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Short answer: if you want it to look identical, change your configuration to this:
odom0_config: [true, true, false,
false, false, true,
false, false, false,
false, false, false,
false, false, false]
(Note that I left Z position as false because you have two_d_mode
set to true). Note, however, that if you plan on fusing other sensors such as IMUs, then you want to continue to use velocities as you are, with one caveat (see below).
The long answer has a few possibilities:
ekf_localization_node
has its own motion model. At every time step, it's going to predict the next state, and then correct it using your sensor data. However, the filter has some trust in its own estimate, so when a measurement comes in, it may not fully accept it.