======Normalized Joint Angle - Method 2======

[[Visual3D:Documentation:Kinematics_and_Kinetics:Normalized_Joint_Angle_-_Method_1|Normalized Joint Angle - Method 1]] illustrated how to align a [[Visual3D:Documentation:Modeling:segments:Virtual_Segments|Virtual Foot Segment]] precisely with the [[Visual3D:Documentation:Modeling:segments:Segment_Coordinate_System|Segment Coordinate System]] for the Shank. The example on this page shows how to create a virtual foot that is aligned with the lab floor. This example uses Tutorial2.cmo from the [[Visual3D:Tutorials:tutorial_files|Visual3D Tutorial Files]] page. Download this file and follow the steps below. [[https://www.has-motion.com/download/examples/Tutorial2.cmo|Tutorial2.cmo]]

Open the Tutorial2.cmo file, click on the Model tab. The model has been completely constructed.

=====Step 1: Create 3 Laboratory Landmarks=====
The first task is to project the markers that were used to define the foot onto the same plane (for convenience we will use the floor of the laboratory). To do so, we must create some laboratory landmarks.

Click on the Model tab and click on the Landmark Tab. Follow these steps to create these landmarks: Lab_Origin, Lab_X, and Lab_Y.

{{ : Lab Origin Landmark Normalized Joint Angle Method 2.png?230x300}}

1. **Create Lab_Origin landmark:** \\
  - Click **Landmarks** button 
  - Click **Add New Landmark** button \\ **Landmark Name:** Lab_Origin \\ **Define Orientation Using:** \\ **Existing Segment:** Lab
  - Offset Using the Following ML/AP/AXIAL Offset: **X=** 0 , **Y=** 0 , **Z=** 0 
  - **DO NOT Check**: Offset by Percent (1.0 = 100%) 
  - **DO NOT Check**: Calibration Only Landmark \\

\\ \\ \\ \\ \\ \\
{{ :Lab X Landmark Normalized Joint Angle Method 2.png?230x300}}

2. **Create Lab_X landmark:** \\
  - Click **Landmarks** button 
  - Click **Add New Landmark** button \\ **Landmark Name:** Lab_X \\ **Define Orientation Using:** \\ **Existing Segment:** Lab
  - Offset Using the Following ML/AP/AXIAL Offset: **X=** 0.1 , **Y=** 0 , **Z=** 0 
  - **DO NOT Check**: Offset by Percent (1.0 = 100%) 
  - **DO NOT Check**: Calibration Only Landmark  \\ 

\\ \\ \\ \\ \\ 
{{ :Lab Y Landmark Normalized Joint Angle Method 2.png?230x300}}

3. **Create Lab_Y landmark:** \\
  - Click **Landmarks** button 
  - Click **Add New Landmark** button \\ **Landmark Name:** Lab_Y \\ **Define Orientation Using:** \\ **Existing Segment:** Lab
  - Offset Using the Following ML/AP/AXIAL Offset: **X=** 0 , **Y=** 0.1 , **Z=** 0 
  - **DO NOT Check**: Offset by Percent (1.0 = 100%) 
  - **DO NOT Check**: Calibration Only Landmark  \\
 \\ \\ \\
=====Step 2: Create 3 floor projected foot landmarks=====

In this step, we will create 3 landmarks (RLA_Floor, RMA_Floor, and RFT1_Floor) that are the projection of the 3 markers used to define the foot (RLA, RMA, and RFT1) onto the floor. We will use the newly created Lab landmarks in Step 1 to project the foot markers on the floor.

{{ :RLA Floor Landmark Normalized Joint Angle Method 2.png?230x300}}

1. Create RLA_Floor landmark: \\
  - Click **Landmarks** button 
  - Click **Add New Landmark** button \\ **Landmark Name:** RLA_Floor \\ **Define Orientation Using:** \\ **Starting Point:** Lab_Origin \\  **Ending Point:** Lab_X \\  **Lateral Object:** Lab_Y \\ **Projection From:** RLA
  - **Check**: Calibration Only Landmark  \\ 
\\ \\ \\ \\ \\
{{ :RMA Floor Landmark Normalized Joint Angle Method 2.png?230x300}}


2. Create RMA_Floor landmark: \\
  - Click **Landmarks** button 
  - Click **Add New Landmark** button \\ **Landmark Name:** RMA_Floor \\ **Define Orientation Using:** \\ **Starting Point:** Lab_Origin \\  **Ending Point:** Lab_X \\  **Lateral Object:** Lab_Y \\ **Projection From:** RMA
  - **Check**: Calibration Only Landmark  \\ RMA Floor Landmark Normalized Joint Angle Method 2.png

\\ \\ \\ \\ \\
{{ :RFT1 Floor Landmark Normalized Joint Angle Method 2.png?230x300}}


3. Create RFT1_Floor landmark: \\
  - Click **Landmarks** button 
  - Click **Add New Landmark** button \\ **Landmark Name:** RFT1_Floor \\ **Define Orientation Using:** \\ **Starting Point:** Lab_Origin \\  **Ending Point:** Lab_X \\  **Lateral Object:** Lab_Y \\ **Projection From:** RFT1
  - **Check**: Calibration Only Landmark  \\ RFT1 Floor Landmark Normalized Joint Angle Method 2.png
\\ \\ \\ \\ \\
=====Step 3: Create Virtual Foot Segment Parallel to the Floor=====

The following method will not set the Ankle Joint Angle to Zero degrees in the standing trial, but it will create a segment coordinate system that is flat to the floor, which is convenient for describing the angle of the foot segment relative to the laboratory, and also produces an ankle joint angle that is close to zero in the standing posture (if the shank is vertical, the angle will be zero).

