns
#mapFactory=fmFactoryA,
#perturbAndMapFactory=fmFactoryB
)
gala = G.gala(settings)
trainingInstance = ngala.galaTrainingInstance(ragTrain, fOpTrain, edgeGt)
gala.addTrainingInstance(trainingInstance)
gala.train()
for x in range(3, 10):
ragTest = makeRag(imgs[x], showSeg=False)
fOpTest, minVal, maxVal = makeFeatureOp(ragTest, imgs[x], minVal,
maxVal)
instance = ngala.galaInstance(ragTest, fOpTest)
edgeGt = makeEdgeGt(ragTest, gts[x])
nodeRes = gala.predict(instance)
pixelNodeRes = nrag.projectScalarNodeDataToPixels(ragTest, nodeRes, -1)
vigra.segShow(imgs[x], pixelNodeRes)
vigra.show()
def makeFeat(rag, raw, labels, show=True):
featureExtractor = graphs.gridRagFeatureExtractor(rag, labels)
featureExtractor.labels = labels
featureExtractor.graph = rag
geoFeat = featureExtractor.geometricFeatures()
topoFeat = featureExtractor.topologicalFeatures()
features = [geoFeat, topoFeat]
# ward facs
wardness = numpy.array([0.0, 0.1, 0.15, 0.25, 0.5, 1.0], dtype='float32')
accFeat = featureExtractor.accumulatedFeatures(raw)
features.append(accFeat)
for s in [2.0, 3.0, 4.0]:
res = vigra.filters.gaussianGradientMagnitude(raw, s)
accFeat = featureExtractor.accumulatedFeatures(res)
features.append(accFeat)
for s in [2.0, 3.0, 4.0]:
res = vigra.filters.laplacianOfGaussian(raw, s)
accFeat = featureExtractor.accumulatedFeatures(res)
features.append(accFeat)
for s in [2.0, 3.0, 4.0]:
res = vigra.gaussianSmoothing(raw, s)
accFeat = featureExtractor.accumulatedFeatures(res)
features.append(accFeat)
# st ev
for s in [2.0, 3.0, 4.0]:
res = stEv(raw, s)
accFeat = featureExtractor.accumulatedFeatures(res)
mean = accFeat[:, 0]
ucm = featureExtractor.ucmTransformFeatures(mean[:, None], wardness)
features.extend([accFeat, ucm])
if False:
for x in range(ucm.shape[1]):
rag.showEdgeFeature(raw, ucm[:, x])
vigra.show()
# hessian ev
for s in [1.0, 3.0, 4.0, 6.0, 8.0]:
img = hessianEv2(raw, s, 2.0)
#vigra.imshow(img)
#vigra.show()
accFeat = featureExtractor.accumulatedFeatures(img)
mean = accFeat[:, 0]
ucm = featureExtractor.ucmTransformFeatures(mean[:, None], wardness)
features.extend([accFeat, ucm])
if False:
for x in range(ucm.shape[1]):
print "x", x
rag.showEdgeFeature(raw, ucm[:, x])
vigra.show()
#break
#
features = numpy.concatenate(features, axis=1)
return features