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tomo/+tomo/remove_projections.m

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+%  REMOVE_PROJECTIONS remove projections and adjust the other relevant paramaters 
+% 
+%  [stack_object,theta,total_shift,par] = remove_projections(stack_object,theta,total_shift,par, which_remove, plot_fnct = @(x)x)
+%
+% Inputs: 
+%  **stack_object        measured projections    
+%  **theta               measured angles 
+%  **total_shift         Nx2 vector or projection shifts 
+%  **par                 parameter structure 
+%  **which_remove        indices or logical array denoting the projection to be removed 
+%  **plot_fnct = @(x)x   function to be used for plotting, default == @(x)x
+% *returns*
+%   ++stack_object,theta,total_shift,par - inputs after projection removal 
+
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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 [stack_object,theta,total_shift,par] = remove_projections(stack_object,theta,total_shift,par, which_remove, plot_fnct, object_ROI)
+
+    if nargin < 6 
+        plot_fnct = @(x)x; 
+    end
+
+    if islogical(which_remove)
+        which_remove = find(which_remove); 
+    end
+    
+    if isempty(which_remove)
+       return 
+    end
+    
+    utils.verbose(1, 'Removing %i/%i projections', length(which_remove), par.num_proj)
+    [Nx,Ny,~] = size(stack_object);
+    title_extra = {}; 
+    for ii = 1:length(which_remove)
+        title_extra{end+1} = sprintf(' N residua: %i',par.nresidua_per_frame(which_remove(ii))); 
+    end
+
+
+    %%% Getting rid of unwanted projections %%%
+    if ~isempty(which_remove)
+        
+        tomo.show_projections(stack_object(:,:,which_remove), theta(which_remove), par, ...
+            'title', 'Projection to be removed','plot_residua', true, 'title_extra', title_extra, 'fnct', plot_fnct, ...
+            'rectangle_pos', [object_ROI{2}(1), object_ROI{2}(end), object_ROI{1}(1), object_ROI{1}(end)]) 
+
+        if strcmpi(input(sprintf('Do you want remove %i missing/wrong projections and keep going (y/N)?',length(which_remove)),'s'),'y') 
+            disp('Removing missing/wrong projections. stack_object, scanstomo, theta and num_proj are modified')
+
+            stack_object(:,:,which_remove) = [];
+            theta(which_remove)=[];
+            total_shift(which_remove,:) = [];
+            
+            par.scanstomo(which_remove)=[];
+            try par.energy(which_remove,:) = []; end
+            try par.nresidua_per_frame(which_remove) = []; end
+            try par.subtomos(which_remove) = []; end
+            par.num_proj = length(par.scanstomo); 
+            
+            disp('Done')
+        end
+    end
+
+
+
+end