fixed multi_person + differenciates X,Y,Z in scaling
This commit is contained in:
davidpagnon
parent
b793ad1c7c
commit
6f7e883cd3
@ -179,7 +179,7 @@ make_c3d = true # also save triangulated data in c3d format
|
||||
make_c3d = true # save triangulated data in c3d format in addition to trc
|
||||
|
||||
|
||||
[opensim]
|
||||
[kinematics]
|
||||
use_augmentation = true # true or false (lowercase) # Set to true if you want to use the model with augmented markers
|
||||
right_left_symmetry = true # true or false (lowercase) # Set to false only if you have good reasons to think the participant is not symmetrical (e.g. prosthetic limb)
|
||||
remove_individual_scaling_setup = true # true or false (lowercase) # If true, the individual scaling setup files are removed to avoid cluttering
|
||||
|
||||
@ -179,7 +179,7 @@
|
||||
# make_c3d = false # save triangulated data in c3d format in addition to trc
|
||||
|
||||
|
||||
# [opensim]
|
||||
# [kinematics]
|
||||
# use_augmentation = true # true or false (lowercase) # Set to true if you want to use the model with augmented markers
|
||||
# right_left_symmetry = true # true or false (lowercase) # Set to false only if you have good reasons to think the participant is not symmetrical (e.g. prosthetic limb)
|
||||
# remove_individual_scaling_setup = true # true or false (lowercase) # If true, the individual scaling setup files are removed to avoid cluttering
|
||||
|
||||
@ -179,7 +179,7 @@ keypoints_to_consider = 'all' # 'all' if all points should be considered, for ex
|
||||
# make_c3d = false # save triangulated data in c3d format in addition to trc
|
||||
|
||||
|
||||
# [opensim]
|
||||
# [kinematics]
|
||||
# use_augmentation = true # true or false (lowercase) # Set to true if you want to use the model with augmented markers
|
||||
# right_left_symmetry = true # true or false (lowercase) # Set to false only if you have good reasons to think the participant is not symmetrical (e.g. prosthetic limb)
|
||||
# remove_individual_scaling_setup = true # true or false (lowercase) # If true, the individual scaling setup files are removed to avoid cluttering
|
||||
|
||||
@ -179,7 +179,7 @@ make_c3d = false # also save triangulated data in c3d format
|
||||
make_c3d = true # save triangulated data in c3d format in addition to trc
|
||||
|
||||
|
||||
[opensim]
|
||||
[kinematics]
|
||||
use_augmentation = true # true or false (lowercase) # Set to true if you want to use the model with augmented markers
|
||||
right_left_symmetry = true # true or false (lowercase) # Set to false only if you have good reasons to think the participant is not symmetrical (e.g. prosthetic limb)
|
||||
remove_individual_scaling_setup = true # true or false (lowercase) # If true, the individual scaling setup files are removed to avoid cluttering
|
||||
|
||||
@ -217,7 +217,7 @@ def poseEstimation(config=None):
|
||||
config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')
|
||||
|
||||
# Set up logging
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '.'))
|
||||
setup_logging(session_dir)
|
||||
|
||||
# Batch process all trials
|
||||
@ -264,7 +264,7 @@ def synchronization(config=None):
|
||||
config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')
|
||||
|
||||
# Set up logging
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '.'))
|
||||
setup_logging(session_dir)
|
||||
|
||||
# Batch process all trials
|
||||
@ -296,7 +296,7 @@ def personAssociation(config=None):
|
||||
or the function can be called without an argument, in which case it the config directory is the current one.
|
||||
'''
|
||||
|
||||
from Pose2Sim.personAssociation import track_2d_all
|
||||
from Pose2Sim.personAssociation import associate_all
|
||||
|
||||
# Determine the level at which the function is called (root:2, trial:1)
|
||||
level, config_dicts = read_config_files(config)
|
||||
@ -308,7 +308,7 @@ def personAssociation(config=None):
|
||||
config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')
|
||||
|
||||
# Set up logging
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '.'))
