rit_examplescript_pipeline.m

% Copyright 2020-2023 Ivana Labounkova(1,2), Rene Labounek(2), Igor Nestrasil(2,3),
%     Jan Odstrcilik(1), Ralf P. Tornow(4), Radim Kolar(1)
% (1) Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
% (2) Division of Clinical Behavioral Neuroscience, Department of Pediatrics, University of Minnesota, Minneapolis, USA
% (3) Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, USA
% (4) Department of Ophthalmology, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
% 
% This file is part of Retina Imaging Toolbox available at: https://github.com/ivanalabounkova/retinaimagingtoolbox
% 
% Retina Imaging Toolbox 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 any later version.
% 
% Retina Imaging Toolbox 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 Retina Imaging Toolbox.  If not, see <https://www.gnu.org/licenses/>.
% 
% Papers related to specific RIT functions are listed in the cite_papers.txt file.
clear all;
close all;
clc;
%% INPUT VIDEO
% dirname = 'C:\Users\User\Videos'; %Folder path where the input video is stored.
% fname = 'RetinaVideo.avi'; % Input video filename.
dirname = '/home/range1-raid1/labounek/data-on-porto/retina_imaging/crop/sub-0001/ses-01'; %Folder path where the input video is stored.
fname = 'sub-0001_ses-01_pos90_run1_06_01_2023_15_52_46_crop_1-661.avi'; % Input video filename.
% Example of non-aligned input video (RetinaVideo.avi) you can download at: https://github.com/ivanalabounkova/retinaimagingtoolbox-data
fnamepath = fullfile(dirname, fname);
%% RESULT DIRECTORY
% save_dir = 'C:\Users\User\Results'; % Folder path where the results are stored.
save_dir = '/home/range1-raid1/labounek/data-on-porto/retina_imaging/results/denoise/sub-0001/ses-01'; % Folder path where the results are stored.
%% RIT INITIALIZATION
% You need to have setup the retinaimagingtoolbox folder in you MATLAB path
% to make basic RIT command such as rit_defaults to work.
% HOME -> Set Path -> Add Folder -> Find the folder at the HDD and add it -> Save (to remember to set path after MATLAB Restart)
rit_defaults % It is enough to execute rit_defaults just once per one MATLAB instance
%% DENOISING
sratio=1.40; % Ratio between amplitude of the image signal and amplitude of estimated noise. The value defines float index of the first principal component
             % which will be zeroed. For the value 1.40, last preserved component will have amplitude of the signal image about 40% higher than amplitude of
             % the estimated noise,
visualization=0; % set to value 1, if you want to see example of components in spectral domain (first half real values, second half imaginery values)
precision = 'double';
% precision = 'single'; % if limitted RAM memory is available
[video, fps, nframes] = rit_videoload(fnamepath, 'gray');
rit_denoise(video,sratio,visualization,nframes,fps,save_dir,fname,precision,fnamepath);
%% RIGID IMAGE REGISTRATION - LUCAS-KANADE (PARAMETERS)
fnamepath_reg=fullfile(save_dir,[fname(1:end-4) '_denoised.avi']);
index_for_reference_frame = 1; %the first frame is the reference frame
Kvessels = 1; % parameter for thresholding during blood vessel detection; it multiplies the threshold during blood vessel detection
ignore_borderPC = 150; % how many border pixels will be ignored in phase correlation step
ignore_borderLK = 50; % how many border pixels will be ignored in Lucas-Kanade step
NwinLK = 31; % window size for Lucas-Kanade tracking - this should be slightly higher than thickenss of large blood-vessels
RGB_flag = 0; % if the video is RGB, then set to 1; monochromatic - set to 0
%% RIGID IMAGE REGISTRATION - LUCAS-KANADE (MASK / REGION OF INTEREST SETUP)
mask = [];
% Example how to manually draw mask defining the region of interest (ROI) insted of the full image ROI:
%
% aviobj = VideoReader( fnamepath );
% x2show = read( aviobj, index_for_reference_frame );
% mask = roipoly( x2show );
% mask = imdilate( mask, strel('disk', 7, 0) );
% figure(1);
% imshow( x2show, [] );
%% RIGID IMAGE REGISTRATION - LUCAS-KANADE (EXECUTE)
rit_registration_lucaskanade(fnamepath_reg,mask, index_for_reference_frame, Kvessels,...
    ignore_borderPC, ignore_borderLK, NwinLK, RGB_flag);
delete([fnamepath_reg(1:end-4) '_phase.avi']);
%% ESTIMATE AVERAGED ANATOMICAL IMAGE
[video, ~, ~] = rit_videoload([fnamepath_reg(1:end-4) '_registered.avi'], 'gray');
video_mean = mean(video,3);
video_mean = (video_mean - min(video_mean(:))) ./ (max(video_mean(:)) - min(video_mean(:)));
imwrite(video_mean,[fnamepath_reg(1:end-4) '_registered_mean.png'])