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When an object has not been replaced by a better overlapping one for age_for_refinement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.