def segmentGC(pred, beta):
'''
This function implements a call to the standard Graph Cut segmentation
in the OpenGM library (http://hci.iwr.uni-heidelberg.de/opengm2/).
Potts model is assumed, with a 4-neighborhood for 2D data and a 6-neighborhood
for 3D data to define the pairwise terms.
Parameters:
-- pred - the unary terms, used directly (no Log applied, do it outside if needed)
This input is assumed to be 3D!
-- beta - the weight of the pairwise potentials, usually called lambda
Return:
-- binary volume, as produced by OpenGM
'''
nz, ny, nx = pred.shape
numVar = pred.size
numLabels = 2
numberOfStates = np.ones(numVar, dtype=opengm.index_type) * numLabels
gm = opengm.graphicalModel(numberOfStates, operator='adder')
# Adding unary function and factors
functions = np.zeros((numVar, 2))
predflat = pred.reshape((numVar, 1))
if (predflat.dtype == np.uint8):
predflat = predflat.astype(np.float32)
predflat = predflat / 256.
functions[:, 0] = predflat[:, 0]
functions[:, 1] = 1 - predflat[:, 0]
unary_fids = gm.addFunctions(functions)
gm.addFactors(unary_fids, np.arange(0, numVar))
# add one binary function (potts fuction)
potts = opengm.PottsFunction([2, 2], 0.0, beta)
binary_fid = gm.addFunction(potts)
# add binary factors
indices = np.arange(numVar, dtype=np.uint32).reshape((nz, ny, nx))
z_edges = np.concatenate([indices[:nz - 1, :, :], indices[1:, :, :]]
).reshape((2, (nz - 1) * ny * nx)).transpose()
y_edges = np.concatenate([indices[:, :ny - 1, :], indices[:, 1:, :]]
).reshape((2, nz * (ny - 1) * nx)).transpose()
x_edges = np.concatenate([indices[:, :, :nx - 1], indices[:, :, 1:]]
).reshape((2, nz * ny * (nx - 1))).transpose()
gm.addFactors(binary_fid, z_edges)
gm.addFactors(binary_fid, y_edges)
gm.addFactors(binary_fid, x_edges)
grcut = opengm.inference.GraphCut(gm)
grcut.infer()
argmin = grcut.arg()
res = argmin.reshape((nz, ny, nx))
if hasattr(pred, 'axistags'):
res = vigra.taggedView(res, pred.axistags)
return res
def segment_adjacency_graph(segment_unaries,
segment_map,
segment_regularizer=None):
"""
Creates a region adjacency graph. Each segment has a variable and adjacent segments are linked by edges
"""
_check_valid_segment_map(segment_map)
_check_compatible_segment_map_unaries(segment_map, segment_unaries)
n_vars = segment_unaries.shape[0]
n_labels = segment_unaries.shape[-1]
edges = segment_map_to_rag_edges(segment_map)
n_edges = edges.shape[0]
# allocate space for the model and all its variables
gm = opengm.graphicalModel([n_labels] * n_vars)
gm.reserveFunctions(
n_vars + n_edges,
'explicit') # the unary functions plus the 3 types of regularizer
gm.reserveFactors(n_vars + n_edges)
gm = add_layer(gm, segment_unaries, edges, segment_regularizer)
gm.finalize()
return gm
def test_constructor_list(self):
numberOfStates=[2,3,4]
gm=opengm.graphicalModel(numberOfStates,operator="adder")
assert(gm.numberOfVariables==3)
assert(gm.numberOfLabels(0)==2)
assert(gm.numberOfLabels(1)==3)
assert(gm.numberOfLabels(2)==4)
def _constructOpenGMModel(self):
openGMModel = opengm.graphicalModel(self.cardinalities, operator="adder")
for factor in self.factors:
members = tuple(map(int, list(factor.members)))
func = openGMModel.addFunction(factor.values)
openGMModel.addFactor(func, members)
return openGMModel
def test_constructor_numpy(self):
numberOfStates=numpy.ones(3,dtype=numpy.uint64)
numberOfStates[0]=2
numberOfStates[1]=3
numberOfStates[2]=4
gm=opengm.graphicalModel(numberOfStates)
assert(gm.numberOfVariables==3)
assert(gm.numberOfLabels(0)==2)
assert(gm.numberOfLabels(1)==3)
assert(gm.numberOfLabels(2)==4)
def fit(self, mapc, th, enc, lambda0):
'''
create a model for the decision fo the word
'''
import opengm
N = len(mapc)
K = self.K
numLabel = [K + 1] * N
self.gm = opengm.graphicalModel(numLabel)
i0 = np.argsort(mapc, axis=0)[:, 0]
self.indice = i0
v = []
unary = []
for i in i0:
p = mapc[i][1]
Eu = []
for k in range(self.K):
Eu.append(1 - p[k])
Eu.append(mapc[i][2])
#Eu.append(max(p))
v.append([mapc[i][0], Eu, mapc[i][3]])
unary.append(Eu)
self.vertices = v
unary = np.array(unary)
assert (unary.shape == (N, K + 1))
fid = self.gm.addFunctions(unary)
vis = np.arange(0, N, dtype=np.uint64)