|
||||
setup_logging(session_dir)
|
||||
|
||||
# Batch process all trials
|
||||
@ -326,7 +326,7 @@ def personAssociation(config=None):
|
||||
logging.info(f"Project directory: {project_dir}")
|
||||
logging.info("---------------------------------------------------------------------\n")
|
||||
|
||||
track_2d_all(config_dict)
|
||||
associate_all(config_dict)
|
||||
|
||||
end = time.time()
|
||||
elapsed = end-start
|
||||
@ -354,7 +354,7 @@ def triangulation(config=None):
|
||||
config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')
|
||||
|
||||
# Set up logging
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '.'))
|
||||
setup_logging(session_dir)
|
||||
|
||||
# Batch process all trials
|
||||
@ -400,7 +400,7 @@ def filtering(config=None):
|
||||
config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')
|
||||
|
||||
# Set up logging
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '.'))
|
||||
setup_logging(session_dir)
|
||||
|
||||
# Batch process all trials
|
||||
@ -441,7 +441,7 @@ def markerAugmentation(config=None):
|
||||
raise ValueError('Please specify the project directory in config_dict:\n \
|
||||
config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')
|
||||
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '.'))
|
||||
setup_logging(session_dir)
|
||||
|
||||
for config_dict in config_dicts:
|
||||
@ -485,7 +485,7 @@ def kinematics(config=None):
|
||||
raise ValueError('Please specify the project directory in config_dict:\n \
|
||||
config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')
|
||||
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '.'))
|
||||
setup_logging(session_dir)
|
||||
|
||||
# Process each configuration dictionary
|
||||
@ -519,7 +519,7 @@ def runAll(config=None, do_calibration=True, do_poseEstimation=True, do_synchron
|
||||
|
||||
# Set up logging
|
||||
level, config_dicts = read_config_files(config)
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
|
||||
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '.'))
|
||||
setup_logging(session_dir)
|
||||
|
||||
currentDateAndTime = datetime.now()
|
||||
|
||||
@ -275,7 +275,7 @@ def dict_segment_marker_pairs(scaling_root, right_left_symmetry=True):
|
||||
|
||||
'''
|
||||
|
||||
measurement_dict = {}
|
||||
segment_markers_dict = {}
|
||||
for measurement in scaling_root.findall(".//Measurement"):
|
||||
# Collect all marker pairs for this measurement
|
||||
marker_pairs = [pair.find('markers').text.strip().split() for pair in measurement.findall(".//MarkerPair")]
|
||||
@ -283,17 +283,22 @@ def dict_segment_marker_pairs(scaling_root, right_left_symmetry=True):
|
||||
# Collect all body scales for this measurement
|
||||
for body_scale in measurement.findall(".//BodyScale"):
|
||||
body_name = body_scale.get('name')
|
||||
axes = body_scale.find('axes').text.strip().split()
|
||||
for axis in axes:
|
||||
body_name_axis = f"{body_name}_{axis}"
|
||||
if right_left_symmetry:
|
||||
measurement_dict[body_name] = marker_pairs
|
||||
segment_markers_dict.setdefault(body_name_axis, []).extend(marker_pairs)
|
||||
else:
|
||||
if body_name.endswith('_r'):
|
||||
marker_pairs_r = [pair for pair in marker_pairs if any([pair[0].startswith('R'), pair[1].startswith('R')])]
