TableOfContents()

Target Outcome

Loading and boundary conditions (kinematics-kinetics) reflecting experimentation, which are represented in model coordinate systems

• Access data in tdms file (outputted by SimVitro) from tibiofemoral joint experimentation

• Process kinematic and kinetic data

  • Input & validation data for FE model

• Analyze reproducibility data (anterior-posterior laxity)

Prerequisites

Include(Infrastructure/AuxiliarySoftware, "Infrastructure", 2, from="= Scripting & Numerical Analysis =", to="= Finite Element Analysis =")

Previous Protocols

• ["Specifications/ExperimentationAnatomicalImaging"]
• ["Specifications/ExperimentationJointMechanics"]
• ["Specifications/Registration"]

Protocols

Tibiofemoral Testing:

Input

• Model coordinate systems and transformation matrices (obtained from imaging)
• Experimentation coordinate systems and transformation matrices (obtained from joint mechanics testing)
• Transformation matrices for registration of imaging and joint testing coordinate systems (obtained from registration)

• Access Python script from source code repository: https://simtk.org/websvn/wsvn/openknee/utl/SimVitro/#_utl_SimVitro_

  • Script: tdms_plotting.py

  • Python module: npTDMS

• Processing data (use script tdms_plotting.py):

  • Tdms files (Main Processed Data File)
    • Filename: Experiment Run Number_Experiment Run Name + “_Main” + “_Processed”
    • File extension: “.tdms”
    • File Format: binary
    • File Type: NI TDMS
  • Text file with paths to tdms files within (include extension for tdms files)

• Reproducibility data (use script tdms_plotting.py):

  • Data from three AP laxity tests at 30 degree flexion
  • Text file with path to the three tdms file within (include extension for tdms files)
• Important Notes
  • Place each path to tdms file on new line of text file.

-- ["aerdemir"] DateTime(2015-06-30T12:33:37Z) Your code should be able to handle paths with spaces. Otherwise the user will need to move files to an approriate path.

-- ["ogad"] DateTime(2015-06-30T20:20:35Z) Thank you. Resolved.

• Paths of tdms files should be relative to your present working directory when running the script.
• Example of running script in terminal: 'python tdms_plotting.py text_file.txt'

Procedures

• Use nptdms module to access data
  • Data file hierarchy of tdms file
    • attachment:datafilehiearchy.png
• Processing data:
  • Find "time windows" during desired kinetics (Channel: Kinetics.JCS.Desired). "Time windows" are periods of time in which a constant force or torque is applied (steps in loading conditions).

    • For each "time window" select last time point. This will be appended to list of key time indices, "time index", which will be used to process data.

    • Raw desired kinetics and processed desired kinetics shown below.
      • attachment:Kinetics.JCS.Desired.png attachment:Kinetics.JCS.Desired_Extracted.png
  • Use "time index" from desired kinetics to process actual kinetics (Channel: State.JCS Load) and actual kinematics (Channel: State.Knee JCS).
    • Examples of processed kinematic and kinetic data.
      • attachment:State.JCS_Load_Extracted.png attachment:State.Knee_JCS_Extracted.png
• Reproducibility testing:
  • Process kinematic/kinetic data from AP laxity 30 degrees flexion tests
    • Enter '1' when prompted to run analysis for reproducibility testing (tdms_plotting.py)
  • Compare differences between all combinations of the three reproducibility tests

    • Compare tests 1 & 2, 1 & 3, 2 & 3 using RMSD

    • RMSD in reproducibility analysis

attachment:State.Knee_JCS_Translations.png attachment:Repro_Plot.png

Output

• Joint kinematics-kinetics information
  • Experimental kinematics and/or kinetics described in a form that can be directly applied to the model as inputs.
  • Experimental kinematics and/or kinetics described in a form that can be directly compared to the model outputs.

• Processed kinematic & kinetic data

  • Folder with tdms file name with directory of tdms files
  • Plots of all raw data (path/filename/group.[png/svg])
  • Plots of processed kinematic/kinetic data (path/filename/group_extracted.[png/svg])
  • Text file with processed kinematic/kinetic data (path/filename/group.txt)
• Reproducibility testing
  • Folder titled Repro_filename with directory of last tdms file (filename = last reproducibility tdms file)
  • Plots comparing forces/torques and rotations/translations between tests (path/Repro_filename/group_forces.[png/svg])
  • Plot of kinetic vs. kinematic data for dominant axis (Anterior-Posterior)
  • Text file with processed kinematic/kinetic data (path/Repro_filename/group_Data_Repro.txt)
  • Text file with RMSD values, maximums, minimums, and means (path/Repro_filename/RMSD_Repro_Table.txt)
    • attachment:RMSD_Repro_Table.txt

Patellofemoral Testing

Input

Input is similar to tibiofemoral testing input, however reproducibility tests do not occur in this script.

• Model coordinate systems and transformation matrices (obtained from imaging)
• Experimentation coordinate systems and transformation matrices (obtained from joint mechanics testing)
• Transformation matrices for registration of imaging and joint testing coordinate systems (obtained from registration)

• Access Python script from source code repository: https://simtk.org/websvn/wsvn/openknee/utl/SimVitro/#_utl_SimVitro_

  • Script: tdms_plottingPF.py

  • Python module: npTDMS

• Processing data (use script tdms_plottingPF.py):

  • Tdms files (Main Processed Data File)
    • Filename: Experiment Run Number_Experiment Run Name + “_Main” + “_Processed”
    • File extension: “.tdms”
    • File Format: binary
    • File Type: NI TDMS
  • Text file with paths to tdms files within (include extension for tdms files)
• Important Notes
  • Place each path to tdms file on new line of text file.

Procedure

Procedure is similar to the tibiofemoral testing above:

• Processing data: Find "time windows" during desired kinetics (Channel: Kinetics.JCS.Desired). "Time windows" are periods of time in which a constant force or torque is applied (steps in loading conditions).

• For each "time window" select last time point. This will be appended to list of key time indices, "time index", which will be used to process data.

• Raw desired kinetics and processed desired kinetics shown below.

attachment:PTKinetics.JCSlDesired.png

attachment:Kinetics.JCS.Desired_Processed.png

Use "time index" from desired kinetics to process actual kinetics (Channel: State.JCS Load) and actual kinematics (Channel: State.Knee JCS).

• Examples of processed kinematic and kinetic data.

attachment:State.Knee%20PTFJ.png

attachment:State.Knee%20PTFJ_Processed.png

Output

• Joint kinematics-kinetics information
  • Experimental kinematics and/or kinetics described in a form that can be directly applied to the model as inputs.
  • Experimental kinematics and/or kinetics described in a form that can be directly compared to the model outputs.

• Processed kinematic & kinetic data

  • Folder with tdms file name with directory of tdms files
  • Plots of all raw data (path/filename/group.[png/svg])
  • Plots of processed kinematic/kinetic data (path/filename/group_extracted.[png/svg])
  • Text file with processed kinematic/kinetic data (path/filename/group.txt)

Test Problem

-- ["aerdemir"] DateTime(2014-11-18T13:58:01Z) Reproducibility tests (30 degrees flexion anterior-posterior laxity) during characterization of tibiofemoral joint kinematics/kinetics can be a good candidate.