def agglomerative_clustering_3d(vol, seg_vol, use_gradient = False): labels = vigra.analysis.labelVolume(seg_vol) volBig = vigra.resize(vol, [ vol.shape[0]*2-1, vol.shape[1]*2-1, vol.shape[2]*2-1 ] ) if use_gradient: sigmaGradMag = 2.0 gradMag = vigra.filters.gaussianGradientMagnitude(volBig, sigmaGradMag) # get 3D grid graph and edgeMap for grid graph # from gradMag of interpolated vloume or plain volume (depending on use_gradient) gridGraph = vigra.graphs.gridGraph(vol.shape[0:2]) gridGraphEdgeIndicator = [] if use_gradient: gridGraphEdgeIndicator = vigra.graphs.edgeFeaturesFromInterpolatedImage(gridGraph, gradMag) else: gridGraphEdgeIndicator = vigra.graphs.edgeFeaturesFromInterpolatedImage(gridGraph, volBig) # get region adjacency graph from super-pixel labels rag = vigra.graphs.regionAdjacencyGraph(gridGraph, labels) # accumalate edge weights from gradient magintude edgeWeights = rag.accumulateEdgeFeatures(gridGraphEdgeIndicator) # agglomerative clustering beta = 0.5 nodeNumStop = 20 clustering = vigra.graphs.agglomerativeClustering(graph = rag, edgeWeights = edgeWeights, beta = beta, nodeNumStop = nodeNumStop) print clustering
def agglomerative_clustering_2d(img, labels, use_gradient = False): labels = vigra.analysis.labelImage(labels) imgBig = vigra.resize(img, [img.shape[0]*2-1, img.shape[1]*2-1]) if use_gradient: # compute the gradient on interpolated image sigmaGradMag = 2.0 gradMag = vigra.filters.gaussianGradientMagnitude(imgBig, sigmaGradMag) # get 2D grid graph and edgeMap for grid graph # from gradMag of interpolated image or from plain image (depending on use_gradient) gridGraph = vigra.graphs.gridGraph(img.shape[0:2]) gridGraphEdgeIndicator = [] if use_gradient: gridGraphEdgeIndicator = vigra.graphs.edgeFeaturesFromInterpolatedImage(gridGraph, gradMag) else: gridGraphEdgeIndicator = vigra.graphs.edgeFeaturesFromInterpolatedImage(gridGraph, imgBig) # get region adjacency graph from super-pixel labels rag = vigra.graphs.regionAdjacencyGraph(gridGraph, labels) # accumalate edge weights from gradient magintude edgeWeights = rag.accumulateEdgeFeatures(gridGraphEdgeIndicator) # agglomerative clustering beta = 0.5 nodeNumStop = 20 clustering = vigra.graphs.agglomerativeClustering(graph = rag, edgeWeights = edgeWeights, beta = beta, nodeNumStop = nodeNumStop) res = np.zeros( labels.shape ) for c in range(len(clustering)): res[ np.where( labels== (c-1) ) ] = clustering[c] res = vigra.Image(res) res = vigra.analysis.labelImage(res) return res
takeNth = 3
if loadN is None:
loadN = 0
imgs = []
gt = []
for i in range(1, loadN + 1):
hName = "horse%03d.jpg" % (i, )
rgbImg = vigra.impex.readImage(imgPath + hName)
gtImg = vigra.impex.readImage(gtPath +
hName).astype('uint32')[::takeNth, ::takeNth]
gtImg[gtImg < 125] = 0
gtImg[gtImg >= 125] = 1
rgbImg = vigra.resize(rgbImg, [gtImg.shape[0], gtImg.shape[1]])
imgs.append(rgbImg)
gt.append(gtImg)
fUnary = [
vigra.colors.transform_RGB2Lab,
vigra.colors.transform_RGB2Luv,
partial(vigra.filters.gaussianGradientMagnitude, sigma=1.0),
partial(vigra.filters.gaussianGradientMagnitude, sigma=2.0),
]
fBinary = [
vigra.colors.transform_RGB2Lab,
vigra.colors.transform_RGB2Luv,
partial(vigra.filters.gaussianGradientMagnitude, sigma=1.0),
partial(vigra.filters.gaussianGradientMagnitude, sigma=2.0),
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))
slicWeight = 10.0 # SLIC color - spatial weight
beta = 0.5 # node vs edge weight
nodeNumStop = 50 # desired num. nodes in result
# load image and convert to LAB
img = vigra.impex.readImage(filepath)
# get super-pixels with slic on LAB image
imgLab = vigra.colors.transform_RGB2Lab(img)
labels, nseg = vigra.analysis.slicSuperpixels(imgLab, slicWeight,
superpixelDiameter)
labels = vigra.analysis.labelImage(labels)
# compute gradient on interpolated image
imgLabBig = vigra.resize(imgLab, [imgLab.shape[0]*2-1, imgLab.shape[1]*2-1])
gradMag = vigra.filters.gaussianGradientMagnitude(imgLabBig, sigmaGradMag)