self.gm.addFactors(fid, vis)
self.edges = []
self.overlap = np.zeros((N, N))
for i, v1 in enumerate(self.vertices):
for j, v2 in enumerate(self.vertices[i + 1:]):
dx = abs(v2[0][0] - v1[0][0])
dy = abs(v2[0][1] - v1[0][1])
w = min(v1[2][0], v2[2][0])
h = min(v1[2][1], v2[2][0])
if dx < th * w and dy < th * h:
intersec = (w - min(w, abs(v2[0][0] - v1[0][0])))
intersec *= (h - min(h, abs(v2[0][1] - v1[0][1])))
intersec *= 100. / (w * h)
v0 = lambda0 * np.exp(-(100 - intersec)**2)
BinaryE = np.ones((K + 1, K + 1)) * v0
BinaryE += self.prior
BinaryE[K, K] = 0
fid = self.gm.addFunction(BinaryE)
self.edges.append((i, j + i + 1, intersec))
self.gm.addFactor(fid, [i, j + i + 1])
def potts_lattice_graph(pixel_unaries, beta):
n_vars = pixel_unaries.shape[0] * pixel_unaries.shape[1]
n_labels = pixel_unaries.shape[-1]
n_edges = calc_n_pixel_edges(pixel_unaries.shape)
gm = opengm.graphicalModel([n_labels] * n_vars)
gm.reserveFunctions(
n_vars + 1,
'explicit') # the unary functions plus the 1 type of regularizer
gm.reserveFactors(n_vars + n_edges)
gm = add_potts_lattice_layer(gm, pixel_unaries, beta)
gm.finalize()
return gm
def makeModel(img, gt):
shape = gt.shape[0:2]
numVar = shape[0] * shape[1]
# make model
gm = graphicalModel(numpy.ones(numVar) * numberOfLabels)
# compute features
unaryFeat = getFeat(fUnary, img)
unaryFeat = numpy.nan_to_num(
numpy.concatenate(unaryFeat, axis=2).view(numpy.ndarray))
unaryFeat = unaryFeat.reshape([numVar, -1])
# add unaries
lUnaries = lUnaryFunctions(
weights=weights,
numberOfLabels=numberOfLabels,
features=unaryFeat,
weightIds=uWeightIds,
featurePolicy=FeaturePolicy.sharedBetweenLabels,
makeFirstEntryConst=numberOfLabels == 2,
addConstFeature=addConstFeature)
fids = gm.addFunctions(lUnaries)
gm.addFactors(fids, numpy.arange(numVar))
if len(fBinary) > 0:
binaryFeat = getFeat(fBinary, img)
binaryFeat = numpy.nan_to_num(
numpy.concatenate(binaryFeat, axis=2).view(numpy.ndarray))
binaryFeat = binaryFeat.reshape([numVar, -1])
# add second order
vis2Order = gridVis(shape[0:2], True)
fU = binaryFeat[vis2Order[:, 0], :]
fV = binaryFeat[vis2Order[:, 1], :]
fB = (fU + fV / 2.0)
lp = lPottsFunctions(weights=weights,
numberOfLabels=numberOfLabels,
features=fB,
weightIds=bWeightIds,
addConstFeature=addConstFeature)
gm.addFactors(gm.addFunctions(lp), vis2Order)
return gm
def buildGM(img,rag,dataImage,numLabels,boundaryPixels,regionPixels,beta,sigma,verbose=False):
print "get region clustering"
regionFeatures=numpy.ones([rag.numberOfRegions(),3],dtype=numpy.float64)
print "lab type in gm" ,type(img)
print "lab type in gm shape" ,img.shape
npimg=numpy.ones(img.shape)
npimg[:,:,:]=img[:,:,:]
print "npimg type in gm shape" ,npimg.shape
for r in range(rag.numberOfRegions()):
for c in range(3):
regionFeatures[r,c]=numpy.mean(npimg[regionPixels[r][:,0],regionPixels[r][:,1]][c])
print "do clustering"
code,dists=doClustering(regionFeatures,k=numLabels,steps=100)
dists=(dists-dists.min())/(dists.max()-dists.min())
if verbose==True : print "get boundary evidence"
boundaryEvidence=numpy.ones(rag.numberOfBoundaries(),dtype=numpy.float64)
be=numpy.ones([rag.numberOfBoundaries(),2],dtype=numpy.float64)
energy=numpy.ones([rag.numberOfBoundaries(),2],dtype=numpy.float64)
for b in range(rag.numberOfBoundaries()):
boundaryEvidence[b]=numpy.mean(dataImage[boundaryPixels[b][:,0],boundaryPixels[b][:,1]])
r=rag.adjacentRegions(b)
boundaryEvidence=(boundaryEvidence-boundaryEvidence.min())/(boundaryEvidence.max()-boundaryEvidence.min())*(1.0-2.0*epsilon) + epsilon
be[:,1]=numpy.exp(-1.0*boundaryEvidence[:]*sigma)
be[:,0]=1.0-be[:,1]
energy [:,0]= (-1.0*numpy.log( (1)*(1.0-beta) ) ) +be[:,0]
energy [:,1]= (-1.0*numpy.log( (1)*(beta) ) ) +be[:,1]
if verbose==True : print "build gm"
gm=opengm.graphicalModel(numpy.ones(rag.numberOfRegions(),dtype=numpy.uint64)*numLabels)
shapePotts=[numLabels,numLabels]
print "add unaries"
for r in range(rag.numberOfRegions()):
f=dists[r,:]*gamma
vis=[r]
gm.addFactor(gm.addFunction(f),vis)
print "add 2.order"
for b in range(rag.numberOfBoundaries()):
f=opengm.pottsFunction(shapePotts, energy[b,0] ,energy[b,1])
vis=rag.adjacentRegions(b)
gm.addFactor(gm.addFunction(f),vis)
