def __init__(self, mainOperator, projectFileGroupName):
slots = [
SerialDictSlot(mainOperator.Parameters, selfdepends=True),
SerialHdf5BlockSlot(mainOperator.OutputHdf5,
mainOperator.InputHdf5,
mainOperator.CleanBlocks,
name="CachedOutput"),
SerialDictSlot(mainOperator.EventsVector,
transform=str,
selfdepends=True),
SerialDictSlot(mainOperator.FilteredLabels,
transform=str,
selfdepends=True),
]
if 'MergerOutput' in mainOperator.outputs:
slots.append(
SerialHdf5BlockSlot(mainOperator.MergerOutputHdf5,
mainOperator.MergerInputHdf5,
mainOperator.MergerCleanBlocks,
name="MergerCachedOutput"), )
if 'CoordinateMap' in mainOperator.outputs:
slots.append(
SerialPickleableSlot(mainOperator.CoordinateMap, 1,
pgmlink.TimestepIdCoordinateMap()))
super(TrackingSerializer, self).__init__(projectFileGroupName,
slots=slots)
def __init__(self, topLevelOperator, projectFileGroupName):
slots = [
SerialDictSlot(topLevelOperator.Parameters, selfdepends=True),
SerialHdf5BlockSlot(topLevelOperator.OutputHdf5,
topLevelOperator.InputHdf5,
topLevelOperator.CleanBlocks,
name="CachedOutput"),
SerialDictSlot(topLevelOperator.EventsVector,
transform=str,
selfdepends=True),
SerialDictSlot(topLevelOperator.FilteredLabels,
transform=str,
selfdepends=True),
SerialSlot(topLevelOperator.DivisionWeight),
SerialSlot(topLevelOperator.DetectionWeight),
SerialSlot(topLevelOperator.TransitionWeight),
SerialSlot(topLevelOperator.AppearanceWeight),
SerialSlot(topLevelOperator.DisappearanceWeight),
SerialSlot(topLevelOperator.MaxNumObjOut)
]
if 'MergerOutput' in topLevelOperator.outputs:
slots.append(
SerialHdf5BlockSlot(topLevelOperator.MergerOutputHdf5,
topLevelOperator.MergerInputHdf5,
topLevelOperator.MergerCleanBlocks,
name="MergerCachedOutput"), )
if 'CoordinateMap' in topLevelOperator.outputs:
slots.append(
SerialPickleableSlot(topLevelOperator.CoordinateMap, 1,
pgmlink.TimestepIdCoordinateMap()))
super(StructuredTrackingSerializer,
self).__init__(projectFileGroupName, slots=slots)
def __init__(self, topLevelOperator, projectFileGroupName):
if WITH_HYTRA:
slots = [
SerialDictSlot(topLevelOperator.Parameters, selfdepends=True),
SerialDictSlot(topLevelOperator.FilteredLabels,
transform=str,
selfdepends=True),
SerialPickledValueSlot(topLevelOperator.ExportSettings),
SerialPickledValueSlot(topLevelOperator.HypothesesGraph),
SerialPickledValueSlot(topLevelOperator.ResolvedMergers),
SerialSlot(topLevelOperator.DivisionWeight),
SerialSlot(topLevelOperator.DetectionWeight),
SerialSlot(topLevelOperator.TransitionWeight),
SerialSlot(topLevelOperator.AppearanceWeight),
SerialSlot(topLevelOperator.DisappearanceWeight),
SerialSlot(topLevelOperator.MaxNumObjOut)
]
else:
try:
import pgmlink
except:
import pgmlinkNoIlpSolver as pgmlink
slots = [
SerialDictSlot(topLevelOperator.Parameters, selfdepends=True),
SerialHdf5BlockSlot(topLevelOperator.OutputHdf5,
topLevelOperator.InputHdf5,
topLevelOperator.CleanBlocks,
name="CachedOutput"),
SerialDictSlot(topLevelOperator.EventsVector,
transform=str,
selfdepends=True),
SerialDictSlot(topLevelOperator.FilteredLabels,
transform=str,
selfdepends=True),
SerialSlot(topLevelOperator.DivisionWeight),
SerialSlot(topLevelOperator.DetectionWeight),
SerialSlot(topLevelOperator.TransitionWeight),
SerialSlot(topLevelOperator.AppearanceWeight),
SerialSlot(topLevelOperator.DisappearanceWeight),
SerialSlot(topLevelOperator.MaxNumObjOut)
]
if 'MergerOutput' in topLevelOperator.outputs:
slots.append(
SerialHdf5BlockSlot(topLevelOperator.MergerOutputHdf5,
topLevelOperator.MergerInputHdf5,
topLevelOperator.MergerCleanBlocks,
name="MergerCachedOutput"), )
if 'CoordinateMap' in topLevelOperator.outputs:
slots.append(
SerialPickleableSlot(topLevelOperator.CoordinateMap, 1,
pgmlink.TimestepIdCoordinateMap()))
super(StructuredTrackingSerializer,
self).__init__(projectFileGroupName,
slots=slots,
operator=topLevelOperator)
def __init__(self, mainOperator, projectFileGroupName):
# Serialization for the new pipeline (HyTra)
if WITH_HYTRA:
slots = [
SerialDictSlot(mainOperator.Parameters, selfdepends=True),
SerialDictSlot(mainOperator.EventsVector,
transform=str,
selfdepends=True),
SerialDictSlot(mainOperator.FilteredLabels,
transform=str,
selfdepends=True),
SerialPickledValueSlot(mainOperator.ExportSettings),
SerialPickleableSlot(mainOperator.HypothesesGraph,
self.VERSION, None),
SerialPickleableSlot(mainOperator.ResolvedMergers,