# get 2D grid graph and edgeMap for grid graph
# from gradMag of interpolated image
gridGraph = graphs.gridGraph(img.shape[0:2])
gridGraphEdgeIndicator = graphs.edgeFeaturesFromInterpolatedImage(gridGraph,
gradMag)
# get region adjacency graph from super-pixel labels
rag = graphs.regionAdjacencyGraph(gridGraph, labels)
# accumulate edge weights from gradient magnitude
edgeWeights = rag.accumulateEdgeFeatures(gridGraphEdgeIndicator)
# accumulate node features from grid graph node map
# which is just a plain image (with channels)
import skneuro
import vigra
from volumina.api import Viewer
from PyQt4.QtGui import QApplication
import skneuro.blockwise_filters as bf
import skneuro.denoising as dn
import pylab
import h5py
if True:
#data = vigra.impex.readHDF5('/mnt/CLAWS1/tbeier/data/knott1000/knott-block-full2/d-gt.h5','sbfsem')[0:100,0:100,0:100].astype('float32')
#dc = data.copy()
data = vigra.impex.readImage(
'/home/tbeier/Desktop/10683114_980333491982687_1214393854_o.jpg'
).astype(numpy.float32)
data = vigra.resize(data, [data.shape[0] / 2, data.shape[1] / 2])
#data = (data[:,:,0]+data[:,:,1]+data[:,:,2])/(3.0)
dc = data.copy().view(numpy.ndarray)
else:
if False:
fp = h5py.File(
"/mnt/CLAWS1/tbeier/data/knott1000_results/pixel_classification/boundary_prob_r1.h5",
"r")
pmap = fp['exported_data'][0:300, 0:300, 0:300, 1]
fd = h5py.File(
"/mnt/CLAWS1/tbeier/data/knott1000/knott-block-full2/d-gt.h5", "r")
data = fd['sbfsem'][0:300, 0:300, 0:300]
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))
import opengm import vigra import numpy import time import sys fname = "135069.jpg" img = vigra.readImage(fname) img = numpy.sum(img, axis=2) img = vigra.resize(img, [s / 1 for s in img.shape]) noise = numpy.random.random(img.size).reshape(img.shape) * 255 print noise.shape img += noise img -= img.min() img /= img.max() print "shape", img.shape vigra.imshow(img) #vigra.show() threshold = 0.24 labelsNaive = img > threshold vigra.imshow(labelsNaive) #vigra.show() nVar = img.size nLabelsPerVar = 2 variableSpace = numpy.ones(nVar) * nLabelsPerVar gm = opengm.gm(variableSpace) t0 = time.time() # add unaries
gamma = 0.15 # exp(-gamma * edgeIndicator)
edgeThreshold = 2.5 # values higher are considered as edges
scale = 1.0 # how much smoothing
iterations = 10 # how man smoothing iterations
# load image and convert to LAB
img = vigra.impex.readImage(filepath)
# get super-pixels with slic on LAB image
imgLab = vigra.colors.transform_RGB2Lab(img)
labels, nseg = vigra.analysis.slicSuperpixels(imgLab, slicWeight,
superpixelDiameter)
labels = vigra.analysis.labelImage(labels)
# compute gradient on interpolated image
imgLabBig = vigra.resize(imgLab,
[imgLab.shape[0] * 2 - 1, imgLab.shape[1] * 2 - 1])
gradMag = vigra.filters.gaussianGradientMagnitude(imgLabBig, sigmaGradMag)
# get 2D grid graph and edgeMap for grid graph
# from gradMag of interpolated image
gridGraph = graphs.gridGraph(img.shape[0:2])
gridGraphEdgeIndicator = graphs.edgeFeaturesFromInterpolatedImage(
gridGraph, gradMag)
# get region adjacency graph from super-pixel labels
rag = graphs.regionAdjacencyGraph(gridGraph, labels)
# accumulate edge weights from gradient magnitude
edgeIndicator = rag.accumulateEdgeFeatures(gridGraphEdgeIndicator)
# accumulate node features from grid graph node map
def eccentricity( img, distFunc = "exponential", showPathImage = False, percentageOfPaths = 100, imgSaveName = "" ):
## Enlarge image by one pixel on each side
img = img.astype(numpy.uint8)
bigImg = numpy.ones( (img.shape[0]+2, img.shape[1]+2) )
bigImg[1:bigImg.shape[0]-1, 1:bigImg.shape[1]-1] = img
## Find borders in img (replace with graph functions)
borderImg = numpy.zeros(bigImg.shape)
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
## regionImageToCrackEdgeImage ( labelImage )
# ## 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[numpy.where(bigImg==0)]=1.0
## Set the outside to a very high value
distImage[numpy.where(bigImg==1)]=10000.0
imgp = distImage.copy()
## Get image graph and its path finder
gridGraph = vigraph.gridGraph(bigImg.shape[0:2],False)
