Merge pull request #1 from qualisys/feature/opensim-44

Update to use OpenSim 4.3 and 4.4

README.md

@@ -9,27 +9,31 @@ To download this example project to your computer, you can either:
 
 ## Preparing Qualisys data for OpenSim processing
 ### Preparation
-1. Install OpenSim 4.2 or later from https://simtk.org/frs/index.php?group_id=91 :
+1. Install OpenSim 4.2, 4.3 or 4.4 from https://simtk.org/frs/index.php?group_id=91
    1. Create an account on SimTK, download and install OpenSim. 
    *Note: OpenSim versions before 4.2 did not support importing data from Type-3 force plates (Kistler) from c3d files exported from Qualisys Track Manager.*
-2. Install Python 3.7.9 (64-bit) from https://www.python.org/ftp/python/3.7.9/python-3.7.9-amd64.exe.
-   1. Select the option to Add Python 3.7 to PATH and click "Install Now" in the first installation step.
+2. Choose the appropriate Python version
+   - If using OpenSim 4.2, then download Python 3.7.9 (64-bit) from https://www.python.org/ftp/python/3.7.9/python-3.7.9-amd64.exe.
+   - If using OpenSim 4.3 or 4.4, then download Python 3.8.10 (64-bit) from https://www.python.org/ftp/python/3.8.10/python-3.8.10-amd64.exe.
+3. Install Python software and packages
+   1. Select the option to Add Python to PATH and click "Install Now" in the first installation step.
    2. Verify Python installation by starting a Windows Command prompt and entering:
       ````
       python --version
       ````
-      This should return "Python 3.7.9". If not, verify that your Python installation folder is listed in Windows Environment variables -> Path
-   3. Install Python packages Start a Windows command prompt and run:
+      This should return the python version that has been installed. If not, verify that your Python installation folder is listed in Windows Environment variables -> Path
+   3. Install Python packages  
+      Start a Windows command prompt and run:
       ````
       pip install numpy
       pip install pandas
       pip install scipy
       pip install matplotlib
       ````
       Matplotlib is optional, only required if you want to generate graphs to verify force data processing.
-   4. Close Windows Command Prompt.
+   4. Close the Windows Command Prompt.
 3. Connect Python with OpenSim
-   1. Insert OpenSim into the System Path:
+   1. *(Only for OpenSim 4.2)* Insert OpenSim into the System Path:
       1. Click the Windows Start icon and type "env". Click "Edit the system environment variables".
       2. Click "Envrionment Variables" button at the bottom.
       3. In "System Variables", locate "Path" and click Edit.
@@ -38,9 +42,10 @@ To download this example project to your computer, you can either:
    2. Run OpenSim setup file from command line:
       1. Open a new Windows Command Prompt
       2. Navigate to the OpenSim installation folder and locate the subfolder sdk\Python:
-         `cd C:\OpenSim 4.2\sdk\Python`
+         `cd C:\OpenSim 4.X\sdk\Python`
       3. Run the setup script:
-         `python setup.py install`
+         - If using OepnSim 4.2: `python setup.py install`
+         - If using OpenSim 4.3 or 4.4: `python setup_win_python38.py` then `python -m pip install .`
       4. Test the installation by typing:
          `python -c "import opensim"` 
          If there is no error, the installation was successful.
@@ -74,7 +79,8 @@ For detailed instructions or if you would like to use a different model, please
    2. Repeat for .mot file (force data)
    3. Extend the ExperimentalData nodes, use Ctrl+click to select .trc and .mot data and select Sync motions
    4. Play files to confirm that marker and force data are aligned as expected.
-   5. Note: to change the orientation of the data, you can modify the settings for rotate_data_table in qtm2opensim.py
+   5. OpenSim 4.4 will offset the forces and markers in the Visualizer window so that they are not on top of each other. This display offset is a display only property. The model itself is never affected by the changes to the display offset but you can remove this offset by right-clicking on the second ExperimentalData node then select Display -> Model Offset 
+   6. Note: to change the orientation of the data, you can modify the settings for rotate_data_table in qtm2opensim.py
 3. Use data in OpenSim:
    1. Use File -> Open Model and load the example models from OpenSim Example\Templates\OpenSim. Examples for CAST and IOR marker sets are included.
    2. Select Tools -> Scale model:
@@ -89,14 +95,15 @@ For detailed instructions or if you would like to use a different model, please
       2. Adjust weights as desired
       3. Click Run
    4. Select Tools -> Inverse Dynamics
-      1. In the *Main settings* tab, select *Loaded Motion* and choose *IKResults*. Check the *Filter coordinates* box and enter a cutoff frequency for your kinematic data
+      1. In the *Main settings* tab, select *Loaded Motion* and choose *IKResults*. Check the *Filter coordinates* box and enter a cutoff frequency for your kinematic data.  
+      Note or change the path of the *Output* directory where the results of the Inverse Dynamics step are written
       2. In the *External Loads* tab, click on the edit icon to open the External Forces window
       3. Load the .mot file in *Force data file*
       4. Click on *Add...* and enter a name for the right foot force assignment, ie "Right", and select *calcn_r* in the list of segments next to *Applied to*. Check *Applies Force* (*Point Force*) and *Applies Torque*. In the various drop downs, select the components of the correct force plate that is in contact with the right foot. Click on *OK*
       5. Replicate the previous step for the left foot force assignment (use *calcn_l*)
       6. Click on *Save* to save your external forces setup
       7. Save your Inverse Dynamics Tool setup (optional) and click on Run
-      8. You can now plot results of your Inverse Dynamics procedure by going to Tools -> Plot. Click on *Y-Quantity* and *Load File* to select the inverse_dynamics.sto output file automatically created at the previous step. Select the signals you want to plot and click *OK*. Click on *X_Quantity* and select *Time*. Finally click on your figure in the *Curves List* and then click on *Add* to see the curve in the graph
+      8. You can now plot results of your Inverse Dynamics procedure by going to Tools -> Plot. Click on *Y-Quantity* and *Load File* to select the inverse_dynamics.sto output file that contains the results of the Inverse Dynamics step (path set in the *Main settings* tab). Select the signals you want to plot and click *OK*. Click on *X_Quantity* and select *Time*. Finally click on your figure in the *Curves List* and then click on *Add* to see the curve in the graph
       9. For more details please refer to the OpenSim documentation, for example https://simtk-confluence.stanford.edu/display/OpenSim/How+to+Use+the+Inverse+Dynamics+Tool and https://simtk-confluence.stanford.edu/display/OpenSim/Tutorial+3+-+Scaling%2C+Inverse+Kinematics%2C+and+Inverse+Dynamics
 
 ## Resources for using the Qualisys Project Automation Framework (PAF)