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subject01.py
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import os
import osimpipeline as osp
import tasks
import helpers
def scale_setup_fcn(util, mset, sset, ikts):
m = util.Measurement('torso', mset)
m.add_markerpair('RASI', 'CLAV')
m.add_markerpair('LASI', 'CLAV')
m.add_markerpair('LPSI', 'C7')
m.add_markerpair('RPSI', 'C7')
m.add_markerpair('RASI',' RACR')
m.add_markerpair('LASI', 'LACR')
m.add_bodyscale('torso')
m = util.Measurement('pelvis_z', mset)
m.add_markerpair('RPSI', 'LPSI')
m.add_markerpair('RASI', 'LASI')
m.add_bodyscale('pelvis', 'Z')
m = util.Measurement('thigh', mset)
m.add_markerpair('LHJC', 'LLFC')
m.add_markerpair('LHJC', 'LMFC')
m.add_markerpair('RHJC', 'RMFC')
m.add_markerpair('RHJC', 'RLFC')
m.add_bodyscale_bilateral('femur')
m = util.Measurement('shank', mset)
m.add_markerpair('LLFC', 'LLMAL')
m.add_markerpair('LMFC', 'LMMAL')
m.add_markerpair('RLFC', 'RLMAL')
m.add_markerpair('RMFC', 'RMMAL')
m.add_bodyscale_bilateral('tibia')
m = util.Measurement('foot', mset)
m.add_markerpair('LCAL', 'LMT5')
m.add_markerpair('LCAL', 'LTOE')
m.add_markerpair('RCAL', 'RTOE')
m.add_markerpair('RCAL',' RMT5')
m.add_bodyscale_bilateral('talus')
m.add_bodyscale_bilateral('calcn')
m.add_bodyscale_bilateral('toes')
m = util.Measurement('humerus', mset)
m.add_markerpair('LSJC', 'LMEL')
m.add_markerpair('LSJC', 'LLEL')
m.add_markerpair('RSJC', 'RLEL')
m.add_markerpair('RSJC', 'RMEL')
m.add_bodyscale_bilateral('humerus')
m = util.Measurement('radius_ulna', mset)
m.add_markerpair('LLEL', 'LFAradius')
m.add_markerpair('LMEL', 'LFAulna')
m.add_markerpair('RMEL', 'RFAulna')
m.add_markerpair('RLEL', 'RFAradius')
m.add_bodyscale_bilateral('ulna')
m.add_bodyscale_bilateral('radius')
m.add_bodyscale_bilateral('hand')
m = util.Measurement('pelvis_Y', mset)
m.add_markerpair('LPSI', 'LHJC')
m.add_markerpair('RPSI', 'RHJC')
m.add_markerpair('RASI', 'RHJC')
m.add_markerpair('LASI', 'LHJC')
m.add_bodyscale('pelvis', 'Y')
m = util.Measurement('pelvis_X', mset)
m.add_markerpair('RASI', 'RPSI')
m.add_markerpair('LASI', 'LPSI')
m.add_bodyscale('pelvis', 'X')
ikts.add_ikmarkertask_bilateral('ASI', True, 15.0)
ikts.add_ikmarkertask_bilateral('PSI', True, 15.0)
ikts.add_ikmarkertask_bilateral('LFC', True, 10.0)
ikts.add_ikmarkertask_bilateral('MFC', True, 10.0)
ikts.add_ikmarkertask_bilateral('LMAL', True, 5.0)
ikts.add_ikmarkertask_bilateral('MMAL', True, 5.0)
ikts.add_ikmarkertask_bilateral('CAL', True, 5.0)
ikts.add_ikmarkertask_bilateral('TOE', True, 5.0)
ikts.add_ikmarkertask_bilateral('MT5', True, 5.0)
ikts.add_ikmarkertask_bilateral('ACR', True, 2.0)
ikts.add_ikmarkertask_bilateral('ASH', True, 2.0)
ikts.add_ikmarkertask_bilateral('PSH', True, 2.0)
ikts.add_ikmarkertask_bilateral('LEL', True, 1.0)
ikts.add_ikmarkertask_bilateral('MEL', True, 1.0)
ikts.add_ikmarkertask_bilateral('HJC', True, 20.0)
ikts.add_ikmarkertask_bilateral('KJC', True, 10.0)
