Track_filter.m

function [trk_filt,tracks]= Track_filter(fits_fname,fits,trackparams,savetracks)
%% Track_filter
% written BPI 6/7/16
% Track_filter is a function to filter based on tracking. Currently just
% tracks and removes and the first and last frame from the track
%
% fits_fname is the name of the fits .mat file, importantly containing an
% array called fits with the fit information with column 9 being the
% goodfit boolean
% 
% fits is the fits structure from Subtract_then_fit.m
%
% trackparams are the tracking parameters, definitions and defaults below
%
% savetracks is an optional Boolean determining whether the output of
% Track3D2 will be saved separately
%
%%%% Outputs %%%%
% trk_filt is a logical vector which indicates whether or not the fit passed
% the filter
%
% tracks is array with the track information and columns
% tracks is made of 1: frame #, 2: x (px), 3: y (px), 4: track #

% the function also can append the fit .mat file with trk_filt

%     Copyright (C) 2018 Benjamin P Isaacoff
%
%     This program 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.
% 
%     You should have received a copy of the GNU General Public License
%     along with this program.  If not, see <http://www.gnu.org/licenses/>.
%

%% Default tracking parameters
if nargin<3
    % TRACKING PARAMETERS
    % minimum merit
    trackparams(1)=0.01;
    % Integration time (ms)
    trackparams(2)=200;
    % gamma
    trackparams(3)=1;
    % maximum step size
    trackparams(4)=3;
    % minimum track length
    trackparams(5)=3;
    % speed estimation window halfsize
    trackparams(6)=1;
    % time delay between consecutive frames (ms)
    trackparams(7)=0;
end

%% Track it

%the logical vector of whether or not the fit passed the tracking filtering
trk_filt=false(size(fits.frame,1),1);

[~,fname] = fileparts(fits_fname);
global verbose
if verbose
disp([char(datetime),'   Tracking ',fname])
end
tracks = Tracking(fits_fname,fits,trackparams,savetracks);
if ~isempty(tracks)
    save(fits_fname,'tracks','trackparams','-append')
    
    % remove the first and last entries of each track
    for ii=1:max(tracks(:,4))
        %the molecules in the current track
        mols_inds=find(tracks(:,4)==ii);
        %remove the first and last entries
        tracks(mols_inds([1,end]),:)=[];
    end
    % trk_filt(ismember(fits(:,1:3),tracks(:,1:3),'rows'))=1;
    trk_filt(ismember([fits.frame,fits.row,fits.col],tracks(:,1:3),'rows'))=1;
else
    trk_filt=false(size(fits.frame,1),1);
end

save(fits_fname,'trk_filt','-append')


end