function Miji(open_imagej) %% This script sets up the classpath to Fiji and optionally starts MIJ %% Author: Jacques Pecreaux & Johannes Schindelin if nargin < 1 open_imagej = true; end %% Get the Fiji directory fiji_directory = fileparts(fileparts(mfilename('fullpath'))); %% Get the Java classpath classpath = javaclasspath('-all'); %% Add all libraries in jars/ and plugins/ to the classpath add_to_classpath(classpath, strcat([fiji_directory filesep 'jars'])); add_to_classpath(classpath, strcat([fiji_directory filesep 'plugins'])); %% Maybe open the ImageJ window if open_imagej cd ..; fprintf('\n\nUse MIJ.exit to end the session\n\n'); MIJ.start(pwd); 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_) javaaddpath(path_, '-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))); end