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It looks like waitForTransform is false by default here. Try adding wait_for_transform parameter to obstacles_detection nodelet:

 <node pkg="nodelet" type="nodelet" name="obstacles_detection"
    args="load rtabmap_ros/obstacles_detection stereo_nodelet">
      <remap from="cloud" to="/pointCloud_downsample"/>
      <remap from="obstacles" to="/pointCloud_obstacles"/>
      <param name="use_sim_time" type="bool" value="true"/>
      <param name="frame_id" type="string" value="base_footprint"/>
      <param name="map_frame_id" type="string" value="map"/>
      <param name="wait_for_transform" type="bool" value="true"/>
      <param name="Grid/MinClusterSize" type="int" value="5"/>
      <param name="Grid/ClusterRadius"       type="double" value="0.1"/>
      <param name="Grid/MaxObstaclesHeight" type="double" value="0.5"/>  
   </node>

The error happens because it is receiving the point cloud before odometry has been completely computed, so it has to wait a little to get TF at that stamp.