self.VERSION, None)
]
# Serialization for backward compatibility (for tracking with pgmlink)
# TODO: Remove this section when Windows supports the new pipeline (HyTra)
else:
try:
import pgmlink
except:
import pgmlinkNoIlpSolver as pgmlink
slots = [
SerialDictSlot(mainOperator.Parameters, selfdepends=True),
SerialHdf5BlockSlot(mainOperator.OutputHdf5,
mainOperator.InputHdf5,
mainOperator.CleanBlocks,
name="CachedOutput"),
SerialDictSlot(mainOperator.EventsVector,
transform=str,
selfdepends=True),
SerialDictSlot(mainOperator.FilteredLabels,
transform=str,
selfdepends=True),
SerialPickledValueSlot(mainOperator.ExportSettings)
]
if 'MergerOutput' in mainOperator.outputs:
slots.append(
SerialHdf5BlockSlot(mainOperator.MergerOutputHdf5,
mainOperator.MergerInputHdf5,
mainOperator.MergerCleanBlocks,
name="MergerCachedOutput"), )
if 'CoordinateMap' in mainOperator.outputs:
slots.append(
SerialPickleableSlot(mainOperator.CoordinateMap, 1,
pgmlink.TimestepIdCoordinateMap()))
super(TrackingSerializer, self).__init__(projectFileGroupName,
slots=slots)
def track(self,
time_range,
x_range,
y_range,
z_range,
size_range=(0, 100000),
x_scale=1.0,
y_scale=1.0,
z_scale=1.0,
maxDist=30,
maxObj=2,
divThreshold=0.5,
avgSize=[0],
withTracklets=False,
sizeDependent=True,
divWeight=10.0,
detWeight=10.0,
transWeight=10.0,
withDivisions=True,
withOpticalCorrection=True,
withClassifierPrior=False,
ndim=3,
cplex_timeout=None,
withMergerResolution=True,
borderAwareWidth=0.0,
withArmaCoordinates=True,
appearance_cost=500,
disappearance_cost=500,
motionModelWeight=10.0,
force_build_hypotheses_graph=False,
max_nearest_neighbors=1,
withBatchProcessing=False,
solverName="ILP",
numFramesPerSplit=0):
if not self.Parameters.ready():
raise Exception("Parameter slot is not ready")
if numFramesPerSplit != 0:
raise Exception(
"PGMLINK tracking does not support sliding window tracking")
# it is assumed that the self.Parameters object is changed only at this
# place (ugly assumption). Therefore we can track any changes in the
# parameters as done in the following lines: If the same value for the
# key is already written in the parameters dictionary, the
# paramters_changed dictionary will get a "False" entry for this key,
# otherwise it is set to "True"
parameters = self.Parameters.value
parameters['maxDist'] = maxDist
parameters['maxObj'] = maxObj
parameters['divThreshold'] = divThreshold
parameters['avgSize'] = avgSize
parameters['withTracklets'] = withTracklets
parameters['sizeDependent'] = sizeDependent
parameters['detWeight'] = detWeight
parameters['divWeight'] = divWeight
parameters['transWeight'] = transWeight
parameters['withDivisions'] = withDivisions
parameters['withOpticalCorrection'] = withOpticalCorrection
parameters['withClassifierPrior'] = withClassifierPrior
parameters['withMergerResolution'] = withMergerResolution
parameters['borderAwareWidth'] = borderAwareWidth
parameters['withArmaCoordinates'] = withArmaCoordinates
parameters['appearanceCost'] = appearance_cost
parameters['disappearanceCost'] = disappearance_cost
parameters['max_nearest_neighbors'] = max_nearest_neighbors
parameters['numFramesPerSplit'] = numFramesPerSplit
do_build_hypotheses_graph = True
if cplex_timeout:
parameters['cplex_timeout'] = cplex_timeout
else:
parameters['cplex_timeout'] = ''
cplex_timeout = float(1e75)
if withClassifierPrior:
if not self.DetectionProbabilities.ready() or len(
self.DetectionProbabilities([0]).wait()[0]) == 0:
raise DatasetConstraintError(
'Tracking',
'Classifier not ready yet. Did you forget to train the Object Count Classifier?'
)
if not self.NumLabels.ready() or self.NumLabels.value < (maxObj +
1):
raise DatasetConstraintError('Tracking', 'The max. number of objects must be consistent with the number of labels given in Object Count Classification.\n' +\
'Check whether you have (i) the correct number of label names specified in Object Count Classification, and (ii) provided at least ' +\
'one training example for each class.')
if len(self.DetectionProbabilities(
[0]).wait()[0][0]) < (maxObj + 1):
raise DatasetConstraintError('Tracking', 'The max. number of objects must be consistent with the number of labels given in Object Count Classification.\n' +\
'Check whether you have (i) the correct number of label names specified in Object Count Classification, and (ii) provided at least ' +\
'one training example for each class.')
