mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 19:39:08 +09:00
initial commit
This commit is contained in:
@@ -0,0 +1,298 @@
|
||||
% This script is to plot, correct and export solution SAXS data to SASfit
|
||||
% accounts for transmission, time and thickness correction
|
||||
% scales the data to a calibration factor
|
||||
% background correction, removal of bad pixels
|
||||
% not suitable for anisotropic data
|
||||
% saves the output to be used in SASfit
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% EDIT HERE
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% give the calibration factor for absolute intensity, calculated previously
|
||||
cal_factor_SAXS = 2.91e-4;
|
||||
cal_factor_WAXS = 2.01e-5 ;
|
||||
|
||||
% where the data is saved (Data10, afs, p-account)
|
||||
base_dir = '~/Data10/';%'/sls/X12SA/Data20/e16598/';
|
||||
save_dir = '~/Data10/';%'/mnt/das-gpfs/work/p16598/';
|
||||
eaccount = beamline.identify_eaccount; % 'e16598';
|
||||
|
||||
% samples and thicknesses
|
||||
Air = 15; % scan used for transmission calculation
|
||||
sample_scan = [34:38]; % should be given
|
||||
sample_thickness = 0.15; % in cm: important for absolute scattering
|
||||
back_scan = []; % used as background, leave it empty [] for no subtraction !!NOT TESTED!!
|
||||
back_thickness = 0.01; % in cm: important for absolute scattering
|
||||
|
||||
% export data for SASfit?
|
||||
export_sasfit = 1;
|
||||
|
||||
%plot curves?
|
||||
plot_curves = 0;
|
||||
|
||||
% save figures?
|
||||
save_fig = 0;
|
||||
|
||||
% average the scan points? 1 = yes, 0 = no
|
||||
average_scan = 1;
|
||||
% scale also the waxs data? yes = 1; no = 0;
|
||||
use_waxs = 0;
|
||||
|
||||
% which bad pixels should be removed
|
||||
bad_pixel = []; %given as a vector [811, 825]
|
||||
|
||||
% use all data measurement points or skip some (faster)
|
||||
skip_measurements = [100]; % use 1 to show all
|
||||
|
||||
% used to reduce noise at the beginning and end of scattering curve
|
||||
skip_first_points = 55;
|
||||
skip_last_points = 150;
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
%% load the diode value for the air
|
||||
S_air = io.spec_read(base_dir,'ScanNr',Air);
|
||||
%scale in case the exposure times are different
|
||||
exp_time = S_air.sec(1,1);
|
||||
scale_air = 1/exp_time;
|
||||
Air_data = load(sprintf('%s/analysis/radial_integration/%s_1_%05d_00000_00000_integ.mat', base_dir, eaccount, Air));
|
||||
I_air = mean(Air_data.I_all, 3);
|
||||
% average over the segments when needed
|
||||
if size(I_air, 2) > 1
|
||||
I_air = (I_air .* Air_data.norm_sum)./sum(Air_data.norm_sum, 2);
|
||||
I_air = sum(I_air, 2);
|
||||
end
|
||||
|
||||
if use_waxs
|
||||
Air_waxs = load(sprintf('%s/analysis/radial_integration_waxs/%s_2_%05d_00000_00000_integ.mat', base_dir, eaccount, Air));
|
||||
I_air_waxs = mean(squeeze(Air_waxs.I_all), 2);
|
||||
end
|
||||
%% background correction
|
||||
if ~isempty(back_scan)
|
||||
for b = 1:length(back_scan)
|
||||
bgr = load(sprintf('%s/analysis/radial_integration/%s_1_%05d_00000_00000_integ.mat', base_dir, eaccount, back_scan(b)));
|
||||
S_back = spec_read(base_dir,'ScanNr',back_scan(b));
|
||||
% in case the burst scan takes place, the transmission is
|
||||
% calculated differently
|
||||
if ~isempty(findstr(S_back.S, 'burst_scan'))
|
||||
delimiter = ' ';
|
||||
formatSpec = '%*s%*s%s%[^\n\r]';
|
||||
fileID = fopen(sprintf('%smcs/S00000-00999/S%05d/%s_%05d.dat', base_dir,back_scan(b), eaccount, back_scan(b)), 'r');
|
||||
dataArray = textscan(fileID, formatSpec, 'Delimiter', delimiter, 'MultipleDelimsAsOne', true, 'ReturnOnError', false);
|
||||
exp_time = dataArray{1,1}{7,1};
|
||||
scale_back = 1/str2num(exp_time);
|
||||
diode = mean(str2num(dataArray{1,1}{9,end}));
