beta test opensim scaling and kinematics with edits

Pose2Sim/Demo_Batch/Config.toml

@@ -136,7 +136,6 @@ calibration_type = 'convert' # 'convert' or 'calculate'
 
 
 [triangulation]
-reorder_trc = false # only checked if multi_person analysis
 reproj_error_threshold_triangulation = 15 # px
 likelihood_threshold_triangulation= 0.3
 min_cameras_for_triangulation = 2
@@ -181,14 +180,10 @@ make_c3d = true # save triangulated data in c3d format in addition to trc
 
 
 [opensim]
-static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
-#            # If this Config.toml file is at the Trial level, set to true or false (lowercase);
-#            # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
-#            # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']
-opensim_bin_path = 'C:\OpenSim 4.4\bin'
-use_augmentation = false  # If using augmented measurements then set it true
-load_trc_name = 'filtered'  # 'default' or 'filtered', if use_augmentation = true, this line will be ignored instead using __LSTM.trc
-IK_timeRange = [] #left empty to IK full range or eg.[0.5,1.0]
+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
+remove_individual_IK_setup = true # true or false (lowercase) # If true, the individual IK setup files are removed to avoid cluttering
 
 
 
@@ -204,7 +199,7 @@ IK_timeRange = [] #left empty to IK full range or eg.[0.5,1.0]
 # Check your model hierarchy with:  for pre, _, node in RenderTree(model): 
 #                                      print(f'{pre}{node.name} id={node.id}')
 [pose.CUSTOM]
-name = "CHip"
+name = "Hip"
 id = "19"
   [[pose.CUSTOM.children]]
   name = "RHip"

Pose2Sim/Demo_Batch/Trial_1/Config.toml

@@ -136,7 +136,6 @@
 
 
 # [triangulation]
-# reorder_trc = false # only checked if multi_person analysis
 # reproj_error_threshold_triangulation = 15 # px
 # likelihood_threshold_triangulation= 0.3
 # min_cameras_for_triangulation = 2
@@ -181,14 +180,10 @@
 
 
 # [opensim]
-#static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
-#            # If this Config.toml file is at the Trial level, set to true or false (lowercase);
-#            # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
-#            # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']
-#opensim_bin_path = 'C:\OpenSim 4.4\bin'
-#use_augmentation = false  # If using augmented measurements then set it true
-#load_trc_name = 'filtered'  # 'default' or 'filtered', if use_augmentation = true, this line will be ignored instead using __LSTM.trc
-#IK_timeRange = [] #left empty to IK full range or eg.[0.5,1.0]
+# 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
+# remove_individual_IK_setup = true # true or false (lowercase) # If true, the individual IK setup files are removed to avoid cluttering
 
 
 
@@ -204,7 +199,7 @@
 # # Check your model hierarchy with:  for pre, _, node in RenderTree(model): 
 # #                                      print(f'{pre}{node.name} id={node.id}')
 # [pose.CUSTOM]
-# name = "CHip"
+# name = "Hip"
 # id = "19"
   # [[pose.CUSTOM.children]]
   # name = "RHip"

Pose2Sim/Demo_Batch/Trial_2/Config.toml

@@ -19,8 +19,8 @@
 
 [project]
 multi_person = true # true for trials with multiple participants. If false, only the main person in scene is analyzed (and it run much faster). 
-participant_height = [1.72, 1.40, 1.86] # m # float if single person, list of float if multi-person (same order as the Static trials) # Only used for marker augmentation
-participant_mass = [70.0, 63.5, 88.0] # kg # Only used for marker augmentation and scaling
+participant_height = [1.72, 1.40] # m # float if single person, list of float if multi-person (same order as the Static trials) # Only used for marker augmentation
+participant_mass = [70.0, 63.5] # kg # Only used for marker augmentation and scaling
 