median_obj_size = [0]
fs, ts, empty_frame, max_traxel_id_at = self._generate_traxelstore(
time_range,
x_range,
y_range,
z_range,
size_range,
x_scale,
y_scale,
z_scale,
median_object_size=median_obj_size,
with_div=withDivisions,
with_opt_correction=withOpticalCorrection,
with_classifier_prior=withClassifierPrior)
if empty_frame:
raise DatasetConstraintError(
'Tracking', 'Can not track frames with 0 objects, abort.')
if avgSize[0] > 0:
median_obj_size = avgSize
logger.info('median_obj_size = {}'.format(median_obj_size))
ep_gap = 0.05
transition_parameter = 5
fov = pgmlink.FieldOfView(
time_range[0] * 1.0,
x_range[0] * x_scale,
y_range[0] * y_scale,
z_range[0] * z_scale,
time_range[-1] * 1.0,
(x_range[1] - 1) * x_scale,
(y_range[1] - 1) * y_scale,
(z_range[1] - 1) * z_scale,
)
logger.info('fov = {},{},{},{},{},{},{},{}'.format(
time_range[0] * 1.0,
x_range[0] * x_scale,
y_range[0] * y_scale,
z_range[0] * z_scale,
time_range[-1] * 1.0,
(x_range[1] - 1) * x_scale,
(y_range[1] - 1) * y_scale,
(z_range[1] - 1) * z_scale,
))
if ndim == 2:
assert z_range[0] * z_scale == 0 and (
z_range[1] -
1) * z_scale == 0, "fov of z must be (0,0) if ndim==2"
if self.tracker is None:
do_build_hypotheses_graph = True
solverType = self.getPgmlinkSolverType(solverName)
if do_build_hypotheses_graph:
print '\033[94m' + "make new graph" + '\033[0m'
self.tracker = pgmlink.ConsTracking(
int(maxObj),
bool(sizeDependent), # size_dependent_detection_prob
float(median_obj_size[0]), # median_object_size
float(maxDist),
bool(withDivisions),
float(divThreshold),
"none", # detection_rf_filename
fov,
"none", # dump traxelstore,
solverType,
ndim)
g = self.tracker.buildGraph(ts, max_nearest_neighbors)
# create dummy uncertainty parameter object with just one iteration, so no perturbations at all (iter=0 -> MAP)
sigmas = pgmlink.VectorOfDouble()
for i in range(5):
sigmas.append(0.0)
uncertaintyParams = pgmlink.UncertaintyParameter(
1, pgmlink.DistrId.PerturbAndMAP, sigmas)
params = self.tracker.get_conservation_tracking_parameters(
0, # forbidden_cost
float(ep_gap), # ep_gap
bool(withTracklets), # with tracklets
float(detWeight), # detection weight
float(divWeight), # division weight
float(transWeight), # transition weight
float(disappearance_cost), # disappearance cost
float(appearance_cost), # appearance cost
bool(withMergerResolution), # with merger resolution
int(ndim), # ndim
float(transition_parameter), # transition param
float(borderAwareWidth), # border width
True, #with_constraints
uncertaintyParams, # uncertainty parameters
float(cplex_timeout), # cplex timeout
None, # transition classifier
solverType,
False, # training to hard constraints
1 # num threads
)
# if motionModelWeight > 0:
# logger.info("Registering motion model with weight {}".format(motionModelWeight))
# params.register_motion_model4_func(swirl_motion_func_creator(motionModelWeight), motionModelWeight * 25.0)
try:
eventsVector = self.tracker.track(params, False)
eventsVector = eventsVector[
0] # we have a vector such that we could get a vector per perturbation
# extract the coordinates with the given event vector
if withMergerResolution:
coordinate_map = pgmlink.TimestepIdCoordinateMap()
self._get_merger_coordinates(coordinate_map, time_range,
eventsVector)
self.CoordinateMap.setValue(coordinate_map)
eventsVector = self.tracker.resolve_mergers(
eventsVector,
params,
coordinate_map.get(),
float(ep_gap),
float(transWeight),
bool(withTracklets),
ndim,
transition_parameter,
max_traxel_id_at,
True, # with_constraints
None) # TransitionClassifier
except Exception as e:
raise Exception, 'Tracking terminated unsuccessfully: ' + str(e)
if len(eventsVector) == 0:
raise Exception, 'Tracking terminated unsuccessfully: Events vector has zero length.'