edgeWeights = vigra.resize(distImage,[distImage.shape[0]*2-1,distImage.shape[1]*2-1],order=0)
edgeWeights = vigra.graphs.edgeFeaturesFromInterpolatedImageCorrected(gridGraph,edgeWeights)
pathFinder = vigraph.ShortestPathPathDijkstra(gridGraph)
## End points for paths (all points on the border)
targets = numpy.where(borderImg==1)
tx,ty = targets
nTargets = len(tx)
## 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):
source = gridGraph.coordinateToNode((int(tx[starts[i]]), int (ty[starts[i]])))
pathFinder.run(edgeWeights, source)
maxPathLength = 0
for j in range(nTargets):
target = gridGraph.coordinateToNode((int(tx[j]), int(ty[j])))
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)
if showPathImage or len(imgSaveName)>1:
val = (imgp.max()+imgp.min())/2
for p in maxPaths:
imgp[p[:,0], p[:,1]] = val
if showPathImage:
plt.figure(distFunc)
plt.imshow(imgp, interpolation='none')
if len(imgSaveName)>1:
scipy.misc.imsave(imgSaveName, imgp)
return maxPathLengths
sps = []
gts = []
pbar = getPbar(len(imgFiles), 'Load Image')
pbar.start()
for i,path in enumerate(imgFiles):
if i>20 :
break
gtPath = gtBasePath + os.path.basename(path)
rgbImg = vigra.impex.readImage(path)
gtImg = vigra.impex.readImage(gtPath).astype('uint32')[::takeNth,::takeNth]
gtImg[gtImg<125] = 0
gtImg[gtImg>=125] = 1
rgbImg = vigra.resize(rgbImg, [gtImg.shape[0],gtImg.shape[1]])
#vigra.imshow(gtImg.astype('float32'))
#vigra.show()
labImg = vigra.colors.transform_RGB2Lab(rgbImg.astype('float32'))
sp,nSeg = vigra.analysis.slicSuperpixels(labImg, intensityScaling=20.0, seedDistance=5)
sp = vigra.analysis.labelImage(sp)-1
#vigra.segShow(rgbImg, sp)
#vigra.show()
gg = vigra.graphs.gridGraph(rgbImg.shape[0:2])
rag = vigra.graphs.regionAdjacencyGraph(gg,sp)
gt,qtq = rag.projectBaseGraphGt(gtImg)
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, 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
import numpy
import skneuro
import vigra
from volumina.api import Viewer
from PyQt4.QtGui import QApplication
import skneuro.blockwise_filters as bf
import skneuro.denoising as dn
import pylab
import h5py
if True:
#data = vigra.impex.readHDF5('/mnt/CLAWS1/tbeier/data/knott1000/knott-block-full2/d-gt.h5','sbfsem')[0:100,0:100,0:100].astype('float32')
#dc = data.copy()
data = vigra.impex.readImage('/home/tbeier/Desktop/10683114_980333491982687_1214393854_o.jpg').astype(numpy.float32)
data = vigra.resize(data, [data.shape[0]/2, data.shape[1]/2])
#data = (data[:,:,0]+data[:,:,1]+data[:,:,2])/(3.0)
dc = data.copy().view(numpy.ndarray)
else :
if False:
fp = h5py.File("/mnt/CLAWS1/tbeier/data/knott1000_results/pixel_classification/boundary_prob_r1.h5","r")
pmap = fp['exported_data'][0:300,0:300,0:300,1]
fd = h5py.File("/mnt/CLAWS1/tbeier/data/knott1000/knott-block-full2/d-gt.h5", "r")
data = fd['sbfsem'][0:300,0:300,0:300]
vigra.impex.writeHDF5(data[0:300, 0:300, 0:300], "sub.h5", "data")
vigra.impex.writeHDF5(pmap[0:300, 0:300, 0:300], "sub.h5", "pmap")
import opengm import vigra import numpy import time import sys fname = "135069.jpg" img = vigra.readImage(fname) img = numpy.sum(img,axis=2) img = vigra.resize(img,[s/1 for s in img.shape]) noise = numpy.random.random(img.size).reshape(img.shape)*255 print noise.shape img += noise img -= img.min() img /= img.max() print "shape", img.shape vigra.imshow(img) #vigra.show() threshold = 0.24 labelsNaive = img > threshold vigra.imshow(labelsNaive) #vigra.show() nVar = img.size nLabelsPerVar = 2 variableSpace = numpy.ones(nVar)*nLabelsPerVar gm = opengm.gm(variableSpace) t0 = time.time()
def getFeatures(rag, img, imgId):
featureNames = ['1-Feature']
############################## Filter ###################################################
filters = []
### Gradient Magnitude ###
imgLab = vigra.colors.transform_RGB2Lab(img)
imgLabBig = vigra.resize(imgLab, [imgLab.shape[0]*2-1, imgLab.shape[1]*2-1]) ##### was ist der Vorteil hiervon? #####
filters.append(vigra.filters.gaussianGradientMagnitude(imgLabBig, 1.))
