fold_slice/ptycho/simulation_electron_FSC.m

%simulate CBED for FSC analysis
%% parameters
addpath(fullfile(pwd,'utils_electron'))
FOV = 60; %fixed FOV in angstrom
N = 128;   % size of diffraction pattern in pixels. only square dp allowed 
scan_step_size = 3; %scan step size in angstrom
N_scans_h = round(FOV/scan_step_size); % number of scan positions along horizontal direction
N_scans_v = round(FOV/scan_step_size); % number of scan positions along vertical direction

maxPosError = 0; %largest randrom position error
dose = 5e4; %total electron dose (e/A^2)
Nc_avg = dose*scan_step_size^2/N^2; %average electron count per detector pixel. For poisson noise, SNR = sqrt(Nc_avg);
base_dir = '/home/beams2/YJIANG/research/algorithm/simulation/FSC_study/electron_ptycho_temp/';

%% load test object
disp('Load test object...')
%load(fullfile(pwd,'utils_electron','CuPcCl.mat'))
load(fullfile(pwd,'utils_electron','amorphous_random.mat'))

%pad object in case of large FOV is needed
%phase_true = padarray(phase_true,[6400,6400],'circular','post');
r = 4; %resample phase
phase_true = imresize(phase_true, 1/r);
%create a complex object
object_true = ones(size(phase_true)).*exp(1i*phase_true);
dx = dx*r; %real-space pixel size in angstrom

N_obj = size(object_true,1); %only square object allowed
ind_obj_center = floor(N_obj/2)+1;

%% generate probe function
disp('Generate probe function...')
par_probe = {};
par_probe.df = 800; %defocus in angstrom
par_probe.C3 = 0; %third-order spherical aberration in angstrom
par_probe.voltage = 300; %beam voltage in keV
par_probe.alpha_max = 18; %semi-convergence angle in mrad
par_probe.plotting = true;
[probe_true, ~] = make_tem_probe(dx,N,par_probe);

%calculate rbf
lambda = 12.398/sqrt((2*511.0+par_probe.voltage).*par_probe.voltage); %angstrom
dk = 1/dx/N; %fourier-space pixel size in 1/A
rbf = par_probe.alpha_max/1e3/lambda/dk;
%% save initial probe and parameters
probe = probe_true;
data_dir = strcat('amorph_ss',num2str(scan_step_size),'_a',num2str(par_probe.alpha_max),'_df',num2str(par_probe.df),'_dose',num2str(dose),'/');
mkdir(fullfile(base_dir,data_dir))
p = {};
p.binning = false;
p.detector.binning = false;
p.dk = dk;
p.N_scans_h = N_scans_h;
p.N_scans_v = N_scans_v;
save(strcat(base_dir,data_dir,'init_probe'),'probe','p','par_probe')

%% Generate scan positions
disp('Generate scan positions...')
pos_h = (1 + (0:N_scans_h-1) *scan_step_size);
pos_v = (1 + (0:N_scans_v-1) *scan_step_size);
% centre this
pos_h  = pos_h - (mean(pos_h));
pos_v  = pos_v - (mean(pos_v));
[Y,X] = meshgrid(pos_h, pos_v);
Y = Y';
X = X';
pos_true_h = X(:); % true posoition
pos_true_v = Y(:);

pos_recon_init_h = pos_true_h;
pos_recon_init_v = pos_true_v;

%add random position errors - to simulate scan noise
pos_recon_init_h = pos_recon_init_h + maxPosError*(rand(size(pos_recon_init_h))*2-1);
pos_recon_init_v = pos_recon_init_v + maxPosError*(rand(size(pos_recon_init_v))*2-1);

%
%calculate indicies for all scans
N_scan = length(pos_true_h);
%position = pi(integer) + pf(fraction)
pv_i = round(pos_true_v/dx);
pv_f = pos_true_v - pv_i*dx;
ph_i = round(pos_true_h/dx);
ph_f = pos_true_h - ph_i*dx;

ind_h_lb = ph_i - floor(N/2) + ind_obj_center;
ind_h_ub = ph_i + ceil(N/2) -1 + ind_obj_center;
ind_v_lb = pv_i - floor(N/2) + ind_obj_center;
ind_v_ub = pv_i + ceil(N/2) -1 + ind_obj_center;
%% generate two datasets (required by FSC)
disp('Generating diffraction patterns...')
close all

for j=1:2
    disp(j)
    
    dp = zeros(N,N,N_scan);
    dp_true = zeros(N,N,N_scan);
    snr = ones(N_scan,1)*inf; %signal-to-noise ratio of each diffraction pattern

    f = waitbar(0,'1','Name','Simulating diffraction patterns...',...
        'CreateCancelBtn','setappdata(gcbf,''canceling'',1)');
    setappdata(f,'canceling',0);

    for i=1:N_scan
        % Check for clicked Cancel button
        if getappdata(f,'canceling')
            break
        end
        % Update waitbar and message
        waitbar(i/N_scan,f,sprintf('No.%d/%d',i,N_scan))

        probe_s = shift(probe_true, dx, dx, ph_f(i), pv_f(i));
        obj_roi = object_true(ind_v_lb(i):ind_v_ub(i),ind_h_lb(i):ind_h_ub(i));
        psi =  obj_roi .* probe_s;

        %FFT to get diffraction pattern
        dp_true(:,:,i) = abs(fftshift(fft2(ifftshift(psi)))).^2;
        dp(:,:,i) = dp_true(:,:,i);

        %Add poisson noise
        if Nc_avg<inf
            dp_true_temp = dp_true(:,:,i);
            dp_temp = dp_true_temp/sum(dp_true_temp(:))*(N^2*Nc_avg);
            dp_temp = poissrnd(dp_temp);
            dp_temp = dp_temp*sum(dp_true_temp(:))/(N^2*Nc_avg);
            snr(i) = mean((dp_true_temp(:)))/std(dp_true_temp(:) - dp_temp(:));
            dp(:,:,i) = dp_temp;
        end
    end
    delete(f)
    disp('Generating diffraction patterns...done')

    % save cbed 
    disp('Saving diffraction patterns...')
    save_dir = fullfile(base_dir,data_dir,strcat('data',num2str(j)));
    mkdir(save_dir)
    
    save_name = strcat('data_roi0_dp.hdf5'); %save diffraction patterns
    h5create(fullfile(save_dir,save_name), '/dp', size(dp),'ChunkSize',[size(dp,1) size(dp,1), 1],'Deflate',4)
    h5write(fullfile(save_dir,save_name), '/dp', dp*100)
    save_name = strcat('data_roi0_para.hdf5'); %save scan positions
    hdf5write(fullfile(save_dir,save_name), '/ppX', pos_true_h)
    hdf5write(fullfile(save_dir,save_name), '/ppY', pos_true_v,'WriteMode','append')
    disp('done')
end

%% run ptychosheleves script to prepare reconstruction parameters
template = 'ptycho_electron_simulation_template';
% you can adjust more parameters in the template
base_path_ptycho = fullfile(base_dir,data_dir); %base path needed by ptychoshelves
grouping = N_scans_h; %adjust group size based on total # of diffraction patterns
run(template)

% start reconstruction
tic
out = core.ptycho_recons(p);
toc

%% To exam the final FSC score, load the .mat file generated by PtychoSheleves
%for example:
load(fullfile(eng.fout,'Niter200.mat'))
fsc = p.dx_spec(1)/outputs.fsc_score{end}.resolution; %unit: angstrom
disp(fsc)