updating default coordinate values

[Riza Bayoglu]

Hi,

I like to change the coordinate values in my model using Python scripting. I am analyzing only one state. Reading through the API documents and the forum questions, I used setValue() property of the coordinates and assemble() afterwards. However, my code below does not seem to update the default coordinate values.

Code: Select all

model     = osim.Model(modelpath)
actuators = osim.ForceSet('mymodel.xml')
forceset  = model.updForceSet()

for i in range(0, actuators.getSize() -1 ):
            
    forceset.cloneAndAppend(actuators.get(i))
    
analyze_tool = osim.AnalyzeTool('staticOpt_Setup.xml')
analyze_tool.setModel(model)
analyze_tool.setStartTime(0)
analyze_tool.setFinalTime(0)  

state      = model.initSystem()
coord_set  = model.getCoordinateSet()
coords     = ['pelvis_tilt',	'Abs_FE',	'Abs_LB',	'Abs_AR',	'L5_S1_FE',	'L5_S1_LB',	'L5_S1_AR',	'L4_L5_FE',	'L4_L5_LB',	'L4_L5_AR',	'L3_L4_FE',	'L3_L4_LB',	'L3_L4_AR',	'L2_L3_FE', 'L2_L3_LB',	'L2_L3_AR',	'L1_L2_FE',	'L1_L2_LB',	'L1_L2_AR',	'T12_L1_FE',	'T12_L1_LB',	'T12_L1_AR',	'T11_T12_FE',	'T11_T12_LB', 'T11_T12_AR',	'T10_T11_FE', 'T10_T11_LB',	'T10_T11_AR', 'T9_T10_FE',	'T9_T10_LB', 'T9_T10_AR',	'T8_T9_FE',	'T8_T9_LB',	'T8_T9_AR',	'T7_T8_FE',	'T7_T8_LB',	'T7_T8_AR',	'T6_T7_FE',	'T6_T7_LB',	'T6_T7_AR',	'T5_T6_FE', 'T5_T6_LB',	'T5_T6_AR',	'T4_T5_FE',	'T4_T5_LB',	'T4_T5_AR',	'T3_T4_FE',	'T3_T4_LB',	'T3_T4_AR',	'T2_T3_FE',	'T2_T3_LB',	'T2_T3_AR',	'T1_T2_FE',	'T1_T2_LB',	'T1_T2_AR',	'T1_head_neck_FE',	'T1_head_neck_LB',	'T1_head_neck_AR',	'T12_r12R_X',	'T12_r12R_Y',	'T12_r12R_Z',	'T11_r11R_X',	'T11_r11R_Y',	'T11_r11R_Z',	'T10_r10R_X',	'T10_r10R_Y',	'T10_r10R_Z',	'T9_r9R_X',	'T9_r9R_Y',	'T9_r9R_Z',	'T8_r8R_X',	'T8_r8R_Y',	'T8_r8R_Z',	'T7_r7R_X',	'T7_r7R_Y',	'T7_r7R_Z',	'T6_r6R_X',	'T6_r6R_Y',	'T6_r6R_Z',	'T5_r5R_X',	'T5_r5R_Y',	'T5_r5R_Z',	'T4_r4R_X',	'T4_r4R_Y',	'T4_r4R_Z',	'T3_r3R_X',	'T3_r3R_Y',	'T3_r3R_Z',	'T2_r2R_X',	'T2_r2R_Y',	'T2_r2R_Z',	'T1_r1R_X',	'T1_r1R_Y',	'T1_r1R_Z',	'T12_r12L_X',	'T12_r12L_Y',	'T12_r12L_Z',	'T11_r11L_X',	'T11_r11L_Y',	'T11_r11L_Z',	'T10_r10L_X',	'T10_r10L_Y',	'T10_r10L_Z',	'T9_r9L_X',	'T9_r9L_Y',	'T9_r9L_Z',	'T8_r8L_X',	'T8_r8L_Y',	'T8_r8L_Z',	'T7_r7L_X',	'T7_r7L_Y',	'T7_r7L_Z',	'T6_r6L_X',	'T6_r6L_Y',	'T6_r6L_Z',	'T5_r5L_X',	'T5_r5L_Y',	'T5_r5L_Z',	'T4_r4L_X',	'T4_r4L_Y',	'T4_r4L_Z',	'T3_r3L_X',	'T3_r3L_Y',	'T3_r3L_Z',	'T2_r2L_X',	'T2_r2L_Y',	'T2_r2L_Z',	'T1_r1L_X',	'T1_r1L_Y',	'T1_r1L_Z',	'SternumX',	'SternumY',	'SternumZ',	'SternumRotX',	'SternumRotY',	'SternumRotZ',	'shoulder_elv_r',	'shoulder_rot_r',	'elv_angle_r',	'elbow_flexion_r',	'pro_sup_r',	'wrist_dev_r',	'wrist_flex_r',	'shoulder_elv_l',	'shoulder_rot_l',	'elv_angle_l',	'elbow_flexion_l',	'pro_sup_l',	'wrist_dev_l',	'wrist_flex_l']
coord_vals = [0,0,0,0,-0.01745,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0] 