featureNames.append('GradMag1')
filters.append(vigra.filters.gaussianGradientMagnitude(imgLabBig, 2.))
featureNames.append('GradMag2')
filters.append(vigra.filters.gaussianGradientMagnitude(imgLabBig, 5.))
featureNames.append('GradMag5')
### Hessian of Gaussian Eigenvalues ###
sigmahoG = 2.0
hoG = vigra.filters.hessianOfGaussianEigenvalues(rgb2gray(imgLab), sigmahoG)
filters.append(hoG[:,:,0])
featureNames.append('HessGauss1')
filters.append(hoG[:,:,1])
featureNames.append('HessGauss2')
### Laplacian of Gaussian ###
loG = vigra.filters.laplacianOfGaussian(imgLab)
loG = loG[:,:,0] # es gilt hier: loG[:,:,i] = loG[:,:,j], i,j = 1,2,3
filters.append(loG)
featureNames.append('LoG')
### Canny Filter ###
scaleCanny = 2.0
thresholdCanny = 2.0
markerCanny = 1
canny = vigra.VigraArray(vigra.analysis.cannyEdgeImage(rgb2gray(img), scaleCanny,
thresholdCanny, markerCanny),
dtype=np.float32)
filters.append(canny)
featureNames.append('Canny')
### Structure Tensor Eigenvalues ###
strucTens = vigra.filters.structureTensorEigenvalues(imgLab, 1.5, 3.0)
filters.append(strucTens[:,:,0])
featureNames.append('StrucTensor1')
filters.append(strucTens[:,:,1])
featureNames.append('StrucTensor2')
n4 = vigra.impex.readImage('images/edgeDetectors/n4/' + imgId + '.png')
filters.append(n4)
featureNames.append('N4')
dollar = vigra.impex.readImage('images/edgeDetectors/dollar/' + imgId + '.png')
filters.append(dollar)
featureNames.append('Dollar')
##########################################################################################
############# Edge Weights Calculation #############
edgeWeightsList = []
featureSpace = np.ones((rag.edgeNum, 1))
for i in range(len(filters)):
gridGraphEdgeIndicator = graphs.edgeFeaturesFromImage(rag.baseGraph, filters[i])
edgeWeights = rag.accumulateEdgeFeatures(gridGraphEdgeIndicator)
#edgeWeights /= edgeWeights.max()
edgeWeights = edgeWeights.reshape(edgeWeights.shape[0], 1)
featureSpace = np.concatenate((featureSpace, edgeWeights), axis=1)
pos = np.where(np.array(featureNames)=='N4')[0][0]
edgeWeights = featureSpace[:,pos] * rag.edgeLengths()
edgeWeights /= edgeWeights.max()
edgeWeights = edgeWeights.reshape(edgeWeights.shape[0], 1)
featureSpace = np.concatenate((featureSpace, edgeWeights), axis=1)
featureNames.append('N4_EdgeLengthWeighted')
pos = np.where(np.array(featureNames)=='Dollar')[0][0]
edgeWeights = featureSpace[:,pos] * rag.edgeLengths()
edgeWeights /= edgeWeights.max()
edgeWeights = edgeWeights.reshape(edgeWeights.shape[0], 1)
featureSpace = np.concatenate((featureSpace, edgeWeights), axis=1)
featureNames.append('Dollar_EdgeLengthWeighted')
rgbDummy = np.array(n4)
rgbDummy = rgbDummy.reshape(rgbDummy.shape[0], rgbDummy.shape[1], 1)
edgeWeights = getEdgeWeightsFromNodesAround3(rag, rgbDummy, 1, variance=True, mean=True, meanRatio=True, medianRatio=True, skewness=True, kurtosis=True)
