"""
Create and update project
"""
import yaml
from pyoviz import FieldsAssignment
from pyosim import Conf, Project
aws_conf = yaml.safe_load(open("../conf.yml"))
local_or_distant = "distant" if aws_conf["distant_id"]["enable"] else "local"
# create Project object
project = Project(path=aws_conf["path"]["project"][local_or_distant])
project.update_participants()
# Create a Conf object
conf = Conf(project_path=aws_conf["path"]["project"][local_or_distant])
# Check if all participants have a configuration file and update it in the project_sample's configuration file
conf.check_confs()
# add some data path in participants' conf file
participants = conf.get_participants_to_process()
d = {}
for iparticipant in participants:
pseudo_in_path = (
iparticipant[0].upper() + iparticipant[1:-1] + iparticipant[-1].upper()
)
trials = (
f"{aws_conf['path']['data'][local_or_distant]}/IRSST_{pseudo_in_path}d/trials"
)
import os
from multiprocessing import Pool
from pathlib import Path
import numpy as np
from pyomeca.obj.analogs import MVC
from pyosim import Conf
from pyosim.obj import Analogs3dOsim
# path
PROJECT_PATH = Path('/home/romain/Dropbox/pyosim_irsst')
MULTIPROC = True
conf = Conf(project_path=PROJECT_PATH)
params = {
'band_pass_cutoff': [10, 425],
'low_pass_cutoff': 5,
'order': 4,
'outlier': 5,
'emg_labels': conf.get_conf_field(participant='dapo', field=['emg', 'targets'])
}
participants = conf.get_participants_to_process()
for iparticipant in participants:
print(f'\nparticipant: {iparticipant}')
directories = conf.get_conf_field(participant=iparticipant, field=['emg', 'data'])
assigned = conf.get_conf_field(participant=iparticipant, field=['emg', 'assigned'])
"""
Static optimization
"""
import yaml
from pyosim import Conf
from pyosim import StaticOptimization
import pandas as pd
aws_conf = yaml.safe_load(open("../conf.yml"))
local_or_distant = "distant" if aws_conf["distant_id"]["enable"] else "local"
conf = Conf(project_path=aws_conf["path"]["project"][local_or_distant])
participants = conf.get_participants_to_process()
conf.check_confs()
model_names = ["wu"]
blacklist = [
"wu_AnnSF6H2_1",
"wu_AnnSF6H2_3",
"wu_SteBF6H2_2",
"wu_JawRH12H4_1",
"wu_JawRH12H3_3",
"wu_JawRH12H3_2",
"wu_JawRH12H2_1",
"wu_JawRH12H1_3",
"wu_NemKH6H2_3",
"wu_NemKH6H1_3",
"wu_NemKH6H1_2",
"wu_NemKH6H1_1",
"""
Example: run joint reaction analysis and export sto
"""
from pathlib import Path
from pyosim import Conf
from pyosim import JointReaction
# path
PROJECT_PATH = Path('/home/romain/Dropbox/pyosim_irsst')
TEMPLATES_PATH = PROJECT_PATH / '_templates'
model_names = ['wu', 'das']
conf = Conf(project_path=PROJECT_PATH)
conf.check_confs()
participants = conf.get_participants_to_process()
for iparticipant in participants:
print(f'\nparticipant: {iparticipant}')
# ignore some trials
blacklist_suffix = '0'
trials = [
ifile for ifile in (PROJECT_PATH / iparticipant /
'1_inverse_kinematic').glob('*.mot')
if not ifile.stem.endswith(blacklist_suffix)
]
"""
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
from pyosim import Conf
from pyosim.obj import Analogs3dOsim
# path
PROJECT_PATH = Path('/home/romain/Dropbox/pyosim_irsst')
# PROJECT_PATH = Path('/home/romain/Documents/codes/pyosim/Misc/project_sample')
CALIBRATION_MATRIX = Path('../tests/data/forces_calibration_matrix.csv')
conf = Conf(project_path=PROJECT_PATH)
conf.check_confs()
calibration_matrix = np.genfromtxt(CALIBRATION_MATRIX, delimiter=',')
