initial commit

2026-09-17 21:49:08 +09:00 · 2026-08-07 15:56:42 +09:00
commit 91ad25aca9
1012 changed files with 159314 additions and 0 deletions
@@ -0,0 +1,120 @@
+%  RADIATION_DAMAGE_ESTIMATION Plot SVD filtered curved of the vertical fluctuations 
+%  tomo invariant to shown if there was radiation damage 
+%
+% radiation_damage_estimation(object, par, varargin)
+%
+% Inputs:
+%     **object      - complex valued projections
+%     **par         - tomography paramter structure 
+%     **varargin    - see the code 
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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.
+
+
+function radiation_damage_estimation(object, par, varargin)
+
+    import plotting.*
+    import math.*
+
+    
+    parser = inputParser;
+    parser.addParameter('N_SVD_modes',  1 , @isnumeric )
+    parser.addParameter('smoothing', 15 , @isnumeric )
+    parser.addParameter('logscale',  true , @islogical ) % threshold for mask estimation 
+    parser.addParameter('invariant',  'derivative' , @isstr ) % threshold for mask estimation 
+    parser.addParameter('vert_range',  [] , @isnumeric ) % threshold for mask estimation 
+
+    parser.parse(varargin{:})
+    r = parser.Results;
+    
+    if ~isempty(r.vert_range)
+        object = object((max(1,r.vert_range(1)):min(end,r.vert_range(end))),:,:);
+    end
+    
+    switch r.invariant
+        case 'phase'
+            %% standard vertical mass fluctuation
+            phase_diff = tomo.get_phase_gradient(object, 2,0.5);
+            phase = -tomo.unwrap2D_fft(phase_diff, 2, par.air_gap);
+            invariant = max(0,squeeze(sum(phase,2)));
+        case 'derivative'
+            %% vertical derivative fluctuation
+            phase_diff_vert = math.get_phase_gradient_1D(object, 1,1);
+            invariant = squeeze(sum(phase_diff_vert,2));
+    end
+
+    % smoothing in the time domain to remove outliers 
+    mass_filt = medfilt2(invariant,[1,floor(r.smoothing/2)*2+1], 'symmetric'); 
+    
+    
+    figure(5);
+    subplot(3,1,1)
+    imagesc(invariant)
+    axis tight xy
+    colormap(franzmap)
+    caxis(sp_quantile(invariant, [0.01, 0.99], 10))
+    title(sprintf('Vertical mass derivative S%05d - S%05d',par.scanstomo(1),par.scanstomo(end)))
+    xlabel('Projection number')
+    grid on 
+    subplot(3,1,2)
+    Navg_slices= 10; % average over last 10 slices 
+    mass_filt_resid = mass_filt - median(mass_filt(:,end-Navg_slices:end),2); 
+    imagesc(mass_filt_resid)
+    axis tight xy
+    if r.logscale
+        set(gca, 'xscale', 'log')
+    end
+    colormap bone
+    caxis(sp_quantile(mass_filt_resid, [0.01, 0.99], 10))
+    title('Filtered change with respect to median')
+    xlabel('Projection number')
+    grid on 
+    
+    subplot(3,1,3)
+    [U,S,V] = svd(mass_filt); 
+    S = S / sqrt(sum(diag(S.^2)));
+    plot( V(:,[2:r.N_SVD_modes+1]) * S(2:r.N_SVD_modes+1,2:r.N_SVD_modes+1) )
+    if r.logscale
+        set(gca, 'xscale', 'log')
+    end
+    title(sprintf('PCA decomposition - shows changes in the sample, Power=%2.3g%%', 100*sum(diag(S(2:end,2:end)).^2)))
+    axis tight
+    xlabel('Aprox projection number')
+    grid on 
+    
+    file_png = fullfile(par.output_folder,'Radiation_damage_curve.png');
+    disp(['Saving ' file_png])
+    
+end