helpers.py

import osimpipeline as osp
import tasks
import pyBTK as btk
import opensim as osm

def filemodifier(self,mocapdir,subject,loadorno,condition,trial):
    # Read in trc file and create acquisition object
    import pdb
    # pdb.set_trace()
    ## old stuff
        # reader = btk.btkAcquisitionFileReader()
        # reader.SetFilename(mocapdir)
        # reader.Update()
        # acq = reader.GetOutput()

        # Set data capture point frequency for all files in case
        # missing from TRC. This is required if the method
        # acq.GetPointFrameNumber() is to be used when adding a new
        # marker.

        # freq = 100.0 # Hz old = 120
        # acq.SetPointFrequency(freq)

        # dont need
            # Remove unused marker recordings from left leg
            # unused_markers = ["LCW", "LLS1", "LLS2", "LLS3", "LLS4",
            #                   "LMS1", "LMS2", "LMS3", "LMS4", "LDAC",
            #                   "LPAC", "LHJC"]
            # for mark in unused_markers:
            #     acq.RemovePoint(mark)
        
    ### read in files

    # Only need to estimate joint centers for static trial
    if loadorno == 'noload':
        if condition == 'static':
            print('\nStatic trial, adding markers...') 
            acq = osm.TimeSeriesTableVec3(mocapdir)
            self.add_virtual_markers(acq)



    # Update acquisition object to reflect changes
    # acq.Update()

    # Write changes to new C3D file
    # writer = btk.btkAcquisitionFileWriter()
    # writer.SetInput(acq)
    # writer.SetFilename(os.path.join(self.preprocess_path, subj,
                                    # '%s.trc' % v))
    # writer.Update()
    ## old version
        # for subj in self.study.all_subjects:
        #     print(subj)
        #     for k, v in self.cond_map.items():
        #         print ('-->', v)

        #         # shouldn't need to do this anymore
        #         # Read in C3D file and create acquisition object
        #         reader = btk.btkAcquisitionFileReader()
        #         reader.SetFilename(os.path.join(self.preprocess_path, subj,
        #                                         '%s.trc' % v))
        #         reader.Update()
        #         acq = reader.GetOutput()

        #         # Set data capture point frequency for all files in case
        #         # missing from TRC. This is required if the method
        #         # acq.GetPointFrameNumber() is to be used when adding a new
        #         # marker.
        #         freq = 120.0 # Hz
        #         acq.SetPointFrequency(freq)

        #         # dont need
        #             # Remove unused marker recordings from left leg
        #             # unused_markers = ["LCW", "LLS1", "LLS2", "LLS3", "LLS4",
        #             #                   "LMS1", "LMS2", "LMS3", "LMS4", "LDAC",
        #             #                   "LPAC", "LHJC"]
        #             # for mark in unused_markers:
        #             #     acq.RemovePoint(mark)
                
        #         # Only need to estimate joint centers for static trial
        #         if k=='static': 
        #             self.add_virtual_markers(acq)

        #         # Update acquisition object to reflect changes
        #         acq.Update()

        #         # Write changes to new C3D file
        #         writer = btk.btkAcquisitionFileWriter()
        #         writer.SetInput(acq)
        #         writer.SetFilename(os.path.join(self.preprocess_path, subj,
        #                                         '%s.trc' % v))
        #         writer.Update()

def generate_mrsmod_task(trial, mrs_setup_tasks, force_level):

    if force_level == 'low': exo_force_level = 1
    elif force_level == 'med': exo_force_level = 2 
    elif force_level == 'high': exo_force_level = 3
    elif force_level == 'max': exo_force_level = 4  
          
    mrsflags = [
        "study='AnkleHipExosuit'",
        "exo_force_level=%s" % exo_force_level, # shift_exo_peaksforce_level,
        "data_path='%s'" % trial.study.config['data_path'],
        "subject='%s'" % trial.subject.name,
        "condition='%s'" % trial.condition.name,
        "shift_exo_peaks=%s" % trial.study.shift_exo_peaks,
        ]

    mrsmod_tasks = trial.add_task_cycles(
        osp.TaskMRSDeGrooteMod,
        force_level,
        'AnkleHipExosuit: apply low exosuit force condition',
        mrsflags,
        setup_tasks=mrs_setup_tasks
        )

    trial.add_task_cycles(tasks.TaskMRSDeGrooteModPost,
        setup_tasks=mrsmod_tasks)

def generate_ik_id_tasks(trial):

    ik_setup_task = trial.add_task(osp.TaskIKSetup)
    trial.add_task(osp.TaskIK, ik_setup_task)
    trial.add_task(osp.TaskIKPost, ik_setup_task,
        error_markers=trial.study.error_markers, side='r')

    trial.add_task(tasks.TaskFilterGRFs)
    trial.add_task(tasks.TaskUpdateGroundReactionColumnLabels)
    id_setup_task = trial.add_task(osp.TaskIDSetup, ik_setup_task)
    trial.add_task(osp.TaskID, id_setup_task)

    # Create Butterworth filter to process net joint moments from ID
    from scipy.signal import butter
    import math     
    
    grf_sample_freq = 2160 # Hz
    cutoff = 200 # Hz

    nyq = 0.5 * grf_sample_freq
    # 1080
    norm_cutoff = cutoff / nyq
    # .185

    b, a = butter(4, 0.15, btype='low', analog=False) # old is 4, 0.15
    butter_polys = (b, a)

    # need to find out where the best and right place to do this filtering and editing

    trial.add_task(osp.TaskIDPost, id_setup_task, 
        butter_polys=butter_polys,  # default is false, this turns off the joint moment filtering
        plot_primary_leg_only=False)