idtrackerai

Source code for model_area

# This file is part of idtracker.ai a multiple animals tracking system
# described in [1].
# Copyright (C) 2017- Francisco Romero Ferrero, Mattia G. Bergomi,
# Francisco J.H. Heras, Robert Hinz, Gonzalo G. de Polavieja and the
# Champalimaud Foundation.
#
# idtracker.ai is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details. In addition, we require
# derivatives or applications to acknowledge the authors by citing [1].
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <https://www.gnu.org/licenses/>.
#
# For more information please send an email (idtrackerai@gmail.com) or
# use the tools available at https://gitlab.com/polavieja_lab/idtrackerai.git.
#
# [1] Romero-Ferrero, F., Bergomi, M.G., Hinz, R.C., Heras, F.J.H., de Polavieja, G.G., Nature Methods, 2019.
# idtracker.ai: tracking all individuals in small or large collectives of unmarked animals.
# (F.R.-F. and M.G.B. contributed equally to this work.
# Correspondence should be addressed to G.G.d.P: gonzalo.polavieja@neuro.fchampalimaud.org)

from confapp import conf

[docs]class ModelArea(object): """Model of the area used to perform a first discrimination between blobs representing single individual and multiple touching animals (crossings) Attributes ---------- median : float median of the area of the blobs segmented from portions of the video in which all the animals are visible (not touching) mean : float mean of the area of the blobs segmented from portions of the video in which all the animals are visible (not touching) std : float standard deviation of the area of the blobs segmented from portions of the video in which all the animals are visible (not touching) std_tolerance : int tolerance factor """ def __init__(self, mean, median, std): self.median = median self.mean = mean self.std = std self.std_tolerance = conf.STD_TOLERANCE def __call__(self, area, std_tolerance = None): if std_tolerance is not None: self.std_tolerance = std_tolerance return (area - self.median) < self.std_tolerance * self.std