def eccentricity( img, distFunc = "exponential", showPathImage = False, percentageOfPaths = 100, imgSaveName = "" ):
img = img.astype(numpy.uint8)
dim = len(img.shape)
## Enlarge image by one pixel on each side
bigShape = []
for s in img.shape:
bigShape.append(s + 2)
bigImg = numpy.ones(bigShape)
slices = []
for i in range(dim):
slices.append(slice(1, bigImg.shape[i]-1))
bigImg[ slices ] = img
inside = numpy.where(bigImg==0)
outside = numpy.where(bigImg==1)
## Apply distanceTransform and modify (outside: high values, inside: low values)
distImage = vigra.filters.distanceTransform2D(bigImg.astype(numpy.float32))
imgp = distImage.copy()
# if showPathImage:
# imgp = distImage.copy()
if distFunc == "exponential":
distImage = numpy.exp(distImage*-gamma)
elif distFunc == "linear":
maxDist = distImage.max()
distImage = maxDist - distImage + 10
elif distFunc == "inverse":
w = numpy.where(distImage!=0)
distImage[w] = 1/distImage[w]
else:
print "wrong parameters for distFunc in eccentricity"
## Distance in the inside between two pixels is 1.0
#distImage = bigImg.copy().astype(numpy.float32)
#distImage[inside]=1.0
# if len(imgSaveName)>1:
# plt.imshow(numpy.swapaxes(distImage, 1, 0))
# plt.savefig(imgSaveName+"_dist.png")
# #scipy.misc.imsave(imgSaveName+"_dist.png", numpy.swapaxes(distImage, 1, 0))
## Set the outside to a very high value
distImage[outside]=1000.0
## Image copy to draw the paths in
#imgp = distImage.copy()
imgp[outside] = 100
## Get image graph and its path finder
gridGraph = vigraph.gridGraph(bigImg.shape[0:dim],False)
graphShape = []
for s in distImage.shape:
graphShape.append(s*2-1)
edgeWeights = vigra.resize(distImage, graphShape, order=0)
#edgeWeights = vigra.graphs.edgeFeaturesFromInterpolatedImage(gridGraph, edgeWeights)
edgeWeights = vigra.graphs.edgeFeaturesFromInterpolatedImageCorrected(gridGraph,edgeWeights)
pathFinder = vigraph.ShortestPathPathDijkstra(gridGraph)
## Find borders in img
if dim == 2:
bigLblImg = vigra.analysis.labelImage(bigImg.astype(numpy.uint8))
else:
bigLblImg = vigra.analysis.labelVolume(bigImg.astype(numpy.uint8))
rag = vigraph.GridRegionAdjacencyGraph(gridGraph, bigLblImg)
node = vigraph.GridRegionAdjacencyGraph.nodeFromId(rag, long( bigLblImg[inside][0] ))
edges = vigraph._ragFindEdges(rag, gridGraph, rag.affiliatedEdges, bigLblImg, node)
borderImg = numpy.zeros(bigImg.shape)
for edge in edges:
slices = []
for d in range(dim):
slices.append( slice(edge[d], edge[d]+1) )
borderImg[slices] = 1
## End points for paths (all points on the border)
targets = numpy.where(borderImg==1)
nTargets = len(targets[0])
## Find the diameter (longest path)
eccLength = numpy.empty(nTargets)
eccLength.fill(-1)
eccTargetPath = {}
vpIndex = 0
vpGraphIndex = []
for d in range(dim):
vpGraphIndex.append(int(targets[d][vpIndex]))
vp = gridGraph.coordinateToNode(vpGraphIndex)
visited = numpy.zeros(nTargets)
while True:
visited[vpIndex] = 1
pathFinder.run(edgeWeights, vp)
eccChanged = False
for j in range(nTargets):
targetIndex = []
for d in range(dim):
targetIndex.append(int(targets[d][j]))
target = gridGraph.coordinateToNode(targetIndex)
pathLength = pathFinder.distance(target)