|
||||
measurement_dict[body_name] = marker_pairs_r
|
||||
marker_pairs_r = [pair for pair in marker_pairs if any([pair[0].upper().startswith('R'), pair[1].upper().startswith('R')])]
|
||||
segment_markers_dict.setdefault(body_name_axis, []).extend(marker_pairs_r)
|
||||
elif body_name.endswith('_l'):
|
||||
marker_pairs_l = [pair for pair in marker_pairs if any([pair[0].startswith('L'), pair[1].startswith('L')])]
|
||||
measurement_dict[body_name] = marker_pairs_l
|
||||
marker_pairs_l = [pair for pair in marker_pairs if any([pair[0].upper().startswith('L'), pair[1].upper().startswith('L')])]
|
||||
segment_markers_dict.setdefault(body_name_axis, []).extend(marker_pairs_l)
|
||||
else:
|
||||
segment_markers_dict.setdefault(body_name_axis, []).extend(marker_pairs)
|
||||
|
||||
return measurement_dict
|
||||
return segment_markers_dict
|
||||
|
||||
|
||||
def dict_segment_ratio(scaling_root, unscaled_model, Q_coords_scaling, markers, right_left_symmetry=True):
|
||||
@ -321,10 +326,15 @@ def dict_segment_ratio(scaling_root, unscaled_model, Q_coords_scaling, markers,
|
||||
# Calculate ratio for each segment
|
||||
segment_ratios = trc_segment_lengths / model_segment_lengths
|
||||
segment_markers_dict = dict_segment_marker_pairs(scaling_root, right_left_symmetry=right_left_symmetry)
|
||||
segment_ratio_dict = segment_markers_dict.copy()
|
||||
segment_ratio_dict.update({key: np.mean([segment_ratios[segment_pairs.index(k)]
|
||||
segment_ratio_dict_temp = segment_markers_dict.copy()
|
||||
segment_ratio_dict_temp.update({key: np.mean([segment_ratios[segment_pairs.index(k)]
|
||||
for k in segment_markers_dict[key]])
|
||||
for key in segment_markers_dict.keys()})
|
||||
# Merge X, Y, Z ratios into single key
|
||||
segment_ratio_dict={}
|
||||
xyz_keys = list(set([key[:-2] for key in segment_ratio_dict_temp.keys()]))
|
||||
for key in xyz_keys:
|
||||
segment_ratio_dict[key] = [segment_ratio_dict_temp[key+'_X'], segment_ratio_dict_temp[key+'_Y'], segment_ratio_dict_temp[key+'_Z']]
|
||||
|
||||
return segment_ratio_dict
|
||||
|
||||
@ -351,11 +361,11 @@ def update_scale_values(scaling_root, segment_ratio_dict):
|
||||
scale_set.remove(scale)
|
||||
|
||||
# Add new Scale elements based on scale_dict
|
||||
for segment, scale in segment_ratio_dict.items():
|
||||
for segment, scales in segment_ratio_dict.items():
|
||||
new_scale = etree.Element('Scale')
|
||||
# scales
|
||||
scales_elem = etree.SubElement(new_scale, 'scales')
|
||||
scales_elem.text = ' '.join([str(scale)]*3)
|
||||
scales_elem.text = ' '.join(map(str, scales))
|
||||
# segment name
|
||||
segment_elem = etree.SubElement(new_scale, 'segment')
|
||||
segment_elem.text = segment
|
||||
@ -394,7 +404,7 @@ def perform_scaling(trc_file, kinematics_dir, osim_setup_dir, model_name, right_
|
||||
scaling_path = get_scaling_setup(model_name, osim_setup_dir)
|
||||
scaling_tree = etree.parse(scaling_path)
|
||||
scaling_root = scaling_tree.getroot()
|
||||
scaling_path_temp = str(kinematics_dir / Path(scaling_path).name)
|
||||
scaling_path_temp = str(kinematics_dir / (trc_file.stem + '_scaling_setup.xml'))
|
||||
|
||||
# Read trc file
|
||||
Q_coords, _, _, markers, _ = read_trc(trc_file)
|
||||
