diff --git a/target/classes/icon-Matlab-function-caller.png b/target/classes/icon-Matlab-function-caller.png deleted file mode 100644 index d66688871bd6a31c7e2aaaf1fe366264097df00d..0000000000000000000000000000000000000000 Binary files a/target/classes/icon-Matlab-function-caller.png and /dev/null differ diff --git a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommandException.class b/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommandException.class deleted file mode 100644 index ddf47582627ec9986df6b2fa519888527b24eecd..0000000000000000000000000000000000000000 Binary files a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommandException.class and /dev/null differ diff --git a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon$1.class b/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon$1.class deleted file mode 100644 index f43b547beca1ad823f5a57e3b70f390a797fa58b..0000000000000000000000000000000000000000 Binary files a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon$1.class and /dev/null differ diff --git a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon$2.class b/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon$2.class deleted file mode 100644 index 88580e2c1e8fd16c84b6980abd1038bd0743a3dd..0000000000000000000000000000000000000000 Binary files a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon$2.class and /dev/null differ diff --git a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon.class b/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon.class deleted file mode 100644 index 282edc07493644b64f0c413b7b0858da6bebe1c4..0000000000000000000000000000000000000000 Binary files a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon.class and /dev/null differ diff --git a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer$1.class b/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer$1.class deleted file mode 100644 index 4492c5e68a75895534dc66851ca4332af4c0591e..0000000000000000000000000000000000000000 Binary files a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer$1.class and /dev/null differ diff --git a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer$2.class b/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer$2.class deleted file mode 100644 index b3136d9c3ab1326d9dc84d9a3005d1479fd8453b..0000000000000000000000000000000000000000 Binary files a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer$2.class and /dev/null differ diff --git a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer$MatlabSocket.class b/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer$MatlabSocket.class deleted file mode 100644 index 4b1ecbbffdae50a25bc488cb604d3efc5366d131..0000000000000000000000000000000000000000 Binary files a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer$MatlabSocket.class and /dev/null differ diff --git a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer.class b/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer.class deleted file mode 100644 index 71c8cf020586649dc9e32c534549894e7425ede4..0000000000000000000000000000000000000000 Binary files a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer.class and /dev/null differ diff --git a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabInterpreter.class b/target/classes/plugins/ylemontag/matlabcommunicator/MatlabInterpreter.class deleted file mode 100644 index 1d2a02e2f139fd83366d2c648465f05d93cf94d5..0000000000000000000000000000000000000000 Binary files a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabInterpreter.class and /dev/null differ diff --git a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabSession.class b/target/classes/plugins/ylemontag/matlabcommunicator/MatlabSession.class deleted file mode 100644 index ecb6b2d1a25336e133f975e0f089d5a8f8f8a268..0000000000000000000000000000000000000000 Binary files a/target/classes/plugins/ylemontag/matlabcommunicator/MatlabSession.class and /dev/null differ diff --git a/target/classes/plugins/ylemontag/matlabcommunicator/icy_command.m b/target/classes/plugins/ylemontag/matlabcommunicator/icy_command.m deleted file mode 100644 index d938ad6b177247db9cbfd069dcf78aa5b9520f85..0000000000000000000000000000000000000000 --- a/target/classes/plugins/ylemontag/matlabcommunicator/icy_command.m +++ /dev/null @@ -1,132 +0,0 @@ - -function args_out = icy_command(class_name, command, args_in)%#ok -% args_out = icy_command(class_name, command, args_in) -% -% Low-level function to execute a command in Icy from Matlab. -% -% This function should not be used directly by final-users. - -% Sessions identifiers -mlock; -persistent client_ID; -persistent path_in ; -persistent path_out ; - -% Loop for session ID renewing -remaining_attemps = 2; -while(true) - - % Get a session ID if necessary - if(~exist('client_ID', 'var') || isempty(client_ID)) - msg_in = cell(1, 1); - msg_in{1} = '?'; - msg_out = send_command(msg_in); - if(length(msg_out)~=4 || ~strcmp(msg_out{1}, 'ID')) - error('Unconsistent answer (expected: ID)'); - end - client_ID = msg_out{2}; - path_in = msg_out{3}; - path_out = msg_out{4}; - end - remaining_attemps = remaining_attemps - 1; - - % Write the in file - if(~exist('args_in', 'var')) - args_in = struct();%#ok - end - save(path_in, '-struct', 'args_in'); - - % Execute the command - msg_in = cell(3, 1); - msg_in{1} = client_ID; - msg_in{2} = class_name; - msg_in{3} = command; - msg_out = send_command(msg_in); - - % Interpret the result - if(length(msg_out)<1) - error('Unconsistent answer (no return code)'); - end - - % Code=='OK' => everything went well - if(strcmp(msg_out{1}, 'OK')) - args_out = load(path_out); - return; - - % Code=='Fail' => error while executing the command - elseif(strcmp(msg_out{1}, 'Fail')) - error_message = ''; - for p = 2:length(msg_out) - error_message = sprintf('%s\n %s', error_message, msg_out{p}); - end - error('Error while executing the command "%s" with the plugin %s:%s', ... - command, class_name, error_message); - - % Code=='Bad ID' => try to renew the client ID once - elseif(strcmp(msg_out{1}, 'Bad ID')) - if(remaining_attemps>0) - client_ID = []; - path_in = []; - path_out = []; - else - error('Invalid client ID: %s', client_ID); - end - - % Code=='Bad class name' => the expected plugin interpreter does not exist on Icy - elseif(strcmp(msg_out{1}, 'Bad class name')) - error('The expected plugin (%s) is not installed on Icy', class_name); - - % Unkown return code - else - error('Unconsistent answer (unknown return code: %s)', msg_out{1}); - end -end - -% Core function -function msg_out = send_command(msg_in) - - % Java stuff - import java.net.Socket - import java.io.