m = max(eccLength[j], pathLength)
if m > eccLength[j]:
eccChanged = True
eccLength[j] = m
eccTargetPath[j] = pathFinder.path(pathType='coordinates', target=target)
vpIndex = numpy.argmax(eccLength)
vpGraphIndex = []
for d in range(dim):
vpGraphIndex.append(int(targets[d][vpIndex]))
vp = gridGraph.coordinateToNode(vpGraphIndex)
if visited[vpIndex] or not eccChanged:
break
## Find the length of the diameter (non-weighted)
path = eccTargetPath[vpIndex]
dMax = 0
for k in range(1, len(path)):
diffCount = 0
for d in range(dim):
if path[k][d] != path[k-1][d]:
diffCount += 1
dMax += numpy.sqrt(diffCount)
## Find the midpoint of the diameter
dMax = dMax/2
if len(path) == 0:
path = numpy.empty( (1, 2), numpy.uint8 )
path[0][0] = targets[0][0]
path[0][1] = targets[1][0]
p1 = path[0]
d1 = 0
for k in range(1, len(path)):
p2 = path[k]
d2 = d1 + numpy.linalg.norm(p2-p1)
if d2 > dMax:
if (abs(d2-dMax) < abs(d1-dMax)):
p1 = p2
break
p1 = p2
d1 = d2
## Compute eccentricity from center (p1) to all points on border
sourceIndex = []
for d in range(dim):
sourceIndex.append(int(p1[d]))
source = gridGraph.coordinateToNode(sourceIndex)
pathFinder.run(edgeWeights, source)
maxPathLength = 0
for j in range(nTargets):
targetIndex = []
for d in range(dim):
targetIndex.append(int(targets[d][j]))
target = gridGraph.coordinateToNode(targetIndex)
pathLength = pathFinder.distance(target)
maxPathLength = max(maxPathLength, pathLength)
imgp[targetIndex[0], targetIndex[1]] = 40*pathLength
imgp[ path[:,0], path[:,1] ] = 12*maxPathLength
imgp[sourceIndex[0], sourceIndex[1]] = 40*maxPathLength
plt.figure(distFunc)
plt.imshow(numpy.swapaxes(imgp, 1, 0), interpolation='none')
if len(imgSaveName)>1:
scipy.misc.imsave(imgSaveName+".png", numpy.swapaxes(imgp, 1, 0))
def eccentricity(img,
label,
distFunc="exponential",
showPathImage=False,
percentageOfPaths=100,
imgSaveName=""):
img = img.astype(numpy.uint8)
dim = len(img.shape)
## Enlarge image by one pixel on each side
bigShape = []
for s in img.shape:
bigShape.append(s + 2)
bigImg = numpy.ones(bigShape)
slices = []
for i in range(dim):
slices.append(slice(1, bigImg.shape[i] - 1))
bigImg[slices] = img
inside = numpy.where(bigImg == 0)
outside = numpy.where(bigImg == 1)
# ## Apply distanceTransform and modify (outside: high values, inside: low values)
# distImage = vigra.filters.distanceTransform2D(bigImg.astype(numpy.float32))
# if showPathImage:
# imgp = distImage.copy()
# if distFunc == "exponential":
# distImage = numpy.exp(distImage*-gamma)
# elif distFunc == "linear":
# maxDist = distImage.max()
# distImage = maxDist - distImage
# elif distFunc == "inverse":
# w = numpy.where(distImage!=0)
# distImage[w] = 1/distImage[w]
# else:
# print "wrong parameters for distFunc in eccentricity"
## Distance in the inside between two pixels is 1.0
distImage = bigImg.copy().astype(numpy.float32)
distImage[inside] = 1.0
## Set the outside to a very high value
distImage[outside] = 10000.0
## Image copy to draw the paths in
imgp = distImage.copy()
imgp[outside] = 100
## Get image graph and its path finder
gridGraph = vigraph.gridGraph(bigImg.shape[0:dim], False)
graphShape = []
for s in distImage.shape:
graphShape.append(s * 2 - 1)