return gm
def makeModel(img,gt):
shape = gt.shape[0:2]
numVar = shape[0] * shape[1]
# make model
gm = graphicalModel(numpy.ones(numVar)*numberOfLabels)
# compute features
unaryFeat = getFeat(fUnary, img)
unaryFeat = numpy.nan_to_num(numpy.concatenate(unaryFeat,axis=2).view(numpy.ndarray))
unaryFeat = unaryFeat.reshape([numVar,-1])
# add unaries
lUnaries = lUnaryFunctions(weights =weights,numberOfLabels = numberOfLabels,
features=unaryFeat, weightIds = uWeightIds,
featurePolicy= FeaturePolicy.sharedBetweenLabels,
makeFirstEntryConst=numberOfLabels==2, addConstFeature=addConstFeature)
fids = gm.addFunctions(lUnaries)
gm.addFactors(fids, numpy.arange(numVar))
if len(fBinary)>0:
binaryFeat = getFeat(fBinary, img)
binaryFeat = numpy.nan_to_num(numpy.concatenate(binaryFeat,axis=2).view(numpy.ndarray))
binaryFeat = binaryFeat.reshape([numVar,-1])
# add second order
vis2Order=gridVis(shape[0:2],True)
fU = binaryFeat[vis2Order[:,0],:]
fV = binaryFeat[vis2Order[:,1],:]
fB = (fU + fV / 2.0)
lp = lPottsFunctions(weights=weights, numberOfLabels=numberOfLabels,
features=fB, weightIds=bWeightIds,
addConstFeature=addConstFeature)
gm.addFactors(gm.addFunctions(lp), vis2Order)
return gm
def getGraphicalModel(words):
#print 1
noNodes = sum(map(lambda x : 1 if x is not None else 0, words))
word_factors_list = []
no_of_states = []
for word in words:
if word is not None:
factors = get_unary_factors(word)
word_factors_list.append(factors)
no_of_states.append(len(factors.keys()))
#print 2
gm = opengm.graphicalModel(no_of_states)
# Add unary factor nodes for each word factor.
for i, word_factors in enumerate(word_factors_list):
factor_handle = gm.addFunction(np.array(word_factors.values()))
gm.addFactor(factor_handle, i)
#print 3
# TODO: Assuming that relation exists only left to right
for i in range(len(word_factors_list) - 1):
# TODO: Just getting the similarity score.
words_i = word_factors_list[i].keys()
words_i1 = word_factors_list[i + 1].keys()
binary_func = []
for word_a in words_i:
word_a_values = []
for word_b in words_i1:
word_a_values.append(cos_sim.get_sim(final_model.get_row(word_a), final_model.get_row(word_b)))
binary_func.append(word_a_values)
factor_handle = gm.addFunction(np.array(binary_func))
gm.addFactor(factor_handle, [i, i+1])
#print 4
#opengm.visualizeGm(gm)
inf = opengm.inference.BeliefPropagation(gm,parameter=opengm.InfParam(damping=0.05))
inf.infer()
#print 5
return inf
def makeModel(img,sp,gt):
assert sp.min() == 0
shape = img.shape[0:2]
gg = vigra.graphs.gridGraph(shape)
rag = vigra.graphs.regionAdjacencyGraph(gg,sp)
numVar = rag.nodeNum
assert rag.nodeNum == rag.maxNodeId +1
# make model
gm = graphicalModel(numpy.ones(numVar)*numberOfLabels)
assert gm.numberOfVariables == rag.nodeNum
assert gm.numberOfVariables == rag.maxNodeId +1
# compute features
unaryFeat = getFeat(fUnary, img)
unaryFeat = numpy.nan_to_num(numpy.concatenate(unaryFeat,axis=2).view(numpy.ndarray)).astype('float32')
unaryFeat = vigra.taggedView(unaryFeat,'xyc')
accList = []
#for c in range(unaryFeat.shape[-1]):
# cUnaryFeat = unaryFeat[:,:,c]
# cAccFeat = rag.accumulateNodeFeatures(cUnaryFeat)[:,None]
# accList.append(cAccFeat)
#accUnaryFeat = numpy.concatenate(accList,axis=1)
accUnaryFeat = rag.accumulateNodeFeatures(unaryFeat)#[:,None]
#print accUnaryFeat.shape
#accUnaryFeat = rag.accumulateNodeFeatures(unaryFeat[:,:,:])
#accUnaryFeat = vigra.taggedView(accUnaryFeat,'nc')
#accUnaryFeat = accUnaryFeat[1:accUnaryFeat.shape[0],:]
#binaryFeat = binaryFeat.reshape([numVar,-1])
# add unaries
lUnaries = lUnaryFunctions(weights =weights,numberOfLabels = numberOfLabels,
features=accUnaryFeat, weightIds = uWeightIds,
featurePolicy= FeaturePolicy.sharedBetweenLabels,
makeFirstEntryConst=numberOfLabels==2, addConstFeature=addConstFeature)
fids = gm.addFunctions(lUnaries)
gm.addFactors(fids, numpy.arange(numVar))
if len(fBinary)>0:
binaryFeat = getFeat(fBinary, img, topoShape=False)
binaryFeat = numpy.nan_to_num(numpy.concatenate(binaryFeat,axis=2).view(numpy.ndarray)).astype('float32')
edgeFeat = vigra.graphs.edgeFeaturesFromImage(gg, binaryFeat)
accBinaryFeat = rag.accumulateEdgeFeatures(edgeFeat)