 # frame_rate = 'auto' # fps # int or 'auto'. If 'auto', finds from video (or defaults to 60 fps if you work with images) 
 # frame_range = [] # For example [10,300], or [] for all frames. 
@@ -136,7 +136,6 @@ keypoints_to_consider = 'all' # 'all' if all points should be considered, for ex
 
 
 # [triangulation]
-# reorder_trc = false # only checked if multi_person analysis
 # reproj_error_threshold_triangulation = 15 # px
 # likelihood_threshold_triangulation= 0.3
 # min_cameras_for_triangulation = 2
@@ -181,14 +180,10 @@ keypoints_to_consider = 'all' # 'all' if all points should be considered, for ex
 
 
 # [opensim]
-#static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
-#            # If this Config.toml file is at the Trial level, set to true or false (lowercase);
-#            # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
-#            # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']
-#opensim_bin_path = 'C:\OpenSim 4.4\bin'
-#use_augmentation = false  # If using augmented measurements then set it true
-#load_trc_name = 'filtered'  # 'default' or 'filtered', if use_augmentation = true, this line will be ignored instead using __LSTM.trc
-#IK_timeRange = [] #left empty to IK full range or eg.[0.5,1.0]
+# 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
+# remove_individual_IK_setup = true # true or false (lowercase) # If true, the individual IK setup files are removed to avoid cluttering
 
 
 
@@ -204,7 +199,7 @@ keypoints_to_consider = 'all' # 'all' if all points should be considered, for ex
 # # Check your model hierarchy with:  for pre, _, node in RenderTree(model): 
 # #                                      print(f'{pre}{node.name} id={node.id}')
 # [pose.CUSTOM]
-# name = "CHip"
+# name = "Hip"
 # id = "19"
   # [[pose.CUSTOM.children]]
   # name = "RHip"

Pose2Sim/Demo_MultiPerson/Config.toml

@@ -19,8 +19,8 @@
 
 [project]
 multi_person = true # true for trials with multiple participants. If false, only the main person in scene is analyzed (and it run much faster). 
-participant_height = [1.72, 1.40, 1.90] # m # float if single person, list of float if multi-person (same order as the Static trials) # Only used for marker augmentation
-participant_mass = [70.0, 63.5, 90.0] # kg # Only used for marker augmentation and scaling
+participant_height = [1.72, 1.40] # m # float if single person, list of float if multi-person (same order as the Static trials) # Only used for marker augmentation
+participant_mass = [70.0, 63.5] # kg # Only used for marker augmentation and scaling
 
 frame_rate = 'auto' # fps # int or 'auto'. If 'auto', finds from video (or defaults to 60 fps if you work with images) 
 frame_range = [] # For example [10,300], or [] for all frames. 
@@ -136,7 +136,6 @@ calibration_type = 'convert' # 'convert' or 'calculate'
 
 
 [triangulation]
-reorder_trc = false # only checked if multi_person analysis
 reproj_error_threshold_triangulation = 15 # px
 likelihood_threshold_triangulation= 0.3
 min_cameras_for_triangulation = 2
@@ -181,14 +180,10 @@ make_c3d = true # save triangulated data in c3d format in addition to trc
 
 
 [opensim]
-static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
-#            # If this Config.toml file is at the Trial level, set to true or false (lowercase);
-#            # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
-#            # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']
-opensim_bin_path = 'C:\OpenSim 4.4\bin'
-use_augmentation = false  # If using augmented measurements then set it true
-load_trc_name = 'filtered'  # 'default' or 'filtered', if use_augmentation = true, this line will be ignored instead using __LSTM.trc
-IK_timeRange = [] #left empty to IK full range or eg.[0.5,1.0]
+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
+remove_individual_IK_setup = true # true or false (lowercase) # If true, the individual IK setup files are removed to avoid cluttering
 
 
 
