mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 21:49:08 +09:00
initial commit
This commit is contained in:
@@ -0,0 +1,220 @@
|
||||
% Another script for STXM evaluation of round roi scans
|
||||
%
|
||||
% Does not use Gaussians centered on grid points which leads to inaccuarate
|
||||
% values at the center positions (due to adding up all the Gaussians)
|
||||
% but rather uses the Matlab's "griddata" function.
|
||||
|
||||
clear all
|
||||
import utils.compile_x12sa_filename
|
||||
import utils.verbose
|
||||
|
||||
%% scan parameters
|
||||
scannumber = 2370;
|
||||
|
||||
scans = ['S' num2str(scannumber,'%05d')];
|
||||
asize = [128 128];
|
||||
%pathdir = sprintf('/afs/psi.ch/project/cxs/CDI/cSAXS_sxdm_2009_05_tomo/analysis/%s/', scans);
|
||||
pathdir = sprintf('../../analysis/%s/', scans);
|
||||
datafile = [pathdir, sprintf('%s_data_%03dx%03d.mat', scans, asize(1), asize(2))];
|
||||
|
||||
scan_type = 'round_roi';
|
||||
dr = 1.5e-6;
|
||||
lx = 30e-6;
|
||||
ly = 36e-6;
|
||||
nth = 5;
|
||||
|
||||
dx_spec = [65.4e-9 65.4e-9];
|
||||
|
||||
export_figures_to_svg = 0;
|
||||
|
||||
%% create positions
|
||||
|
||||
rmax = sqrt((lx/2)^2 + (ly/2)^2);
|
||||
nr = 1 + floor(rmax/dr);
|
||||
positions = [];
|
||||
for ir=1:nr+1
|
||||
rr = ir*dr;
|
||||
dth = 2*pi / (nth*ir);
|
||||
for ith=0:nth*ir-1
|
||||
th = ith*dth;
|
||||
x1 = rr * cos(th);
|
||||
x2 = rr * sin(th);
|
||||
if( abs(x1) > lx/2 || (abs(x2) >= ly/2) )
|
||||
continue
|
||||
end
|
||||
positions(end+1,:) = [x1/dx_spec(2) x2/dx_spec(2)]; %#ok<AGROW>
|
||||
end
|
||||
end
|
||||
numpts = size(positions,1);
|
||||
|
||||
%% load data
|
||||
if ~exist(datafile,'file')
|
||||
while ~exist(compile_x12sa_filename(scannumber,numpts-1),'file');
|
||||
disp(['Waiting for scan ' scans ' to finish.'])
|
||||
pause(10)
|
||||
end
|
||||
verbose(1); core.prepare_data_2d(asize, numpts, scannumber, [100,268],'','','',147576);
|
||||
end
|
||||
|
||||
load(datafile)
|
||||
|
||||
|
||||
|
||||
%% intialize variables for STXM analysis and upsampling
|
||||
|
||||
upsample =4;
|
||||
ndx = ceil(upsample*(2+lx/dr));
|
||||
ndy = ceil(upsample*(2+ly/dr));
|
||||
[xx,yy] = meshgrid((1:ndx) - ndx/2, (1:ndy) - ndy/2);
|
||||
|
||||
pos = positions;
|
||||
pos(:,1) = upsample*pos(:,1)*dx_spec(1)/dr;
|
||||
pos(:,2) = upsample*pos(:,2)*dx_spec(2)/dr;
|
||||
|
||||
trans = zeros(ndy,ndx);
|
||||
dpcx = zeros(ndy,ndx);
|
||||
dpcy = zeros(ndy,ndx);
|
||||
|
||||
% put the STXM results into linear vectors first
|
||||
lin_trans = zeros(numpts,1);
|
||||
lin_dpcx = zeros(numpts,1);
|
||||
lin_dpcy = zeros(numpts,1);
|
||||
|
||||
%% STXM analysis loop
|
||||
|
||||
for ii=1:numpts
|
||||
s1 = sum(data(:,:,ii),1);
|
||||
s2 = sum(data(:,:,ii),2);
|
||||
Atrans = sum(s1);
|
||||
Adpcx = sum(((1:asize(1))-asize(1)/2).*s1)/Atrans;
|
||||
Adpcy = sum(((1:asize(1))-asize(1)/2)'.*s2)/Atrans;
|
||||
