JMP XML Reference

<NMSMPipelineDocument Version="1.5.0">
<JointModelPersonalizationTool>
    <!--Name of the directory where results are written. Be default this is the directory in which the setup file is be  executed.-->
    <results_directory>JMPResults</results_directory>
    <!--Directory for input files.-->
    <input_directory>JMPInputsDir</input_directory>
    <!--Name of file containing input model, if using the application this has no effect as current model is used.-->
    <input_model_file>model.osim</input_model_file>
    <!--Name of file containing output model after tool executaion.-->
    <output_model_file>model_jmp.osim</output_model_file>
    <!--The accuracy to compare against, depends on model/data units (0.01 == 1cm for data in units meters).-->
    <allowable_error>0.005</allowable_error>
    <!--List of tasks to be completed by the tool, each Task is a separate optimization.-->
    <JMPTaskList>
        <JMPTask>
            <!--Indicate whether the task is enabled or not.-->
            <is_enabled>true</is_enabled>
            <!--Integer to indicate the order that this task should be completed-->
            <index>1</index>
            <!--Name of marker file with required data for this JMP task.-->
            <marker_file_name>marker_file.trc</marker_file_name>
            <!--Space separated list of marker names to be included in this task-->
            <marker_names>marker_1 marker_2 marker_3</marker_names>
            <!--Time range from marker file to be used to optimize joint personalization.-->
            <time_range>0 1</time_range>
            <!--Joints that will be optimized in this task.-->
            <JMPJointSet>
                <!--A joint that will be personalized in this task. Add a joint by changing the name of the <JMPJoint> element-->
                <JMPJoint name="JointName">
                    <!--Joint Parent Frame.-->
                    <parent_frame_transformation>
                        <!--Three boolean values (separated by spaces) for if the joint translation parameter is to be optimized.-->
                        <translation>true true false</translation>
                        <!--Three boolean values (separated by spaces) for if the joint orientation parameter is to be optimized.-->
                        <orientation>true true false</orientation>
                        <!--Translation bounds set the upper and lower limits of the search range around the initial value.-->
                        <translation_bounds>0.05</translation_bounds>
                        <!--Orientation bounds set the upper and lower limits of the search range around the initial value.-->
                        <orientation_bounds>0.5</orientation_bounds>
                    </parent_frame_transformation>
                    <!--Joint Child Frame.-->
                    <child_frame_transformation>
                        <!--Three boolean values (separated by spaces) for if the joint translation parameter is to be optimized.-->
                        <translation>false false false</translation>
                        <!--Three boolean values (separated by spaces) for if the joint orientation parameter is to be optimized.-->
                        <orientation>false false false</orientation>
                        <!--Translation bounds set the upper and lower limits of the search range around the initial value.-->
                        <translation_bounds>0.05</translation_bounds>
                        <!--Orientation bounds set the upper and lower limits of the search range around the initial value.-->
                        <orientation_bounds>0.5</orientation_bounds>
                    </child_frame_transformation>
                </JMPJoint>
            </JMPJointSet>
            <JMPBodySet>
                <JMPBody name="BodyName">
                    <!--Boolean value for whether the body, with task name, is to be scaled.-->
                    <scale_body>true</scale_body>
                    <!--Three boolean values (separated by spaces) for which axes the markers should be free to move in (x, y, z) order.-->
                    <move_markers>false true true</move_markers>
                </JMPBody>
            </JMPBodySet>
        </JMPTask>
    </JMPTaskList>
    <!--*Optional* The accuracy of the IKSolver solution in absolute terms. Default is 1e-5. It determines the number of significant digits to which the solution can be trusted.-->
    <accuracy>1e-06</accuracy>
    <!--*Optional* The minimum step of the least squares algorithm. Default is 1e-4 which means the solution will be optimized to 0.1 mm resolution-->
    <diff_min_change>1e-04</diff_min_change>
    <!--*Optional* The step tolerance determines when the lsqnonlin algorithm stops. The larger it is, the earlier the algorithm stops, but with lower accuracy-->
    <step_tolerance>1e-06</step_tolerance>
    <!--*Optional* The optimality tolerance determines when the lsqnonlin algorithm stops. The larger it is, the earlier the algorithm stops, but with lower accuracy-->
    <optimality_tolerance>1e-6</optimality_tolerance>
    <!--*Optional* The function tolerance determines when the lsqnonlin algorithm stops. The larger it is, the earlier the algorithm stops, but with lower accuracy-->
    <function_tolerance>1e-6</function_tolerance>
    <!--*Optional* The number of allowed iterations for the lsqnonlin, setting this lower can help cancel an optimization that won't converge-->
    <max_function_evaluations>5000</max_function_evaluations>
</JointModelPersonalizationTool>
</NMSMPipelineDocument>