% filename_with_path = find_ptycho_filename(base_analysis_path,scan_number,fileprefix,filesuffix)
% Looks for a ptychography reconstruction name inside the path given as
% initial argument. I will look in the folder given and also try with
% adding analysis. If the scan_number is given it will compile an analysis
% folder and look for it.  e.g. find_ptycho_filename('~/Data10',235);
% Use verbose(2) in order to see all directories and names attempted.
% Inputs
% base_analysis_path    % String with path to start looking
% scan_number           % (optional) Number with the scan number, used to 
                        % compile folder
% fileprefix            % String specifying the starting of the name
% filesuffix            % String specifying the ending of the name

% Output
% filename_with_path    % String with the first file found that satisfies
                        % the input arguments
% 15 June 2015; 
% September 2017 Return all files matching the criteria;

% 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 [ filename_with_path ] = find_ptycho_filename( base_analysis_path, varargin)
import utils.verbose
% Checks and defaults
if nargin < 5
    fileextension = 'h5';
else
    fileextension = varargin{4};
end

if nargin < 4
    filesuffix = [];
else
    filesuffix = varargin{3};
end

if nargin < 3
    fileprefix = [];
else
    fileprefix = varargin{2};
end

if nargin < 2   
    scan_number = [];
else
    scan_number = varargin{1}; 
end

%%% Give all matching files
trial_path = fullfile(base_analysis_path, utils.compile_x12sa_dirname(scan_number));



if isempty(filesuffix)
    searchstring = [fileprefix '*.' fileextension];
else    
    searchstring = [fileprefix '*' filesuffix '*.' fileextension];
end
search_filename = fullfile(trial_path, searchstring);
output = dir(search_filename);



if numel(output) == 0
    verbose(2,['Did not find any file matching' search_filename]);
    % Then see if analysis folder exists here
    trial_path = fullfile(base_analysis_path,'analysis');
    if exist(trial_path,'dir')~=0
        search_filename = fullfile(trial_path,searchstring);
        output = dir(search_filename);
    else
        trial_path = base_analysis_path;
    end
    
    if numel(output) == 0
        verbose(2,['Did not find any file matching' search_filename]);
        if ~isempty(scan_number)
            % Then add the string for the scan folder
            trial_path = fullfile(trial_path,sprintf('S%05d',scan_number));
            search_filename = fullfile(trial_path,searchstring);
            output = dir(search_filename);
            if numel(output) == 0
                verbose(2,['Did not find any file matching' search_filename]);
                filename_with_path = [];
%                 return
            end
        else
            verbose(2,['Did not find any file matching' search_filename]);
            filename_with_path = [];
%             return
        end
    end
end


for ii = 1:length(output)
    filename_with_path{ii} = fullfile(trial_path, output(ii).name); 
end

if numel(filename_with_path)~=0
    if iscell(filename_with_path) && numel(filename_with_path)==1
        filename_with_path = filename_with_path{1};
    else
        verbose(1,'Found %d file matching the criteria -> providing all in cell', numel(filename_with_path))
    end
else
    verbose(1,'Found no file matching %s', fullfile(base_analysis_path, utils.compile_x12sa_dirname(scan_number),searchstring ))
    filename_with_path = [];
end







end