retinaLayersSegmentation.m

% Copyright (C) 2017, Javier Mazzaferri, Luke Beaton, Santiago Costantino 
% Hopital Maisonneuve-Rosemont, 
% Centre de Recherche
% www.biophotonics.ca
%
% 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/>.

function retinaLayersSegmentation(dirlist)

% This function segments the retina interface, RPE, Bruchs membrane and the
% coroid-sclera interface, in each frame in the array bscanstore in the
% file RegisteredImages.mat for each directory in varargin{1}.

% if     ispc,  workersAvailable = Inf; %Uses parallel computing
% elseif ismac, workersAvailable = 0;   %Uses 1 worker computing
% else          workersAvailable = Inf; %Uses 1 worker computing
% end

%Close parallel pool when the process exits the scope of this function
% if workersAvailable > 0
%    finishup = onCleanup(@() delete(gcp('nocreate'))); 
% end

% Iterate over subjects
nDirs = numel(dirlist);

for k = 1:nDirs
    try
        folder = dirlist{k};
        
        savedir = fullfile(folder,'Results');
        if ~exist(savedir,'dir'), mkdir(savedir), end
        
        disp(logit(folder,['Starting retinaLayersSegmentation: ' num2str(k) ' of ' num2str(nDirs) ' - ' folder]))
        
        if ~exist(fullfile(savedir,'flattenedBscans.mat'),'file')
            preProcessFrames(folder); 
        end
        
        varStruct    = load(fullfile(savedir,'flattenedBscans.mat'),'avgScans','indToProcess','RPEheight');
        avgScans     = varStruct.avgScans;
        indToProcess = varStruct.indToProcess;
        RPEheight    = varStruct.RPEheight;
        
        if exist(fullfile(savedir,'segmentationResults.mat'),'file')
            varStruct  = load(fullfile(savedir,'segmentationResults.mat'),'traces','other','EndHeights');
            traces     = varStruct.traces; 
            other      = varStruct.other;
            EndHeights = varStruct.EndHeights;
        end
    
        dispInline('init',logit(folder,'Starting retinaLayersSegmentation.'))
%         parfor (frame = indToProcess, workersAvailable)
        for frame = indToProcess 

            try
                
                bscan = avgScans{frame};
                
                yCSI = segmentCSI(bscan,RPEheight(frame));
                
                if isempty(yCSI), continue, end
                
                EndHeights(frame,:) = [NaN NaN];
                
                traces(frame).RPEheight = RPEheight(frame);
                traces(frame).CSI       = yCSI;
                
                dispInline('update',logit(folder,['retinaLayersSegmentation. Frame done: ' num2str(frame)]));
                
            catch localExc
                errString = ['Error frame:' num2str(frame) ' ' localExc.message];
                errString = [errString buildCallStack(localExc)];
                dispInline('end',logit(folder,errString));   
            end
        end
        
        save(fullfile(savedir,'segmentationResults.mat'),'traces','other','EndHeights');
        
        dispInline('end',logit(folder,['Done retinaLayersSegmentation: ' folder]));
        
    catch exception
        
        errString = ['Error in retinaLayersSegmentation. Message: ' exception.message];
        errString = [errString buildCallStack(exception)];
        dispInline('end',logit(folder,errString)); 
        continue
        
    end
end

end