uvIds = numpy.sort(rag.uvIds(), axis=1)
assert uvIds.min()==0
assert uvIds.max()==gm.numberOfVariables-1
lp = lPottsFunctions(weights=weights, numberOfLabels=numberOfLabels,
features=accBinaryFeat, weightIds=bWeightIds,
addConstFeature=addConstFeature)
fids = gm.addFunctions(lp)
gm.addFactors(fids, uvIds)
return gm
def makeModel(img, sp, gt):
assert sp.min() == 0
shape = img.shape[0:2]
gg = vigra.graphs.gridGraph(shape)
rag = vigra.graphs.regionAdjacencyGraph(gg, sp)
numVar = rag.nodeNum
assert rag.nodeNum == rag.maxNodeId + 1
# make model
gm = graphicalModel(numpy.ones(numVar) * numberOfLabels)
assert gm.numberOfVariables == rag.nodeNum
assert gm.numberOfVariables == rag.maxNodeId + 1
# compute features
unaryFeat = getFeat(fUnary, img)
unaryFeat = numpy.nan_to_num(
numpy.concatenate(unaryFeat,
axis=2).view(numpy.ndarray)).astype('float32')
unaryFeat = vigra.taggedView(unaryFeat, 'xyc')
accList = []
#for c in range(unaryFeat.shape[-1]):
# cUnaryFeat = unaryFeat[:,:,c]
# cAccFeat = rag.accumulateNodeFeatures(cUnaryFeat)[:,None]
# accList.append(cAccFeat)
#accUnaryFeat = numpy.concatenate(accList,axis=1)
accUnaryFeat = rag.accumulateNodeFeatures(unaryFeat) #[:,None]
#print accUnaryFeat.shape
#accUnaryFeat = rag.accumulateNodeFeatures(unaryFeat[:,:,:])
#accUnaryFeat = vigra.taggedView(accUnaryFeat,'nc')
#accUnaryFeat = accUnaryFeat[1:accUnaryFeat.shape[0],:]
#binaryFeat = binaryFeat.reshape([numVar,-1])
# add unaries
lUnaries = lUnaryFunctions(
weights=weights,
numberOfLabels=numberOfLabels,
features=accUnaryFeat,
weightIds=uWeightIds,
featurePolicy=FeaturePolicy.sharedBetweenLabels,
makeFirstEntryConst=numberOfLabels == 2,
addConstFeature=addConstFeature)
fids = gm.addFunctions(lUnaries)
gm.addFactors(fids, numpy.arange(numVar))
if len(fBinary) > 0:
binaryFeat = getFeat(fBinary, img, topoShape=False)
binaryFeat = numpy.nan_to_num(
numpy.concatenate(binaryFeat, axis=2).view(
numpy.ndarray)).astype('float32')
edgeFeat = vigra.graphs.edgeFeaturesFromImage(gg, binaryFeat)
accBinaryFeat = rag.accumulateEdgeFeatures(edgeFeat)
uvIds = numpy.sort(rag.uvIds(), axis=1)
assert uvIds.min() == 0
assert uvIds.max() == gm.numberOfVariables - 1
lp = lPottsFunctions(weights=weights,
numberOfLabels=numberOfLabels,
features=accBinaryFeat,
weightIds=bWeightIds,
addConstFeature=addConstFeature)
fids = gm.addFunctions(lp)
gm.addFactors(fids, uvIds)
return gm
import numpy
import opengm
img = numpy.random.rand(4, 4)
dimx = img.shape[0]
dimy = img.shape[1]
numVar = dimx * dimy
numLabels = 2
beta = 0.3
numberOfStates = numpy.ones(numVar, dtype=opengm.index_type) * numLabels
gm = opengm.graphicalModel(numberOfStates, operator='adder')
#Adding unary function and factors
for y in range(dimy):
for x in range(dimx):
f = numpy.ones(2, dtype=numpy.float32)
f[0] = img[x, y]
f[1] = 1.0 - img[x, y]
fid = gm.addFunction(f)
gm.addFactor(fid, (x * dimy + y, ))
#Adding binary function and factors"
vis = numpy.ones(5, dtype=opengm.index_type)
#add one binary function (potts fuction)
f = numpy.ones(pow(numLabels, 2), dtype=numpy.float32).reshape(
numLabels, numLabels) * beta
for l in range(numLabels):
f[l, l] = 0
fid = gm.addFunction(f)
dimx=100
dimy=100
numVar=dimx*dimy
numLabels=20
beta=0.8
# ---------------------------------
# reserve factors and functions can
# save a lot of time
# ---------------------------------
t=time.time()
numberOfStates=numpy.ones(numVar,dtype=opengm.index_type)*numLabels
gm=opengm.graphicalModel(numberOfStates,operator='adder')
#Adding unary function and factors
for y in range(dimy):
for x in range(dimx):
f1=numpy.random.random(numLabels).astype(numpy.float32)
fid=gm.addFunction( f1)
gm.addFactor(fid,(x+dimx*y,))
#Adding binary function and factors"
vis=numpy.ones(5,dtype=opengm.index_type)
#add one binary function (potts fuction)
f=numpy.ones(pow(numLabels,2)).reshape(numLabels,numLabels)*beta
for l in range(numLabels):
f[l,l]=0
fid=gm.addFunction(f)
#add binary factors
for y in range(dimy):
def segment_overlap_graph(pixel_unaries,
segment_map,
segment_unaries,
pixel_regularizer=None,
segment_regularizer=None,
inter_layer_regularizer=None):
"""
greates a graphical model comprised of two layers.