|
||||
transm_back = ((diode*scale_back)/(mean(S_air.diode)*scale_air));
|
||||
fclose(fileID);
|
||||
else
|
||||
%scale in case the exposure times are different
|
||||
exp_time = S_back.sec(1,1);
|
||||
scale_back = 1/exp_time;
|
||||
transm_back = (mean(S_back.diode)/mean(S_back.bpm4i))/(mean(S_air.diode)/mean(S_air.bpm4i));
|
||||
end
|
||||
%average background
|
||||
I_bgr = mean(bgr.I_all, 3);
|
||||
if size(I_bgr, 2) > 1
|
||||
I_bgr = (I_bgr .* bgr.norm_sum)./sum(bgr.norm_sum, 2);
|
||||
I_bgr = sum(I_bgr, 2);
|
||||
end
|
||||
I_bgr = ((((I_bgr*scale_back)*1/transm_back)-(I_air*scale_air))*1/back_thickness);
|
||||
I_bgr = I_bgr * cal_factor_SAXS;
|
||||
if use_waxs
|
||||
%average background_WAXS
|
||||
bgr_waxs = importdata(sprintf('%s/analysis/radial_integration_waxs/%s_2_%05d_00000_00000_integ.mat', base_dir, eaccount, back_scan(b)));
|
||||
I_bgr_waxs = mean(squeeze(bgr_waxs.I_all), 2);
|
||||
I_bgr_waxs = ((((I_bgr_waxs*scale_back)*1/transm_back)-(I_air_waxs*scale_air))*1/back_thickness);
|
||||
I_bgr_waxs = I_bgr_waxs * cal_factor_WAXS;
|
||||
end
|
||||
end
|
||||
else
|
||||
I_bgr_waxs = 0;
|
||||
I_bgr = 0;
|
||||
end
|
||||
|
||||
%% load and correct the sample
|
||||
for s = 1:length(sample_scan)
|
||||
sample_filename=sprintf('%s/analysis/radial_integration/%s_1_%05d_00000_00000_integ.mat', base_dir, eaccount, sample_scan(s));
|
||||
if exist(sample_filename) == 2
|
||||
display(['reading file ',sample_filename])
|
||||
sample = load(sample_filename);
|
||||
else
|
||||
continue
|
||||
end
|
||||
S_s = io.spec_read(base_dir,'ScanNr',sample_scan(s));
|
||||
if ~isempty(findstr(S_s.S, 'burst_scan'))
|
||||
delimiter = ' ';
|
||||
formatSpec = '%*s%*s%s%[^\n\r]';
|
||||
fileID = fopen(sprintf('%smcs/S00000-00999/S%05d/%s_%05d.dat', base_dir,sample_scan(s), eaccount,sample_scan(s)), 'r');
|
||||
dataArray = textscan(fileID, formatSpec, 'Delimiter', delimiter, 'MultipleDelimsAsOne', true, 'ReturnOnError', false);
|
||||
exp_time = dataArray{1,1}{7,1};
|
||||
scale_s = 1/str2num(exp_time);
|
||||
diode = mean(str2num(dataArray{1,1}{9,end}));
|
||||
transm_sample = ((diode*scale_s)/(mean(S_air.diode)*scale_air));
|
||||
fclose(fileID);
|
||||
else
|
||||
%scale in case the exposure times are different
|
||||
exp_time = S_s.sec(1,1);
|
||||
scale_s = 1/exp_time;
|
||||
transm_sample = (mean(S_s.diode)/mean(S_s.bpm4i))/(mean(S_air.diode)/mean(S_air.bpm4i));
|
||||
end
|
||||
%load the sample
|
||||
I_sample = squeeze(sample.I_all);
|
||||
q_sample = sample.q';
|
||||
|
||||
if use_waxs
|
||||
%average background_WAXS
|
||||
sample_waxs = load(sprintf('%s/analysis/radial_integration_waxs/%s_2_%05d_00000_00000_integ.mat', base_dir, eaccount, sample_scan(s)));
|
||||
I_sample_waxs = (sample_waxs.I_all);
|
||||
q_sample_waxs = sample_waxs.q';
|
||||
else
|
||||
q_sample_waxs = [];
|
||||
I_sample_waxs = [];
|
||||
end
|
||||
if average_scan
|
||||
I_sample = mean(I_sample, 3);
|
||||
I_std = mean(sample.I_std, 3);
|
||||
if size(I_sample, 2) > 1
|
||||
I_sample = (I_sample .* sample.norm_sum)./sum(sample.norm_sum, 2);
|
||||
I_std = (I_std .* sample.norm_sum)./sum(sample.norm_sum, 2);
|
||||
I_std = sum(I_std, 2).*cal_factor_SAXS;
|
||||
I_sample = sum(I_sample, 2);
|
||||
end
|
||||
I_std = I_std(skip_first_points:end-skip_last_points,:);
|
||||
I_sample = ((((I_sample*scale_s)*1/transm_sample)-(I_air*scale_air))*1/sample_thickness);
|
||||
if ~isempty(bad_pixel)
|
||||
I_sample(bad_pixel,1) = (I_sample(bad_pixel-1,1)+I_sample(bad_pixel+1,1))/2;
|
||||
end
|
||||
I_sample = I_sample * cal_factor_SAXS;
|
||||
I_cor = (I_sample-I_bgr);
|
||||
I_cor = I_cor(skip_first_points:end-skip_last_points,:);
|
||||
|
||||
if use_waxs
|
||||
hold on
|
||||
I_sample_waxs = median(I_sample_waxs,3);
