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bfCheckJavaPath.m
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bfCheckJavaPath.m
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function status = bfCheckJavaPath(varargin)
% bfCheckJavaPath check Bio-Formats is included in the Java class path
%
% SYNOPSIS bfCheckJavaPath
% status = bfCheckJavaPath(autoloadBioFormats)
%
% Input
%
% autoloadBioFormats - Optional. A boolean specifying the action to take
% if loci_tools is not in the java path. If true, add loci_tools to the
% dynamic java path. Default - true
%
% Output
%
% status - Boolean. True if loci_tools is part of the Java library.
% Input check
ip=inputParser;
ip.addOptional('autoloadBioFormats',true,@isscalar);
ip.parse(varargin{:});
% Check if loci_tools is in the Java class path (static or dynamic)
jPath = javaclasspath('-all');
isLociTools = cellfun(@(x) ~isempty(regexp(x,'.*loci_tools.jar$','once')),...
jPath);
status = any(isLociTools);
% Return if loci_tools is in the java path or autoloadBioFormats is off
if status || ~ip.Results.autoloadBioFormats, return; end
% Assume the jar is in Matlab path or under the same folder as this file
path =which('loci_tools.jar');
if isempty(path)
path = fullfile(fileparts(mfilename('fullpath')), 'loci_tools.jar');
end
assert(~isempty(path),'Cannot automatically locate loci_tools.jar');
% Add loci_tools to dynamic Java class path
javaaddpath(path);
status = true;