added ptychography scripts

2026-09-17 23:59:11 +09:00 · 2026-08-07 16:31:16 +09:00
parent 3700c783e4
commit 5945346784
19 changed files with 5599 additions and 0 deletions
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+% This script prepares experimental electron ptycho. data for PtychoShelves
+function prepare_data(parfile)
+    %% Step 1: download sample data (rawdata_1x_crop.mat) from the link provided in 
+    % https://www.nature.com/articles/s41467-020-16688-6
+    % Note: it's a good practice to store data (and reconstructions) in a
+    % different folder from fold_slice 
+    
+    %% Step 2: load data
+    par = parameter_builder(parfile);  % load the struct with parameters
+    load(par.raw_data);
+    
+    %% Step 3: go back to .../fold_slice/ptycho and pre-process data
+    % load the parameters in case it is not saved in the raw data
+    df = par.defocus;
+    voltage = par.voltage;
+    rbf = par.rbf;
+    ADU = par.ADU;
+    alpha0 = par.alpha_max;
+    
+    addpath(strcat(pwd,'/utils_electron/'))
+    Np_p = [par.CBED_size, par.CBED_size]; % size of diffraction patterns used during reconstruction. can also pad to 256
+    % pad cbed
+    [ndpy,ndpx,npy,npx]=size(cbed);
+    if ndpy < Np_p(1) % pad zeros
+        dp=padarray(cbed,[(Np_p(1)-ndpy)/2,(Np_p(2)-ndpx)/2,0,0],0,'both');
+    else
+        dp=crop_pad(cbed,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);
+    dk=alpha0/1e3/rbf/lambda; %%% PtychoShelves script needs this %%%
+    
+    %% Step 4: save CBED in a .hdf5 file (needed by Ptychoshelves)
+    scan_number = par.scan_number; %Ptychoshelves needs
+    save_dir = strcat(par.result_dir,num2str(scan_number),'/');
+    disp(save_dir);
+    mkdir(save_dir)
+    roi_label = par.roi_label;
+    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 = df;
+    par_probe.voltage = voltage;
+    par_probe.alpha_max = alpha0;
+    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')
+end