<<TableOfContents>>

== Target ==
 1. Create visualization of experimental tests in modeling (image) coordinate system. 
 1. Prepare experimental data for model inputs. 

== Registration ==
 1. Download joint mechanics .zip file from Downloads page. 
 1. Download the desired registration markers and bone STLs (place in folder named geometry-oks00x, where x is the specimen ID). 
   * For tibiofemoral joint mechanics:
     * 3 registration marker stls for tibia
     * 3 registration marker stls for femur
     * stl for tibia bone (only needed for visualization)
     * stl for femur bone (only needed for visualization)
   * For patellofemoral joint mechanics (in addition to TF joint mechanics):
     * 3 registration marker stls for patella
     * stl for patella (only needed for visualization)
 1. Add digitizing order of femur and tibia in a [[https://simtk.org/svn/openknee/utl/Registration/Registration_final/ReadMe_Notes.txt|ReadMe_Notes.txt]] file within the main Configuration folder of the tibiofemoral test directory. 
 1. Create registration xml ([[https://simtk.org/svn/openknee/utl/Registration/Registration_final/oks001_registration_01.xml| Example Registration XML]]). Place in registration-00x_xx folder within the registration-00x directory. 
 1. Run script from command line [[https://simtk.org/svn/openknee/utl/Registration/Registration_final/convert_to_image_CS.py|Registration Script]]
  1. Change directory to desired !OpenKnee specimen (e.g. oks001)
  1. Run '''convert_to_image_CS.py <oks00x_registration_0x.xml> <1>'''
     * Inputs: 
        * Registration xml 
        * Boolean: 0-does not show visualization figure, 1-shows visualization figure
     * Outputs:
        * Transformation matrices saved within .npz file for each trial that has processed data. 

'''Example using oks001 - 004_passive flexion''' <<BR>>
White stls - segmentation from MRI. Colored registration marker stls - spheres from calculated center of digitized points. <<BR>>
{{attachment:OK_reg1.png||height=300}}

== Re-sample Data for Model Input ==
 1. Create text file with desired tdms file(s) you would like to re-sample. Place this text file in either the !KinematicsKinetics directory of the !PatellofemoralJoint or !TibiofemoralJoint mechanics directories depending on which data you are interested in re-sampling. [[attachment:oks001_PF.txt|Example text file for PatellofemoralJoint]]
 1. Place in the appropriate directory !KinematicsKinetics of either the !TibioFemoral or !PatelloFemoral test directories. 
 1. Run script from command line [[https://simtk.org/svn/openknee/utl/Registration/Registration_final/resampling_plotting.py|Re-sampling Script]]
   1. Change directory to desired !OpenKnee specimen (e.g. oks001)
   1. Run '''resampling_plotting.py <oks00x_registration_0x.xml> <oks0x_xF.txt>
See [[attachment:005_Passive Flexion 0-60_main_processed.mp4|Sample Passive Flexion Video]] for video example.