inference_cfg.yaml

# Hyperparameters for combinatorics code to assemble individuals.
# Mathis et al. xyz

variant: 0

##############################################################################
#### Assembly of PAFs to individuals (should be crossvalidated)
#### Happens in evaluation step.
##############################################################################

# Filtering bodyparts:
# Least strength of a bodypart detection (to be included in assembly)
detectionthresholdsquare: 0.1

# Filtering connections:
# Least strength of a paf cost (to be included in assembly)
pafthreshold: 0.1

# before assembly exclude all bpts more apart than:
distnormalization: 1000
# and closer than:
distnormalizationLOWER: 0

#For edgewisecondition (slack variables)
upperbound_factor: 1.25 # edges that are > upperbound_factor * maximum edge length
lowerbound_factor: .5   # edges that are < lowerbound_factor * minimum edge length

# weighing an edge by paf costs + addlikelihoods*geometric mean of detection likelihood
addlikelihoods: .15
method: 'm1'

# Assembly:
#least number of connections (to actually form an animal)
minimalnumberofconnections: willbeautomaticallyupdatedbycreate_training_datasetcode
#reasonable default: len(cfg['multianimalbodyparts'])/2

# Least average score (average over paf costs of all edges)
averagescore: 0.1
# max. number of objects to keep:
topktoretain: willbeautomaticallyupdatedbycreate_training_datasetcode
#reasonable default: len(cfg['individuals'])+1*(len(cfg['uniquebodyparts'])>0)

# Also extract ID:
withid: False #TODO: set automatically (if >0 id channels!)

##############################################################################
#### Tracker variables (should be crossvalidated)
##############################################################################
#p/m pixels in width and height for increasing bounding boxes.
boundingboxslack : 0

# Intersection over Union (IoU) threshold for linking two bounding boxes
iou_threshold: .2
# maximum duration of a tracklet and length
max_age: 100
min_hits: 3