im_browser_deploy.m

function im_browser_deploy
% try
%     javaaddpath('c:\Science\Fiji\jars\', '-end');
% catch err
%     sprintf('%s', err.identifier)
% end

% the reason for the following Java connecting code is that javaaddpath function is not completely compatible with the
% deployed version of im_browser

% Copyright (C) 12.05.2014 Ilya Belevich, University of Helsinki (ilya.belevich @ helsinki.fi)
% part of Microscopy Image Browser, http:\\mib.helsinki.fi 
% This program is free software; you can redistribute it and/or
% modify it under the terms of the GNU General Public License
% as published by the Free Software Foundation; either version 2
% of the License, or (at your option) any later version.
%
% Updates
% 


% get java library paths

% see more on path
% http://blogs.mathworks.com/loren/2008/08/11/path-management-in-deployed-applications/

fijiJavaPath = 0;
omeroJavaPath = 0;

% % the following code finds where MIB is installed
% if isunix()
%     %[~, user_name] = system('whoami'); 
%     %pathName = fullfile('./Users', user_name(1:end-1), 'Documents/MIB');
%     [status, result] = system('path');
%     pathName = char(regexpi(result, 'Path=(.*?);', 'tokens', 'once'));
% else
%     %pathName = pwd;
%     [status, result] = system('path');
%     pathName = char(regexpi(result, 'Path=(.*?);', 'tokens', 'once'));
% end

if ispc
    pathName = userpath();
else
    % find directory to store preferences
    pathName = getenv('HOME');
    pathName = fullfile(pathName, 'Documents', 'MATLAB');
    if isdir(pathName) == 0;
        mkdir(pathName);
    end
end
if pathName(end) == ';'; pathName(end) = []; end;

javaPathfn = fullfile(pathName, 'mib_java_path.txt');
if exist(javaPathfn,'file') ~= 2
    fid = fopen(javaPathfn, 'w');
    if fid == -1; 
        warndlg(sprintf('A Java-path file for Java libraries can not be created in\n%s\n\nPlease modify permissions for this folder', javaPathfn),'Can not create file');
        pause;
    end
    fprintf(fid, 'c:\\Tools\\Science\\Fiji.app\\\nc:\\Matlab\\Scripts\\OMERO_5\\libs\n/Applications/Fiji.app/\n/Users/ibelev/Documents/MATLAB/OMERO_5/libs');
    fclose(fid);
    warndlg(sprintf('A path-file for Java libraries was not found!\n\nA template file (mib_java_path.txt) was created in %s\n\nPlease modify it with the list of JAR directories (for example: "C:\\Fiji.app" or "c:\\OMERO\\libs")', javaPathfn),'Missing Fiji JARs');
end

sprintf('Reading java-directories from:\n%s', javaPathfn)

fid = fopen(javaPathfn);
tline = fgetl(fid);
while ischar(tline)
    if isunix()   % in MacOS the path should not have :
        if ~isempty(strfind(lower(tline), 'fiji')) && isempty(strfind(tline, ':'))
            fijiJavaPath = tline;
        elseif ~isempty(strfind(lower(tline), 'omero')) && isempty(strfind(tline, ':'))
            omeroJavaPath = tline;
        end
    else
        if ~isempty(strfind(lower(tline), 'fiji')) && ~isempty(strfind(tline, ':'))
            fijiJavaPath = tline;
        elseif ~isempty(strfind(lower(tline), 'omero')) && ~isempty(strfind(tline, ':'))
            omeroJavaPath = tline;
        elseif ~isempty(strfind(lower(tline), 'imaris')) && ~isempty(strfind(tline, ':'))
            imarisJavaPath = tline;
            if exist(imarisJavaPath, 'file') == 0   % check presense of imaris library
                imarisJavaPath = 0;
            end
        end
    end
    tline = fgetl(fid);
end
fclose(fid);

% Load Fiji libraries
if fijiJavaPath == 0
    sprintf('Fiji path was not found!\n\nPlease add it (for example: "C:\\Fiji.app\\") to "mib_java_path.txt" file at (%s)', javaPathfn)
else
    if exist(fijiJavaPath,'dir') ~= 7    % not a folder
        sprintf('Fiji path was not correct!\n\nPlease fix it (for example: "C:\\Fiji.app\\") in "mib_java_path.txt" file at (%s)', javaPathfn);
    else
        % add Fiji libraries
        % Get the Fiji directory
        %fiji_directory = fileparts(fijiJavaPath);
        fiji_directory = fijiJavaPath;
        
        % Get the Java classpath
        classpath = javaclasspath('-all');
        
        % Add all libraries in jars/ and plugins/ to the classpath
        
        % Switch off warning
        warning_state = warning('off');
        add_to_classpath(classpath, fullfile(fiji_directory, 'jars'));
        classpath = javaclasspath('-all');
        add_to_classpath(classpath, fullfile(fiji_directory, 'plugins'));
        
        % Switch warning back to initial settings
        warning(warning_state);
        
        % Set the Fiji directory (and plugins.dir which is not Fiji.app/plugins/)
        java.lang.System.setProperty('ij.dir', fiji_directory);
        java.lang.System.setProperty('plugins.dir', fiji_directory);
    end
end

% Load Omero libraries
if omeroJavaPath == 0
    sprintf('Omero Java libraries path was not found!\n\nPlease add it (for example: "C:\\Omero\\libs") to "mib_java_path.txt" file at the im_browser directory (%s)', javaPathfn)
else
    if exist(omeroJavaPath,'dir') ~= 7    % not a folder
        sprintf('Fiji Java libraries path was not correct!\n\nPlease fix it (for example: "C:\\Omero\\libs") in "mib_java_path.txt" file at the im_browser directory (%s)', javaPathfn);
    else
        % add Omero libraries
        OmeroClient_Jar = fullfile(omeroJavaPath, 'omero_client.jar');
        javaaddpath(OmeroClient_Jar);
        import omero.*;
    end
end
   
% add BioFormats
% Switch off warning
warning_state = warning('off');

javaaddpath(fullfile(fileparts(mfilename('fullpath')),'File_formats','BioFormats','bioformats_package.jar'));
% Switch warning back to initial settings
warning(warning_state);

% the following wrapper is needed for im_browser
global running
running = 1;
im_browser;
while running
    pause(0.05);
end
end

function add_to_classpath(classpath, directory)
% Get all .jar files in the directory
test = dir(strcat([directory filesep '*.jar']));
path_= cell(0);
for i = 1:length(test)
    if not_yet_in_classpath(classpath, test(i).name)
        path_{length(path_) + 1} = strcat([directory filesep test(i).name]);
    end
end

% Add them to the classpath
if ~isempty(path_)
    try
        javaaddpath(path_, '-end');
    catch err
        sprintf('%s', err.identifier);
    end
end
end

function test = not_yet_in_classpath(classpath, filename)
% Test whether the library was already imported
%expression = strcat([filesep filename '$']);
%test = isempty(cell2mat(regexp(classpath, expression)));
expression = strcat([filesep filename]);
test = isempty(cell2mat(strfind(classpath, expression)));
end