def _updateHypothesesGraph(self, arcFlowMap):
"""
After running merger resolving, insert new nodes, remove de-merged nodes
and also update the links in the hypotheses graph.
This also stores the new solution (`value` property) in the new nodes and links
"""
# update nodes
for n in self.unresolvedGraph.nodes_iter():
# skip non-mergers
if not 'newIds' in self.unresolvedGraph.node[n] or len(
self.unresolvedGraph.node[n]['newIds']) < 2:
continue
# for this merger, insert all new nodes into the HG
assert (len(self.unresolvedGraph.node[n]['newIds']) ==
self.unresolvedGraph.node[n]['count'])
for newId, fit in zip(self.unresolvedGraph.node[n]['newIds'],
self.unresolvedGraph.node[n]['fits']):
traxel = Traxel()
traxel.Id = newId
traxel.Timestep = n[0]
traxel.Features = self._fitToRegionCenter(fit)
self.hypothesesGraph.addNodeFromTraxel(traxel, value=1)
# remove merger from HG, which also removes all edges that would otherwise be dangling
self.hypothesesGraph._graph.remove_node(n)
# add new links
for edge in self.resolvedGraph.edges_iter():
srcId = self.resolvedGraph.node[edge[0]]['id']
destId = self.resolvedGraph.node[edge[1]]['id']
value = arcFlowMap[(srcId, destId)]
self.hypothesesGraph._graph.add_edge(edge[0], edge[1], value=value)
def test_trackletgraph():
h = hg.HypothesesGraph()
h._graph.add_path([(0,1),(1,1),(2,1),(3,1)])
for i in [(0,1),(1,1),(2,1),(3,1)]:
t = Traxel()
t.Timestep = i[0]
t.Id = i[1]
h._graph.node[i]['traxel'] = t
t = h.generateTrackletGraph()
assert(t.countArcs() == 1)
assert(t.countNodes() == 2)
assert('tracklet' in t._graph.node[(0,1)])
def _updateHypothesesGraph(self, arcFlowMap):
"""
After running merger resolving, insert new nodes, remove de-merged nodes
and also update the links in the hypotheses graph.
This also stores the new solution (`value` property) in the new nodes and links
"""
# update nodes
for n in self.unresolvedGraph.nodes_iter():
# skip non-mergers
if not 'newIds' in self.unresolvedGraph.node[n] or len(self.unresolvedGraph.node[n]['newIds']) < 2:
continue
# for this merger, insert all new nodes into the HG
assert(len(self.unresolvedGraph.node[n]['newIds']) == self.unresolvedGraph.node[n]['count'])
for newId, fit in zip(self.unresolvedGraph.node[n]['newIds'], self.unresolvedGraph.node[n]['fits']):
traxel = Traxel()
traxel.Id = newId
traxel.Timestep = n[0]
traxel.Features = {'com': self._fitToRegionCenter(fit)}
self.hypothesesGraph.addNodeFromTraxel(traxel, value=1, mergerValue=n[1], divisionValue=False)
# remove merger from HG, which also removes all edges that would otherwise be dangling
self.hypothesesGraph._graph.remove_node(n)
# add new links only for merger nodes
for edge in self.resolvedGraph.edges_iter():
# Add new edges that are connected to new merger nodes
if 'mergerValue' in self.hypothesesGraph._graph.node[edge[0]] or 'mergerValue' in self.hypothesesGraph._graph.node[edge[1]]:
srcId = self.resolvedGraph.node[edge[0]]['id']
destId = self.resolvedGraph.node[edge[1]]['id']
edgeValue = arcFlowMap[(srcId, destId)]
# edges connected to mergers are set to "not used" in order to prevent multiple active outgoing edges from single nodes. The correct edges will be added later.
if edgeValue > 0 and not self.resolvedGraph.node[edge[0]]['division']:
for outEdge in self.hypothesesGraph._graph.out_edges(edge[0]):
self.hypothesesGraph._graph.edge[outEdge[0]][outEdge[1]]['value'] = 0
for inEdge in self.hypothesesGraph._graph.in_edges(edge[1]):
self.hypothesesGraph._graph.edge[inEdge[0]][inEdge[1]]['value'] = 0
# Add new edge connected to merger node
self.hypothesesGraph._graph.add_edge(edge[0], edge[1], value=edgeValue)
def _updateHypothesesGraph(self, arcFlowMap):
"""
After running merger resolving, insert new nodes, remove de-merged nodes
and also update the links in the hypotheses graph.
