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%CREATE_MASK
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% create a binary mask for the current figure
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% The following arguments have to be given as name/value pairs. However,
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% they can also be set within the GUI.
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%
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% *optional*
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% ** mask initial mask; either a file, an array or a structure (indicies + asize)
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% ** fig pass figure handle; default: current figure
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% ** ind convert mask to indicies
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% ** file save mask to disk; specify path + filename
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%
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% returns:
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% ++ out 2D binary mask or structure containing the asize and the indicies
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%
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% EXAMPLE:
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% img = io.image_read('~/Data10/pilatus_1/S00000-00999/S00170/*.cbf'); % load image stack
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% plotting.imagesc3D(log10(img.data)); axis equal tight xy; % plot image stack
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% beamline.create_mask(); % open the GUI and create the mask
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%
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% see also: beamline.mask2ind
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% Academic License Agreement
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%
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% Source Code
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%
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% Introduction
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% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
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% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
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% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
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%
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% Terms and Conditions of the LICENSE
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% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
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% hereinafter set out and until termination of this license as set forth below.
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% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
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% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
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% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
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% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
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% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
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% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
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% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
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% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
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% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
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% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
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% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
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% in the commercial use, application or exploitation of works similar to the PROGRAM.
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% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
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% another computing language:
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% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
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% Scherrer Institut, Switzerland."
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%
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% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
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% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
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% (doi: 10.1126/science.1158573),
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% for maximum likelihood:
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% P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012).
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% (doi: 10.1088/1367-2630/14/6/063004),
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% for mixed coherent modes:
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% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
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% and/or for multislice:
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% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
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% (doi: 10.1364/OE.24.029089).
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% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
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% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
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% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
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% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
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% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
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% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
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% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
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% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
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% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
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% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
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% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
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% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
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% the courts of Zürich, Switzerland.
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function [out] = create_mask(varargin)
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check_input_mask = @(x) ischar(x) || (isnumeric(x)|| islogical(x)) || isstruct(x);
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par = inputParser;
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par.addParameter('mask', [], check_input_mask)
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par.addParameter('fig', [], @ishandle)
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par.addParameter('ind', false, @islogical)
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par.addParameter('file', [], @ischar)
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par.parse(varargin{:})
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vars = par.Results;
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% Check screen size
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try
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scrsz = get(0,'ScreenSize');
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catch
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scrsz = [1 1 2560 1024];
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end
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% get fig
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if isempty(vars.fig)
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fig = gcf;
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end
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current_pos = fig.Position;
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new_fig_pos(2:4) = current_pos(2:4);
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if current_pos(1)+current_pos(3)/2 - scrsz(3)/2 > 0
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% figure to the left
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new_fig_pos(1) = current_pos(1)-current_pos(3);
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else
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% figure to the right
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new_fig_pos(1) = current_pos(1)+current_pos(3);
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end
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% get axis
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ax = gca;
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% get current data size
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if ~isempty(ax.Children)
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asize = size(ax.Children.CData);
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else
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fig = gcf;
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close(fig)
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error('Failed to connect to figure instance.')
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end
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% prepare mask
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if isempty(vars.mask)
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mask = ones(asize);
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else
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if ischar(vars.mask)
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% load a mask from disk
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try
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f = load(vars.mask);
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mask = f.mask;
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clear f
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catch
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fprintf('Failed to load mask. Using empty mask instead.\n')
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mask = ones(asize);
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end
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elseif isnumeric(vars.mask) || islogical(vars.mask)
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mask = vars.mask;
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elseif isstruct(vars.mask)
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mask = beamline.ind2mask(vars.mask);
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else
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error('Unknown mask data format.')
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end
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assert(all(size(mask)==asize), 'Mask size and data size does not match')
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end
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pause(0.1)
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% apply mask
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CData_orig = ax.Children.CData;
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if ax.isprop('img')
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img_orig = ax.img;
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ax.img = ax.img .* mask;
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mask_dims = ndims(img_orig);
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if mask_dims==3
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mask3D = true;
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else
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mask3D = false;
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end
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mask_dims = size(img_orig,3);
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else
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mask3D = false;
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mask_dims = 1;
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end
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ax.Children.CData = ax.Children.CData .* mask;
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s = create_mask_GUI_export('mask', mask, 'mask3D', mask3D, 'mask_dims', mask_dims);
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s.figure1.UserData.ax = ax;
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s.figure1.UserData.fig = fig;
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s.figure1.UserData.asize = asize;
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s.figure1.UserData.CData = CData_orig;
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if ax.isprop('img')
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s.figure1.UserData.img_orig = img_orig;
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if s.figure1.UserData.mask3D
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orig_fig_listener = s.figure1.UserData.ax.slider_handle.listener('Value','PostSet',@(src, evnt)orig_fig_slice_update(s));
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end
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end
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try
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while ~s.figure1.UserData.done
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mask = s.figure1.UserData.mask;
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pause(0.1)
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end
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set(groot,'CurrentFigure',fig);
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ax.Children.CData = CData_orig;
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if ax.isprop('img')
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ax.img = img_orig;
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end
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catch
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if ~isprop(s, 'figure1')
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fprintf('Lost connection to GUI.\n')
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end
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end
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try
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if s.figure1.UserData.mask3D
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delete(orig_fig_listener)
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end
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delete(s.figure1)
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catch
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end
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% if needed, convert 2D mask to indicies
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if vars.ind
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out = beamline.mask2ind(mask);
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else
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out = mask;
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end
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% save to disk
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if ~isempty(vars.file)
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valid_mask = out;
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try
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utils.savefast_safe(vars.file, 'valid_mask');
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catch
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fprintf('Failed to save mask to disk.');
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end
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end
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end
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function orig_fig_slice_update(s)
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val = s.figure1.UserData.ax.slider_handle.Value;
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set(s.axes1.slider_handle, 'Value', val);
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set(s.axes1.edit_handle, 'String', num2str(val));
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s.axes1.update_fig(s.axes1);
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end
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