params = {
'low_pass_cutoff':
30,
'order':
4,
'forces_labels':
conf.get_conf_field(participant='dapo', field=['analogs', 'targets'])
}
participants = conf.get_participants_to_process()
for iparticipant in participants:
Example: run inverse kinematic and export mot
"""
from pathlib import Path
from pyosim import Conf
from pyosim import InverseKinematics
# path
PROJECT_PATH = Path('/home/romain/Dropbox/pyosim_irsst')
TEMPLATES_PATH = PROJECT_PATH / '_templates'
model_names = ['wu', 'das']
offset = 0.05 # take 1 second before and after onsets
conf = Conf(project_path=PROJECT_PATH)
conf.check_confs()
participants = conf.get_participants_to_process()
for iparticipant in participants:
print(f'\nparticipant: {iparticipant}')
trials = [
ifile
for ifile in (PROJECT_PATH / iparticipant / '0_markers').glob('*.trc')
]
onsets = conf.get_conf_field(iparticipant, ['onset'])
onsets = {
key: [values[0] - offset, values[1] + offset]
for key, values in onsets.items()
"""
Example: export markers to trc
"""
from pathlib import Path
import numpy as np
from pyosim import Conf
from pyosim.obj import Markers3dOsim
# path
PROJECT_PATH = Path('/home/romain/Dropbox/pyosim_irsst')
conf = Conf(project_path=PROJECT_PATH)
markers_labels = conf.get_conf_field(participant='dapo',
field=['markers', 'targets'])
participants = conf.get_participants_to_process()
for iparticipant in participants:
print(f'\nparticipant: {iparticipant}')
directories = conf.get_conf_field(participant=iparticipant,
field=['markers', 'data'])
assigned = conf.get_conf_field(participant=iparticipant,
field=['markers', 'assigned'])
for idir in directories:
print(f'\n\tdirectory: {idir}')
from multiprocessing import Pool
from pathlib import Path
import numpy as np
import yaml
from pyomeca import MVC
from pyosim import Conf
from pyosim import Analogs3dOsim
# path
MULTIPROC = True
aws_conf = yaml.safe_load(open("../conf.yml"))
local_or_distant = "distant" if aws_conf["distant_id"]["enable"] else "local"
conf = Conf(project_path=aws_conf["path"]["project"][local_or_distant])
participants = conf.get_participants_to_process()
params = {
"band_pass_cutoff": [10, 425],
"low_pass_cutoff":
5,
"order":
4,
"outlier":
5,
"emg_labels":
conf.get_conf_field(participant=participants[0], field=["emg", "targets"]),
}
for i, iparticipant in enumerate(participants):
"""
from pathlib import Path
from pyosim import Conf
from pyosim import Scale
# path
WU_MASS_FACTOR = 24.385 / 68.2
PROJECT_PATH = Path('/home/romain/Dropbox/pyosim_irsst')
MODELS_PATH = PROJECT_PATH / '_models'
TEMPLATES_PATH = PROJECT_PATH / '_templates'
model_names = ['wu', 'das']
conf = Conf(project_path=PROJECT_PATH)
conf.check_confs()
participants = conf.get_participants_to_process()
for iparticipant in participants:
print(f'\nparticipant: {iparticipant}')
pseudo_in_path = iparticipant[0].upper() + iparticipant[1:-1] + iparticipant[-1].upper()
static_path = f"{PROJECT_PATH / iparticipant / '0_markers' / 'IRSST_'}{pseudo_in_path}d0.trc"
mass = conf.get_conf_field(iparticipant, ['mass'])
height = conf.get_conf_field(iparticipant, ['height'])
for imodel in model_names:
if imodel == 'wu':
# mass of the upper limb + torso
mass = mass * WU_MASS_FACTOR
"""
Scaling
"""
import yaml
from pyosim import Conf
from pyosim import Scale
aws_conf = yaml.safe_load(open("../conf.yml"))
local_or_distant = "distant" if aws_conf["distant_id"]["enable"] else "local"
conf = Conf(project_path=aws_conf["path"]["project"][local_or_distant])