- The first layer is a pixel lattice
- The second layer is a region adjacency graph over segments
- Connections exist between pixels where they are overlapped by a segment
Parameters:
- pixel_unaries - a 3D array of shape (width, height, n_labels).
- segment_map - a 2d array of shape (width, height). Each element >= 0 is a segment id that maps the corresponding pixel to that id. -1 represents no segment and no corresponding node will be added
- segment_unaries - a 2d arry of shape (n_segments, n_labels)
- pixel_regularizer (optional) - a pairwise opengm function e.g. opengm.PottsFunction([2,2],0.0,beta) or list of opengm functions of length n_pixels
- segment_regularizer (optional) - a pairwise opengm function, same requirements as pixel_regularizer
- inter_layer_regularizer (optional) - a pairwise opengm function, same requirements as pixel_regularizer
"""
_check_valid_segment_map(segment_map)
_check_compatible_segment_map_unaries(segment_map, segment_unaries)
# calculate how many variables and factors will be required
n_pixels = pixel_unaries.shape[0] * pixel_unaries.shape[1]
n_segments = segment_unaries.shape[0]
n_variables = n_pixels + n_segments
n_labels_pixels = pixel_unaries.shape[-1]
n_labels_segments = segment_unaries.shape[-1]
# calculate the region adjacency graph for the segments
rag_edges = segment_map_to_rag_edges(segment_map)
rag_edges += n_pixels #segment indices start at n_pixels remember!
n_pixel_edges = (pixel_unaries.shape[0] - 1) * pixel_unaries.shape[1] + (
pixel_unaries.shape[1] - 1) * pixel_unaries.shape[0]
n_segment_edges = rag_edges.shape[0] #check this is right
n_inter_edges = n_pixels
n_edges = n_pixel_edges + n_segment_edges + n_inter_edges
# allocate space for the model and all its variables
gm = opengm.graphicalModel([n_labels_pixels] * n_pixels +
[n_labels_segments] * n_segments)
gm.reserveFunctions(
n_variables + 3,
'explicit') # the unary functions plus the 3 types of regularizer
gm.reserveFactors(n_variables + n_edges)
# add unary functions and factors
fids = gm.addFunctions(pixel_unaries.reshape([n_pixels, n_labels_pixels]))
gm.addFactors(fids, np.arange(n_pixels), finalize=False)
fids = gm.addFunctions(segment_unaries)
gm.addFactors(fids, n_pixels + np.arange(n_segments), finalize=False)
## add pairwise functions
# pixel lattice
if pixel_regularizer is not None:
fid = gm.addFunction(pixel_regularizer)
vis = opengm.secondOrderGridVis(pixel_unaries.shape[0],
pixel_unaries.shape[1])
gm.addFactors(fid, vis, finalize=False)
# segment rag
if segment_regularizer is not None:
fid = gm.addFunction(segment_regularizer)
gm.addFactors(fid, np.sort(rag_edges, axis=1), finalize=False)
# inter-layer
if inter_layer_regularizer is not None:
fid = gm.addFunction(inter_layer_regularizer)
vis = np.dstack([
np.arange(n_pixels).reshape(pixel_unaries.shape[:2]), segment_map
]).reshape((-1, 2))
vis = _remove_rows_with_negative(vis)
vis[:, 1] += n_pixels
gm.addFactors(fid, vis, finalize=False)
gm.finalize()
return gm
def build_factor_graph(G,
nodes,
edges,
n_annots,
n_names,
lookup_annot_idx,
use_unaries=True,
edge_probs=None,
operator='multiplier'):
node_state_card = np.ones(n_annots, dtype=index_type) * n_names
numberOfStates = node_state_card
# n_edges = len(edges)
# n_edge_states = 2
# edge_state_card = np.ones(n_edges, dtype=index_type) * n_edge_states
# numberOfStates = np.hstack([node_state_card, edge_state_card])
# gm = opengm.graphicalModel(numberOfStates, operator='adder')
gm = opengm.graphicalModel(numberOfStates, operator=operator)
annot_idxs = list(range(n_annots))
# edge_idxs = list(range(n_annots, n_annots + n_edges))
import scipy.special
if use_unaries:
unaries = np.ones((n_annots, n_names)) / n_names
# unaries[0][0] = 1
# unaries[0][1:] = 0
for annot_idx in annot_idxs:
fid = gm.addFunction(unaries[annot_idx])
gm.addFactor(fid, annot_idx)
# Add Potts function for each edge
pairwise_factor_idxs = []
for count, (aid1, aid2) in enumerate(edges, start=len(list(gm.factors()))):
varx1, varx2 = ut.take(lookup_annot_idx, [aid1, aid2])
var_indicies = np.array([varx1, varx2])
if edge_probs is None:
p_same, p_diff = get_edge_id_probs(G, aid1, aid2, n_names)
else:
p_same, p_diff = edge_probs[count]
use_logit = operator == 'adder'
if use_logit:
eps = 1E-9
p_same = np.clip(p_same, eps, 1.0 - eps)
same_weight = scipy.special.logit(p_same)
# valueEqual = -same_weight
valueEqual = 0
valueNotEqual = same_weight
if not np.isfinite(valueNotEqual):
"""
python -m plottool.draw_func2 --exec-plot_func --show --range=-1,1 --func=scipy.special.logit
