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ptycho/examples/PSO_science/prepare_data_PSO_science.m

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+% This script prepares experimental electron ptycho. data for PtychoShelves
+
+%% Step 1: download the sample data from the PARADIM website:
+% https://data.paradim.org/doi/ssmm-2j11/
+% Note: it's a good practice to store data (and reconstructions) in a
+% different folder from fold_slice 
+
+%% Step 2: load data
+data_dir = '/home/beams2/YJIANG/ptychography/electron/PrScO3/science/'; %change this
+load(strcat(data_dir,'sample_data_PrScO3.mat'))
+
+%% Step 3: go back to .../fold_slice/ptycho and pre-process data
+addpath(strcat(pwd,'/utils_electron/'))
+Np_p = [256,256]; % size of diffraction patterns used during reconstruction. can also pad to 256
+% pad cbed
+[ndpy,ndpx,npy,npx]=size(dp);
+if ndpy < Np_p(1) % pad zeros
+    dp=padarray(dp,[(Np_p(1)-ndpy)/2,(Np_p(2)-ndpx)/2,0,0],0,'both');
+else
+    dp=crop_pad(dp,Np_p);
+end
+
+dp = dp / ADU; % convert to electron count
+dp=reshape(dp,Np_p(1),Np_p(2),[]);
+Itot=mean(squeeze(sum(sum(dp,1),2))); %need this for normalizting initial probe
+
+% calculate pxiel size (1/A) in diffraction plane
+[~,lambda]=electronwavelength(voltage);
+
+rbf=26; % radius of center disk in pixels
+dk=alpha/1e3/rbf/lambda; %%% PtychoShelves script needs this %%%
+
+%% Step 4: save CBED in a .hdf5 file (needed by Ptychoshelves)
+scan_number = 1; %Ptychoshelves needs
+save_dir = strcat(data_dir,num2str(scan_number),'/');
+mkdir(save_dir)
+roi_label = '0_Ndp256';
+saveName = strcat('data_roi',roi_label,'_dp.hdf5');
+h5create(strcat(save_dir,saveName), '/dp', size(dp),'ChunkSize',[size(dp,1), size(dp,2), 1],'Deflate',4)
+h5write(strcat(save_dir,saveName), '/dp', dp)
+
+%% Step 5: prepare initial probe
+dx=1/Np_p(1)/dk; %% pixel size in real space (angstrom)
+
+par_probe = {};
+par_probe.df = defocus;
+par_probe.voltage = voltage;
+par_probe.alpha_max = alpha;
+par_probe.plotting = true;
+probe = make_tem_probe(dx, Np_p(1), par_probe);
+
+probe=probe/sqrt(sum(sum(abs(probe.^2))))*sqrt(Itot)/sqrt(Np_p(1)*Np_p(2));
+probe=single(probe);
+% add parameters for PtychoShelves
+p = {};
+p.binning = false;
+p.detector.binning = false;
+
+%% Step 6: save initial probe
+save(strcat(save_dir,'/init_probe.mat'),'probe','p')