This also stores the new solution (`value` property) in the new nodes and links
"""
# update nodes
for n in self.unresolvedGraph.nodes_iter():
# skip non-mergers
if not 'newIds' in self.unresolvedGraph.node[n] or len(self.unresolvedGraph.node[n]['newIds']) < 2:
continue
# for this merger, insert all new nodes into the HG
assert(len(self.unresolvedGraph.node[n]['newIds']) == self.unresolvedGraph.node[n]['count'])
for newId, fit in zip(self.unresolvedGraph.node[n]['newIds'], self.unresolvedGraph.node[n]['fits']):
traxel = Traxel()
traxel.Id = newId
traxel.Timestep = n[0]
traxel.Features = {'com': self._fitToRegionCenter(fit)}
self.hypothesesGraph.addNodeFromTraxel(traxel, value=1, mergerValue=True, divisionValue=False)
# remove merger from HG, which also removes all edges that would otherwise be dangling
self.hypothesesGraph._graph.remove_node(n)
# add new links only for merger nodes
for edge in self.resolvedGraph.edges_iter():
# Add new edges that are connected to new merger nodes
if 'mergerValue' in self.hypothesesGraph._graph.node[edge[0]] or 'mergerValue' in self.hypothesesGraph._graph.node[edge[1]]:
srcId = self.resolvedGraph.node[edge[0]]['id']
destId = self.resolvedGraph.node[edge[1]]['id']
edgeValue = arcFlowMap[(srcId, destId)]
# edges connected to mergers are set to "not used" in order to prevent multiple active outgoing edges from single nodes. The correct edges will be added later.
if edgeValue > 0 and not self.resolvedGraph.node[edge[0]]['division']:
for outEdge in self.hypothesesGraph._graph.out_edges(edge[0]):
self.hypothesesGraph._graph.edge[outEdge[0]][outEdge[1]]['value'] = 0
for inEdge in self.hypothesesGraph._graph.in_edges(edge[1]):
self.hypothesesGraph._graph.edge[inEdge[0]][inEdge[1]]['value'] = 0
# Add new edge connected to merger node
self.hypothesesGraph._graph.add_edge(edge[0], edge[1], value=edgeValue)
def toHypothesesGraph(self):
'''
From a json graph representation (and possibly a json result),
set up a hypotheses graph with the respective links.
WARNING: only builds the structure of the graph at the moment,
features/probabilities are not inserted!
WARNING: builds the trackletgraph, not the full graph!