The following definition will create the Segment Coordinate System for the Virtual Foot Segment aligned parallel to the floor. This can be accomplished by using the projected landmarks just created in Step 2.

{{ :Right Virtual Foot Segment Normalized Joint Angle Method 2.png?300x380}}

**Create Right Virtual Foot Segment:**

  - In the **Segments** tab, type Right Virtual Foot 1 in the Segment Name box.
  - **Check** Kinematic Only
  - Click on the **Create Segment** button.
  - In the **Right Virtual Foot** tab, enter these values: \\ \\ **Define Proximal Joint and Radius** \\ **Lateral:** RLA_Floor     **Joint:** None     **Medial:** RMA_Floor     \\ **Radius:** numbers grayed out \\ \\ **Define Distal Joint and Radius** \\ **Lateral:** RFT1_Floor     **Joint:** None     **Medial:** None     \\ **Radius:** 0.06 \\ \\ **Extra Target to Define Orientation** \\ **Location:** None     None \\ **Select Tracking Targets:** \\ **Check** RFT1, RFT2, RFT3 \\
  - Click on **Build Model**. Since it is a Kinematic Only segment, no new image will be appear.
  - Click on **Close Tab** before proceeding. \\ Right Virtual Foot Segment Normalized Joint Angle Method 2.png

=====Step 4: Rotate Virtual Foot Segment Coordinate System=====

Note that the segment coordinate system is parallel to the floor with the z-axis in the plane of the floor rather than vertical (e.g. aligned more-or-less with the shank coordinate system). To resolve this, we need to rotate the coordinate system.

Rotate Segment Coordinate System:

  - In the **Right Virtual Foot** segment, click on the **Segment Properties** tab.
  - Click on **Modify Segment Coordinate System** \\ **Select A/P Axis=** +Z \\ **Select Distal to Proximal=** -Y
  - Click **Ok**

The coordinate system is now aligned with z-axis vertical.

=====Step 5: Plot Angles for Comparison======

Let's plot both ankle joint angles (shank with respect to foot and shank with respect to virtual foot) to see the difference.

**1. Create the angles**

**Create Right Ankle Angle - Right Foot with respect to Right Shank:**
  - In the **Model** menu, select **Compute Model Based Data**.
  - In the dialog enter the following: \\ **Data Name:** Right Ankle Angle \\ **Model based Item Properties:** Joint_Angle \\ **Segment:** Right Foot \\ **Reference Segment:** Right Shank
  - Click on **Create**
  - Click on **Close** before proceeding. \\ Right Ankle Angle Normalized Joint Angle Method 1.png

**Create the Normalized Right joint angle - Right Virtual Foot with respect to Right Shank:**

  - In the **Model** menu, select **Compute Model Based Data**.
  - In the dialog enter the following: \\ **Data Name:** Right Ankle Angle Virtual Foot 1 \\ **Model based Item Properties:** Joint_Angle \\ **Segment:** Right Virtual Foot 1 \\ **Reference Segment:** Right Shank
  - Click on **Create**
  - Click on **Close** before proceeding. \\ Right Ankle Angle Virtual Foot Normalized Joint Angle Method 2.png
  - 
{{ :Graphs Normalized Joint Angle Method 2.png?500}}
**2. Graph the Angles for Comparison**

Now let's graph the two angles and compare their signals.

**Graph the Right Ankle Angle and Right Ankle Angle Virtual Foot**

  - **Graph the Right Ankle Angle**
    - In the **Signal and Events** tab, make the Walking Trial 1.c3d active
    - Select the **Link_Model_Based** to expand the folder
    - **Right-click** on the Right Ankle Angle to bring up the submenu
    - From the submenu, select **Graph X,Y, and Z** to plot all three components of the right ankle angle.
    - Another submenu will appear, select **New Graph** to plot all 3 components in the pane to the right.
  - **Add the Right Ankle Angle Virtual Foot 1 to the Graph**
    - In the **Signal and Events** tab, select the **Link_Model_Based** folder.
    - Right-click on the **Right Ankle Angle Virtual Foot 1** to bring up the submenu
    - From the submenu, select **Graph X,Y, and Z** to plot all three components of the right ankle angle virtual foot.
    - Another submenu will appear, select **Add to Existing** to add all 3 components to the existing graph. 

The top graph represents ankle dorsi/plantarflexion angle. Two signals are shown. The top most signal is right ankle angle and the bottom signal is the normalized angle angle (wrt to virtual foot).

=====Other Normalization Methods=====
For another normalization method, go to [[Visual3D:Documentation:Kinematics_and_Kinetics:Normalized_Joint_Angle_-_Method_1|Normalized Joint Angle - Method 1]]. In addition, there is a great tutorial Tutorial: Foot and Ankle Angles that discusses normalization.