events = get_events(eventsVector)
self.Parameters.setValue(parameters, check_changed=False)
self.EventsVector.setValue(events, check_changed=False)
self.RelabeledImage.setDirty()
if not withBatchProcessing:
merger_layer_idx = self.parent.parent.trackingApplet._gui.currentGui(
).layerstack.findMatchingIndex(lambda x: x.name == "Merger")
tracking_layer_idx = self.parent.parent.trackingApplet._gui.currentGui(
).layerstack.findMatchingIndex(lambda x: x.name == "Tracking")
if 'withMergerResolution' in parameters.keys(
) and not parameters['withMergerResolution']:
self.parent.parent.trackingApplet._gui.currentGui().layerstack[merger_layer_idx].colorTable = \
self.parent.parent.trackingApplet._gui.currentGui().merger_colortable
else:
self.parent.parent.trackingApplet._gui.currentGui().layerstack[merger_layer_idx].colorTable = \
self.parent.parent.trackingApplet._gui.currentGui().tracking_colortable
def track(self,
time_range,
x_range,
y_range,
z_range,
size_range=(0, 100000),
x_scale=1.0,
y_scale=1.0,
z_scale=1.0,
maxDist=30,
maxObj=2,
divThreshold=0.5,
avgSize=[0],
withTracklets=False,
sizeDependent=True,
divWeight=10.0,
transWeight=10.0,
withDivisions=True,
withOpticalCorrection=True,
withClassifierPrior=False,
ndim=3,
cplex_timeout=None,
withMergerResolution=True,
borderAwareWidth=0.0,
withArmaCoordinates=True,
appearance_cost=500,
disappearance_cost=500):
if not self.Parameters.ready():
raise Exception("Parameter slot is not ready")
parameters = self.Parameters.value
parameters['maxDist'] = maxDist
parameters['maxObj'] = maxObj
parameters['divThreshold'] = divThreshold
parameters['avgSize'] = avgSize
parameters['withTracklets'] = withTracklets
parameters['sizeDependent'] = sizeDependent
parameters['divWeight'] = divWeight
parameters['transWeight'] = transWeight
parameters['withDivisions'] = withDivisions
parameters['withOpticalCorrection'] = withOpticalCorrection
parameters['withClassifierPrior'] = withClassifierPrior
parameters['withMergerResolution'] = withMergerResolution
parameters['borderAwareWidth'] = borderAwareWidth
parameters['withArmaCoordinates'] = withArmaCoordinates
parameters['appearanceCost'] = appearance_cost
parameters['disappearanceCost'] = disappearance_cost
if cplex_timeout:
parameters['cplex_timeout'] = cplex_timeout
else:
parameters['cplex_timeout'] = ''
cplex_timeout = float(1e75)
if withClassifierPrior:
if not self.DetectionProbabilities.ready() or len(
self.DetectionProbabilities([0]).wait()[0]) == 0:
raise Exception, 'Classifier not ready yet. Did you forget to train the Object Count Classifier?'
if not self.NumLabels.ready() or self.NumLabels.value != (maxObj +
1):
raise Exception, 'The max. number of objects must be consistent with the number of labels given in Object Count Classification.\n'\
'Check whether you have (i) the correct number of label names specified in Object Count Classification, and (ii) provided at least' \
'one training example for each class.'
if len(self.DetectionProbabilities(
[0]).wait()[0][0]) != (maxObj + 1):
raise Exception, 'The max. number of objects must be consistent with the number of labels given in Object Count Classification.\n'\
'Check whether you have (i) the correct number of label names specified in Object Count Classification, and (ii) provided at least' \
'one training example for each class.'
median_obj_size = [0]
coordinate_map = pgmlink.TimestepIdCoordinateMap()
if withArmaCoordinates:
coordinate_map.initialize()
ts, empty_frame = self._generate_traxelstore(
time_range,
x_range,
y_range,
z_range,
size_range,
x_scale,
y_scale,
z_scale,
median_object_size=median_obj_size,
with_div=withDivisions,
with_opt_correction=withOpticalCorrection,
with_coordinate_list=
withMergerResolution, # no vigra coordinate list, that is done by arma
with_classifier_prior=withClassifierPrior,
coordinate_map=coordinate_map)
if empty_frame:
raise Exception, 'cannot track frames with 0 objects, abort.'
if avgSize[0] > 0:
median_obj_size = avgSize
logger.info('median_obj_size = {}'.format(median_obj_size))
ep_gap = 0.05
transition_parameter = 5
fov = pgmlink.FieldOfView(
time_range[0] * 1.0,
x_range[0] * x_scale,
y_range[0] * y_scale,
z_range[0] * z_scale,
time_range[-1] * 1.0,
(x_range[1] - 1) * x_scale,
(y_range[1] - 1) * y_scale,
(z_range[1] - 1) * z_scale,
)
logger.info('fov = {},{},{},{},{},{},{},{}'.format(
time_range[0] * 1.0,
x_range[0] * x_scale,
y_range[0] * y_scale,
z_range[0] * z_scale,
time_range[-1] * 1.0,
(x_range[1] - 1) * x_scale,
(y_range[1] - 1) * y_scale,
(z_range[1] - 1) * z_scale,
))
if ndim == 2:
assert z_range[0] * z_scale == 0 and (
z_range[1] -
1) * z_scale == 0, "fov of z must be (0,0) if ndim==2"
tracker = pgmlink.ConsTracking(
maxObj,
float(maxDist),
float(divThreshold),
"none", # detection_rf_filename
sizeDependent, # size_dependent_detection_prob
0, # forbidden_cost
float(ep_gap), # ep_gap
float(median_obj_size[0]), # median_object_size
withTracklets,
divWeight,
transWeight,
withDivisions,
disappearance_cost, # disappearance cost
appearance_cost, # appearance cost
withMergerResolution,
ndim,
transition_parameter,
borderAwareWidth,
fov,
True, #with_constraints
cplex_timeout,
"none" # dump traxelstore
)
try:
eventsVector = tracker(ts, coordinate_map.get())
except Exception as e:
raise Exception, 'Tracking terminated unsuccessfully: ' + str(e)
if len(eventsVector) == 0:
raise Exception, 'Tracking terminated unsuccessfully: Events vector has zero length.'