"""
print('valueNotEqual = %r' % (valueNotEqual, ))
print('p_same = %r' % (p_same, ))
raise ValueError('valueNotEqual')
else:
valueEqual = p_same
valueNotEqual = p_diff
p_same, p_diff = get_edge_id_probs(G, aid1, aid2, n_names)
pairwise_factor_idxs.append(count)
potts_func = opengm.PottsFunction((n_names, n_names),
valueEqual=valueEqual,
valueNotEqual=valueNotEqual)
potts_func_id = gm.addFunction(potts_func)
gm.addFactor(potts_func_id, var_indicies)
gm.pairwise_factor_idxs = pairwise_factor_idxs
gm.G = G
return gm
def infer(self):
logging.info("Running Inference")
###########################
# define binary variables #
###########################
# two binary variables:
#var 0 (stage S1): dimension is 2
#var 1 (event E1): dimension is 2
variables = [2, 2]
################################
# # construct the Factor Graph #
################################
gm = opengm.graphicalModel(variables, operator='multiplier')
########################################################################################
# TODO: Fill in values in g_func, and g_var, according to the provided tables #
########################################################################################
f_func = np.array([0.1, 0.9]) # priors f
f_var = [0] # f(S1) using S1 as variable 0
g_func = np.array([[0, 0.2], [0, 0.5]]) # factor function g
g_var = [0, 1] # g(S1, S2)
############
# END TODO #
############
##################################
# connect factor functions to FG #
##################################
gm.addFactor(gm.addFunction(f_func), f_var) # add prior to event
gm.addFactor(gm.addFunction(g_func),
g_var) # add factor function to event (E1) and stage (S1)
##################################
# # belief propagation inference #
##################################
inf = opengm.inference.BeliefPropagation(gm, accumulator='maximizer')
inf.infer()
##############
# get argmax #
##############
arg = inf.arg()
print("Inference result: ", arg)
##############################
# get marginal probabilities #
##############################
marginals = inf.marginals(range(len(variables)))
#############################################################
# # get marginal of the state variable (variable index = 0) #
#############################################################
vars = [0]
max_marg = marginals[0]
max_val = 0
for i in vars:
marginals_xi = marginals[i]
if marginals_xi > max_marg:
max_val = i
max_marg = marginals_xi
marginals_xi /= np.sum(marginals_xi)
print("x_{} marginal: {}".format(i, marginals_xi))
pass
def classifyTissue(heatingParam): numLabels = 3 dxdy, noParam = heatingParam.shape heatingParam = np.reshape(heatingParam, (640, 480, noParam)) shape = heatingParam.shape dimx, dimy, noParam = shape[0], shape[1], shape[2] numVar = dimx * dimy dimx, dimy = shape[0], shape[1] numberOfStates = np.ones(numVar, dtype=opengm.index_type) * numLabels gm = opengm.graphicalModel(numberOfStates) # create unary potentials for CRF f = np.ones(numLabels, dtype=np.float32) for y in range(dimy): for x in range(dimx): f = np.ones(numLabels, dtype=np.float32) beta = abs(heatingParam[x, y, 2] - heatingParam[x, y, 3]) f[0] = abs(heatingParam[x, y, 2]) # * (1/beta) f[1] = beta f[2] = abs(1 + heatingParam[x, y, 2]) # * (1/beta) fid = gm.addFunction(f) gm.addFactor(fid, (x * dimy + y,)) # create pairwise potentials for y in range(dimy): for x in range(dimx): f_pw = np.ones(numLabels * numLabels, dtype=np.float32).reshape(numLabels, numLabels) if (x+1 < dimx): beta_i = abs(heatingParam[x, y, 2] - heatingParam[x, y, 3]) beta_j = abs(heatingParam[x+1, y, 2] - heatingParam[x+1, y, 3]) scaling_f = 1 / abs(beta_i - beta_j) f_pw[0, 0] = 0 f_pw[1, 1] = 0 f_pw[2, 2] = 0 f_pw[0, 1] = scaling_f f_pw[0, 2] = scaling_f * 2 f_pw[1, 0] = scaling_f f_pw[1, 2] = scaling_f f_pw[2, 0] = f_pw[0, 2] f_pw[2, 1] = f_pw[1, 2] fid = gm.addFunction(f_pw) gm.addFactor(fid, np.array([x * dimy + y, (x + 1) * dimy + y], dtype=opengm.index_type)) if (y+1 < dimy): beta_i = abs(heatingParam[x, y, 2] - heatingParam[x, y, 3]) beta_j = abs(heatingParam[x, y+1, 2] - heatingParam[x, y+1, 3]) scaling_f = 1 / abs(beta_i - beta_j) f_pw[0, 0] = 0 f_pw[1, 1] = 0 f_pw[2, 2] = 0 f_pw[0, 1] = scaling_f f_pw[0, 2] = scaling_f * 2 f_pw[1, 0] = scaling_f f_pw[1, 2] = scaling_f f_pw[2, 0] = f_pw[0, 2] f_pw[2, 1] = f_pw[1, 2] fid = gm.addFunction(f_pw) gm.addFactor(fid, [x * dimy + y, x * dimy + (y + 1)]) parameterBP = opengm.InfParam(steps=noIter,damping=0.5) parameter = opengm.InfParam(steps=noIter) # inf = opengm.inference.GraphCut(gm) # inf = opengm.inference.TrwsExternal(gm, parameter=parameter) # inf = opengm.inference.TreeReweightedBp(gm, parameter=parameter) inf = opengm.inference.BeliefPropagation(gm, parameter=parameterBP) callback = PyCallback((dimx, dimy), numLabels) # visitor = inf.pythonVisitor(callback, visitNth=1) # inf.infer(visitor) print "*** INFERENCE" startTime = time.time() inf.infer() endTime = time.time() labelVector = inf.arg() E = gm.evaluate(labelVector) print "FINAL E " + str(E) + " dt " + str(endTime - startTime) + "s" return labelVector
