%[p object probe] = ptycho_show_recons(file,param1,val1,...)
% Receives a path+filename, reads it and makes plots of the ptychography
% reconstruction, in default it will also save the plotted images 
%
% Optional parameters 
%   'imagesavefolder'   '~/Data10/analysis/online/ptycho/show_recons/'
%                           (default = [], which means no plot is saved)
%   param can be updated with another struct
%       [p, probe, object] = core.ptycho_show_recons(filepath, p_updated)
%
%   and / or with single field names
%       [p, probe, object] = core.ptycho_show_recons(filepath, p_updated, 'windowautopos', 1, 'extrastringtitle', 'Final recon')

% 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") 
%   will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS 
%   ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
%
% Terms and Conditions of the LICENSE
% 1.	LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions 
%       hereinafter set out and until termination of this license as set forth below.
% 2.	LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements 
%       or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the 
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%       HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE 
%       OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4.	LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively, 
%       "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same 
%       license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for 
%       profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged 
%       in the commercial use, application or exploitation of works similar to the PROGRAM.
% 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 cSAXS ptychography MATLAB 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 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 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).
% 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.
% 7.	Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE 
%       agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to 
%       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.
% 9.	DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate 
%       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, 
%       in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software 
%       in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 10.	This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before 
%       the courts of Zürich, Switzerland. 

function [p, object, probe] = ptycho_show_recons(file,varargin)

import utils.param_protect_field
import utils.update_param
import utils.find_latest_file
import io.*

msk = {'*recons*.h5', '*recons*.mat', '*recons*.cxs'};
if nargin==0
    file = find_latest_file('../../', msk);
elseif ischar(file) && isdir(file)
    file = find_latest_file(file, msk);
elseif isnumeric(file)
    file = find_latest_file('../../', msk, file);
end


%% load file
fprintf('Showing reconstruction: %s\n',file)
[object, probe, p] = load_ptycho_recons(file);
p.save.store_images = true;
p.use_display = true;

%% update p struct
p.windowautopos = 1;

if ~isempty(varargin)
    p.plot = update_param(p.plot, varargin{:});
end

% orthogonalize probes
if p.ortho_probes && size(p.probes,4)>1   
    p.probes = core.probe_modes_ortho(p.probes);
end

% to allow different screen sizes
try
    p.scrsz = get(0,'ScreenSize');
catch
    p.scrsz = [1 1 2560 1024];
end

% to allow different save paths
if isfield(p, 'imagesavefolder')
    imagesavefolder = p.imagesavefolder;
else
    imagesavefolder = [];
end

% back compatibility
if ~isfield(p, 'numscans')
    p.numscans  = length(p.scan); 
end

for ii = 1:p.numscans     
    p.scanidxs{ii} = p.scanindexrange(ii,1):p.scanindexrange(ii,2); 
end

%% plot
core.analysis.plot_results(p, 'use_display', p.use_display, 'store_images', p.save.store_images, 'final', 1);


return