fully documented all matlab functions with comments

matlab_functions/alignClasses.m

@@ -20,12 +20,7 @@
 %   Output:
 %       superParticle_class: the resulting fused particle
 %
-%   NOTE:
-%       First, the function concatenates all the particles as they are.
-%       Then, each particle is extracted from the stack and registered to
-%       the rest. This is done until all particles are registered to the
-%       rest. Once done, the whole process is iterated iter times.
-
+%
 % (C) Copyright 2017                    QI Group
 %     All rights reserved               Faculty of Applied Physics
 %                                       Delft University of Technology

matlab_functions/all2all_class.m

@@ -1,14 +1,12 @@
-% all2all   performs all 2 all registration for a given set of particles
+% all2all_class   performs all2all registration for a given set of particles
 %
 % SYNOPSIS:
-%   all2all(Particles, outdir, scale)
+%   all2all_class(Particles, scale)
 %
 % INPUT
 %   Particles
 %       Cell arrays of particles with localization in the point field and
 %       squared uncertainties in the sigma field.
-%   outdir
-%       Output directory where rows of all2all matrix are stored
 %   scale
 %       scale parameter for gmm registration
 %

matlab_functions/one2all_class.m

@@ -19,7 +19,7 @@
 %       superParticle
 %
 %   NOTE:
-%       This function is essentially equivalent to 'one2allm, but without 
+%       This function is essentially equivalent to 'one2all.m', but without 
 %       saving the outputFirst, the function concatenates all the particles 
 %       as they are. Then, each particle is extracted from the stack and 
 %       registered to the rest. This is done until all particles are 
@@ -34,7 +34,7 @@
 %
 % Teun Huijben, Dec 2020.
 
-function [superParticle, MT,Particles] = one2all_class(Particles, iter, oldM, scale)
+function [superParticle, MT, Particles] = one2all_class(Particles, iter, oldM, scale)
 
     disp('Bootstapping is started  !');
     initParticle.points = [];

matlab_functions/outlier_removal_class.m

@@ -10,14 +10,15 @@
 %           Cell array of particles of size 1xN
 %       Results
 %           Structure outputted by all2all_class
+%       members
+%           Cell array where each cell contains a vector with the indices
+%           of the images that belong to one class
 %
 %   Output:
 %       initAlginedParticles: the aligned particles after outlier removal
 %       M_new: Transformation parameters (rotation+translation), a 4x4xN
 %       matrix where N is the number of particles.
 %
-%   NOTE:
-%
 %
 % (C) Copyright 2017                    QI Group
 %     All rights reserved               Faculty of Applied Physics
@@ -33,20 +34,12 @@
     disp('Lie-algebraic averaging started  !');
     path_matlab = genpath('Optimization');
     addpath(path_matlab)
-%     cvx_solver mosek;
-%     cvx_solver
 
     % initialization
     RM = zeros(4,4,1);
     I = zeros(2,1);
     iter = 1;   
 
-    % load all2all registration matrix rows from file
-%     allRows = dir(all2all_dir);
-%     allNames = {allRows(~[allRows.isdir]).name};
-%     allNames = natsortfiles(allNames);
-%     nRows = numel(allNames);
-
     % stack all relative motion parameteres in RM
     for j=1:size(Results,1)