Configuration File

Example Configuration

Configuration files follow the INI format. Sections are introduced by [section name]. In a section, parameters are defined by parameter_name = value. Comments start with the hash character # and end with the end of the line. Below are examples of the main sections.

General detection section:

[mpp]
n_iterations            = 1000 # Number of detection iterations
n_births_per_iteration  = 50   # Number of object proposals per iteration

Section about constraints on detected objects. Currently, only one constraint is implemented: non-overlapping between any 2 objects, with some tolerance:

[constraints]
overlap_tolerance       = 20.0 # Accepts up to 20% in overlapping between 2 objects

Detection refinement section (can be safely removed):

[refinement]
age_for_refinement      = 40
n_refinement_attempts   = 40
refinement_fraction     = 0.2

When an object has not been replaced by a better overlapping one for age_for_refinement number of iterations, n_refinement_attempts slight variations of it are generated (how “slight” the variations are is defined by refinement_fraction), the best of which replaces the object if better.

Execution feedback:

[feedback]
status_period           = 2 # Period of reporting of current detection state

Sections about the a priori on the objects of interest:

[object]
object_type             = circle # Idealized shape of objects of interest

# Section of the ranges of the object mark(s)
[object ranges]
radius_rng              = (20, 35, 0.5) # Range of the mark "radius": min value, max value, and precision

Section about the object quality measure:

[quality]
object_quality          = dark_on_bright_gradient # Python "function" to compute the quality measure
min_quality             = 0.75                    # Minimal quality measure of detected objects

Section about the signal to look for objects in:

[signal]
signal_loading_function = SingleChannelOfImage # Python function able to load the signal file
signal_path             = microscopy.png       # Name of signal file

# Section of the parameters of the signal loading function (if any)
[signal loading prm]
channel                 = gray

# Section of the parameter(s) of the signal transformation function
[signal processing prm]
unitary                 = False

The quality measure computation might operate on a transformation of the loaded signal. This transformation might take tunable parameters, which are then specified in the signal processing prm section. Actually, to each quality measure corresponds a signal transformation, be it the no-op.

Section about how the detected objects are presented and/or stored:

[output]
console                 = True

result_output_function  = OutputObjectsOnSingleChannelBackground

Generic Configurations

More details about available sections and parameters: Generic Configurations.