How can I connect Amira visualization to my computation code?
You can write simulation results (e.g., time steps) to files and than tell a running Amira to read them. To do that use the -cmd option of Amira, i.e. call Amira -cmd somecmd where somecmd typically will be a Tcl procedure. If you have the Amira Developer Pack version, you can either embed your simulation code in an Amira module (possibly as a separate thread), or you can write a module which communicates with your simulation via sockets or shared memory.
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