edgeWeights = vigra.resize(distImage, graphShape, order=0)
edgeWeights = vigra.graphs.edgeFeaturesFromInterpolatedImageCorrected(
gridGraph, edgeWeights)
pathFinder = vigraph.ShortestPathPathDijkstra(gridGraph)
## Find borders in img
if dim == 2:
bigLblImg = vigra.analysis.labelImage(bigImg.astype(numpy.uint8))
else:
bigLblImg = vigra.analysis.labelVolume(bigImg.astype(numpy.uint8))
rag = vigraph.GridRegionAdjacencyGraph(gridGraph, bigLblImg)
node = vigraph.GridRegionAdjacencyGraph.nodeFromId(
rag, long(bigLblImg[inside][0]))
edges = vigraph._ragFindEdges(rag, gridGraph, rag.affiliatedEdges,
bigLblImg, node)
# ## Remove duplicates
# edges_a = numpy.ascontiguousarray(edges)
# unique_edges = numpy.unique(edges_a.view([('', edges_a.dtype)]*edges_a.shape[1]))
# edges = unique_edges.view(edges_a.dtype).reshape((unique_edges.shape[0], edges_a.shape[1]))
borderImg = numpy.zeros(bigImg.shape)
for edge in edges:
slices = []
for d in range(dim):
slices.append(slice(edge[d], edge[d] + 1))
borderImg[slices] = 1
# ## Find borders in img
# borderImg = numpy.zeros(bigImg.shape)
# if dim == 2:
# for y in range(bigImg.shape[1]-1):
# for x in range(bigImg.shape[0]-1):
# if bigImg[x,y] == 0:
# if bigImg[x+1,y] == 1 or bigImg[x,y+1] == 1:
# borderImg[x, y] = 1
# else:
# if bigImg[x+1,y] == 0:
# borderImg[x+1, y] = 1
# if bigImg[x,y+1] == 0:
# borderImg[x, y+1] = 1
# else:
# for z in range(bigImg.shape[2]-1):
# for y in range(bigImg.shape[1]-1):
# for x in range(bigImg.shape[0]-1):
# if bigImg[x,y,z] == 0:
# if bigImg[x+1,y,z] == 1 or bigImg[x,y+1,z] == 1 or bigImg[x,y,z+1] == 1:
# borderImg[x, y, z] = 1
# else:
# if bigImg[x+1,y,z] == 0:
# borderImg[x+1,y,z] = 1
# if bigImg[x,y+1,z] == 0:
# borderImg[x,y+1,z] = 1
# if bigImg[x,y,z+1] == 0:
# borderImg[x,y,z+1] = 1
## End points for paths (all points on the border)
targets = numpy.where(borderImg == 1)
nTargets = len(targets[0])
## Indices of start points for paths (random)
nPoints = int(numpy.ceil(percentageOfPaths * nTargets / 100.0))
numpy.random.seed(42)
starts = numpy.random.permutation(range(nTargets))[:nPoints]
## Compute paths
maxPaths = []
maxPathLengths = []
for i in range(nPoints):
sourceIndex = []
for d in range(dim):
sourceIndex.append(int(targets[d][starts[i]]))
source = gridGraph.coordinateToNode(sourceIndex)
pathFinder.run(edgeWeights, source)
maxPathLength = 0
for j in range(nTargets):
targetIndex = []
for d in range(dim):
targetIndex.append(int(targets[d][j]))
target = gridGraph.coordinateToNode(targetIndex)
path = pathFinder.path(pathType='coordinates', target=target)
pathLength = pathFinder.distance(target)
if pathLength > maxPathLength or maxPathLength == 0:
maxPathLength = pathLength
maxPath = path
maxPaths.append(maxPath)
maxPathLengths.append(maxPathLength)
imgp[sourceIndex[0],
sourceIndex[1]] = 3 * maxPathLength * maxPathLength
if showPathImage:
val = (imgp.max() + imgp.min()) / 2
for p in maxPaths:
imgp[p[:, 0], p[:, 1]] = val
if showPathImage:
plt.figure(distFunc)
plt.imshow(numpy.swapaxes(imgp, 1, 0), interpolation='none')
if len(imgSaveName) > 1:
scipy.misc.imsave(imgSaveName, numpy.swapaxes(imgp, 1, 0))
return maxPathLengths
