%%%%%%%%%%%%%AFFINE_MATRIX_SEARCH%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Code to evaluate the affine matrix angle using GPU engine
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% it uses ptychography position refinement to estimate the optimal affine
% matrix correction , optimal camera rotation, and sample to camera
% distance 


%%  CALIBRATION OF GEOMETRY FOR PTYCHOTOMO
% 1) collected mirror scans at 0 and 180 deg with sufficienlty large overlapping FOV (~10x10um)
% 2) create a reconstruction template "working_template"
% 3) fill in "working_template" and both scan numbers variables to the EDIT section below 
% 4) run template and wait for final report 
%       we think we should use geometry_model = {'rotation', 'shear'};
% 5) run afterwards with 
%       find_camera_distance = true 
%       find_scanning_geometry = false
%       if necessary with the new distance find again the matrix
% NOTES: mirrored scans are critical to find camera rotation and
% p.affine_matrix but p.z estimation needs well centered mirror scans or
% use a single scan 

%%  CALIBRATION OF FAST FZP SCANNER 
% 0) perform measurement without zoneplate scanner and find the affine
%       matrix for positions of sample scanner, and detector distance
%       by doing the Calibration of geometry for ptycho tomo (above) 
% 1) collected single scan without sample motion 
% 2) create a reconstruction template "working_template"
% 3) fill in "working_template" and the scan number variables to the EDIT section below 
%       use geometry_model = {'scale','asymmetry','rotation', 'shear'}; 
% 4) run template and wait for final report 


%%  CALIBRATION OF LAMINOGRAPHY
% 1) collected several scans (more than two)
% 2) create a reconstruction template "working_template"
% 3) fill in "working_template" and the scan numbers variables to the EDIT section below
%       we think we should use geometry_model = {'rotation', 'shear'}; 
% 4) run template and wait for final report 

%%
close all; clear

addpath('utils')
addpath(core.find_base_package)
assert(gpuDeviceCount>0, 'Run this template on a GPU computational node')

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% EDIT THIS SECTION %%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% CHOOSE ACTION(S): 
find_camera_rotation = false; 
find_camera_distance = false; 
find_scanning_geometry = true; 
geometry_model = {'rotation', 'shear'}; % list of free parameters in the geometry model, choose from: {'scale', 'asymmetry', 'rotation', 'shear'}

% SET PARAMETERS:
working_template = 'template_ptycho_online.m';   % name of online ptychogrpahy template which can be used to load defaults, paths etc
run(working_template); 
p.   scan_number = [122 128] ;  % provide here 0 and 180 deg scans  
p.   asize = [400 400]; 

p.   gpu_id = [];                  % default GPU id, [] means choosen by matlab

Niter_MLc = 10000;                 % number of iterations in the GPU-MLc refinement 
p.   plot.interval = 100; 
p.   plot.log_scale = [1,1]; 
p.   plot.prepared_data = false;               % plot prepared data


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


%% ENGINES
% --------- GPU engines  -------------   See for more details: Odstrčil M, et al., Optics express. 2018 Feb 5;26(3):3108-23.

p.engines = {};
eng = struct();                 % reset settings for this engine 
eng. name = 'GPU';    

%% DIFFERENCE MAPS PRESOLVER 

% general 
eng. number_iterations = 100;   % number of iterations for selected method 
eng. method = 'DM';             % choose GPU solver: DM, ePIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
eng. grouping = inf;            % size of the processed bunches in parallel, inf = automatic

[p, ~] = core.append_engine(p, eng);    % Adds this engine to the reconstruction process

%% ML solver with geometry refinement for mirrored object 

% general 
eng. method = 'MLc';            % choose GPU solver: DM, ePIE, hPIE, MLc, Mls, -- recommended are MLc and MLs
eng. number_iterations = Niter_MLc;   % number of iterations for selected method 

% basic recontruction parameters 
% PIE / ML methods              % See for more details: Odstrčil M, et al., Optics express. 2018 Feb 5;26(3):3108-23.
eng. momentum = 0;              % add momentum term to the MLc method, eng.momentum = multiplication gain for velocity
eng. accelerated_gradients_start = 2;   % iteration number from which the Nesterov gradient acceleration should be applied, this option is supposted only for MLc method 


%% GEOMETRY REFINEMENT OPTIONS                     See for more details: Odstrčil M, et al., Optics express. 2018 Feb 5;26(3):3108-23.
% position refinement 
if find_scanning_geometry
    eng. probe_position_search = 1;          % reconstruct probe positions, from iteration == probe_position_search, assume they have to match geometry model with error less than probe_position_error_max
    eng. probe_geometry_model = geometry_model;  % list of free parameters in the geometry model, choose from: {'scale', 'asymmetry', 'rotation', 'shear'}
    eng. probe_position_error_max = 40e-9; % max expected random position error of the stages 
end


if find_camera_rotation
    % rotation of tomography axis to the camera 
    assert( length(p.scan_number) == 2, 'Use two scans, one at 0 and one at 180 degrees for camera rotation estimation')
    eng. detector_rotation_search = 20;    % optimize the detector rotation angle 
    eng. mirror_objects = true;           % mirror objects, useful for 0/180deg scan sharing -> geometry refinement for tomography
    eng. share_object = true;  
end

if find_camera_distance
    % detector rotation refinement : can be unstable 
    eng. detector_scale_search = 20;    % optimize the detector scale (sample to detector distance)
    warning  off backtrace
    warning('It is recommended to run this refinement with find_scanning_geometry=false and find_camera_rotation=false and without scan mirroring')
    warning  on backtrace
    pause(5)
end
        

[p, ~] = core.append_engine(p, eng);    % Adds this engine to the reconstruction process

    


%% Run the reconstruction
out = core.ptycho_recons(p);



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% Source Code
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% Introduction 
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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 
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%       © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017. 
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