convert dynamo dipoleSet models into oversampled vesicle models

dipoles2vesicles.m

function dipoles2vesicles(catalogue_name, distance_between_particles)
%%% to be run in the folder which holds your catalogue
%%%
%%% catalogue name - name of catalogue containing your dipoleSet models
%%% distance_between_particles - expected distance between particles in px
%%% (output points will be oversampled relative to this value)
%%%
%%% if you want to restart - !rm */*/*/*/*rawVesicle*.omd
    p = [catalogue_name,'/tomograms/*/models/*.omd'];
    model_files = dir(p);


    for model_idx = 1:length(model_files)
        current_file = model_files(model_idx)
        model_file = fullfile(current_file.folder, current_file.name)
        fprintf('Now reading %s\n', model_file);
        vesicles_from_dipoles(model_file, distance_between_particles)
    end


end


function vesicles_from_dipoles(model_file, expected_inter_particle_distance)
    ds = dread(model_file);

    % checks the number of individual dipoles
    disp(sprintf('Found %d dipoles in the set',length(ds.dipoles)));

    % loops on all the dipoles present in the set
    for i=1:length(ds.dipoles);

        % selects the i-th individual dipole in the set
        dipole = ds.dipoles{i};

        % creates a vesicle model   
        v = dmodels.vesicle();

        % prepares a name for each individual dipole
        v.name = sprintf('%s_rawVesicle_%d',ds.name,i);

        % links the created model with the catalogued volume 
        % of the dipole set module
        v.cvolume = ds.cvolume;

        % initiates the vesicle model
        v.center = dipole.center;
        v.radius = norm(dipole.center - dipole.north);
        
        % add in info about average distance between particle positions on
        % surface
        v.separation = expected_inter_particle_distance / 1.5;
        v.updateCrop();

        % saves the model back into the catalogue
        v.saveInCatalogue();

    end
end