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54 lines
2.0 KiB
Matlab
54 lines
2.0 KiB
Matlab
%hdf5_pos loads ptycho scan positions from hdf5 files
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%Written by YJ
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function [ p ] = hdf5_pos( p )
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for ii = 1:p.numscans
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switch p.scan.type
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case 'default'
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pos_file = strcat(p.base_path,sprintf(p.scan.format, p.scan_number(ii)),'/data_roi',p.scan.roi_label,'_para.hdf5');
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if exist(pos_file,'file')
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ppX = h5read(pos_file,'/ppX');
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ppY = h5read(pos_file,'/ppY');
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ppX = ppX(:);
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ppY = ppY(:);
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positions_real = zeros(length(ppX),2);
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positions_real(:,1) = -ppY;
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positions_real(:,2) = -ppX;
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else
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disp(strcat(p.base_path,sprintf(p.scan.format, p.scan_number(ii)),'/data_roi',p.scan.roi_label,'_para.hdf5'))
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error('Could not find function or data file %s', pos_file);
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end
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case 'custom'
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if ~isempty(p.scan.custom_positions_source) %guess the position file name from base path
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pos_file = p.scan.custom_positions_source;
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else
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error('Position file is not given');
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end
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try
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r_output = load(pos_file,'outputs');
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r_p = load(pos_file,'p');
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ppX = r_output.outputs.probe_positions(:,1)*r_p.p.dx_spec(1);
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ppY = r_output.outputs.probe_positions(:,2)*r_p.p.dx_spec(2);
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ppX = ppX(:);
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ppY = ppY(:);
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positions_real = zeros(length(ppX),2);
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positions_real(:,1) = -ppY;
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positions_real(:,2) = -ppX;
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catch
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error('Failed to load positions from %s', pos_file);
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end
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otherwise
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error('Unknown scan type %s.', p.scan.type);
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end
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utils.verbose(2, strcat('Loaded scan positions from:', pos_file))
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p.numpts(ii) = size(positions_real,1);
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p.positions_real = [p.positions_real ; positions_real]; %append position
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end
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end
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