featureSpace = np.concatenate((featureSpace, edgeWeights), axis=1)
featureNames.extend(('N4_Variance_1', 'N4_Mean_1', 'N4_MeanRatio_1', 'N4_MedianRatio_1', 'N4_Skewness_1', 'N4_Kurtosis_1'))
edgeWeights = getEdgeWeightsFromNodesAround3(rag, rgbDummy, 3, variance=True, mean=True, meanRatio=True, medianRatio=True, skewness=True, kurtosis=True)
featureSpace = np.concatenate((featureSpace, edgeWeights), axis=1)
featureNames.extend(('N4_Variance_3', 'N4_Mean_3', 'N4_MeanRatio_3', 'N4_MedianRatio_3', 'N4_Skewness_3', 'N4_Kurtosis_3'))
rgbDummy = np.array(dollar)
rgbDummy = rgbDummy.reshape(rgbDummy.shape[0], rgbDummy.shape[1], 1)
edgeWeights = getEdgeWeightsFromNodesAround3(rag, rgbDummy, 1, variance=True, mean=True, meanRatio=True, medianRatio=True, skewness=True, kurtosis=True)
featureSpace = np.concatenate((featureSpace, edgeWeights), axis=1)
featureNames.extend(('Dollar_Variance_1', 'Dollar_Mean_1', 'Dollar_MeanRatio_1', 'Dollar_MedianRatio_1', 'Dollar_Skewness_1', 'Dollar_Kurtosis_1'))
edgeWeights = getEdgeWeightsFromNodesAround3(rag, rgbDummy, 3, variance=True, mean=True, meanRatio=True, medianRatio=True, skewness=True, kurtosis=True)
featureSpace = np.concatenate((featureSpace, edgeWeights), axis=1)
featureNames.extend(('Dollar_Variance_3', 'Dollar_Mean_3', 'Dollar_MeanRatio_3', 'Dollar_MedianRatio_3', 'Dollar_Skewness_3', 'Dollar_Kurtosis_3'))
edgeWeights = getEdgeWeightsFromNodesAround3(rag, imgLab, 1, variance=True, mean=True, meanRatio=True, medianRatio=True, skewness=True, kurtosis=True)
featureSpace = np.concatenate((featureSpace, edgeWeights), axis=1)
featureNames.extend(('Variance_1_R', 'Variance_1_G', 'Variance_1_B',
'Mean_1_R', 'Mean_1_G', 'Mean_1_B',
'MeanRatio_1_R', 'MeanRatio_1_G', 'MeanRatio_1_B',
'MedianRatio_1_R', 'MedianRatio_1_G', 'MedianRatio_1_B',
'Skewness_1_R', 'Skewness_1_G', 'Skewness_1_B',
'Kurtosis_1_R', 'Kurtosis_1_G', 'Kurtosis_1_B'))
edgeWeights = getEdgeWeightsFromNodesAround3(rag, imgLab, 3, variance=True, mean=True, meanRatio=True, medianRatio=True, skewness=True, kurtosis=True)
featureSpace = np.concatenate((featureSpace, edgeWeights), axis=1)
featureNames.extend(('Variance_3_R', 'Variance_3_G', 'Variance_3_B',
'Mean_3_R', 'Mean_3_G', 'Mean_3_B',
'MeanRatio_3_R', 'MeanRatio_3_G', 'MeanRatio_3_B',
'MedianRatio_3_R', 'MedianRatio_3_G', 'MedianRatio_3_B',
'Skewness_3_R', 'Skewness_3_G', 'Skewness_3_B',
'Kurtosis_3_R', 'Kurtosis_3_G', 'Kurtosis_3_B'))
featureSpace = featureSpace.astype(np.float64)
### Normalize to [-1, 1]
'''for edgeWeights in featureSpace.transpose():
if (edgeWeights.min() < 0):
edgeWeights -= edgeWeights.min()
maximum = edgeWeights.max()
edgeWeights *= 2
edgeWeights /= maximum
edgeWeights -= 1
'''
### Normalize to [0, 1]
for edgeWeights in featureSpace.transpose():
if (edgeWeights.min() < 0):
edgeWeights -= edgeWeights.min()
edgeWeights /= edgeWeights.max()
return featureSpace, featureNames
