initial commit

+beamline/update_mask.m

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