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I want to my own global path planner to make two/three of different plans. All these plans will require to remove the inbuilt Dijkstra's algorithm, implemented inside navfn.cpp and used inside navfn_ros.cpp. Will a single plugin serve my purpose or I have to make different plugins and make them switchable to decide the proper plan?

The global planner interface is defined so that you only return one plan. In order to use the navigation frame work as is, a global planner can only return one plan. That said, you could make several plans and then only return the best one.

Why two makePlan() methods are used (see here)?

The one with the tolerance parameter allows for a plan that does not find the exact goal position, but instead has some tolerance.

In the link ( http://www.iroboapp.org/index.php?tit... ); they have not told anything about modification about navfn.cpp. .

I'm not familiar with that tutorial.

Finally, where the should I place the code specific to this plugin? Should I create a separate library containing all the files similar to navfn?

Yes.