events = get_events(eventsVector)
self.Parameters.setValue(parameters, check_changed=False)
self.EventsVector.setValue(events, check_changed=False)
def track(self,
time_range,
x_range,
y_range,
z_range,
size_range=(0, 100000),
x_scale=1.0,
y_scale=1.0,
z_scale=1.0,
maxDist=30,
maxObj=2,
divThreshold=0.5,
avgSize=[0],
withTracklets=False,
sizeDependent=True,
divWeight=10.0,
transWeight=10.0,
withDivisions=True,
withOpticalCorrection=True,
withClassifierPrior=False,
ndim=3,
cplex_timeout=None,
withMergerResolution=True,
borderAwareWidth=0.0,
withArmaCoordinates=True,
appearance_cost=500,
disappearance_cost=500,
force_build_hypotheses_graph=False):
if not self.Parameters.ready():
raise Exception("Parameter slot is not ready")
# it is assumed that the self.Parameters object is changed only at this
# place (ugly assumption). Therefore we can track any changes in the
# parameters as done in the following lines: If the same value for the
# key is already written in the parameters dictionary, the
# paramters_changed dictionary will get a "False" entry for this key,
# otherwise it is set to "True"
parameters = self.Parameters.value
parameters_changed = {}
self._setParameter('maxDist', maxDist, parameters, parameters_changed)
self._setParameter('maxObj', maxObj, parameters, parameters_changed)
self._setParameter('divThreshold', divThreshold, parameters,
parameters_changed)
self._setParameter('avgSize', avgSize, parameters, parameters_changed)
self._setParameter('withTracklets', withTracklets, parameters,
parameters_changed)
self._setParameter('sizeDependent', sizeDependent, parameters,
parameters_changed)
self._setParameter('divWeight', divWeight, parameters,
parameters_changed)
self._setParameter('transWeight', transWeight, parameters,
parameters_changed)
self._setParameter('withDivisions', withDivisions, parameters,
parameters_changed)
self._setParameter('withOpticalCorrection', withOpticalCorrection,
parameters, parameters_changed)
self._setParameter('withClassifierPrior', withClassifierPrior,
parameters, parameters_changed)
self._setParameter('withMergerResolution', withMergerResolution,
parameters, parameters_changed)
self._setParameter('borderAwareWidth', borderAwareWidth, parameters,
parameters_changed)
self._setParameter('withArmaCoordinates', withArmaCoordinates,
parameters, parameters_changed)
self._setParameter('appearanceCost', appearance_cost, parameters,
parameters_changed)
self._setParameter('disappearanceCost', disappearance_cost, parameters,
parameters_changed)
# if self._graphBuildingParameterChanged(parameters_changed):
# do_build_hypotheses_graph = True
# else:
# do_build_hypotheses_graph = force_build_hypotheses_graph
do_build_hypotheses_graph = True
if cplex_timeout:
parameters['cplex_timeout'] = cplex_timeout
else:
parameters['cplex_timeout'] = ''
cplex_timeout = float(1e75)
if withClassifierPrior:
if not self.DetectionProbabilities.ready() or len(
self.DetectionProbabilities([0]).wait()[0]) == 0:
raise Exception, 'Classifier not ready yet. Did you forget to train the Object Count Classifier?'
if not self.NumLabels.ready() or self.NumLabels.value < (maxObj +
1):
raise Exception, 'The max. number of objects must be consistent with the number of labels given in Object Count Classification.\n'\
'Check whether you have (i) the correct number of label names specified in Object Count Classification, and (ii) provided at least ' \
'one training example for each class.'
if len(self.DetectionProbabilities(
[0]).wait()[0][0]) < (maxObj + 1):
raise Exception, 'The max. number of objects must be consistent with the number of labels given in Object Count Classification.\n'\
'Check whether you have (i) the correct number of label names specified in Object Count Classification, and (ii) provided at least ' \
'one training example for each class.'
median_obj_size = [0]
ts, empty_frame = self._generate_traxelstore(
time_range,
x_range,
y_range,
z_range,
size_range,
x_scale,
y_scale,
z_scale,
median_object_size=median_obj_size,
with_div=withDivisions,
with_opt_correction=withOpticalCorrection,
with_classifier_prior=withClassifierPrior)
if empty_frame:
raise Exception, 'cannot track frames with 0 objects, abort.'