lin_trans(ii) = Atrans;
|
||||
lin_dpcx(ii) = Adpcx;
|
||||
lin_dpcy(ii) = Adpcy;
|
||||
end
|
||||
|
||||
%% upsample
|
||||
|
||||
trans=griddata(pos(:,1),pos(:,2),lin_trans,xx,yy,'linear');
|
||||
dpcx_nearest=griddata(pos(:,1),pos(:,2),lin_dpcx,xx,yy,'nearest');
|
||||
dpcx_linear =griddata(pos(:,1),pos(:,2),lin_dpcx,xx,yy,'linear');
|
||||
%dpcy=griddata(pos(:,1),pos(:,2),lin_dpcy,xx,yy,'linear');
|
||||
|
||||
%I0 = mean(trans(10:20,3));
|
||||
[n,x] = hist(trans(:),asize(1));
|
||||
I0 = x(find(diff(n)>0,1,'last')+1);
|
||||
|
||||
% Compute integrated linear attenuation coefficient
|
||||
mu = -log(trans./ I0 );
|
||||
|
||||
%% plot
|
||||
|
||||
%figure(1)
|
||||
% scatter(positions(:,1),positions(:,2),300,lin_dpcx,'filled');
|
||||
% colormap bone(256)
|
||||
%colorbar
|
||||
% title([scans ': scattered photons per diffraction pattern'])
|
||||
% axis ij image off
|
||||
|
||||
% figure(2);
|
||||
%imagesc(dpcx_nearest);
|
||||
%axis image ij tight off
|
||||
%colormap bone(256); colorbar
|
||||
%title([scans ': scattered photons (upsampled by a factor of ' num2str(upsample) ', nearest neighbour interpolation)'])
|
||||
%scalebar(dr,'fontsize',20, 'linewidth',10)
|
||||
|
||||
figure(1);
|
||||
imagesc(dpcx_linear);
|
||||
axis image ij tight off
|
||||
colormap bone(256); colorbar
|
||||
title([scans ': DPC x'])
|
||||
scalebar(upsample*dx_spec(1),'fontsize',20, 'linewidth',10)
|
||||
|
||||
figure(4)
|
||||
imagesc(trans)
|
||||
axis image ij tight off
|
||||
colormap bone(256); colorbar
|
||||
scalebar(upsample*dx_spec(1),'fontsize',20, 'linewidth',10)
|
||||
title([scans ': transmission'])
|
||||
|
||||
figure(5)
|
||||
imagesc(mu)
|
||||
axis image ij tight off
|
||||
colormap bone(256); colorbar
|
||||
scalebar(upsample*dx_spec(1),'fontsize',20, 'linewidth',10)
|
||||
|
||||
%
|
||||
% roi_half = floor(upsample*nr/sqrt(2));
|
||||
% roi_mask = zeros(size(trans));
|
||||
% roi_mask(size(trans,1)/2-roi_half+1:size(trans,1)/2+roi_half,...
|
||||
% size(trans,2)/2-roi_half+1:size(trans,2)/2+roi_half) =1;
|
||||
% roi_mask(size(trans,1)/2-upsample+1:size(trans,1)/2+upsample,...
|
||||
% size(trans,2)/2-upsample+1:size(trans,2)/2+upsample) =0;
|
||||
%
|
||||
% roi_ind = find(roi_mask == 1);
|
||||
|
||||
%% export figures
|
||||
|
||||
if export_figures_to_svg
|
||||
saveas(1,fullfile(pathdir,'/S00327_dpcx_scatterplot.png'))
|
||||
%plot2svg(fullfile(pathdir,'/S00327_dpcx_scatterplot.svg'),1)
|
||||
plot2svg(fullfile(pathdir,'/S00327_dpcx_interpol_nearest.svg'),2)
|
||||
plot2svg(fullfile(pathdir,'/S00327_dpcx_interpol_linear.svg'),3)
|
||||
plot2svg(fullfile(pathdir,'/S00327_trans_interpol_linear.svg'),4)
|
||||
plot2svg(fullfile(pathdir,'/S00327_abs_mu_interpol_linear.svg'),5)
|
||||
disp(['Image files saved.']);
|
||||
end
|
||||
|
||||
% 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.
|
||||
Reference in New Issue
Block a user