ikts.add_ikmarkertask_bilateral('AJC', True, 10.0)
ikts.add_ikmarkertask_bilateral('SJC', True, 1.0)
ikts.add_ikmarkertask_bilateral('EJC', True, 1.0)
ikts.add_ikmarkertask_bilateral('FAsuperior', False, 0.0)
ikts.add_ikmarkertask_bilateral('FAradius', False, 0.0)
ikts.add_ikmarkertask_bilateral('FAulna', False, 0.0)
ikts.add_ikmarkertask('CLAV', True, 2.0)
ikts.add_ikmarkertask('C7', True, 2.0)
ikts.add_ikmarkertask_bilateral('TH1', False, 0.0)
ikts.add_ikmarkertask_bilateral('TH2', False, 0.0)
ikts.add_ikmarkertask_bilateral('TH3', False, 0.0)
ikts.add_ikmarkertask_bilateral('TB1', False, 0.0)
ikts.add_ikmarkertask_bilateral('TB2', False, 0.0)
ikts.add_ikmarkertask_bilateral('TB3', False, 0.0)
ikts.add_ikmarkertask_bilateral('UA1', False, 0.0)
ikts.add_ikmarkertask_bilateral('UA2', False, 0.0)
ikts.add_ikmarkertask_bilateral('UA3', False, 0.0)
def add_to_study(study):
subject = study.add_subject(1, 72.85)
cond_args = dict()
subject.cond_args = cond_args
static = subject.add_condition('static')
static_trial = static.add_trial(1, omit_trial_dir=True)
# `os.path.basename(__file__)` should be `subject01.py`.
scale_setup_task = subject.add_task(osp.TaskScaleSetup,
init_time=0,
final_time=0.5,
mocap_trial=static_trial,
edit_setup_function=scale_setup_fcn,
addtl_file_dep=['dodo.py', os.path.basename(__file__)])
subject.add_task(osp.TaskScale,
scale_setup_task=scale_setup_task,
#scale_max_isometric_force=True,
)
subject.add_task(tasks.TaskScaleMuscleMaxIsometricForce)
marker_adjustments = dict()
marker_adjustments['RTOE'] = (1, 0.0170717)
marker_adjustments['RMT5'] = (1, 0.011679)
marker_adjustments['LTOE'] = (1, 0.0170708)
marker_adjustments['LMT5'] = (1, 0.0116779)
subject.add_task(tasks.TaskAdjustScaledModelMarkers, marker_adjustments)
subject.scaled_model_fpath = os.path.join(subject.results_exp_path,
'%s_final.osim' % subject.name)
## walk1 condition
walk1 = subject.add_condition('walk1', metadata={'walking_speed': 1.00})
# GRF gait landmarks
# walk1_trial_temp = walk1.add_trial(99, omit_trial_dir=True)
# walk1_trial_temp.add_task(osp.TaskGRFGaitLandmarks)
# walk1_trial_temp.add_task(tasks.TaskUpdateGroundReactionColumnLabels)
gait_events = dict()
gait_events['right_strikes'] = [0.487, 1.757, 3.020, 4.302]
gait_events['left_toeooffs'] = [0.716, 1.980, 3.256]
gait_events['left_strikes'] = [1.125, 2.393, 3.663]
gait_events['right_toeoffs'] = [1.351, 2.624, 3.886]
walk1_trial = walk1.add_trial(1,
gait_events=gait_events,
omit_trial_dir=True,
)
# walk1: main study tasks
mrs_setup_tasks = helpers.generate_main_tasks(walk1_trial)
helpers.generate_exotopology_tasks(walk1_trial, mrs_setup_tasks)
helpers.generate_coupled_controls_tasks(walk1_trial, mrs_setup_tasks)
## walk2 condition
walk2 = subject.add_condition('walk2', metadata={'walking_speed': 1.25})
# GRF gait landmarks
# walk2_trial_temp = walk2.add_trial(99, omit_trial_dir=True)
# walk2_trial_temp.add_task(osp.TaskGRFGaitLandmarks)
# Trial to use
gait_events = dict()