for i in range(len(coords)):

    curr_coord = coord_set.get(coords[i])
    curr_coord.setValue(state, coord_vals[i], False)

state = model.initSystem()
model.assemble(state)
analyze_tool.run()

[/size]

Afterwards, I use these codes to display if the values are updated, but they do not.

Code: Select all

coord_set = model.getCoordinateSet()     
print(coord_set.get(coords[4]).getName())    
print(coord_set.get(coords[4]).getValue(state))

Any help is appreciated.

[Thomas Uchida]

The line "state = model.initSystem()" immediately after the "for" loop is creating a fresh underlying computational system and assigning it to the variable "state" in Matlab, so anything that was done to the "state" variable before that line will be lost. Please try removing that line.

[Riza Bayoglu]

Hi Thomas,

Thanks for the help. My original scripts do not include the code piece, state = model.initSystem() after the second for loop. I accidentally copied that line when I was copying the clean version of my codes here, my bad. For the sake of clarity, my current codes are below. I am using Python v3.11 and Opensim v4.4 that I installed with Conda. I still can't get the joint coordinate values updated in the model.

Code: Select all

model      = osim.Model(modelpath)
actuators = osim.ForceSet('mymodel.xml')
forceset   = model.updForceSet()

for i in range(0, actuators.getSize() -1 ):
            
    forceset.cloneAndAppend(actuators.get(i))
    
analyze_tool = osim.AnalyzeTool('staticOpt_Setup.xml')
analyze_tool.setModel(model)
analyze_tool.setStartTime(0)
analyze_tool.setFinalTime(0)  