'''
from hytra.core.hypothesesgraph import HypothesesGraph
from hytra.core.probabilitygenerator import Traxel
# set up graph
hypothesesGraph = HypothesesGraph()
for s in self.model['segmentationHypotheses']:
tracklet = self.uuidToTraxelMap[s['id']]
assert (len(tracklet) > 0)
traxel = Traxel()
traxel.Timestep = tracklet[0][0]
traxel.Id = tracklet[0][1]
hypothesesGraph.addNodeFromTraxel(traxel, tracklet=tracklet)
# adding nodes automatically assigns UUIDs, we replace them by the loaded one
hypothesesGraph._graph.node[(traxel.Timestep,
traxel.Id)]['id'] = s['id']
# insert edges
for l in self.model['linkingHypotheses']:
try:
srcTracklet = self.uuidToTraxelMap[l['src']]
destTracklet = self.uuidToTraxelMap[l['dest']]
except:
getLogger().warning(
"Failed finding {} from JSON['linkingHypotheses'] in uuidToTraxelMap"
.format((l['dest'], l['src'])))
hypothesesGraph._graph.add_edge(
(srcTracklet[0][0], srcTracklet[0][1]),
((destTracklet[0][0], destTracklet[0][1])))
# insert result
if self.result is not None:
hypothesesGraph.insertSolution(self.result)
return hypothesesGraph
def test_insertEnergies():
skipLinkBias = 20
h = hg.HypothesesGraph()
h._graph.add_path([(0, 1), (1, 1), (2, 1), (3, 1)])
for uuid, i in enumerate([(0, 1), (1, 1), (2, 1), (3, 1)]):
t = Traxel()
t.Timestep = i[0]
t.Id = i[1]
# fill in detProb, divProb, and center of mass
t.Features['detProb'] = [0.2, 0.8]
t.Features['divProb'] = [0.2, 0.8]
t.Features['com'] = [float(i[0]), 0.0]
h._graph.node[i]['traxel'] = t
h._graph.node[i]['id'] = uuid
# set up some dummy functions to compute probabilities from a traxel
def detProbFunc(traxel):
return traxel.Features['detProb']
def divProbFunc(traxel):
return traxel.Features['divProb']
def boundaryCostFunc(traxel, forAppearance):
return 1.0
def transProbFunc(traxelA, traxelB):
dist = np.linalg.norm(
np.array(traxelA.Features['com']) -
np.array(traxelB.Features['com']))
return [1.0 - np.exp(-dist), np.exp(-dist)]
h.insertEnergies(1, detProbFunc, transProbFunc, boundaryCostFunc,
divProbFunc, skipLinkBias)
for n in h.nodeIterator():
assert ('features' in h._graph.node[n])
assert (h._graph.node[n]['features'] == [[1.6094379124341003],
[0.22314355131420971]])
assert ('divisionFeatures' in h._graph.node[n])
assert (h._graph.node[n]['divisionFeatures'] == [[1.6094379124341003],
[0.22314355131420971]
])
assert ('appearanceFeatures' in h._graph.node[n])
assert (h._graph.node[n]['appearanceFeatures'] == [[0.0], [1.0]])
assert ('disappearanceFeatures' in h._graph.node[n])
assert (h._graph.node[n]['disappearanceFeatures'] == [[0.0], [1.0]])
for a in h.arcIterator():
assert ('features' in h._graph.edge[a[0]][a[1]])
srcTraxel = h._graph.node[h.source(a)]['traxel']
destTraxel = h._graph.node[h.target(a)]['traxel']
frame_gap = destTraxel.Timestep - srcTraxel.Timestep
assert (h._graph.edge[a[0]][a[1]]['features'] == [[
0.45867514538708193
], [1.0 + skipLinkBias * (frame_gap - 1)]])
def toHypothesesGraph(self):
'''
From a json graph representation (and possibly a json result),
set up a hypotheses graph with the respective links.
WARNING: only builds the structure of the graph at the moment,
features/probabilities are not inserted!
WARNING: builds the trackletgraph, not the full graph!
'''
from hytra.core.hypothesesgraph import HypothesesGraph
from hytra.core.probabilitygenerator import Traxel
# set up graph
hypothesesGraph = HypothesesGraph()
for s in self.model['segmentationHypotheses']:
tracklet = self.uuidToTraxelMap[s['id']]
assert(len(tracklet) > 0)
traxel = Traxel()
traxel.Timestep = tracklet[0][0]
traxel.Id = tracklet[0][1]
hypothesesGraph.addNodeFromTraxel(traxel, tracklet=tracklet)
# adding nodes automatically assigns UUIDs, we replace them by the loaded one
hypothesesGraph._graph.node[(traxel.Timestep, traxel.Id)]['id'] = s['id']
# insert edges
for l in self.model['linkingHypotheses']:
try:
srcTracklet = self.uuidToTraxelMap[l['src']]
destTracklet = self.uuidToTraxelMap[l['dest']]
except:
getLogger().warning("Failed finding {} from JSON['linkingHypotheses'] in uuidToTraxelMap".format((l['dest'], l['src'])))
hypothesesGraph._graph.add_edge((srcTracklet[0][0], srcTracklet[0][1]),
((destTracklet[0][0], destTracklet[0][1])))
# insert result
if self.result is not None:
hypothesesGraph.insertSolution(self.result)
return hypothesesGraph
def test_trackletgraph():
h = hg.HypothesesGraph()
h._graph.add_path([(0, 1), (1, 1), (2, 1), (3, 1)])
for i in [(0, 1), (1, 1), (2, 1), (3, 1)]:
t = Traxel()
t.Timestep = i[0]
t.Id = i[1]
h._graph.node[i]['traxel'] = t
t = h.generateTrackletGraph()
assert (t.countArcs() == 1)
assert (t.countNodes() == 2)
assert ('tracklet' in t._graph.node[(0, 1)])
def test_insertEnergies():
skipLinkBias = 20
h = hg.HypothesesGraph()
h._graph.add_path([(0,1),(1,1),(2,1),(3,1)])
for uuid, i in enumerate([(0,1),(1,1),(2,1),(3,1)]):
t = Traxel()
t.Timestep = i[0]
t.Id = i[1]
# fill in detProb, divProb, and center of mass
t.Features['detProb'] = [0.2, 0.8]
t.Features['divProb'] = [0.2, 0.8]
t.Features['com'] = [float(i[0]), 0.0]
h._graph.node[i]['traxel'] = t
h._graph.node[i]['id'] = uuid
# set up some dummy functions to compute probabilities from a traxel
def detProbFunc(traxel):
return traxel.Features['detProb']
def divProbFunc(traxel):
return traxel.Features['divProb']
def boundaryCostFunc(traxel, forAppearance):
return 1.0
def transProbFunc(traxelA, traxelB):
dist = np.linalg.norm(np.array(traxelA.Features['com']) - np.array(traxelB.Features['com']))
return [1.0 - np.exp(-dist), np.exp(-dist)]
h.insertEnergies(1, detProbFunc, transProbFunc, boundaryCostFunc, divProbFunc, skipLinkBias)
for n in h.nodeIterator():
assert('features' in h._graph.node[n])
assert(h._graph.node[n]['features'] == [[1.6094379124341003], [0.22314355131420971]])
assert('divisionFeatures' in h._graph.node[n])
assert(h._graph.node[n]['divisionFeatures'] == [[1.6094379124341003], [0.22314355131420971]])
assert('appearanceFeatures' in h._graph.node[n])
assert(h._graph.node[n]['appearanceFeatures'] == [[0.0], [1.0]])
assert('disappearanceFeatures' in h._graph.node[n])
assert(h._graph.node[n]['disappearanceFeatures'] == [[0.0], [1.0]])
for a in h.arcIterator():
assert('features' in h._graph.edge[a[0]][a[1]])
srcTraxel = h._graph.node[h.source(a)]['traxel']
destTraxel = h._graph.node[h.target(a)]['traxel']
frame_gap = destTraxel.Timestep - srcTraxel.Timestep
assert(h._graph.edge[a[0]][a[1]]['features'] == [[0.45867514538708193], [1.0 + skipLinkBias*(frame_gap-1)]])
def tracklet_graph():
# / 2 4
# 0 -> 1 /
# \ 3
# \
# 5
#
# 6 -> 7 -> 8
#
# t: 0 1 2 3
h = HypothesesGraph()
h._graph.add_path([(0, 0), (1, 1), (2, 2)])
h._graph.add_path([(1, 1), (2, 3), (3, 4)])
h._graph.add_path([(2, 3), (3, 5)])
h._graph.add_path([(1, 6), (2, 7), (3, 8)])
for n in h._graph.nodes:
h._graph.nodes[n]["id"] = n[1]
h._graph.nodes[n]["traxel"] = Traxel()
h._graph.nodes[n]["traxel"].Id = n[1]
h._graph.nodes[n]["traxel"].Timestep = n[0]
return h
def _generate_traxelstore(self,
time_range,
x_range,
y_range,
z_range,
size_range,
x_scale=1.0,
y_scale=1.0,
z_scale=1.0,
with_div=False,
with_local_centers=False,
with_classifier_prior=False):
logger.info("generating traxels")
self.progressVisitor.showState("Object features")
self.progressVisitor.showProgress(0)
traxelstore = ProbabilityGenerator()
logger.info("fetching region features and division probabilities")
feats = self.ObjectFeatures(time_range).wait()
if with_div:
if not self.DivisionProbabilities.ready() or len(
self.DivisionProbabilities([0]).wait()[0]) == 0:
msgStr = "\nDivision classifier has not been trained! " + \
"Uncheck divisible objects if your objects don't divide or " + \
"go back to the Division Detection applet and train it."