if avgSize[0] > 0:
median_obj_size = avgSize
logger.info('median_obj_size = {}'.format(median_obj_size))
ep_gap = 0.05
transition_parameter = 5
fov = pgmlink.FieldOfView(
time_range[0] * 1.0,
x_range[0] * x_scale,
y_range[0] * y_scale,
z_range[0] * z_scale,
time_range[-1] * 1.0,
(x_range[1] - 1) * x_scale,
(y_range[1] - 1) * y_scale,
(z_range[1] - 1) * z_scale,
)
logger.info('fov = {},{},{},{},{},{},{},{}'.format(
time_range[0] * 1.0,
x_range[0] * x_scale,
y_range[0] * y_scale,
z_range[0] * z_scale,
time_range[-1] * 1.0,
(x_range[1] - 1) * x_scale,
(y_range[1] - 1) * y_scale,
(z_range[1] - 1) * z_scale,
))
if ndim == 2:
assert z_range[0] * z_scale == 0 and (
z_range[1] -
1) * z_scale == 0, "fov of z must be (0,0) if ndim==2"
if self.tracker is None:
do_build_hypotheses_graph = True
if do_build_hypotheses_graph:
print '\033[94m' + "make new graph" + '\033[0m'
self.tracker = pgmlink.ConsTracking(
maxObj,
sizeDependent, # size_dependent_detection_prob
float(median_obj_size[0]), # median_object_size
float(maxDist),
withDivisions,
float(divThreshold),
"none", # detection_rf_filename
fov,
"none" # dump traxelstore
)
self.tracker.buildGraph(ts)
try:
eventsVector = self.tracker.track(
0, # forbidden_cost
float(ep_gap), # ep_gap
withTracklets,
divWeight,
transWeight,
disappearance_cost, # disappearance cost
appearance_cost, # appearance cost
ndim,
transition_parameter,
borderAwareWidth,
True, #with_constraints
cplex_timeout)
# extract the coordinates with the given event vector
if withMergerResolution:
coordinate_map = pgmlink.TimestepIdCoordinateMap()
self._get_merger_coordinates(coordinate_map, time_range,
eventsVector)
self.CoordinateMap.setValue(coordinate_map)
eventsVector = self.tracker.resolve_mergers(
eventsVector,
coordinate_map.get(),
float(ep_gap),
transWeight,
withTracklets,
ndim,
transition_parameter,
True, # with_constraints
False) # with_multi_frame_moves
except Exception as e:
raise Exception, 'Tracking terminated unsuccessfully: ' + str(e)
if len(eventsVector) == 0:
raise Exception, 'Tracking terminated unsuccessfully: Events vector has zero length.'
events = get_events(eventsVector)
self.Parameters.setValue(parameters, check_changed=False)
self.EventsVector.setValue(events, check_changed=False)
self.RelabeledImage.setDirty()
merger_layer_idx = self.parent.parent.trackingApplet._gui.currentGui(
).layerstack.findMatchingIndex(lambda x: x.name == "Merger")
tracking_layer_idx = self.parent.parent.trackingApplet._gui.currentGui(
).layerstack.findMatchingIndex(lambda x: x.name == "Tracking")
if 'withMergerResolution' in parameters.keys(
) and not parameters['withMergerResolution']:
self.parent.parent.trackingApplet._gui.currentGui().layerstack[merger_layer_idx].colorTable = \
self.parent.parent.trackingApplet._gui.currentGui().merger_colortable
else:
self.parent.parent.trackingApplet._gui.currentGui().layerstack[merger_layer_idx].colorTable = \
self.parent.parent.trackingApplet._gui.currentGui().tracking_colortable
def track(self,
time_range,
x_range,
y_range,
z_range,
size_range=(0, 100000),
x_scale=1.0,
y_scale=1.0,
z_scale=1.0,
maxDist=30,
maxObj=2,
divThreshold=0.5,
avgSize=[0],
withTracklets=False,
sizeDependent=True,
detWeight=10.0,
divWeight=10.0,
transWeight=10.0,
withDivisions=True,
withOpticalCorrection=True,
withClassifierPrior=False,
ndim=3,
cplex_timeout=None,
withMergerResolution=True,
borderAwareWidth=0.0,
withArmaCoordinates=True,
appearance_cost=500,
disappearance_cost=500,
graph_building_parameter_changed=True,
trainingToHardConstraints=False,
max_nearest_neighbors=1):
if not self.Parameters.ready():
raise Exception("Parameter slot is not ready")
# it is assumed that the self.Parameters object is changed only at this
# place (ugly assumption). Therefore we can track any changes in the
# parameters as done in the following lines: If the same value for the
# key is already written in the parameters dictionary, the
# paramters_changed dictionary will get a "False" entry for this key,
# otherwise it is set to "True"
parameters = self.Parameters.value
parameters['maxDist'] = maxDist
parameters['maxObj'] = maxObj
parameters['divThreshold'] = divThreshold
parameters['avgSize'] = avgSize
parameters['withTracklets'] = withTracklets
parameters['sizeDependent'] = sizeDependent
parameters['divWeight'] = divWeight
parameters['transWeight'] = transWeight
parameters['withDivisions'] = withDivisions
parameters['withOpticalCorrection'] = withOpticalCorrection
parameters['withClassifierPrior'] = withClassifierPrior
parameters['withMergerResolution'] = withMergerResolution
parameters['borderAwareWidth'] = borderAwareWidth
parameters['withArmaCoordinates'] = withArmaCoordinates
parameters['appearanceCost'] = appearance_cost
parameters['disappearanceCost'] = disappearance_cost
do_build_hypotheses_graph = True
if cplex_timeout:
parameters['cplex_timeout'] = cplex_timeout
else:
parameters['cplex_timeout'] = ''
cplex_timeout = float(1e75)
if withClassifierPrior:
if not self.DetectionProbabilities.ready() or len(
self.DetectionProbabilities([0]).wait()[0]) == 0:
raise DatasetConstraintError(
'Tracking',
'Classifier not ready yet. Did you forget to train the Object Count Classifier?'