def eccentricity(img,
distFunc="exponential",
showPathImage=False,
percentageOfPaths=100,
imgSaveName=""):
img = img.astype(numpy.uint8)
dim = len(img.shape)
## Enlarge image by one pixel on each side
bigShape = []
for s in img.shape:
bigShape.append(s + 2)
bigImg = numpy.ones(bigShape)
slices = []
for i in range(dim):
slices.append(slice(1, bigImg.shape[i] - 1))
bigImg[slices] = img
inside = numpy.where(bigImg == 0)
outside = numpy.where(bigImg == 1)
## Apply distanceTransform and modify (outside: high values, inside: low values)
distImage = vigra.filters.distanceTransform2D(bigImg.astype(numpy.float32))
imgp = distImage.copy()
# if showPathImage:
# imgp = distImage.copy()
if distFunc == "exponential":
distImage = numpy.exp(distImage * -gamma)
elif distFunc == "linear":
maxDist = distImage.max()
distImage = maxDist - distImage + 10
elif distFunc == "inverse":
w = numpy.where(distImage != 0)
distImage[w] = 1 / distImage[w]
else:
print "wrong parameters for distFunc in eccentricity"
## Distance in the inside between two pixels is 1.0
#distImage = bigImg.copy().astype(numpy.float32)
#distImage[inside]=1.0
# if len(imgSaveName)>1:
# plt.imshow(numpy.swapaxes(distImage, 1, 0))
# plt.savefig(imgSaveName+"_dist.png")
# #scipy.misc.imsave(imgSaveName+"_dist.png", numpy.swapaxes(distImage, 1, 0))
## Set the outside to a very high value
distImage[outside] = 1000.0
## Image copy to draw the paths in
#imgp = distImage.copy()
imgp[outside] = 100
## Get image graph and its path finder
gridGraph = vigraph.gridGraph(bigImg.shape[0:dim], False)
graphShape = []
for s in distImage.shape:
graphShape.append(s * 2 - 1)
edgeWeights = vigra.resize(distImage, graphShape, order=0)
#edgeWeights = vigra.graphs.edgeFeaturesFromInterpolatedImage(gridGraph, edgeWeights)
edgeWeights = vigra.graphs.edgeFeaturesFromInterpolatedImageCorrected(
gridGraph, edgeWeights)
pathFinder = vigraph.ShortestPathPathDijkstra(gridGraph)
## Find borders in img
if dim == 2:
bigLblImg = vigra.analysis.labelImage(bigImg.astype(numpy.uint8))
else:
bigLblImg = vigra.analysis.labelVolume(bigImg.astype(numpy.uint8))
rag = vigraph.GridRegionAdjacencyGraph(gridGraph, bigLblImg)
node = vigraph.GridRegionAdjacencyGraph.nodeFromId(
rag, long(bigLblImg[inside][0]))
edges = vigraph._ragFindEdges(rag, gridGraph, rag.affiliatedEdges,
bigLblImg, node)
borderImg = numpy.zeros(bigImg.shape)
for edge in edges:
slices = []
for d in range(dim):
slices.append(slice(edge[d], edge[d] + 1))
borderImg[slices] = 1
## End points for paths (all points on the border)
targets = numpy.where(borderImg == 1)
nTargets = len(targets[0])
## Find the diameter (longest path)
eccLength = numpy.empty(nTargets)
eccLength.fill(-1)
eccTargetPath = {}
vpIndex = 0
vpGraphIndex = []
for d in range(dim):
vpGraphIndex.append(int(targets[d][vpIndex]))
vp = gridGraph.coordinateToNode(vpGraphIndex)
visited = numpy.zeros(nTargets)
while True:
visited[vpIndex] = 1
pathFinder.run(edgeWeights, vp)
eccChanged = False
for j in range(nTargets):
targetIndex = []
for d in range(dim):
targetIndex.append(int(targets[d][j]))
target = gridGraph.coordinateToNode(targetIndex)
pathLength = pathFinder.distance(target)