num_unary_feats = num_labels * X[0][0].shape[1]
num_weights = num_unary_feats + num_edge_feats
# create and initialize weights
print 'num_weights =', num_weights
print 'num_instances =', len(X)
ogm_ds = learning.createDataset(num_weights, numInstances=len(X), loss="generalized-hamming")
weights = ogm_ds.getWeights()
for idx, (x, y) in enumerate(zip(X, Y)):
y[y==-1]=0 # FIXME: introduce a void label, so long: make the void label background
unary_feats, edges, edge_feats = x
num_vars = unary_feats.shape[0]
states = np.ones(num_vars, dtype=opengm.index_type) * num_labels
gm = opengm.graphicalModel(states, operator='adder')
lossParam = learning.GeneralizedHammingLossParameter()
lossParam.setLabelLossMultiplier(np.array(label_weights))
# add unary factors
weight_ids = np.arange(0, num_labels * unary_feats.shape[1]).reshape((num_labels, -1))
for feat_idx, unary_feat in enumerate(unary_feats):
# make that each label sees all features, but use their own weights
unary_feat_array = np.repeat(unary_feat.reshape((-1,1)), num_labels, axis=1)
f = learning.lUnaryFunction(weights, num_labels, unary_feat_array, weight_ids)
var_idxs = np.array([feat_idx], dtype=np.uint64)
fid = gm.addFunction(f)
gm.addFactor(fid, var_idxs)
#var_idxs = np.arange(0, num_vars, dtype=np.uint64)
#gm.addFactors(fids, var_idxs)
# model parameter
gridSize = [3, 3] # size of grid
beta = 0.7 # bias to choose between under- and over-segmentation
high = 100 # closedness-enforcing soft-constraint value for forbidden configurations
# size of the topological grid
tGridSize = [2 * gridSize[0] - 1, 2 * gridSize[1] - 1]
nrOfVariables = gridSize[1] * (gridSize[0] - 1) + gridSize[0] * (gridSize[1] -
1)
cToVi = TopologicalCoordinateToIndex(gridSize)
# some random data on a grid
data = numpy.random.random(gridSize[0] * gridSize[1]).astype(
numpy.float32).reshape(gridSize[0], gridSize[1])
# construct gm
numberOfLabels = numpy.ones(nrOfVariables, dtype=opengm.label_type) * 2
gm = opengm.graphicalModel(numberOfLabels)
# 4th closedness-function
fClosedness = numpy.zeros(pow(2, 4), dtype=numpy.float32).reshape(2, 2, 2, 2)
for x1 in range(2):
for x2 in range(2):
for x3 in range(2):
for x4 in range(2):
labelsum = x1 + x2 + x3 + x4
if labelsum is not 2 and labelsum is not 0:
fClosedness[x1, x2, x3, x4] = high
fidClosedness = gm.addFunction(fClosedness)
# for each boundary in the grid, i.e. for each variable
# of the model, add one 1st order functions
# and one 1st order factor
# and for each junction of four inter-pixel edges on the grid,
sys.stdout.write("\n")
# model parameter
gridSize=[10,10] # size of grid
beta=0.7 # bias to choose between under- and over-segmentation
high=100 # closedness-enforcing soft-constraint value for forbidden configurations
# size of the topological grid
tGridSize=[2*gridSize[0] -1,2*gridSize[1] -1]
nrOfVariables=gridSize[1]*(gridSize[0]-1)+gridSize[0]*(gridSize[1]-1)
cToVi=TopologicalCoordinateToIndex(gridSize)
# some random data on a grid
data=numpy.random.random(gridSize[0]*gridSize[1]).astype(numpy.float32).reshape(gridSize[0],gridSize[1])
# construct gm
numberOfLabels=numpy.ones(nrOfVariables,dtype=numpy.uint64)*2
gm=opengm.graphicalModel(numberOfLabels)
# 4th closedness-function
fClosedness=numpy.zeros( pow(2,4),dtype=numpy.float32).reshape(2,2,2,2)
for x1 in range(2):
for x2 in range(2):
for x3 in range(2):
for x4 in range(2):
labelsum=x1+x2+x3+x4
if labelsum is not 2 and labelsum is not 0 :
fClosedness[x1,x2,x3,x4]=high
fidClosedness=gm.addFunction(fClosedness)
# for each boundary in the grid, i.e. for each variable
# of the model, add one 1st order functions
# and one 1st order factor
# and for each junction of four inter-pixel edges on the grid,
def _update_state_opengm(model,
weight_key='cut_prob',
name_label_key='name_label'):
import opengm
import scipy.special
graph = model.graph
n_annots = len(model.graph)
n_names = n_annots