gait_events['right_strikes'] = [1.179, 2.282, 3.361, 4.488] #, 5.572]
gait_events['left_toeooffs'] = [1.368, 2.471, 3.578] #, 4.680]
gait_events['left_strikes'] = [1.728, 2.836, 3.943] #, 5.051]
gait_events['right_toeoffs'] = [1.934, 3.033, 4.137] #, 5.252]
walk2_trial = walk2.add_trial(1,
gait_events=gait_events,
omit_trial_dir=True,
)
walk2_trial.add_task(tasks.TaskUpdateGroundReactionColumnLabels)
# walk2: main study tasks
helpers.generate_sensitivity_tasks(walk2_trial)
mrs_setup_tasks = helpers.generate_main_tasks(walk2_trial)
helpers.generate_exotopology_tasks(walk2_trial, mrs_setup_tasks)
helpers.generate_coupled_controls_tasks(walk2_trial, mrs_setup_tasks)
## walk3 condition
walk3 = subject.add_condition('walk3', metadata={'walking_speed': 1.50})
# GRF gait landmarks
# walk3_trial_temp = walk3.add_trial(99, omit_trial_dir=True)
# walk3_trial_temp.add_task(osp.TaskGRFGaitLandmarks)
# walk3_trial_temp.add_task(tasks.TaskUpdateGroundReactionColumnLabels)
gait_events = dict()
gait_events['right_strikes'] = [0.911, 1.934, 3.978, 5.008]
gait_events['left_toeoffs'] = [1.081, 2.089, 4.146]
gait_events['left_strikes'] = [1.428, 2.440, 4.495]
gait_events['right_toeoffs'] = [1.598, 2.614, 4.661]
gait_events['stride_times'] = [1.934-0.911, 3.978-2.934, 5.008-3.978]
walk3_trial = walk3.add_trial(1,
gait_events=gait_events,
omit_trial_dir=True,
)
# walk3: main study tasks
mrs_setup_tasks = helpers.generate_main_tasks(walk3_trial)
helpers.generate_exotopology_tasks(walk3_trial, mrs_setup_tasks)
helpers.generate_coupled_controls_tasks(walk3_trial, mrs_setup_tasks)
## walk4 condition
walk4 = subject.add_condition('walk4', metadata={'walking_speed': 1.75})
# GRF gait landmarks
# walk4_trial_temp = walk4.add_trial(99, omit_trial_dir=True)
# walk4_trial_temp.add_task(osp.TaskGRFGaitLandmarks)
# walk4_trial_temp.add_task(tasks.TaskUpdateGroundReactionColumnLabels)
gait_events = dict()
gait_events['right_strikes'] = [1.156, 2.112, 3.069, 4.033]
gait_events['left_toeooffs'] = [1.307, 2.257, 3.218]
gait_events['left_strikes'] = [1.646, 2.594, 3.532]
gait_events['right_toeoffs'] = [1.801, 2.754, 3.714]
walk4_trial = walk4.add_trial(1,
gait_events=gait_events,
omit_trial_dir=True,
)
# walk4: main study tasks
mrs_setup_tasks = helpers.generate_main_tasks(walk4_trial)
helpers.generate_exotopology_tasks(walk4_trial, mrs_setup_tasks)
helpers.generate_coupled_controls_tasks(walk4_trial, mrs_setup_tasks)
# multi-phase parameter calibration (trial does not matter)
calibrate_setup_task = walk3_trial.add_task(
tasks.TaskCalibrateParametersMultiPhaseSetup,
['walk1','walk2','walk3','walk4'],
['cycle01'],
study.param_dict,
study.cost_dict,
passive_precalibrate=True)
walk3_trial.add_task(
tasks.TaskCalibrateParametersMultiPhase,
calibrate_setup_task)
walk3_trial.add_task(
tasks.TaskCalibrateParametersMultiPhasePost,
calibrate_setup_task)