mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 17:29:09 +09:00
96 lines
3.9 KiB
Matlab
96 lines
3.9 KiB
Matlab
%% 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.
|
||
|