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This might be a stupid answer, but have you tried this?

<link name="base_footprint">
</link>
<joint name="base_footprint_joint" type="fixed">
    <parent link="base_footprint"/>
    <child link="base_link"/>
    <origin xyz="0 0 0" rpy="0 0 0"/>
</joint>

This might be a stupid answer, but have you tried this?

<link name="base_footprint">
</link>
<joint name="base_footprint_joint" type="fixed">
    <parent link="base_footprint"/>
    <child link="base_link"/>
    <origin xyz="0 0 0" rpy="0 0 0"/>
</joint>

Although my spider sense tells me that you should modify your setup so that gazebo publishes the transform "odom -> base_footprint" instead of "odom -> base_link"