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https://github.com/c-sooyoung/fold_slice.git
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69 lines
2.4 KiB
Matlab
69 lines
2.4 KiB
Matlab
% This script prepares experimental electron ptycho. data for PtychoShelves
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%% Step 1: download sample data (rawdata_1x_crop.mat) from the link provided in
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% https://www.nature.com/articles/s41467-020-16688-6
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% Note: it's a good practice to store data (and reconstructions) in a
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% different folder from fold_slice
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%% Step 2: load data
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load("parameter.mat"); % load the struct with parameters
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% data_dir = 'BO_tests/'; %change this
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data_dir = par.data_dir;
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% load(strcat(data_dir,'rawdata_1x_crop.mat'))
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load(strcat(data_dir, par.file_name));
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%% Step 3: go back to .../fold_slice/ptycho and pre-process data
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% load the parameters in case it is not saved in the raw data
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df = par.defocus;
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voltage = par.voltage;
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rbf = par.rbf;
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ADU = par.ADU;
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alpha0 = par.alpha_max;
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addpath(strcat(pwd,'/utils_electron/'))
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Np_p = [128,128]; % size of diffraction patterns used during reconstruction. can also pad to 256
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% pad cbed
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[ndpy,ndpx,npy,npx]=size(cbed);
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if ndpy < Np_p(1) % pad zeros
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dp=padarray(cbed,[(Np_p(1)-ndpy)/2,(Np_p(2)-ndpx)/2,0,0],0,'both');
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else
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dp=crop_pad(cbed,Np_p);
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end
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dp = dp / ADU; % convert to electron count
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dp=reshape(dp,Np_p(1),Np_p(2),[]);
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Itot=mean(squeeze(sum(sum(dp,1),2))); %need this for normalizting initial probe
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% calculate pxiel size (1/A) in diffraction plane
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[~,lambda]=electronwavelength(voltage);
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dk=alpha0/1e3/rbf/lambda; %%% PtychoShelves script needs this %%%
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%% Step 4: save CBED in a .hdf5 file (needed by Ptychoshelves)
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scan_number = 1; %Ptychoshelves needs
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save_dir = strcat(data_dir,num2str(scan_number),'/');
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mkdir(save_dir)
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% roi_label = '0_Ndp128';
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roi_label = par.roi_label;
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saveName = strcat('data_roi',roi_label,'_dp.hdf5');
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h5create(strcat(save_dir,saveName), '/dp', size(dp),'ChunkSize',[size(dp,1), size(dp,2), 1],'Deflate',4)
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h5write(strcat(save_dir,saveName), '/dp', dp)
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%% Step 5: prepare initial probe
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dx=1/Np_p(1)/dk; %% pixel size in real space (angstrom)
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par_probe = {};
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par_probe.df = df;
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par_probe.voltage = voltage;
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par_probe.alpha_max = alpha0;
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par_probe.plotting = true;
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probe = make_tem_probe(dx, Np_p(1), par_probe);
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probe=probe/sqrt(sum(sum(abs(probe.^2))))*sqrt(Itot)/sqrt(Np_p(1)*Np_p(2));
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probe=single(probe);
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% add parameters for PtychoShelves
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p = {};
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p.binning = false;
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p.detector.binning = false;
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%% Step 6: save initial probe
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save(strcat(save_dir,'/init_probe.mat'),'probe','p') |