@ -415,8 +425,7 @@ def perform_scaling(trc_file, kinematics_dir, osim_setup_dir, model_name, right_
|
||||
scaling_root[0].find(".//scaling_order").text = ' manualScale measurements'
|
||||
deactivate_measurements(scaling_root)
|
||||
update_scale_values(scaling_root, segment_ratio_dict)
|
||||
for mk_f in scaling_root[0].findall(".//marker_file"):
|
||||
mk_f.text = "Unassigned"
|
||||
for mk_f in scaling_root[0].findall(".//marker_file"): mk_f.text = "Unassigned"
|
||||
scaling_root[0].find('ModelScaler').find('output_model_file').text = str(scaled_model_path)
|
||||
|
||||
etree.indent(scaling_tree, space='\t', level=0)
|
||||
@ -448,7 +457,7 @@ def perform_IK(trc_file, kinematics_dir, osim_setup_dir, model_name, remove_IK_s
|
||||
try:
|
||||
# Retrieve data
|
||||
ik_path = get_IK_Setup(model_name, osim_setup_dir)
|
||||
ik_path_temp = str(kinematics_dir / Path(ik_path).name)
|
||||
ik_path_temp = str(kinematics_dir / (trc_file.stem + '_ik_setup.xml'))
|
||||
scaled_model_path = (kinematics_dir / (trc_file.stem + '.osim')).resolve()
|
||||
output_motion_file = Path(kinematics_dir, trc_file.stem + '.mot').resolve()
|
||||
if not trc_file.exists():
|
||||
@ -546,7 +555,7 @@ def kinematics(config_dict):
|
||||
elif not type(subject_mass) == list:
|
||||
subject_mass = [subject_mass]
|
||||
elif len(subject_mass) < len(trc_files):
|
||||
logging.warning("Number of subject masses does not match number of TRC files. Missing masses are set to 70kg.")
|
||||
logging.warning("Number of subject masses does not match number of TRC files. Missing masses are set to 70kg.\n")
|
||||
subject_mass += [70] * (len(trc_files) - len(subject_mass))
|
||||
|
||||
# Perform scaling and IK for each trc file
|
||||
@ -558,7 +567,7 @@ def kinematics(config_dict):
|
||||
logging.info(f"\tDone. OpenSim logs saved to {opensim_logs_file.resolve()}.")
|
||||
logging.info(f"\tScaled model saved to {(kinematics_dir / (trc_file.stem + '_scaled.osim')).resolve()}")
|
||||
|
||||
logging.info("\nInverse Kinematics...")
|
||||
logging.info("Inverse Kinematics...")
|
||||
perform_IK(trc_file, kinematics_dir, osim_setup_dir, model_name, remove_IK_setup=remove_IK_setup)
|
||||
logging.info(f"\tDone. OpenSim logs saved to {opensim_logs_file.resolve()}.")
|
||||
logging.info(f"\tJoint angle data saved to {(kinematics_dir / (trc_file.stem + '.mot')).resolve()}\n")
|
||||
|
||||
@ -604,7 +604,7 @@ def recap_tracking(config_dict, error=0, nb_cams_excluded=0):
|
||||
logging.info(f'\nTracked json files are stored in {os.path.realpath(poseTracked_dir)}.')
|
||||
|
||||
|
||||
def track_2d_all(config_dict):
|
||||
def associate_all(config_dict):
|
||||
'''
|
||||
For each frame,
|
||||
- Find all possible combinations of detected persons
|
||||
|
||||
@ -191,6 +191,7 @@ def sort_people(Q_kpt_old, Q_kpt):
|
||||
frame_by_frame_dist = []
|
||||
for comb in personsIDs_comb:
|
||||
frame_by_frame_dist += [euclidean_distance(Q_kpt_old[comb[0]],Q_kpt[comb[1]])]
|
||||
frame_by_frame_dist = np.mean(frame_by_frame_dist, axis=1)
|
||||
|
||||
# sort correspondences by distance
|
||||
minL, _, associated_tuples = min_with_single_indices(frame_by_frame_dist, personsIDs_comb)
|
||||
|
||||
Loading…
Reference in New Issue
Block a user