notes.txt

2025/1/7

Note: after writing a scaling file from Matlab fclose('all') needs to be called
otherwise Matlab blocks OpenSim from using the file. This was time-consuming
to debug.

Ok. To dos:

1. Apply Scale programmatically and see if it works

2. IK script:
  a. Read in the pose of the joints from the static file. Write these in 
     as the manually set values for the IK coordinate tasks
  b. Update the IK setup once
  
  c. For each TRC file, update the IK setup:
    <time_range> 			: Have to check the TRC file for this one.
	                          Make an option to produce a trimmed file: 
								autodetect motion, then add +/- 0.5 sec.
    <output_motion_file>	: Same name as the Take, but with mot, and maybe
	                          all spaces filled with '_'
	<marker_file>
--------------------------------------------------
Questions:
1. What is the height of the (passenger) model?
2. Participant:
a. Height is in the data sheet
b. Normalized torso segment lengths
	DeLeva (Table 4)
	:C7 to hip joint: 
		male 	603.3 / 1741 
			= 0.3465249856404365
		female	614.8 / 1735 
			= 0.3543515850144092
	:STR to hip joint:
		male 	(603.3 - 71.4) / 1741
			= 0.3055140723721999
		female	(614.8 - 71.4 (614.8/603.3))/ 1735
				(614.8 - 72.8)/ 1735
			= 0.3123919308357349
					
		
1. Template model:
opensim2022/models/passengerModel.osim
             x,     y,    z       
	C7 (-0.327, 0.596, 0.00)
	HC ( 0.000, 0.0816, 0.067
C7-HC  (-0.327  -0.514, (not incl)

	l  0.6095 m
	
	This is very close to the 1.74m male. In deed, the Vasavada model has been constructed for a 1.74m tall male.

2. Scaling:
a. Programmatic preliminaries
 - Evaluate l_c7_HC from the default model.
 - Evaluate l_c7_HC using De Leva and the participant's height 
 - Calculate the manual scaling factor for the torso.
 - Update the Scaling script with these updated manual scaling terms.
b. Apply the model scaling using the marker based measures.
c. Save the model as "subjectXX_scaled.xml"

3. Marker positioning
a. Load the trial and time of a good neutral pose
b. Apply IK.
c. Update the position of the markers.
d. Save the model as "subjectXX_scaled_aligned.xml"

4. Then ... on with the pipline.