pose2sim/Pose2Sim/Utilities/bodykin_from_mot_osim.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-


'''
    ##################################################
    ## Build csv from mot and osim files            ##
    ##################################################
    
    Build a csv file which stores locations and orientations of all bodies
    calculated from a .mot motion file and a .osim model file.
    
    Equivalent to OpenSim Analysis -> BodyKinematics but without the bugs in 
    orientations due to their use of Euler angle instead of homography matrices

    Transforms from OpenSim's yup to Blender's zup unless you set direction = 'yup'
    
    Usage: 
    from Pose2Sim.Utilities import bodykin_from_mot_osim; bodykin_from_mot_osim.bodykin_from_mot_osim_func(r'<input_mot_file>', r'<output_osim_file>', r'<output_csv_file>')
    python -m bodykin_from_mot_osim -m input_mot_file -o input_osim_file
    python -m bodykin_from_mot_osim -m input_mot_file -o input_osim_file -c output_csv_file
'''


## INIT
import os
import numpy as np
import opensim as osim
import argparse

direction = 'zup' # 'zup' or 'yup'

## AUTHORSHIP INFORMATION
__author__ = "David Pagnon, Jonathan Camargo"
__copyright__ = "Copyright 2023, BlendOSim & Sim2Blend"
__credits__ = ["David Pagnon", "Jonathan Camargo"]
__license__ = "MIT License"
__version__ = "0.0.1"
__maintainer__ = "David Pagnon"
__email__ = "contact@david-pagnon.com"
__status__ = "Development"


def bodykin_from_mot_osim_func(*args):
    '''
    Build a csv file which stores locations and orientations of all bodies
    calculated from a .mot motion file and a .osim model file.
    
    Equivalent to OpenSim Analysis -> BodyKinematics but without the bugs in 
    orientations due to their use of Euler angle instead of homography matrices
    
    Usage: 
    from Pose2Sim.Utilities import bodykin_from_mot_osim; bodykin_from_mot_osim.bodykin_from_mot_osim_func(r'<input_mot_file>', r'<output_osim_file>', r'<output_csv_file>')
    python -m bodykin_from_mot_osim -m input_mot_file -o input_osim_file
    python -m bodykin_from_mot_osim -m input_mot_file -o input_osim_file -t output_csv_file
    '''
    
    try:
        motion_path = args[0]['input_mot_file'] # invoked with argparse
        osim_path = args[0]['input_osim_file']
        if args[0]['csv_output_file'] == None:
            output_csv_file = motion_path.replace('.mot', '.csv')
        else:
            output_csv_file = args[0]['csv_output_file']
    except:
        motion_path = args[0] # invoked as a function
        osim_path = args[1]
        try:
            output_csv_file = args[2]
        except:
            output_csv_file = motion_path.replace('.mot', '.csv')
    
    
    # Read model and motion files
    model = osim.Model(osim_path)
    motion_data = osim.TimeSeriesTable(motion_path)

    # Model: get model coordinates and bodies
    model_coordSet = model.getCoordinateSet()
    coordinates = [model_coordSet.get(i) for i in range(model_coordSet.getSize())]
    coordinateNames = [c.getName() for c in coordinates]
    model_bodySet = model.getBodySet()
    bodies = [model_bodySet.get(i) for i in range(model_bodySet.getSize())]
    bodyNames = [b.getName() for b in bodies]

    # Motion: read coordinates and convert to radians
    times = motion_data.getIndependentColumn()
    motion_data_np = motion_data.getMatrix().to_numpy()
    for i in range(len(coordinates)):
        if coordinates[i].getMotionType() == 1: # 1: rotation, 2: translation, 3: coupled
            motion_data_np[:,i] = motion_data_np[:,i] * np.pi/180 # if rotation, convert to radians

    # Animate model
    state = model.initSystem()
    loc_rot_frame_all = []
    H_zup = np.array([[1,0,0,0], [0,0,-1,0], [0,1,0,0], [0,0,0,1]])
    for n in range(motion_data.getNumRows()):
        
        # Set model struct in each time state
        for c, coord in enumerate(coordinateNames):
            model.getCoordinateSet().get(coord).setValue(state, motion_data_np[n,c])
        
        # Use state of model to get body coordinates in ground
        loc_rot_frame = []
        for b in bodies:
            H_swig = b.getTransformInGround(state)
            T = H_swig.T().to_numpy()
            R_swig = H_swig.R()
            R = np.array([[R_swig.get(0,0), R_swig.get(0,1), R_swig.get(0,2)],
                [R_swig.get(1,0), R_swig.get(1,1), R_swig.get(1,2)],
                [R_swig.get(2,0), R_swig.get(2,1), R_swig.get(2,2)]])
            H = np.block([ [R,T.reshape(3,1)], [np.zeros(3), 1] ])
            
            # y-up to z-up
            if direction=='zup':
                H = H_zup @ H
            
            # Convert matrix to loc and rot, and export to csv
            loc_x, loc_y, loc_z = H[0:3,3]
            R_mat = H[0:3,0:3]
            sy = np.sqrt(R_mat[1,0]**2 +  R_mat[0,0]**2) # singularity when y angle is +/- pi/2
            if sy>1e-6:
                rot_x = np.arctan2(R_mat[2,1], R_mat[2,2])
                rot_y = np.arctan2(-R_mat[2,0], sy)
                rot_z = np.arctan2(R_mat[1,0], R_mat[0,0])
            else: # to be verified
                rot_x = np.arctan2(-R_mat[1,2], R_mat[1,1])
                rot_y = np.arctan2(-R[2,0], sy)
                rot_z = 0
            loc_rot_frame.extend([loc_x, loc_y, loc_z, rot_x, rot_y, rot_z])
        
        loc_rot_frame_all.append(loc_rot_frame)

    # Export to csv
    loc_rot_frame_all_np = np.array(loc_rot_frame_all)
    loc_rot_frame_all_np = np.insert(loc_rot_frame_all_np, 0, times, axis=1) # insert time column
    bodyHeader = 'times, ' + ''.join([f'{b}_x, {b}_y, {b}_z, {b}_rotx, {b}_roty, {b}_rotz, ' for b in bodyNames])[:-2]
    np.savetxt(os.path.splitext(output_csv_file)[0]+'.csv', loc_rot_frame_all_np, delimiter=',', header=bodyHeader)
    
    
if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument('-m', '--input_mot_file', required = True, help='input mot file')
    parser.add_argument('-o', '--input_osim_file', required = True, help='input osim file')
    parser.add_argument('-c', '--csv_output_file', required=False, help='csv output file')
    args = vars(parser.parse_args())
    
    bodykin_from_mot_osim_func(args)