/* Feb 22, 2008
edited by Anne Schmitz to use Shriners markers instead of UW markers 
April 1, 2008
modified by Schmitz to include LTHI */

optStoppingCriterion  0.000001
retainExtraMarkers 0

/*******************************************************************************
Transformation matrix for redefining the kinematic coordinate system if so desired
1st row are the measured x, y and z components corresponding to the output X direction
2nd row are the measured x, y and z components corresponding to the output Y direction
3rd row are the measured x, y and z components corresponding to the output Z direction
*******************************************************************************/

/* transforms Shriners kinematic data into SIMM frame 
Shriners frame x transformation = SIMM frame */

begintransformationmatrix 
0.0	1.0	0.0
0.0	0.0	1.0
1.0	0.0	0.0
endtransformationmatrix 

/*******************************************************************************
Flag to denote whether the data represents an upright calibration trial         
(1=YES, 0=NO)                                                                   
*******************************************************************************/
uprighttrial 1                                                                  


/*******************************************************************************
Flag to denote whether the user wishes to reset the anatomical marker locations 
after calibrating to the upright calibration trial                              
(1=YES, 0=NO)                                                                   
*******************************************************************************/
resetanatomicalmarkers 1             

/*******************************************************************************
Anatomical markers are used in computing the generalized coordinates for an
upright static calibration trial.  These markers should exist in both the joint
file and the trc file.  Note that the local coordinates of these markers are
reset after the upright joint angles are computed.  This ensures that the model
and measured marker locations coincide for the calibration data.
*******************************************************************************/
beginanatomicalmarkers      
/* Shriners Markers */
RASI	    30.
LASI	    30.
RPSI	    15.
LPSI	    15.
RLK		5.0
RMK		5.0
LLK		5.0
LMK		5.0
RMA		5.0
RLA		5.0
LLA 	5.0
LMA		1.0
RLT      1.0
RMT      1.0
RLE       1.0
RME       1.0
LLE       1.0
LME       1.0
RLF	1.0
RMF	1.0
LLF	1.0
LMF	1.0
RLHD  1.0
RMHD  1.0
RLS   1.0
LLS   1.0
RMW   1.0
LMW   1.0
RLW		1.0
LLW		1.0
RB5   1.0
LB5   1.0
RHE   1.0
LHE   1.0
RALH    1.0
RAMH    1.0
RPLH    1.0
RPMH    1.0
RLH     1.0
LLH     1.0
RC7     1.0
endanatomicalmarkers        

/* UW Markers
R.ASIS	    30.
S2          15.
L.ASIS	    30.
R.PSIS	    15.
L.PSIS	    15.
R.Shoulder      1.0
R.Elbow         1.0
R.MElbow        1.0
R.Wrist         1.0
L.Shoulder      1.0
L.Elbow         1.0
L.MElbow        1.0
L.Wrist         1.0
R.Knee		5.0
R.MKnee		5.0
R.MAnkle		5.0
R.Ankle		5.0
R.MT5		1.0
R.MT1		1.0
L.Knee		5.0
L.MKnee		5.0
L.Ankle		5.0
L.MAnkle		1.0
L.MT5		1.0
L.MT1		1.0
*/
                            
/*******************************************************************************
Tracking markers are NOT used in computing the generalized coordinates for an
upright static calibration trial.  These markers should exist in both the joint
file and the trc file.  Note that the local coordinates of these markers are
determined after the upright joint angles are computed.  This ensures that the model
and measured tracking marker locations coincide for the calibration data.
*******************************************************************************/
begintrackingmarkers  
/* Shriners markers */
RTHI	0.0
RPPT	0.0
RAPT	0.0
RADT	0.0
RPDT	0.0
LTHI  0.0
LPPT	0.0
LAPT	0.0
LADT	0.0
LPDT	0.0
RPPS	0.0
RADS	0.0
RPDS	0.0
RAPS	0.0
LPPS	0.0
LADS	0.0
LPDS	0.0
LAPS	0.0
RLP	0.0
RMP	0.0
RPDA      0.0
RPPA      0.0
RAPA      0.0
RADA      0.0
LPDA      0.0
LPPA      0.0
LAPA      0.0
LADA      0.0
LPUN    0.0
LDUN    0.0
LPMF    0.0
LPLF    0.0
RPUN    0.0
RDUN    0.0
RPMF    0.0
RPLF    0.0
RLSX    0.0
RMSX    0.0
RLIX    0.0
LPLW    0.0
RPLW    0.0
LDLW    0.0
RDLW    0.0
RFT4    0.0
RFT5    0.0
LFT4    0.0
LFT5    0.0
endtrackingmarkers

