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You are defining the parameters in different namespaces. Try defining the obstacle_sources under each costmap, i.e.:

obstacle_range: 2.5
raytrace_range: 3.0
max_obstacle_height: 2.0
footprint: [[0.285, 0.6365], [0.285, -0.6365], [-0.285, -0.6365], [-0.285, 0.6365]]
inflation_radius: 0.3

global_costmap/observation_sources: laser_scan_sensor point_cloud_sensor
local_costmap/observation_sources: laser_scan_sensor point_cloud_sensor

laser_scan_sensor: {sensor_frame: camera_depth_frame, data_type: LaserScan, topic: /scan, marking: true, clearing: true}

point_cloud_sensor: {sensor_frame: camera_frame, data_type: PointCloud, topic: /camera/depth/points, marking: true, clearing: true}


planner_patience: 5.0
shutdown_costmaps: false


TrajectoryPlannerROS:
  max_vel_x: 0.45
  min_vel_x: 0.1
  max_rotational_vel: 1.0
  min_in_place_rotational_vel: 0.4

  acc_lim_th: 2.0
  acc_lim_x: 2.0
  acc_lim_y: 2.0

  sim_time: 1.0

  pdist_scale: 0.6
  gdist_scale: 0.8
  occdist_scale: 0.01

  holonomic_robot: true


global_costmap:
  global_frame: map
  robot_base_frame: base_footprint
  update_frequency: 5.0
  publish_frequency: 2.0
  static_map: true


local_costmap:
  global_frame: odom
  robot_base_frame: base_footprint
  update_frequency: 5.0
  publish_frequency: 2.0
  static_map: false
  rolling_window: true
  width: 3.0
  height: 3.0
  resolution: 0.01

You are defining the parameters in different namespaces. Try defining the obstacle_sources under each costmap, i.e.:

obstacle_range: 2.5
raytrace_range: 3.0
max_obstacle_height: 2.0
footprint: [[0.285, 0.6365], [0.285, -0.6365], [-0.285, -0.6365], [-0.285, 0.6365]]
inflation_radius: 0.3

global_costmap/observation_sources: laser_scan_sensor point_cloud_sensor
local_costmap/observation_sources: laser_scan_sensor point_cloud_sensor

laser_scan_sensor: global_costmap/laser_scan_sensor: {sensor_frame: camera_depth_frame, data_type: LaserScan, topic: /scan, marking: true, clearing: true}

point_cloud_sensor: global_costmap/point_cloud_sensor: {sensor_frame: camera_frame, data_type: PointCloud, topic: /camera/depth/points, marking: true, clearing: true}

local_costmap/laser_scan_sensor: {sensor_frame: camera_depth_frame, data_type: LaserScan, topic: /scan, marking: true, clearing: true}

local_costmap/point_cloud_sensor: {sensor_frame: camera_frame, data_type: PointCloud, topic: /camera/depth/points, marking: true, clearing: true}

planner_patience: 5.0
shutdown_costmaps: false


TrajectoryPlannerROS:
  max_vel_x: 0.45
  min_vel_x: 0.1
  max_rotational_vel: 1.0
  min_in_place_rotational_vel: 0.4

  acc_lim_th: 2.0
  acc_lim_x: 2.0
  acc_lim_y: 2.0

  sim_time: 1.0

  pdist_scale: 0.6
  gdist_scale: 0.8
  occdist_scale: 0.01

  holonomic_robot: true


global_costmap:
  global_frame: map
  robot_base_frame: base_footprint
  update_frequency: 5.0
  publish_frequency: 2.0
  static_map: true


local_costmap:
  global_frame: odom
  robot_base_frame: base_footprint
  update_frequency: 5.0
  publish_frequency: 2.0
  static_map: false
  rolling_window: true
  width: 3.0
  height: 3.0
  resolution: 0.01

Source: http://wiki.ros.org/costmap_2d/hydro/obstacles#VoxelCostmapPlugin

I assumed that you want marking and clearing in both costmaps (which I do not think it is a common setup).