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134 lines
5.1 KiB
Matlab
134 lines
5.1 KiB
Matlab
% prepare_real_deform_data - load already prealigned and fixed projections
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%
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%[dphase, shift_3D_all_0, angles, par] = ...
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% prepare_real_deform_data(path_to_projections, projection_filename, sample_name, par_0)
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%
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% Inputs:
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% **path_to_projections path where are stored preloaded data
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% **projection_filename name of the file where are the preloaded data
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% **sample_name name of the sample, it used for cache file reparation
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% **par_0 initial paramters structure that will be merged with the loaded paramters
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% Outputs:
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% ++dphase phase difference for the complex project
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% ++shift_3D_all_0 original deformation = {}
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% ++angles angles for each of the projection
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% ++par merged parameter structure
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% ++object complex valued projections
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%*-----------------------------------------------------------------------*
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%| |
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%| Except where otherwise noted, this work is licensed under a |
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%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
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%| International (CC BY-NC-SA 4.0) license. |
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%| |
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%| Copyright (c) 2018 by Paul Scherrer Institute (http://www.psi.ch) |
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%| |
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%| Author: CXS group, PSI |
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%*-----------------------------------------------------------------------*
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% You may use this code with the following provisions:
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%
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% If the code is fully or partially redistributed, or rewritten in another
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% computing language this notice should be included in the redistribution.
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%
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% If this code, or subfunctions or parts of it, is used for research in a
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% publication or if it is fully or partially rewritten for another
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% computing language the authors and institution should be acknowledged
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% in written form in the publication: “Data processing was carried out
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% using the “cSAXS matlab package” developed by the CXS group,
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% Paul Scherrer Institut, Switzerland.”
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% Variations on the latter text can be incorporated upon discussion with
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% the CXS group if needed to more specifically reflect the use of the package
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% for the published work.
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%
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% A publication that focuses on describing features, or parameters, that
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% are already existing in the code should be first discussed with the
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% authors.
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%
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% This code and subroutines are part of a continuous development, they
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% are provided “as they are” without guarantees or liability on part
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% of PSI or the authors. It is the user responsibility to ensure its
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% proper use and the correctness of the results.
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function [dphase, shift_3D_all_0, angles, par, object] = ...
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prepare_real_deform_data(path_to_projections, projection_filename, sample_name, par_0)
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import utils.*
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import math.*
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import plotting.*
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shift_3D_all_0 = {};
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if ~exist('cache', 'dir')
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mkdir('cache')
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end
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cached_file = fullfile(path_to_projections, ['cache_nonrigid_tomo', sample_name,'.mat']);
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% try to load cached data
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verbose(0, 'Loading prepared data from %s', fullfile(path_to_projections, projection_filename))
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%% load complex valued projections
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d = load(fullfile(path_to_projections, projection_filename));
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verbose(0, 'Loading done')
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%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%% create data and geometry
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%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%%%%%%%%%%%%%%%%%%%%%%%%%%%
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if isfield(d, 'dphase')
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dphase = d.dphase;
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else
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object = complex(d.stack_object_r,d.stack_object_i);
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object_ROI = d.object_ROI;
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object = object(object_ROI{:},:);
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object = smooth_edges(object);
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dphase = tomo.block_fun(@math.get_phase_gradient_1D,object, 2);
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end
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if isfield(d, 'angles')
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angles = d.angles;
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else
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angles = d.theta;
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end
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dphase = smooth_edges(dphase);
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try
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par = d.par;
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catch
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par = struct();
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end
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% rewrite loaded params by some defaults
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for field = fields(par_0)'
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par.(field{1}) = par_0.(field{1});
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end
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par.output_folder = path_to_projections;
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if debug()
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% plot angular blocks
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figure
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plot(angles, '.-')
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for ii = 1:Nblocks
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plotting.vline(ii*Bsize)
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end
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xlabel('Projection #')
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ylabel('Angle [deg]')
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title('Angular block splitting')
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drawnow
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end
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end |