state         = model.initSystem()
coord_set  = model.getCoordinateSet()
coords       = ['pelvis_tilt',	'Abs_FE',	'Abs_LB',	'Abs_AR',	'L5_S1_FE',	'L5_S1_LB',	'L5_S1_AR',	'L4_L5_FE',	'L4_L5_LB',	'L4_L5_AR',	'L3_L4_FE',	'L3_L4_LB',	'L3_L4_AR',	'L2_L3_FE', 'L2_L3_LB',	'L2_L3_AR',	'L1_L2_FE',	'L1_L2_LB',	'L1_L2_AR',	'T12_L1_FE',	'T12_L1_LB',	'T12_L1_AR',	'T11_T12_FE',	'T11_T12_LB', 'T11_T12_AR',	'T10_T11_FE', 'T10_T11_LB',	'T10_T11_AR', 'T9_T10_FE',	'T9_T10_LB', 'T9_T10_AR',	'T8_T9_FE',	'T8_T9_LB',	'T8_T9_AR',	'T7_T8_FE',	'T7_T8_LB',	'T7_T8_AR',	'T6_T7_FE',	'T6_T7_LB',	'T6_T7_AR',	'T5_T6_FE', 'T5_T6_LB',	'T5_T6_AR',	'T4_T5_FE',	'T4_T5_LB',	'T4_T5_AR',	'T3_T4_FE',	'T3_T4_LB',	'T3_T4_AR',	'T2_T3_FE',	'T2_T3_LB',	'T2_T3_AR',	'T1_T2_FE',	'T1_T2_LB',	'T1_T2_AR',	'T1_head_neck_FE',	'T1_head_neck_LB',	'T1_head_neck_AR',	'T12_r12R_X',	'T12_r12R_Y',	'T12_r12R_Z',	'T11_r11R_X',	'T11_r11R_Y',	'T11_r11R_Z',	'T10_r10R_X',	'T10_r10R_Y',	'T10_r10R_Z',	'T9_r9R_X',	'T9_r9R_Y',	'T9_r9R_Z',	'T8_r8R_X',	'T8_r8R_Y',	'T8_r8R_Z',	'T7_r7R_X',	'T7_r7R_Y',	'T7_r7R_Z',	'T6_r6R_X',	'T6_r6R_Y',	'T6_r6R_Z',	'T5_r5R_X',	'T5_r5R_Y',	'T5_r5R_Z',	'T4_r4R_X',	'T4_r4R_Y',	'T4_r4R_Z',	'T3_r3R_X',	'T3_r3R_Y',	'T3_r3R_Z',	'T2_r2R_X',	'T2_r2R_Y',	'T2_r2R_Z',	'T1_r1R_X',	'T1_r1R_Y',	'T1_r1R_Z',	'T12_r12L_X',	'T12_r12L_Y',	'T12_r12L_Z',	'T11_r11L_X',	'T11_r11L_Y',	'T11_r11L_Z',	'T10_r10L_X',	'T10_r10L_Y',	'T10_r10L_Z',	'T9_r9L_X',	'T9_r9L_Y',	'T9_r9L_Z',	'T8_r8L_X',	'T8_r8L_Y',	'T8_r8L_Z',	'T7_r7L_X',	'T7_r7L_Y',	'T7_r7L_Z',	'T6_r6L_X',	'T6_r6L_Y',	'T6_r6L_Z',	'T5_r5L_X',	'T5_r5L_Y',	'T5_r5L_Z',	'T4_r4L_X',	'T4_r4L_Y',	'T4_r4L_Z',	'T3_r3L_X',	'T3_r3L_Y',	'T3_r3L_Z',	'T2_r2L_X',	'T2_r2L_Y',	'T2_r2L_Z',	'T1_r1L_X',	'T1_r1L_Y',	'T1_r1L_Z',	'SternumX',	'SternumY',	'SternumZ',	'SternumRotX',	'SternumRotY',	'SternumRotZ',	'shoulder_elv_r',	'shoulder_rot_r',	'elv_angle_r',	'elbow_flexion_r',	'pro_sup_r',	'wrist_dev_r',	'wrist_flex_r',	'shoulder_elv_l',	'shoulder_rot_l',	'elv_angle_l',	'elbow_flexion_l',	'pro_sup_l',	'wrist_dev_l',	'wrist_flex_l']
coord_vals = [0,0,0,0,-0.01745,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0] 

for i in range(len(coords)):

    curr_coord = coord_set.get(coords[i])
    curr_coord.setValue(state, coord_vals[i], False)

model.assemble(state)
analyze_tool.run()

[Riza Bayoglu]

I still need help with this. Does anyone have suggestions? Thank you.

[Mohammadreza Rezaie]

Hi, I never used AnalyzeTool in that way. You can set your motion file using setCoordinatesFileName.

These may help:

1. update coordinates values followed by model.assemble(state) and model.realizePosition(state) before analyze_tool.setModel(model) line.
2. use setLoadModelAndInput before analyze_tool.run().