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Directions for Running Customization Script

1. Febio and Geometry file template models should already be generated. Check that the Names of all geometry parts are according the the Data Management page on the OpenKnee(S) simtk site. For Example: 'FMB' for Femur, 'PTC' for Patella Cartilage, 'MNS-M' for Medial Meniscus. NOTE: Use these names in the Connectivity Xml when running StlToMed.py and MedToFebio.py, so you won't have to change them in the template model. 

2. Create an xml file containing the Model Propeties, which includes Material properties, and manually chosen anatomical lankmarks. see ModelProperties.xml located in this folder for the proper xml structure. 

3. Locate the following anatomical landmarks manually, and save their coordinates in the Landmarks element of the Model Properties xml. Use the naming convention in the brackets below. 

medial tibial spine  (MTS)
lateral tibial spine (LTS) 
approximate center of medial tibial plateau (MTP)
approximate center of lateral tibial plateau (LTP)
most distal point on the posterior surface of the femur, midway between the medial and lateral condyles (DFP)
medial femoral condyle (most distal point on posterior surface) (MFC)
lateral femoral condyle (most distal point on posterior surface) (LFC)
Medial Patella Ridge (MPR)
Lateral Patella Ridge (LPR)

3. Save the scripts FebCustomization.py, and AnatomicalLandmarks.py in the same folder 

4. Run FebCustomization.py from python in the terminal with the first argument as the Febio file, and the second argument the Model Properties xml file

python FebCustomization.py Febio.feb ModelProperties.xml

The script generates two files: 
a. the customized febio file, in the same location as the original febio template file
b. the customized geometry file, in the same location as the original geometry file (provided in the 'Gemoetry' section of the febio file)

The script also adds landmarks that were calculated to the Model Properties xml, such as joint origins and axes, in case they need to be checked. 

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Directions for Runnin Model Reduction Script.

1. Create the customized febio file (see directions above)

2. Run ModelRedudiction.py from python in the terminal, with the first argument as the customized febio file, and the second argument a list of names of parts you would like to keep in the reduced model. For example:
python ModelReduction.py febio_custom.feb ['FMB','ACL','TBB']

The script generates a new febio file, where all the unused geometry materials are turned into rigid bodies, fixed in place, and all contacts/ties between them are removed. Note that the new febio file will still reference the same geometry file as the input febio file. 
Simulation boundary conditions and constraints should be manually edited as needed for test cases. 

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Directions for Running LogPostProcessing.py

Run LogPostProcessing.py from python in the terminal with the first argument as the output file (.log) , and the second argument the ModelPropeties.xml document.

The script generates the following graphs:
1. joint translations and rotations for the patellofemoral and tibiofemoral joints. 
2. translation of tibia and patella relative to the femur in the femur coordinate system