mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 23:39:08 +09:00
initial commit
This commit is contained in:
@@ -0,0 +1,134 @@
|
||||
% 14-11-2012
|
||||
% Integrates frames from a loopscan
|
||||
%
|
||||
% Syntax:
|
||||
% [int] = integrate_frames(base_path,scan_num,plotfigure,det_num,savedata,maskfilename)
|
||||
% Needed parameters: base_path (e.g. '~/Data10/')
|
||||
% scan_num (scan number)
|
||||
% Optional parameters: plotfigure (figure number for fial plot, 0 for no plotting, by default is 0)
|
||||
% det_num (detector number, default 1)
|
||||
% savedata (=1 to save data in 'analysis/integrated_frames/', default 0)
|
||||
% maskfilename (valid mask file name. If empty [], no mask used)
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 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
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% 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
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 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
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% 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
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% 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
|
||||
% 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
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 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
|
||||
% another computing language:
|
||||
% "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
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for maximum likelihood:
|
||||
% P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012).
|
||||
% (doi: 10.1088/1367-2630/14/6/063004),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% and/or for multislice:
|
||||
% 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).
|
||||
% (doi: 10.1364/OE.24.029089).
|
||||
% 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
|
||||
% 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.
|
||||
% 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
|
||||
% 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
|
||||
% 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:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% 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,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 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
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
function [int] = integrate_frames(base_path,scan_num,plotfigure,det_num,savedata,maskfile)
|
||||
import beamline.pilatus_valid_pixel_roi
|
||||
import io.image_read
|
||||
import io.spec_read
|
||||
import plotting.integrate_frames
|
||||
|
||||
if exist('det_num') == 0
|
||||
det_num=1;
|
||||
end
|
||||
if exist('savedata') == 0
|
||||
savedata=0;
|
||||
end
|
||||
if exist('maskfile') == 0
|
||||
maskfile=[];
|
||||
end
|
||||
if exist('plotfigure') == 0
|
||||
plotfigure = 0;
|
||||
end
|
||||
|
||||
%maskfile=[];
|
||||
if savedata
|
||||
savefolder=[base_path 'analysis/integrated_frames/'];
|
||||
if savefolder ~= 7
|
||||
mkdir(savefolder)
|
||||
end
|
||||
end
|
||||
|
||||
path=sprintf('%spilatus_%01d',base_path,det_num);
|
||||
filename0=compile_x12sa_filename(scan_num,0);
|
||||
data0=image_read(filename0);
|
||||
img0=data0.data;
|
||||
dims=size(img0);
|
||||
S=spec_read(base_path,'ScanNr',scan_num);
|
||||
num=size(S.bpm4i,1);
|
||||
|
||||
if ~isempty(maskfile)
|
||||
load(maskfile)
|
||||
valid_mask = pilatus_valid_pixel_roi(valid_mask,'RoiSize',size(img0));
|
||||
mask = zeros(size(img0));
|
||||
mask(valid_mask.indices) = 1;
|
||||
else
|
||||
mask = ones(size(img0));
|
||||
end
|
||||
|
||||
int=img0*0;
|
||||
stack=zeros(dims(1),dims(2),num);
|
||||
|
||||
for jj=1:num
|
||||
filename=compile_x12sa_filename(scan_num,jj-1);
|
||||
data1=image_read(filename);
|
||||
img=data1.data.*mask;
|
||||
int=int+img;
|
||||
stack(:,:,jj)=img;
|
||||
end
|
||||
|
||||
if plotfigure ~= 0
|
||||
figure(plotfigure)
|
||||
figure_position=[187 295 817 650];
|
||||
set(gcf,'Position',figure_position);
|
||||
imagesc(log10(int)); axis xy equal tight; colorbar; colormap jet
|
||||
title(sprintf('integrated frames S%05d',scan_num))
|
||||
end
|
||||
if savedata
|
||||
savefilename=sprintf('%s/S%05d_%01d_integrated_frames',savefolder,scan_num,det_num);
|
||||
save([savefilename '.mat'],'int')
|
||||
print('-f2','-djpeg','-r300',[ savefilename '.jpg'] );
|
||||
print('-f2','-depsc','-r1200',[savefilename '.eps'] );
|
||||
end
|
||||
Reference in New Issue
Block a user