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

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 script from source code repository: https://simtk.org/websvn/wsvn/openknee/utl/SimVitro/#_utl_SimVitro_
- Script: tdms_plotting.py
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
- Ensure there are no spaces in paths to tdms files placed in text file (change to underscores using following script found in source code repository).
  - space_underscore.py

-- ["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. ~~~~

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_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.JCS%20Load_Processed.png attachment:State.Knee%20JCS_Processed.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
  - Normalization of RMS errors in reproducibility analysis

attachment:State.Knee%20JCS_Translations.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_processed.[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])
- Text file with processed kinematic/kinetic data (path/Repro_filename/group_Data_Repro.txt)
- Text file with normalized RMSD values (path/Repro_filename/RMSD_Repro_Table.txt)
  - attachment:RMSD_Repro_Table.txt
- Text file with maximum, minimum, and mean values (path/Repro_filename/Data_Info_Repro_Table.txt)
  - attachment:Data_Info_Repro_Table.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.