)
if not self.NumLabels.ready() or self.NumLabels.value != (maxObj +
1):
raise DatasetConstraintError('Tracking', 'The max. number of objects must be consistent with the number of labels given in Object Count Classification.\n'+\
'Check whether you have (i) the correct number of label names specified in Object Count Classification, and (ii) provided at least' +\
'one training example for each class.')
if len(self.DetectionProbabilities(
[0]).wait()[0][0]) != (maxObj + 1):
raise DatasetConstraintError('Tracking', 'The max. number of objects must be consistent with the number of labels given in Object Count Classification.\n'+\
'Check whether you have (i) the correct number of label names specified in Object Count Classification, and (ii) provided at least' +\
'one training example for each class.')
median_obj_size = [0]
fs, ts, empty_frame, max_traxel_id_at = self._generate_traxelstore(
time_range,
x_range,
y_range,
z_range,
size_range,
x_scale,
y_scale,
z_scale,
median_object_size=median_obj_size,
with_div=withDivisions,
with_opt_correction=withOpticalCorrection,
with_classifier_prior=withClassifierPrior)
if empty_frame:
raise DatasetConstraintError(
'Tracking', 'Can not track frames with 0 objects, abort.')
if avgSize[0] > 0:
median_obj_size = avgSize
logger.info('median_obj_size = {}'.format(median_obj_size))
ep_gap = 0.05
fov = pgmlink.FieldOfView(
time_range[0] * 1.0,
x_range[0] * x_scale,
y_range[0] * y_scale,
z_range[0] * z_scale,
time_range[-1] * 1.0,
(x_range[1] - 1) * x_scale,
(y_range[1] - 1) * y_scale,
(z_range[1] - 1) * z_scale,
)
logger.info('fov = {},{},{},{},{},{},{},{}'.format(
time_range[0] * 1.0,
x_range[0] * x_scale,
y_range[0] * y_scale,
z_range[0] * z_scale,
time_range[-1] * 1.0,
(x_range[1] - 1) * x_scale,
(y_range[1] - 1) * y_scale,
(z_range[1] - 1) * z_scale,
))
if ndim == 2:
assert z_range[0] * z_scale == 0 and (
z_range[1] -
1) * z_scale == 0, "fov of z must be (0,0) if ndim==2"
if (self.consTracker == None or graph_building_parameter_changed
): # or do_build_hypotheses_graph):
foundAllArcs = False
new_max_nearest_neighbors = max_nearest_neighbors - 1
while not foundAllArcs:
new_max_nearest_neighbors += 1
logger.info('\033[94m' + "make new graph" + '\033[0m')
self.consTracker = pgmlink.ConsTracking(
maxObj,
sizeDependent, # size_dependent_detection_prob
float(median_obj_size[0]), # median_object_size
float(maxDist),
withDivisions,
float(divThreshold),
"none", # detection_rf_filename
fov,
"none", # dump traxelstore,
pgmlink.ConsTrackingSolverType.CplexSolver,
ndim)
hypothesesGraph = self.consTracker.buildGraph(
ts, new_max_nearest_neighbors)
self.features = self.ObjectFeatures(
range(0, self.LabelImage.meta.shape[0])).wait()
foundAllArcs = True
if trainingToHardConstraints:
logger.info(
"Tracking: Adding Training Annotations to Hypotheses Graph"
)
# could be merged with code in structuredTrackingGui
self.consTracker.addLabels()
for cropKey in self.Annotations.value.keys():
if foundAllArcs:
crop = self.Annotations.value[cropKey]
if "labels" in crop.keys():
labels = crop["labels"]
for time in labels.keys():
if not foundAllArcs:
break
for label in labels[time].keys():
if not foundAllArcs:
break
trackSet = labels[time][label]
center = self.features[time][
'Default features'][
'RegionCenter'][label]
trackCount = len(trackSet)
for track in trackSet:
if not foundAllArcs:
logger.info(
"[opStructuredTracking] Increasing max nearest neighbors!"
)
break
# is this a FIRST, INTERMEDIATE, LAST, SINGLETON(FIRST_LAST) object of a track (or FALSE_DETECTION)
type = self._type(
cropKey, time, track
) # returns [type, previous_label] if type=="LAST" or "INTERMEDIATE" (else [type])
if type[0] == "LAST" or type[
0] == "INTERMEDIATE":
previous_label = int(type[1])
previousTrackSet = labels[
time - 1][previous_label]
intersectionSet = trackSet.intersection(
previousTrackSet)
trackCountIntersection = len(
intersectionSet)
foundAllArcs &= self.consTracker.addArcLabel(
time - 1,
int(previous_label),
int(label),
float(
trackCountIntersection)
)
if not foundAllArcs:
logger.info(
"[opStructuredTracking] Increasing max nearest neighbors!"
)
break
if type[0] == "FIRST":
self.consTracker.addFirstLabels(
time, int(label),
float(trackCount))
if time > self.Crops.value[
cropKey]["time"][0]:
self.consTracker.addDisappearanceLabel(
time, int(label), 0.0)
elif type[0] == "LAST":
self.consTracker.addLastLabels(
time, int(label),
float(trackCount))
if time < self.Crops.value[
cropKey]["time"][1]:
self.consTracker.addAppearanceLabel(
time, int(label), 0.0)
elif type[0] == "INTERMEDIATE":
self.consTracker.addIntermediateLabels(
time, int(label),
float(trackCount))
if "divisions" in crop.keys():
divisions = crop["divisions"]
for track in divisions.keys():
if not foundAllArcs:
logger.info(
"[opStructuredTracking] Increasing max nearest neighbors!"
