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ptycho/examples/Planar_Interface/prepare_data_Planar_Interface.m

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+% This script prepares experimental electron ptycho. data for PtychoShelves
+%% Step 1: download sample data from Zenodo:
+% DOI : 
+% link: 
+% Note: it's a good practice to store data (and reconstructions) in a
+% different folder from fold_slice 
+
+%% Step 2: load data
+data_dir = '/path/to/file/'; %change this
+dp = h5read(strcat(data_dir,'SupFig1a_MEP_Planar_Interface.hdf5'), '/dp');
+
+%% Step 3: any preprocessing steps if required
+ADU = 3661; % Analog to Digital units for EMPAD-1 detector
+dp = dp / ADU; % convert to electron count
+
+%% Step 4: save .hdf5 file in the folder structure used in PtychoShelves
+scan_number = 1; %Ptychoshelves needs
+save_dir = strcat(data_dir,num2str(scan_number),'/');
+mkdir(save_dir)
+roi_label = '0_Ndp255';
+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)