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96 lines
3.9 KiB
Matlab
96 lines
3.9 KiB
Matlab
%% UDPATE_MASK
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% This small script guides you to update an alread existing mask for
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% ptychography. The main tool for creating a new mask is
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% beamline.create_mask, a GUI that lets you select bad/hot pixels.
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% UPDATE_MASK loads the data, specified by file_path, plots it and starts
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% the GUI. Although you can create a 3D mask, i.e. a mask which varies from
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% frame to frame, a 2D mask is sufficient for most datasets.
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% You can load an already existing mask within the GUI.
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close all
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file_path = '~/Data10/eiger_4/S00000-00999/S00089/run_00089_000000000000.h5';
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single_file = true; % if you have multiple files use * in file_path
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H5Location = '/entry/data/eiger_4/'; % check the location within the h5 file in ptycho/+detector
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orientation = [1 0 0]; % check the detector orientation in ptycho/+detector
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%% load the data
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image_read_args = [];
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image_read_args{1} = 'Orientation';
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image_read_args{2} = orientation;
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image_read_args{3} = 'OrientByExtension';
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image_read_args{4} = false;
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if ~single_file
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image_read_args{end+1} = 'IsFmask';
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image_read_args{end+1} = 1;
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end
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if ~isempty(H5Location)
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image_read_args{end+1} = 'H5Location';
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image_read_args{end+1} = H5Location;
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end
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data = io.image_read(file_path, image_read_args(:));
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%% plot the data
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figure(1),
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plotting.imagesc3D(abs(log10(double(data.data)+1)));
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colorbar
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axis xy equal tight
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colorbar
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title('Detector raw data')
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colormap jet
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%% iterative step for a mask update (add dead pixels to the current mask)
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mask = beamline.create_mask;
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%% check it again
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figure (2),
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imagesc(mask); axis equal tight xy
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title('Final mask')
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%*-----------------------------------------------------------------------*
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%| |
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%| Except where otherwise noted, this work is licensed under a |
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%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
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%| International (CC BY-NC-SA 4.0) license. |
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%| |
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%| Copyright (c) 2018 by Paul Scherrer Institute (http://www.psi.ch) |
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%| |
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%| Author: CXS group, PSI |
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%*-----------------------------------------------------------------------*
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% You may use this code with the following provisions:
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%
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% If the code is fully or partially redistributed, or rewritten in another
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% computing language this notice should be included in the redistribution.
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%
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% If this code, or subfunctions or parts of it, is used for research in a
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% publication or if it is fully or partially rewritten for another
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% computing language the authors and institution should be acknowledged
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% in written form in the publication: “Data processing was carried out
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% using the “cSAXS matlab package” developed by the CXS group,
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% Paul Scherrer Institut, Switzerland.”
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% Variations on the latter text can be incorporated upon discussion with
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% the CXS group if needed to more specifically reflect the use of the package
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% for the published work.
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%
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% A publication that focuses on describing features, or parameters, that
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% are already existing in the code should be first discussed with the
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% authors.
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%
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% This code and subroutines are part of a continuous development, they
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% are provided “as they are” without guarantees or liability on part
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% of PSI or the authors. It is the user responsibility to ensure its
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% proper use and the correctness of the results.
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