m = max(eccLength[j], pathLength)
if m > eccLength[j]:
eccChanged = True
eccLength[j] = m
eccTargetPath[j] = pathFinder.path(pathType='coordinates',
target=target)
vpIndex = numpy.argmax(eccLength)
vpGraphIndex = []
for d in range(dim):
vpGraphIndex.append(int(targets[d][vpIndex]))
vp = gridGraph.coordinateToNode(vpGraphIndex)
if visited[vpIndex] or not eccChanged:
break
## Find the length of the diameter (non-weighted)
path = eccTargetPath[vpIndex]
dMax = 0
for k in range(1, len(path)):
diffCount = 0
for d in range(dim):
if path[k][d] != path[k - 1][d]:
diffCount += 1
dMax += numpy.sqrt(diffCount)
## Find the midpoint of the diameter
dMax = dMax / 2
if len(path) == 0:
path = numpy.empty((1, 2), numpy.uint8)
path[0][0] = targets[0][0]
path[0][1] = targets[1][0]
p1 = path[0]
d1 = 0
for k in range(1, len(path)):
p2 = path[k]
d2 = d1 + numpy.linalg.norm(p2 - p1)
if d2 > dMax:
if (abs(d2 - dMax) < abs(d1 - dMax)):
p1 = p2
break
p1 = p2
d1 = d2
## Compute eccentricity from center (p1) to all points on border
sourceIndex = []
for d in range(dim):
sourceIndex.append(int(p1[d]))
source = gridGraph.coordinateToNode(sourceIndex)
pathFinder.run(edgeWeights, source)
maxPathLength = 0
for j in range(nTargets):
targetIndex = []
for d in range(dim):
targetIndex.append(int(targets[d][j]))
target = gridGraph.coordinateToNode(targetIndex)
pathLength = pathFinder.distance(target)
maxPathLength = max(maxPathLength, pathLength)
imgp[targetIndex[0], targetIndex[1]] = 40 * pathLength
imgp[path[:, 0], path[:, 1]] = 12 * maxPathLength
imgp[sourceIndex[0], sourceIndex[1]] = 40 * maxPathLength
plt.figure(distFunc)
plt.imshow(numpy.swapaxes(imgp, 1, 0), interpolation='none')
if len(imgSaveName) > 1:
scipy.misc.imsave(imgSaveName + ".png", numpy.swapaxes(imgp, 1, 0))
def eccentricity( img, label, distFunc = "exponential", showPathImage = False, percentageOfPaths = 100, imgSaveName = "" ):
img = img.astype(numpy.uint8)
dim = len(img.shape)
## Enlarge image by one pixel on each side
bigShape = []
for s in img.shape:
bigShape.append(s + 2)
bigImg = numpy.ones(bigShape)
slices = []
for i in range(dim):
slices.append(slice(1, bigImg.shape[i]-1))
bigImg[ slices ] = img
inside = numpy.where(bigImg==0)
outside = numpy.where(bigImg==1)
# ## Apply distanceTransform and modify (outside: high values, inside: low values)
# distImage = vigra.filters.distanceTransform2D(bigImg.astype(numpy.float32))
# if showPathImage:
# imgp = distImage.copy()
# if distFunc == "exponential":
# distImage = numpy.exp(distImage*-gamma)
# elif distFunc == "linear":
# maxDist = distImage.max()
# distImage = maxDist - distImage
# elif distFunc == "inverse":
# w = numpy.where(distImage!=0)
# distImage[w] = 1/distImage[w]
# else:
# print "wrong parameters for distFunc in eccentricity"
## Distance in the inside between two pixels is 1.0
distImage = bigImg.copy().astype(numpy.float32)
distImage[inside]=1.0
## Set the outside to a very high value
distImage[outside]=10000.0
## Image copy to draw the paths in
imgp = distImage.copy()
imgp[outside] = 100
## Get image graph and its path finder
gridGraph = vigraph.gridGraph(bigImg.shape[0:dim],False)
graphShape = []
for s in distImage.shape:
graphShape.append(s*2-1)
edgeWeights = vigra.resize(distImage, graphShape, order=0)
edgeWeights = vigra.graphs.edgeFeaturesFromInterpolatedImageCorrected(gridGraph, edgeWeights)
pathFinder = vigraph.ShortestPathPathDijkstra(gridGraph)
## Find borders in img
if dim == 2:
bigLblImg = vigra.analysis.labelImage(bigImg.astype(numpy.uint8))
else:
bigLblImg = vigra.analysis.labelVolume(bigImg.astype(numpy.uint8))
rag = vigraph.GridRegionAdjacencyGraph(gridGraph, bigLblImg)
node = vigraph.GridRegionAdjacencyGraph.nodeFromId(rag, long( bigLblImg[inside][0] ))
edges = vigraph._ragFindEdges(rag, gridGraph, rag.affiliatedEdges, bigLblImg, node)
# ## Remove duplicates
# edges_a = numpy.ascontiguousarray(edges)
# unique_edges = numpy.unique(edges_a.view([('', edges_a.dtype)]*edges_a.shape[1]))
# edges = unique_edges.view(edges_a.dtype).reshape((unique_edges.shape[0], edges_a.shape[1]))
borderImg = numpy.zeros(bigImg.shape)
for edge in edges:
slices = []
for d in range(dim):
slices.append( slice(edge[d], edge[d]+1) )
borderImg[slices] = 1
# ## Find borders in img
# borderImg = numpy.zeros(bigImg.shape)
# if dim == 2:
# for y in range(bigImg.shape[1]-1):
# for x in range(bigImg.shape[0]-1):
# if bigImg[x,y] == 0:
# if bigImg[x+1,y] == 1 or bigImg[x,y+1] == 1:
# borderImg[x, y] = 1
# else:
# if bigImg[x+1,y] == 0:
# borderImg[x+1, y] = 1
# if bigImg[x,y+1] == 0:
# borderImg[x, y+1] = 1
# else:
# for z in range(bigImg.shape[2]-1):
# for y in range(bigImg.shape[1]-1):
# for x in range(bigImg.shape[0]-1):
# if bigImg[x,y,z] == 0:
# if bigImg[x+1,y,z] == 1 or bigImg[x,y+1,z] == 1 or bigImg[x,y,z+1] == 1:
# borderImg[x, y, z] = 1
# else:
# if bigImg[x+1,y,z] == 0:
# borderImg[x+1,y,z] = 1
# if bigImg[x,y+1,z] == 0:
# borderImg[x,y+1,z] = 1
# if bigImg[x,y,z+1] == 0:
# borderImg[x,y,z+1] = 1
## End points for paths (all points on the border)
targets = numpy.where(borderImg==1)
nTargets = len(targets[0])
## Indices of start points for paths (random)
nPoints = int(numpy.ceil(percentageOfPaths * nTargets / 100.0))
numpy.random.seed(42)
starts = numpy.random.permutation(range(nTargets))[:nPoints]
## Compute paths
maxPaths = []
maxPathLengths = []
for i in range(nPoints):
sourceIndex = []
for d in range(dim):
sourceIndex.append(int(targets[d][starts[i]]))
source = gridGraph.coordinateToNode(sourceIndex)
pathFinder.run(edgeWeights, source)
maxPathLength = 0
for j in range(nTargets):
targetIndex = []
for d in range(dim):
targetIndex.append(int(targets[d][j]))
target = gridGraph.coordinateToNode(targetIndex)
path = pathFinder.path(pathType='coordinates', target=target)
pathLength = pathFinder.distance(target)
if pathLength > maxPathLength or maxPathLength == 0:
maxPathLength = pathLength
maxPath = path
maxPaths.append(maxPath)
maxPathLengths.append(maxPathLength)
imgp[sourceIndex[0], sourceIndex[1]] = 3*maxPathLength*maxPathLength
if showPathImage:
val = (imgp.max()+imgp.min())/2
for p in maxPaths:
imgp[p[:,0], p[:,1]] = val
if showPathImage:
plt.figure(distFunc)
plt.imshow(numpy.swapaxes(imgp, 1, 0), interpolation='none')
if len(imgSaveName)>1:
scipy.misc.imsave(imgSaveName, numpy.swapaxes(imgp, 1, 0))
return maxPathLengths