/* UW Markers
R.Iliac	0.0
L.Iliac	0.0
R.Clavicle   0.0
R.Bicep      0.0
R.Forearm    0.0
L.Clavicle   0.0
L.Scapula    0.0
L.Bicep      0.0
L.Forearm    0.0
R.TH1	0.0
R.TH2	0.0
R.TH3	0.0
R.SH1	0.0
R.SH2	0.0
R.SH3	0.0
R.SH4	0.0
L.TH1	0.0
L.TH2	0.0
L.TH3	0.0
L.TH4	0.0
L.SH1	0.0
L.SH2	0.0
L.SH3	0.0
*/
                             
/*******************************************************************************
Segment scaling markers are used to compute segment lengths 
The avg distance between each pair of markers following a segment is computed
This ratio of this distance to the distance between skeleton fixed markers is then
computed
The avg ratio for a segment is used as the segment scaling factor in the segment's
x, y and z directions
One can specify separate scaling rules for different directions by using the
_x, _y or _z designations, e.g.
   pelvis_z        R.ASIS L.ASIS
   
*******************************************************************************/

/* replaced UW names with Shriners marker names so all algorithms are the same as UW */

/* questions: what do I replace R.Clavicle, L.Clavicle,
R.Wrist, and L.Wrist with? these UW markers don't have
a Shriners equivalent? */

beginsegmentscalemarkers
pelvis_x 	RASI RLK 	LASI LLK
pelvis_y 	RASI RLK 	LASI LLK	
pelvis_z 	RASI RLK 	LASI LLK
femur_r 	RASI RLK 		LASI LLK
femur_l 	RASI RLK 		LASI LLK
patella_r 	RASI RLK 		LASI  LLK
patella_l 	RASI RLK 		LASI  LLK
tibia_r 	RLK RLA 		LLK LLA
tibia_l 	RLK RLA 		LLK LLA
talus_r 	RLK RLA 		LLK LLA
talus_l 	RLK RLA 		LLK LLA
foot_r 	RASI RLK 	LASI LLK	RLK RLA 		LLK LLA
foot_l 	RASI RLK 	LASI LLK	RLK RLA 		LLK LLA
toes_r 	RASI RLK 	LASI LLK	RLK RLA 		LLK LLA
toes_l 	RASI RLK 	LASI LLK	RLK RLA 		LLK LLA
torso	RASI RLT	LASI RMT
neckhead	RASI RLT	LASI RMT
humerus_r	RLT RLE	RMT LLE
humerus_l	RLT RLE	RMT LLE
ulna_r	RLE RLW		LLE LLW
ulna_l	RLE RLW		LLE LLW
radius_r	RLE RLW		LLE LLW
radius_l	RLE RLW		LLE LLW
hand_r	RLE RLW		LLE LLW
hand_l	RLE RLW		LLE LLW
endsegmentscalemarkers

/* UW Rules with question markers
ulna_r	RLE R.Wrist		LLE L.Wrist
ulna_l	RLE R.Wrist		LLE L.Wrist
radius_r	RLE R.Wrist		LLE L.Wrist
radius_l	RLE R.Wrist		LLE L.Wrist
hand_r	RLE R.Wrist		LLE L.Wrist
hand_l	RLE R.Wrist		LLE L.Wrist
neckhead	RASI R.Clavicle	LASI L.Clavicle
torso	RASI R.Clavicle	LASI L.Clavicle */

/*******************************************************************************
Can reset the gencoord range that will restrict the solutions of the
optimization based inverse dynamics routine
*******************************************************************************/
begingencoordrange
pelvis_tx 		-5.0	5.0
pelvis_ty		-5.0	5.0
pelvis_tz		-5.0	5.0
pelvis_list		-60.0	60.0
pelvis_rot		-200.0	200.0
pelvis_tilt		-60.0	60.0
lumbar_latbend		-0.1	 0.1
lumbar_rot		-0.1	 0.1
lumbar_ext		-60.0	60.0
neck_latbend		-60.0	60.0
neck_rot		-60.0	60.0
neck_ext		-60.0	60.0
arm_add_r		-120.0 	60.0
arm_rot_r		-90.0 	90.0
arm_flex_r		-90.0 	120.0
elbow_flex_r		0.0	160.0
pro_sup_r		50.0 	70.0
wrist_flex_r		-0.001	0.001
arm_add_l		-120.0 	60.0
arm_rot_l		-90.0 	90.0
arm_flex_l		-90.0 	120.0
elbow_flex_l		0.0	160.0
pro_sup_l		50.0	70.0
wrist_flex_l		-0.001	0.001
hip_flex_r		-60.0	150.0
hip_add_r		-60.0	60.0
hip_rot_r		-60.0	60.0	
knee_flex_r		-2.5	160.0
ankle_flex_r		-60.0	60.0
subt_angle_r	-0.001	0.001
toe_angle_r		-60.0 	60.0
hip_flex_l		-60.0	150.0
hip_add_l		-60.0	60.0
hip_rot_l		-60.0	60.0	
knee_flex_l		-2.5	160.0
ankle_flex_l	-60.0	60.0
subt_angle_l	-0.001	0.001
toe_angle_l		-0.001	0.001
endgencoordrange