raise DatasetConstraintError("Tracking", msgStr)
self.progressVisitor.showState("Division probabilities")
self.progressVisitor.showProgress(0)
divProbs = self.DivisionProbabilities(time_range).wait()
if with_local_centers:
localCenters = self.RegionLocalCenters(time_range).wait()
if with_classifier_prior:
if not self.DetectionProbabilities.ready() or len(
self.DetectionProbabilities([0]).wait()[0]) == 0:
msgStr = "\nObject count classifier has not been trained! " + \
"Go back to the Object Count Classification applet and train it."
raise DatasetConstraintError("Tracking", msgStr)
self.progressVisitor.showState("Detection probabilities")
self.progressVisitor.showProgress(0)
detProbs = self.DetectionProbabilities(time_range).wait()
logger.info("filling traxelstore")
filtered_labels = {}
total_count = 0
empty_frame = False
numTimeStep = len(list(feats.keys()))
countT = 0
stepStr = "Creating traxel store"
self.progressVisitor.showState(stepStr +
" ")
for t in list(feats.keys()):
countT += 1
self.progressVisitor.showProgress(
old_div(countT, float(numTimeStep)))
rc = feats[t][default_features_key]['RegionCenter']
lower = feats[t][default_features_key]['Coord<Minimum>']
upper = feats[t][default_features_key]['Coord<Maximum>']
if rc.size:
rc = rc[1:, ...]
lower = lower[1:, ...]
upper = upper[1:, ...]
ct = feats[t][default_features_key]['Count']
if ct.size:
ct = ct[1:, ...]
logger.debug("at timestep {}, {} traxels found".format(
t, rc.shape[0]))
count = 0
filtered_labels_at = []
for idx in range(rc.shape[0]):
traxel = Traxel()
# for 2d data, set z-coordinate to 0:
if len(rc[idx]) == 2:
x, y = rc[idx]
z = 0
x_lower, y_lower = lower[idx]
x_upper, y_upper = upper[idx]
z_lower = 0
z_upper = 0
elif len(rc[idx]) == 3:
x, y, z = rc[idx]
x_lower, y_lower, z_lower = lower[idx]
x_upper, y_upper, z_upper = upper[idx]
else:
raise DatasetConstraintError(
"Tracking",
"The RegionCenter feature must have dimensionality 2 or 3."
)
size = ct[idx]
if (x_upper < x_range[0] or x_lower >= x_range[1]
or y_upper < y_range[0] or y_lower >= y_range[1]
or z_upper < z_range[0] or z_lower >= z_range[1]
or size < size_range[0] or size >= size_range[1]):
filtered_labels_at.append(int(idx + 1))
continue
else:
count += 1
traxel.Id = int(idx + 1)
traxel.Timestep = int(t)
traxel.set_x_scale(x_scale)
traxel.set_y_scale(y_scale)
traxel.set_z_scale(z_scale)
# Expects always 3 coordinates, z=0 for 2d data
traxel.add_feature_array("com", 3)
for i, v in enumerate([x, y, z]):
traxel.set_feature_value('com', i, float(v))
traxel.add_feature_array("CoordMinimum", 3)
for i, v in enumerate(lower[idx]):
traxel.set_feature_value("CoordMinimum", i, float(v))
traxel.add_feature_array("CoordMaximum", 3)
for i, v in enumerate(upper[idx]):
traxel.set_feature_value("CoordMaximum", i, float(v))
if with_div:
traxel.add_feature_array("divProb", 2)
# idx+1 because rc and ct start from 1, divProbs starts from 0
prob = float(divProbs[t][idx + 1][1])
prob = float(prob)
if prob < 0.0000001:
prob = 0.0000001
if prob > 0.99999999:
prob = 0.99999999
traxel.set_feature_value("divProb", 0, 1.0 - prob)
traxel.set_feature_value("divProb", 1, prob)
if with_classifier_prior:
traxel.add_feature_array("detProb",
len(detProbs[t][idx + 1]))
for i, v in enumerate(detProbs[t][idx + 1]):
val = float(v)
if val < 0.0000001:
val = 0.0000001
if val > 0.99999999:
val = 0.99999999
traxel.set_feature_value("detProb", i, float(val))