conf.check_confs()
participants = conf.get_participants_to_process()
model_names = ["wu"]
WU_MASS_FACTOR = 24.385 / 68.2
for i, iparticipant in enumerate(participants):
print(f"\nparticipant #{i}: {iparticipant}")
pseudo_in_path = (iparticipant[0].upper() + iparticipant[1:-1] +
iparticipant[-1].upper())
static_path = f"{conf.project_path / iparticipant / '0_markers' / 'IRSST_'}{pseudo_in_path}d0.trc"
mass = conf.get_conf_field(iparticipant, ["mass"])
height = conf.get_conf_field(iparticipant, ["height"])
for imodel in model_names:
if imodel[:2] == "wu":
# mass of the upper limb + torso
mass = mass * WU_MASS_FACTOR
path_kwargs = {
"""
Export forces to sto
"""
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import yaml
from pyosim import Conf
from pyosim import Analogs3dOsim
aws_conf = yaml.safe_load(open("../conf.yml"))
local_or_distant = "distant" if aws_conf["distant_id"]["enable"] else "local"
conf = Conf(project_path=aws_conf["path"]["project"][local_or_distant])
participants = conf.get_participants_to_process()
calibration_matrix = np.genfromtxt(
conf.project_path / "forces_calibration_matrix.csv", delimiter=","
)
params = {
"low_pass_cutoff": 30,
"order": 4,
"forces_labels": conf.get_conf_field(
participant=participants[0], field=["analogs", "targets"]
),
}
for i, iparticipant in enumerate(participants[:]):
print(f"\nparticipant #{i}: {iparticipant}")
directories = conf.get_conf_field(
participant=iparticipant, field=["analogs", "data"]
"""
Export markers to trc
"""
from pathlib import Path
import yaml
import numpy as np
from pyosim import Conf, Markers3dOsim
aws_conf = yaml.safe_load(open("../conf.yml"))
local_or_distant = "distant" if aws_conf["distant_id"]["enable"] else "local"
conf = Conf(project_path=aws_conf["path"]["project"][local_or_distant])
participants = conf.get_participants_to_process()
conf.check_confs()
markers_labels = conf.get_conf_field(participant=participants[0],
field=["markers", "targets"])
for i, iparticipant in enumerate(participants[:]):
print(f"\nparticipant #{i}: {iparticipant}")
directories = conf.get_conf_field(participant=iparticipant,
field=["markers", "data"])
assigned = conf.get_conf_field(participant=iparticipant,
field=["markers", "assigned"])
for idir in directories:
print(f"\n\tdirectory: {idir}")
for itrial in Path(idir).glob("*.c3d"):
blacklist = False
# try participant's channel assignment
# remove project if already exists (you don't need to do this)
if PROJECT_PATH.is_dir():
shutil.rmtree(PROJECT_PATH)
# create Project object
project = Project(path=PROJECT_PATH)
# create project directory
project.create_project()
# add participants from the template conf file
shutil.copy(CONF_TEMPLATE, PROJECT_PATH)
project.update_participants()
# Create a Conf object
conf = Conf(project_path=PROJECT_PATH)
# Check if all participants have a configuration file and update it in the project's configuration file
conf.check_confs()
# add some data path in participants' conf file
participants = conf.get_participants_to_process()
d = {}
for iparticipant in participants:
pseudo_in_path = iparticipant[0].upper(
) + iparticipant[1:-1] + iparticipant[-1].upper()
trials = f'/media/romain/F/Data/Shoulder/RAW/IRSST_{pseudo_in_path}d/trials'
score = f'/media/romain/F/Data/Shoulder/RAW/IRSST_{pseudo_in_path}d/MODEL2'
mvc = f'/media/romain/E/Projet_MVC/data/C3D_original_files/irsst_hf/{pseudo_in_path}'
d.update({