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tomo/+nonrigid/prepare_real_deform_data.m

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+% prepare_real_deform_data - load already prealigned and fixed projections
+%
+%[dphase, shift_3D_all_0, angles, par] = ...
+%                 prepare_real_deform_data(path_to_projections, projection_filename, sample_name, par_0)
+%
+% Inputs:
+%    **path_to_projections     path where are stored preloaded data  
+%    **projection_filename     name of the file where are the preloaded data 
+%    **sample_name             name of the sample, it used for cache file reparation 
+%    **par_0                   initial paramters structure that will be merged with the loaded paramters 
+% Outputs: 
+%    ++dphase               phase difference for the complex project 
+%    ++shift_3D_all_0       original deformation = {}
+%    ++angles               angles for each of the projection 
+%    ++par                  merged parameter structure 
+%    ++object               complex valued projections 
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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) 2018 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 [dphase, shift_3D_all_0, angles, par, object] = ...
+                 prepare_real_deform_data(path_to_projections, projection_filename, sample_name, par_0)
+
+     import utils.*
+     import math.*
+     import plotting.*
+             
+    shift_3D_all_0 = {};
+    if ~exist('cache', 'dir')
+        mkdir('cache')
+    end
+    
+    cached_file = fullfile(path_to_projections, ['cache_nonrigid_tomo', sample_name,'.mat']); 
+    % try to load cached data 
+
+        verbose(0, 'Loading prepared data from %s', fullfile(path_to_projections, projection_filename))
+        %% load complex valued projections  
+        d = load(fullfile(path_to_projections, projection_filename));
+        verbose(0, 'Loading done')
+
+        %%%%%%%%%%%%%%%%%%%%%%%%%%%
+        %% create data and geometry
+        %%%%%%%%%%%%%%%%%%%%%%%%%%%
+        %%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+         if isfield(d, 'dphase')
+            dphase = d.dphase; 
+         else
+            object = complex(d.stack_object_r,d.stack_object_i); 
+
+            object_ROI = d.object_ROI;
+
+            
+            object = object(object_ROI{:},:);
+            
+
+            object = smooth_edges(object); 
+
+            dphase = tomo.block_fun(@math.get_phase_gradient_1D,object, 2);
+
+         end
+         if isfield(d, 'angles')
+            angles = d.angles; 
+         else
+            angles = d.theta; 
+         end
+         
+         
+        dphase = smooth_edges(dphase); 
+
+        
+        
+
+        try
+            par = d.par; 
+        catch
+            par = struct(); 
+        end
+        
+        
+
+    % rewrite loaded params by some defaults 
+   for field = fields(par_0)'
+        par.(field{1}) = par_0.(field{1}); 
+   end
+   
+   par.output_folder = path_to_projections; 
+   
+   if debug()
+        % plot angular blocks 
+        figure
+        plot(angles, '.-')
+        for ii = 1:Nblocks
+           plotting.vline(ii*Bsize) 
+        end
+        xlabel('Projection #')
+        ylabel('Angle [deg]')
+        title('Angular block splitting')
+        drawnow 
+   end
+
+   
+end