# FIXME: check whether it is 2d or 3d data!
if with_local_centers:
traxel.add_feature_array("localCentersX",
len(localCenters[t][idx + 1]))
traxel.add_feature_array("localCentersY",
len(localCenters[t][idx + 1]))
traxel.add_feature_array("localCentersZ",
len(localCenters[t][idx + 1]))
for i, v in enumerate(localCenters[t][idx + 1]):
traxel.set_feature_value("localCentersX", i,
float(v[0]))
traxel.set_feature_value("localCentersY", i,
float(v[1]))
traxel.set_feature_value("localCentersZ", i,
float(v[2]))
traxel.add_feature_array("count", 1)
traxel.set_feature_value("count", 0, float(size))
if (x_upper < x_range[0] or x_lower >= x_range[1]
or y_upper < y_range[0] or y_lower >= y_range[1]
or z_upper < z_range[0] or z_lower >= z_range[1]
or size < size_range[0] or size >= size_range[1]):
logger.info("Omitting traxel with ID: {} {}".format(
traxel.Id, t))
print("Omitting traxel with ID: {} {}".format(
traxel.Id, t))
else:
logger.debug("Adding traxel with ID: {} {}".format(
traxel.Id, t))
traxelstore.TraxelsPerFrame.setdefault(
int(t), {})[int(idx + 1)] = traxel
if len(filtered_labels_at) > 0:
filtered_labels[str(int(t) -
time_range[0])] = filtered_labels_at
logger.debug("at timestep {}, {} traxels passed filter".format(
t, count))
if count == 0:
empty_frame = True
logger.info('Found empty frames for time {}'.format(t))
total_count += count
self.parent.parent.trackingApplet.progressSignal(100)
self.FilteredLabels.setValue(filtered_labels, check_changed=True)
return traxelstore
def _generate_traxelstore(self,
time_range,
x_range,
y_range,
z_range,
size_range,
x_scale=1.0,
y_scale=1.0,
z_scale=1.0,
with_div=False,
with_local_centers=False,
with_classifier_prior=False):
logger.info("generating traxels")
traxelstore = ProbabilityGenerator()
logger.info("fetching region features and division probabilities")
feats = self.ObjectFeatures(time_range).wait()
if with_div:
if not self.DivisionProbabilities.ready() or len(self.DivisionProbabilities([0]).wait()[0]) == 0:
msgStr = "\nDivision classifier has not been trained! " + \
"Uncheck divisible objects if your objects don't divide or " + \
"go back to the Division Detection applet and train it."
raise DatasetConstraintError ("Tracking",msgStr)
divProbs = self.DivisionProbabilities(time_range).wait()
if with_local_centers:
localCenters = self.RegionLocalCenters(time_range).wait()
if with_classifier_prior:
if not self.DetectionProbabilities.ready() or len(self.DetectionProbabilities([0]).wait()[0]) == 0:
msgStr = "\nObject count classifier has not been trained! " + \
"Go back to the Object Count Classification applet and train it."
raise DatasetConstraintError ("Tracking",msgStr)
detProbs = self.DetectionProbabilities(time_range).wait()
logger.info("filling traxelstore")
filtered_labels = {}
total_count = 0
empty_frame = False
for t in feats.keys():
rc = feats[t][default_features_key]['RegionCenter']
lower = feats[t][default_features_key]['Coord<Minimum>']
upper = feats[t][default_features_key]['Coord<Maximum>']
if rc.size:
rc = rc[1:, ...]