|
||||
I_sample_waxs = ((((I_sample_waxs.*scale_s).*1/transm_sample)-(I_air_waxs.*scale_air)).*1/sample_thickness);
|
||||
I_sample_waxs = I_sample_waxs * cal_factor_WAXS;
|
||||
I_cor_waxs = (I_sample_waxs-I_bgr_waxs);
|
||||
|
||||
else
|
||||
I_cor_waxs = [];
|
||||
end
|
||||
I_total = [I_cor; I_cor_waxs];
|
||||
|
||||
q_total = [q_sample(skip_first_points: end-skip_last_points,:); q_sample_waxs];
|
||||
[q_total, index] = sort(q_total);
|
||||
I_total = I_total(index);
|
||||
|
||||
if plot_curves
|
||||
figure
|
||||
plot(q_total*10, I_total);
|
||||
set(gca,'XScale','log', 'YScale','log');
|
||||
grid on;
|
||||
box on;
|
||||
xlabel('scattering vector q (nm^{-1})');
|
||||
ylabel('differential scattering cross-section (cm^{-1})');
|
||||
hold on
|
||||
end
|
||||
if export_sasfit
|
||||
save_data = [q_total*10, I_total, I_std];
|
||||
filename = sprintf('scan_%05d_avg', sample_scan);
|
||||
save(sprintf('%sanalysis/dat_files/%s.dat', save_dir , filename) , 'save_data', '-ascii');
|
||||
end
|
||||
else
|
||||
if plot_curves
|
||||
figure
|
||||
hold on
|
||||
end
|
||||
for i = 1:skip_measurements:size(sample.I_all, 3)
|
||||
I_point = sample.I_all(:,:,i);
|
||||
I_point_std = sample.I_std(:,:, i);
|
||||
if size(I_point, 2) > 1
|
||||
I_point = (I_point .* sample.norm_sum)./sum(sample.norm_sum, 2);
|
||||
I_point = sum(I_point, 2);
|
||||
I_point_std = (I_point_std .* sample.norm_sum)./sum(sample.norm_sum, 2);
|
||||
I_point_std = sum(I_point_std, 2).*cal_factor_SAXS;
|
||||
end
|
||||
I_point_std = I_point_std(skip_first_points:end-skip_last_points,:);
|
||||
if ~isempty(bad_pixel)
|
||||
I_point(bad_pixel,1) = (I_point(bad_pixel-1,1) + I_point(bad_pixel+1,1))/2;
|
||||
end
|
||||
I_point = ((((I_point*scale_s)*1/transm_sample)-(I_air*scale_air))*1/sample_thickness);
|
||||
I_point = I_point * cal_factor_SAXS;
|
||||
I_cor = (I_point-I_bgr);
|
||||
I_cor = I_cor(skip_first_points: end-skip_last_points,:);
|
||||
|
||||
if use_waxs
|
||||
I_point_waxs = I_sample_waxs(:,i);
|
||||
I_point_waxs = ((((I_point_waxs*scale_s)*1/transm_sample)-(I_air_waxs*scale_air))*1/sample_thickness);
|
||||
I_point_waxs = I_point_waxs * cal_factor_WAXS;
|
||||
I_cor_waxs = (I_point_waxs-I_bgr_waxs);
|
||||
I_point_std_WAXS = I_sample_waxs(:,:, i);
|
||||
I_point_std_WAXS = I_point_std_WAXS.*cal_factor_WAXS;
|
||||
I_point_std_WAXS = sum(I_point_std_WAXS, 2).*cal_factor_SAXS;
|
||||
else
|
||||
I_cor_waxs = [];
|
||||
end
|
||||
I_total = [I_cor; I_cor_waxs];
|
||||
q_total = [q_sample(skip_first_points: end-skip_last_points,:); q_sample_waxs];
|
||||
[q_total, index] = sort(q_total);
|
||||
I_total = I_total(index);
|
||||
I_point_std_total= [I_point_std; I_point_std_WAXS];
|
||||
if plot_curves
|
||||
plot(q_total*10, I_total);
|
||||
grid on;
|
||||
box on;
|
||||
set(gca,'XScale','log', 'YScale','log');
|
||||
xlabel('scattering vector q (nm^{-1})');
|
||||
ylabel('differential scattering cross-section (cm^{-1})');
|
||||
axis tight
|
||||
hold on
|
||||
drawnow
|
||||
end
|
||||
if export_sasfit
|
||||
save_data = [q_total*10, I_total, I_point_std_total];
|
||||
filename = sprintf('scan_%05d_pt_%05d', sample_scan(s), i);
|
||||
save(sprintf('%sanalysis/dat-files/%s.dat', save_dir , filename) , 'save_data', '-ascii');
|
||||
end
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
end
|
||||
if save_fig
|
||||
%save the results
|
||||
saveas(gcf, sprintf('%sanalysis/scanNr_%05d.jpg', save_dir , sample_scan))
|
||||
end
|
||||
|
||||
%*-----------------------------------------------------------------------*
|
||||
%| |
|
||||
%| 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) 2017 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.
|
||||
Reference in New Issue
Block a user