* - - % Establish the connection - socket = Socket('localhost', 8732); - out = socket.getOutputStream; - in = socket.getInputStream ; - - % Send the list of strings - for k=1:length(msg_in) - buffer_in = uint8(sprintf('%s\n', msg_in{k})); - %fprintf('In: %s', buffer_in); - out.write(buffer_in); - end - out.flush(); - - % Wait for the answer and close the connection - msg_out = cell(0, 1); - msg_idx = 0; - buffer_out = zeros(1, 256); - buffer_idx = 0; - while(true) - current_char = in.read(); - if(current_char<0) - error('End of stream reached unexpectedly'); - elseif(current_char==10 || current_char==13) - current_answer = char(buffer_out(1:buffer_idx)); - %fprintf('Out: %s\n', current_answer); - if(strcmp(current_answer, 'EOF')) - break; - end - msg_idx = msg_idx + 1; - msg_out{msg_idx} = current_answer; - buffer_out = zeros(1, 256); - buffer_idx = 0; - else - buffer_idx = buffer_idx + 1; - buffer_out(buffer_idx) = current_char; - end - end - socket.close(); -end - -end diff --git a/target/classes/plugins/ylemontag/matlabcommunicator/icy_init.m b/target/classes/plugins/ylemontag/matlabcommunicator/icy_init.m deleted file mode 100644 index 7e98a3ab3a8d272f7222eba74d9c2bf9f3497d3b..0000000000000000000000000000000000000000 --- a/target/classes/plugins/ylemontag/matlabcommunicator/icy_init.m +++ /dev/null @@ -1,39 +0,0 @@ - -function icy_init() -% icy_init() -% -% Append to the PATH Matlab environment variable all the folders that contain -% Matlab functions in the Icy plugin directory. -% -% To initialize the functions provided by the Matlab<->Icy interaction plugins, -% you have to execute the following commands each time you start Matlab: -% -% >> addpath('path/to/icy/plugins/ylemontag/matlabcommunicator'); -% >> icy_init(); -% -% This operation can be done automatically using a startup.m file (please -% consult the Matlab documentation for more details). - -% Current path -myself = mfilename('fullpath'); - -% Text file containing the list of source folders -sep = find(myself=='/', 1, 'last'); -communicator_root = myself(1:sep); -source_folder_file = [communicator_root 'source_folders.txt']; - -% Exit now if the source file does not exist -if(~exist(source_folder_file, 'file')) - return; -end - -% Read the file -fid = fopen(source_folder_file, 'r'); -line = fgetl(fid); -while(ischar(line)) - if(exist(line, 'dir')) - addpath(line); - end - line = fgetl(fid); -end -fclose(fid); diff --git a/target/classes/tooltip-Matlab-function-caller.png b/target/classes/tooltip-Matlab-function-caller.png deleted file mode 100644 index bfcfb9de757eeb8e787ae894aeb0b567fda8ac93..0000000000000000000000000000000000000000 Binary files a/target/classes/tooltip-Matlab-function-caller.png and /dev/null differ diff --git a/target/matlab-communicator-1.0.5.jar b/target/matlab-communicator-1.0.5.jar deleted file mode 100644 index 87d14160f6c44088116c739dd471e59933350402..0000000000000000000000000000000000000000 Binary files a/target/matlab-communicator-1.0.5.jar and /dev/null differ diff --git a/target/maven-archiver/pom.properties b/target/maven-archiver/pom.properties deleted file mode 100644 index bd431e01ba9125e40e11cb0d16a3fad0d3d066e1..0000000000000000000000000000000000000000 --- a/target/maven-archiver/pom.properties +++ /dev/null @@ -1,3 +0,0 @@ -artifactId=matlab-communicator -groupId=org.bioimageanalysis.icy -version=1.0.5 diff --git a/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst b/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst deleted file mode 100644 index 074afaafc1b7f2505b2b09245412feed70f79619..0000000000000000000000000000000000000000 --- a/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst +++ /dev/null @@ -1,10 +0,0 @@ -plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon$1.class -plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon.class -plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon$2.class -plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer$2.class -plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer$1.class -plugins/ylemontag/matlabcommunicator/MatlabSession.class -plugins/ylemontag/matlabcommunicator/MatlabCommandException.class -plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer$MatlabSocket.class -plugins/ylemontag/matlabcommunicator/MatlabInterpreter.class -plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer.class diff --git a/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst b/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst deleted file mode 100644 index 5397b449497d6317529200cf561226b3a9970aec..0000000000000000000000000000000000000000 --- a/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst +++ /dev/null @@ -1,5 +0,0 @@ -/run/media/kitwaii/Dev/kitwaii/pasteur/Plugins/matlab-communicator/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer.java -/run/media/kitwaii/Dev/kitwaii/pasteur/Plugins/matlab-communicator/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabCommandException.java -/run/media/kitwaii/Dev/kitwaii/pasteur/Plugins/matlab-communicator/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabSession.java -/run/media/kitwaii/Dev/kitwaii/pasteur/Plugins/matlab-communicator/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabInterpreter.java -/run/media/kitwaii/Dev/kitwaii/pasteur/Plugins/matlab-communicator/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon.java