lower = lower[1:, ...]
upper = upper[1:, ...]
ct = feats[t][default_features_key]['Count']
if ct.size:
ct = ct[1:, ...]
logger.debug("at timestep {}, {} traxels found".format(t, rc.shape[0]))
count = 0
filtered_labels_at = []
for idx in range(rc.shape[0]):
traxel = Traxel()
# for 2d data, set z-coordinate to 0:
if len(rc[idx]) == 2:
x, y = rc[idx]
z = 0
elif len(rc[idx]) == 3:
x, y, z = rc[idx]
else:
raise DatasetConstraintError ("Tracking", "The RegionCenter feature must have dimensionality 2 or 3.")
size = ct[idx]
if (x < x_range[0] or x >= x_range[1] or
y < y_range[0] or y >= y_range[1] or
z < z_range[0] or z >= z_range[1] or
size < size_range[0] or size >= size_range[1]):
filtered_labels_at.append(int(idx + 1))
continue
else:
count += 1
traxel.Id = int(idx + 1)
traxel.Timestep = int(t)
traxel.set_x_scale(x_scale)
traxel.set_y_scale(y_scale)
traxel.set_z_scale(z_scale)
# Expects always 3 coordinates, z=0 for 2d data
traxel.add_feature_array("com", 3)
for i, v in enumerate([x, y, z]):
traxel.set_feature_value('com', i, float(v))
traxel.add_feature_array("CoordMinimum", 3)
for i, v in enumerate(lower[idx]):
traxel.set_feature_value("CoordMinimum", i, float(v))
traxel.add_feature_array("CoordMaximum", 3)
for i, v in enumerate(upper[idx]):
traxel.set_feature_value("CoordMaximum", i, float(v))
if with_div:
traxel.add_feature_array("divProb", 2)
# idx+1 because rc and ct start from 1, divProbs starts from 0
prob = float(divProbs[t][idx + 1][1])
prob = float(prob)
if prob < 0.0000001:
prob = 0.0000001
if prob > 0.99999999:
prob = 0.99999999
traxel.set_feature_value("divProb", 0, 1.0 - prob)
traxel.set_feature_value("divProb", 1, prob)
if with_classifier_prior:
traxel.add_feature_array("detProb", len(detProbs[t][idx + 1]))
for i, v in enumerate(detProbs[t][idx + 1]):
val = float(v)
if val < 0.0000001:
val = 0.0000001
if val > 0.99999999:
val = 0.99999999
traxel.set_feature_value("detProb", i, float(val))
# FIXME: check whether it is 2d or 3d data!
if with_local_centers:
traxel.add_feature_array("localCentersX", len(localCenters[t][idx + 1]))
traxel.add_feature_array("localCentersY", len(localCenters[t][idx + 1]))
traxel.add_feature_array("localCentersZ", len(localCenters[t][idx + 1]))
for i, v in enumerate(localCenters[t][idx + 1]):
traxel.set_feature_value("localCentersX", i, float(v[0]))
traxel.set_feature_value("localCentersY", i, float(v[1]))
traxel.set_feature_value("localCentersZ", i, float(v[2]))
traxel.add_feature_array("count", 1)
traxel.set_feature_value("count", 0, float(size))
# Add traxel to traxelstore after checking position, time, and size ranges
if (x < x_range[0] or x >= x_range[1] or
y < y_range[0] or y > y_range[1] or
z < z_range[0] or z > z_range[1] or
size < size_range[0] or size > size_range[1]):
logger.info("Omitting traxel with ID: {}".format(traxel.Id))
else:
traxelstore.TraxelsPerFrame.setdefault(int(t), {})[int(idx + 1)] = traxel
if len(filtered_labels_at) > 0:
filtered_labels[str(int(t) - time_range[0])] = filtered_labels_at
logger.debug("at timestep {}, {} traxels passed filter".format(t, count))
if count == 0:
empty_frame = True
logger.info('Found empty frames')
total_count += count
self.FilteredLabels.setValue(filtered_labels, check_changed=True)
return traxelstore