nodes = sorted(graph.nodes())
edges = [tuple(sorted(e)) for e in graph.edges()]
edges = ut.sortedby2(edges, edges)
index_type = opengm.index_type
node_state_card = np.ones(n_annots, dtype=index_type) * n_names
numberOfStates = node_state_card
annot_idxs = list(range(n_annots))
lookup_annot_idx = ut.dzip(nodes, annot_idxs)
gm = opengm.graphicalModel(numberOfStates, operator='adder')
# annot_idxs = list(range(n_annots))
# edge_idxs = list(range(n_annots, n_annots + n_edges))
# if use_unaries:
# unaries = np.ones((n_annots, n_names)) / n_names
# # unaries[0][0] = 1
# # unaries[0][1:] = 0
# for annot_idx in annot_idxs:
# fid = gm.addFunction(unaries[annot_idx])
# gm.addFactor(fid, annot_idx)
# Add Potts function for each edge
pairwise_factor_idxs = []
for count, (aid1, aid2) in enumerate(edges,
start=len(list(gm.factors()))):
varx1, varx2 = ut.take(lookup_annot_idx, [aid1, aid2])
var_indicies = np.array([varx1, varx2])
p_same = graph.get_edge_data(aid1, aid2)['cut_prob']
# p_diff = 1 - p_same
eps = 1E-9
p_same = np.clip(p_same, eps, 1.0 - eps)
same_weight = scipy.special.logit(p_same)
# valueEqual = -same_weight
valueEqual = 0
valueNotEqual = same_weight
if not np.isfinite(valueNotEqual):
"""
python -m plottool.draw_func2 --exec-plot_func --show --range=-1,1 --func=scipy.special.logit
"""
print('valueNotEqual = %r' % (valueNotEqual, ))
print('p_same = %r' % (p_same, ))
raise ValueError('valueNotEqual')
pairwise_factor_idxs.append(count)
potts_func = opengm.PottsFunction((n_names, n_names),
valueEqual=valueEqual,
valueNotEqual=valueNotEqual)
potts_func_id = gm.addFunction(potts_func)
gm.addFactor(potts_func_id, var_indicies)
model.gm = gm
matplot.subplot(2, 2, 3)
matplot.imshow(N_spec2)
matplot.title('speuclar theta 2')
matplot.show()
N_solutions = np.dstack((N_diff_solutions, N_spec_solutions))
Diff_flag = np.hstack((Diff_flag1, Diff_flag2))
rows, cols = mask1.shape
# matplot.imshow(N)
# matplot.show()
##=================> Optimised based on opengm
noofNodes = np.sum(mask1)
nodeStates = np.ones(noofNodes, dtype=opengm.index_type) * 4 # Possible answer are N or T*N
gm = opengm.graphicalModel(nodeStates)
# gm = opengm.adder.GraphicalModel(np.ones(noofNodes, dtype=opengm.index_type), reserveNumFactorsPerVariable=3)
spec_threshold = 0.99
specmask_valid = specmask[mask1 == 1]
flip_factor = 7
w_u = 1
# 1. add node factor
for i in range(noofNodes):
nState = np.int32(nodeStates[i])
f = np.zeros(nState, dtype=np.float32)
Ng_i = N_guide_valid[i, :]
if np.any(np.isnan(Ng_i)):
for k in range(nState):
numVar = dimx * dimy
numLabels = 2
numberOfStates = numpy.ones(numVar, dtype=opengm.index_type) * numLabels
vis2Order = opengm.secondOrderGridVis(dimx, dimy)
numFac = len(vis2Order)
randf = numpy.random.rand(numFac, numLabels, numLabels).astype(numpy.float64)
print randf.shape
print "numVar", numVar, "numFac", numFac
print "# METHOD A"
with opengm.Timer():
gm = opengm.graphicalModel(numberOfStates, operator="adder", reserveNumFactorsPerVariable=4)
gm.reserveFunctions(numFac, "explicit")
fids = gm.addFunctions(randf)
gm.addFactors(fids, vis2Order)
print "# METHOD B"
with opengm.Timer():
# (reserve reserveNumFactorsPerVariable does not make sense if we not "finalize" factors directely)
gm = opengm.graphicalModel(numberOfStates, operator="adder")
gm.reserveFactors(numFac)
gm.reserveFunctions(numFac, "explicit")
fids = gm.addFunctions(randf)
gm.addFactors(fids, vis2Order, finalize=False)
gm.finalize()
print 'num_weights =', num_weights
print 'num_instances =', len(X)
ogm_ds = learning.createDataset(num_weights,
numInstances=len(X),
loss="generalized-hamming")
weights = ogm_ds.getWeights()
for idx, (x, y) in enumerate(zip(X, Y)):
y[y ==
-1] = 0 # FIXME: introduce a void label, so long: make the void label background
unary_feats, edges, edge_feats = x
num_vars = unary_feats.shape[0]
states = np.ones(num_vars, dtype=opengm.index_type) * num_labels
gm = opengm.graphicalModel(states, operator='adder')
lossParam = learning.GeneralizedHammingLossParameter()
lossParam.setLabelLossMultiplier(np.array(label_weights))
# add unary factors
weight_ids = np.arange(0, num_labels * unary_feats.shape[1]).reshape(
(num_labels, -1))
for feat_idx, unary_feat in enumerate(unary_feats):
# make that each label sees all features, but use their own weights
unary_feat_array = np.repeat(unary_feat.reshape((-1, 1)),
num_labels,
axis=1)
f = learning.lUnaryFunction(weights, num_labels, unary_feat_array,
weight_ids)
var_idxs = np.array([feat_idx], dtype=np.uint64)