% example usage of generate_simulated_spots and centroid_image

clear all
close all



%% example 1 - 
%----------------------------------------------------------
npixels = 1024;          % the number of pixels in the image
digitize = 0;         % =1, therefore digitize to 12-bits
IntensityNoise = 0;   % =0, therefore do NOT add photo-electron shot noise
positionNoise = 0;    % =0, therefore keep the nominal positions of the spots regular

ONOFF(1).str = 'OFF';
ONOFF(2).str = 'ON';

% report
disp('EXAMPLE 1')
disp('---------')
disp(['- Number of pixels = ', num2str(npixels)])
disp(['- 12-bit digitization is ', ONOFF(digitize+1).str])
disp(['- photo-electron shot noise is ', ONOFF(IntensityNoise+1).str])
disp(['- position-noise is ', ONOFF(positionNoise+1).str])


% generate the spot image
genSpots = generate_simulated_spots(npixels, digitize, ...
                                    IntensityNoise, positionNoise);
% initialize centroids - and set the background level to subtract   
clear centroids
centroids.background = genSpots.image(1, 1);
centroids = centroid_image(genSpots.image, centroids);

% display the RMS deviation between the calculated centroids and the
% nominal centroids
diff = sort(centroids.current_centroids) - sort(genSpots.positions);
RMS = sqrt(sum(diff(:, 1).^2 + diff(:, 2).^2)/numel(diff));
disp(['The RMS spot error for example 1 is ',num2str(RMS), ' pixels' ])
disp(' ')
imagesc(genSpots.image);
%----------------------------------------------------------


%% example 2 - 
%----------------------------------------------------------
npixels = 400;          % the number of pixels in the image
digitize = 1;         % =1, therefore digitize to 12-bits
IntensityNoise = 0;   % =0, therefore do NOT add photo-electron shot noise
positionNoise = 0;    % =0, therefore keep the nominal positions of the spots regular

ONOFF(1).str = 'OFF';
ONOFF(2).str = 'ON';

% report
disp('EXAMPLE 2')
disp('---------')
disp(['- Number of pixels = ', num2str(npixels)])
disp(['- 12-bit digitization is ', ONOFF(digitize+1).str])
disp(['- photo-electron shot noise is ', ONOFF(IntensityNoise+1).str])
disp(['- position-noise is ', ONOFF(positionNoise+1).str])


% generate the spot image
genSpots = generate_simulated_spots(npixels, digitize, ...
                                    IntensityNoise, positionNoise);
% initialize centroids - and set the background level to subtract  
clear centroids
centroids.background = genSpots.image(1, 1);
centroids = centroid_image(genSpots.image, centroids);

% display the RMS deviation between the calculated centroids and the
% nominal centroids
diff = sort(centroids.current_centroids) - sort(genSpots.positions);
RMS = sqrt(sum(diff(:, 1).^2 + diff(:, 2).^2)/numel(diff));
disp(['The RMS spot error for example 1 is ',num2str(RMS), ' pixels' ])
disp(' ');
%----------------------------------------------------------


%% example 3 - 
%----------------------------------------------------------
npixels = 400;          % the number of pixels in the image
digitize = 0;         % =1, therefore digitize to 12-bits
IntensityNoise = 1;   % =0, therefore do NOT add photo-electron shot noise
positionNoise = 0;    % =0, therefore keep the nominal positions of the spots regular

ONOFF(1).str = 'OFF';
ONOFF(2).str = 'ON';

% report
disp('EXAMPLE 3')
disp('---------')
disp(['- Number of pixels = ', num2str(npixels)])
disp(['- 12-bit digitization is ', ONOFF(digitize+1).str])
disp(['- photo-electron shot noise is ', ONOFF(IntensityNoise+1).str])
disp(['- position-noise is ', ONOFF(positionNoise+1).str])


% generate the spot image
genSpots = generate_simulated_spots(npixels, digitize, ...
                                    IntensityNoise, positionNoise);
% initialize centroids - and set the background level to subtract 
clear centroids
centroids.background = genSpots.image(1, 1);
centroids = centroid_image(genSpots.image, centroids);

% display the RMS deviation between the calculated centroids and the
% nominal centroids
diff = sort(centroids.current_centroids) - sort(genSpots.positions);
RMS = sqrt(sum(diff(:, 1).^2 + diff(:, 2).^2)/numel(diff));
disp(['The RMS spot error for example 1 is ',num2str(RMS), ' pixels' ])
disp('NOTE: the RMS error with realistic photo-electron shot noise')
disp('      will be approximately 0.1%-0.3% of a pixel')
disp('')
%----------------------------------------------------------



%% example 4 - 
%----------------------------------------------------------
npixels = 400;          % the number of pixels in the image
digitize = 0;         % =1, therefore digitize to 12-bits
IntensityNoise = 0;   % =0, therefore do NOT add photo-electron shot noise
positionNoise = 1;    % =0, therefore keep the nominal positions of the spots regular

ONOFF(1).str = 'OFF';
ONOFF(2).str = 'ON';

% report
disp('EXAMPLE 4')
disp('---------')
disp(['- Number of pixels = ', num2str(npixels)])
disp(['- 12-bit digitization is ', ONOFF(digitize+1).str])
disp(['- photo-electron shot noise is ', ONOFF(IntensityNoise+1).str])
disp(['- position-noise is ', ONOFF(positionNoise+1).str])


% generate the spot image
genSpots = generate_simulated_spots(npixels, digitize, ...
                                    IntensityNoise, positionNoise);
% initialize centroids - and set the background level to subtract
clear centroids
centroids.background = genSpots.image(1, 1);
centroids = centroid_image(genSpots.image, centroids);

% display the RMS deviation between the calculated centroids and the
% nominal centroids
diff = sort(centroids.current_centroids) - sort(genSpots.positions);
RMS = sqrt(sum(diff(:, 1).^2 + diff(:, 2).^2)/numel(diff));
disp(['The RMS spot error for example 1 is ',num2str(RMS), ' pixels' ])
disp('')
%----------------------------------------------------------