Interprocess Communication

[AvocadoMoon]

Currently you need to copy the link in which the remote N5 file is exported to and this can be viewed as a problem for people who don't understand that the link needs to be copied.

[AvocadoMoon]

Can have OS environmental variables set by executing terminal commands with Java, having some set of conditional statements that change the terminal command executed based on the OS VCell is ran on.

[AvocadoMoon]

Some other potential solutions

[AvocadoMoon]

Process builder to execute Fiji app, shared file to store data that is needed.

[AvocadoMoon]

The current predicament: ImageJ plugins seem to be able to accept parameter arguments but it may be tricky to implement since it'll have to be done using the context manager and @Parameter decorator most likely. Also some of the problems that can happen while wanting the VCell application to automatically retrieve the URI from the VCell application is as follows:

• Exporting multiple models, which model exportation link should be used
• What if the user doesn't want ImageJ to automatically launch everytime an N5 file is exported
• Due to the method of creating a new process in Java a new global variable will be needed to keep a handle on the ImageJ process class
• If the ImageJ plugin name changes at any time, then the plugin won't be executed
• It's difficult to continually pass in parameters after initialization to the plugin
  • The method I can think of is opening some server client communication through sockets on the localhost interface. The reason being that even with shared file or memory, there needs to be something that causes an alert that status has changed. The user can also do it manually with a refresh button maybe.

It may be better to teach the users how to copy the URI link into the ImageJ plugin and create some "Exported" tab in the VCell app which lists all the exports a user had already did along with the details about that export job such as simulation, parameters, variables etc...

[AvocadoMoon]

Currently for inter-process communication regarding exports a JSON file is saved within the VCell applications home directory. It doesn't allow for a one button click and other consequences, but it seems to be the best available option for quick communication that is safe.