%AFFINE_MATRIX_SEARCH
% Code to evaluate the affine matrix angle for a series of 
% reconstructions
%
% Each reconstruction should have preffix 'affine' in the name
% and contain a field called p.affine_angle
%
% see also: aligned_FSC_template


close all; clear all; 
addpath('utils')
%%
scans=[74 78];

filename_search_mask = '*affine*recons*.h5';

path1=sprintf('~/Data10/analysis/S00000-00999/S%05d/',scans(1));
path2=sprintf('~/Data10/analysis/S00000-00999/S%05d/',scans(2));

params_fsc.plotting = true;
params_fsc.flipped_images = true;
params_fsc.thickring = 30;
params_fsc.remove_ramp = true; 
params_fsc.GUIguess = false; 
params_fsc.prop_obj = false;
%params_fsc.guessx=18;
%params_fsc.guessy=74;
%params_fsc.crop= {701:1031,584:1820};
files1 = dir(fullfile(path1,filename_search_mask));
files2 = dir(fullfile(path2,filename_search_mask));

if numel(files1)==0
    error(sprintf('I did not find any files in %s matching %s',path1,filename_search_mask))
elseif numel(files2)==0
    error(sprintf('I did not find any files in %s matching %s',path2,filename_search_mask))
end

for idx = 1:numel(files1)

    file1 = fullfile(path1,files1(idx).name);
    file2 = fullfile(path2,files2(idx).name);
    disp(['loading ' file1])
     p1 = io.load_ptycho_recons(file1);
    disp(['loading ' file2])
     p2 = io.load_ptycho_recons(file2);

    if all(all(p1.p.affine_matrix ~= p2.p.affine_matrix))
        error(['The affine angle is not the same in files, ' file1 ' and ' file2])
    else
        angle_array(idx) = atan(p1.p.affine_matrix(2,1))/pi*180;
    end
    
    [resol stat] = aligned_FSC(file1,file2,params_fsc);
    resolution(idx,:) = resol;
    fsc_mean_1nm(idx) = stat.fsc_mean_1nm;
    SNR_avg(idx) = stat.SNR_avg;
end    

%% 
FS = 15; 
figure;
len = length(resolution(:,1));
X=angle_array(1:len);
Y=resolution(:,1);
F0 = fit(X', Y, 'poly2'); 
xx=(X(1):0.01:X(end));
yy=F0.p1*xx.^2 + F0.p2*xx + F0.p3;
vertex=-F0.p2/(2*F0.p1);
plot(angle_array(1:len), resolution(:,1),'r^-','linewidth',2); grid on;
hold on;
plot(angle_array(1:len), resolution(:,2),'bo-','linewidth',2);
plot(xx,yy,'-c')
hold off;
xlabel('Angle');
ylabel('Resolution (nm)')
set(gca,'fontsize',FS,'fontweight','bold');


display(sprintf('The vertex of the fitted parabola is at angle = %4.2f degrees',vertex))

legend ('First intersection point with FSC','Last intersection point with FSC')

title(sprintf('FSC S%05d/S%05d',scans(1),scans(2)))

figure(2);
clf
plot(angle_array(1:len), fsc_mean_1nm,'r^','linewidth',2); grid on;
xlabel('Angle [degrees]')
title('FSC mean [inverse nm]')

% Academic License Agreement
%
% Source Code
%
% Introduction 
% •	This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR") 
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% 5.	LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into 
%       another computing language:
%       "Data processing was carried out using the PtychoShelves package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul 
%       Scherrer Institut, Switzerland."
%
% Additionally, any publication using the package, or any translation of the code into another computing language should cite 
% K. Wakonig, H.-C. Stadler, M. Odstrčil, E.H.R. Tsai, A. Diaz, M. Holler, I. Usov, J. Raabe, A. Menzel, M. Guizar-Sicairos, PtychoShelves, a versatile 
% high-level framework for high-performance analysis of ptychographic data, J. Appl. Cryst. 53(2) (2020). (doi: 10.1107/S1600576720001776)
% and for difference map:
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008). 
%   (doi: 10.1126/science.1158573),
% for maximum likelihood:
% P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012). 
%   (doi: 10.1088/1367-2630/14/6/063004),
% for LSQ-ML:
% M. Odstrčil, A. Menzel, and M. Guizar-Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Opt. Express 26(3), 3108 (2018). 
%   (doi: 10.1364/OE.26.003108),
% for mixed coherent modes:
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
% and/or for multislice:
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016). 
%   (doi: 10.1364/OE.24.029089),
% and/or for OPRP:
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby,  Ptychographic coherent diffractive imaging with orthogonal probe relaxation. 
% Opt. Express 24.8 (8360-8369) 2016. (doi: 10.1364/OE.24.008360).
% 6.	Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the 
%       names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
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%       make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies: 
%       © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017. 
% 8.	The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
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%       to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents, 
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