)
break
division = divisions[track]
time = int(division[1])
parent = int(
self.getLabelInCrop(
cropKey, time, track))
if parent >= 0:
self.consTracker.addDivisionLabel(
time, parent, 1.0)
self.consTracker.addAppearanceLabel(
time, parent, 1.0)
self.consTracker.addDisappearanceLabel(
time, parent, 1.0)
child0 = int(
self.getLabelInCrop(
cropKey, time + 1,
division[0][0]))
self.consTracker.addDisappearanceLabel(
time + 1, child0, 1.0)
self.consTracker.addAppearanceLabel(
time + 1, child0, 1.0)
foundAllArcs &= self.consTracker.addArcLabel(
time, parent, child0, 1.0)
if not foundAllArcs:
logger.info(
"[opStructuredTracking] Increasing max nearest neighbors!"
)
break
child1 = int(
self.getLabelInCrop(
cropKey, time + 1,
division[0][1]))
self.consTracker.addDisappearanceLabel(
time + 1, child1, 1.0)
self.consTracker.addAppearanceLabel(
time + 1, child1, 1.0)
foundAllArcs &= self.consTracker.addArcLabel(
time, parent, child1, 1.0)
if not foundAllArcs:
logger.info(
"[opStructuredTracking] Increasing max nearest neighbors!"
)
break
logger.info("max nearest neighbors={}".format(
new_max_nearest_neighbors))
drawer = self.parent.parent.trackingApplet._gui.currentGui()._drawer
if new_max_nearest_neighbors > max_nearest_neighbors:
max_nearest_neighbors = new_max_nearest_neighbors
drawer.maxNearestNeighborsSpinBox.setValue(max_nearest_neighbors)
self.parent.parent.trackingApplet._gui.currentGui(
)._maxNearestNeighbors = max_nearest_neighbors
# create dummy uncertainty parameter object with just one iteration, so no perturbations at all (iter=0 -> MAP)
sigmas = pgmlink.VectorOfDouble()
for i in range(5):
sigmas.append(0.0)
uncertaintyParams = pgmlink.UncertaintyParameter(
1, pgmlink.DistrId.PerturbAndMAP, sigmas)
self.detectionWeight = drawer.detWeightBox.value()
self.divisionWeight = drawer.divWeightBox.value()
self.transitionWeight = drawer.transWeightBox.value()
self.appearanceWeight = drawer.appearanceBox.value()
self.disappearanceWeight = drawer.disappearanceBox.value()
logger.info("detectionWeight= {}".format(self.detectionWeight))
logger.info("divisionWeight={}".format(self.divisionWeight))
logger.info("transitionWeight={}".format(self.transitionWeight))
logger.info("appearanceWeight={}".format(self.appearanceWeight))
logger.info("disappearanceWeight={}".format(self.disappearanceWeight))
consTrackerParameters = self.consTracker.get_conservation_tracking_parameters(
0, # forbidden_cost
float(ep_gap),
withTracklets,
self.detectionWeight,
self.divisionWeight,
self.transitionWeight,
self.disappearanceWeight,
self.appearanceWeight,
withMergerResolution,
ndim,
self.transition_parameter,
borderAwareWidth,
True, #with_constraints
uncertaintyParams,
cplex_timeout,
None, # TransitionClassifier
pgmlink.ConsTrackingSolverType.CplexSolver,
trainingToHardConstraints,
1) # default: False
# will be needed for python defined TRANSITION function
# consTrackerParameters.register_transition_func(self.track_transition_func)
fixLabeledNodes = False
try:
eventsVector = self.consTracker.track(consTrackerParameters,
fixLabeledNodes)
eventsVector = eventsVector[
0] # we have a vector such that we could get a vector per perturbation
if withMergerResolution:
coordinate_map = pgmlink.TimestepIdCoordinateMap()
self._get_merger_coordinates(coordinate_map, time_range,
eventsVector)
self.CoordinateMap.setValue(coordinate_map)
eventsVector = self.consTracker.resolve_mergers(
eventsVector,
consTrackerParameters,
coordinate_map.get(),
float(ep_gap),
transWeight,
withTracklets,
ndim,
self.transition_parameter,
max_traxel_id_at,
True, # with_constraints
None) # TransitionClassifier
except Exception as e:
if trainingToHardConstraints:
raise Exception, 'Tracking: Your training can not be extended to a feasible solution! ' + \
'Turn training to hard constraints off or correct your tracking training. '
else:
raise Exception, 'Tracking terminated unsuccessfully: ' + str(
e)
if len(eventsVector) == 0:
raise Exception, 'Tracking terminated unsuccessfully: Events vector has zero length.'
events = get_events(eventsVector)
self.Parameters.setValue(parameters, check_changed=False)
self.EventsVector.setValue(events, check_changed=False)
self.RelabeledImage.setDirty()
merger_layer_idx = self.parent.parent.trackingApplet._gui.currentGui(
).layerstack.findMatchingIndex(lambda x: x.name == "Merger")
tracking_layer_idx = self.parent.parent.trackingApplet._gui.currentGui(
).layerstack.findMatchingIndex(lambda x: x.name == "Tracking")
if 'withMergerResolution' in parameters.keys(
) and not parameters['withMergerResolution']:
self.parent.parent.trackingApplet._gui.currentGui().layerstack[merger_layer_idx].colorTable = \
self.parent.parent.trackingApplet._gui.currentGui().merger_colortable
else:
self.parent.parent.trackingApplet._gui.currentGui().layerstack[merger_layer_idx].colorTable = \
self.parent.parent.trackingApplet._gui.currentGui().tracking_colortable