@@ -204,7 +199,7 @@ IK_timeRange = [] #left empty to IK full range or eg.[0.5,1.0]
 # Check your model hierarchy with:  for pre, _, node in RenderTree(model): 
 #                                      print(f'{pre}{node.name} id={node.id}')
 [pose.CUSTOM]
-name = "CHip"
+name = "Hip"
 id = "19"
   [[pose.CUSTOM.children]]
   name = "RHip"

Pose2Sim/Demo_SinglePerson/Config.toml

@@ -53,9 +53,9 @@ output_format = 'openpose' # 'openpose', 'mmpose', 'deeplabcut', 'none' or a lis
 [synchronization]
 display_sync_plots = true # true or false (lowercase)
 keypoints_to_consider = ['RWrist'] # 'all' if all points should be considered, for example if the participant did not perform any particicular sharp movement. In this case, the capture needs to be 5-10 seconds long at least
-                           # ['RWrist', 'RElbow'] list of keypoint names if you want to specify the keypoints to consider.
+                           # ['RWrist', 'RElbow'] list of keypoint names if you want to specify keypoints with a sharp vertical motion.
 approx_time_maxspeed = 'auto' # 'auto' if you want to consider the whole capture (default, slower if long sequences)
-                           # [10.0, 2.0, 8.0, 11.0] list of times in seconds, one value per camera if you want to specify the approximate time of a clear vertical event by one person standing alone in the scene
+                           # [10.0, 2.0, 8.0, 11.0] list of times (seconds) if you want to specify the approximate time of a clear vertical event for each camera
 time_range_around_maxspeed = 2.0 # Search for best correlation in the range [approx_time_maxspeed - time_range_around_maxspeed, approx_time_maxspeed  + time_range_around_maxspeed]
 likelihood_threshold = 0.4 # Keypoints whose likelihood is below likelihood_threshold are filtered out
 filter_cutoff = 6 # time series are smoothed to get coherent time-lagged correlation
@@ -136,7 +136,6 @@ calibration_type = 'convert' # 'convert' or 'calculate'
 
 
 [triangulation]
-reorder_trc = false # only checked if multi_person analysis
 reproj_error_threshold_triangulation = 15 # px
 likelihood_threshold_triangulation= 0.3
 min_cameras_for_triangulation = 2
@@ -180,17 +179,11 @@ make_c3d = true # also save triangulated data in c3d format
 make_c3d = true # save triangulated data in c3d format in addition to trc
 
 
-[opensim]
-static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
-#            # If this Config.toml file is at the Trial level, set to true or false (lowercase);
-#            # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
-#            # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']
-opensim_bin_path = 'C:\OpenSim 4.4\bin'
-use_augmentation = false  # If using augmented measurements then set it true
-load_trc_name = 'filtered'  # 'default' or 'filtered', if use_augmentation = true, this line will be ignored instead using __LSTM.trc
-IK_timeRange = [] #left empty to IK full range or eg.[0.5,1.0]
-
-
+[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
+remove_individual_IK_setup = true # true or false (lowercase) # If true, the individual IK setup files are removed to avoid cluttering
 
 
 
@@ -206,7 +199,7 @@ IK_timeRange = [] #left empty to IK full range or eg.[0.5,1.0]
 # Check your model hierarchy with:  for pre, _, node in RenderTree(model): 
 #                                      print(f'{pre}{node.name} id={node.id}')
 [pose.CUSTOM]
-name = "CHip"
+name = "Hip"
 id = "19"
   [[pose.CUSTOM.children]]
   name = "RHip"

Pose2Sim/OpenSim_Setup/Model_Pose2Sim_Coco133.osim

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 <OpenSimDocument Version="40000">
-	<Model name="Pose2Sim_AlphaPose">
+	<Model name="Pose2Sim_RTMPose">
 		<!--The model's ground reference frame.-->
 		<Ground name="ground">
 			<!--The geometry used to display the axes of this Frame.-->

Pose2Sim/OpenSim_Setup/Model_Pose2Sim_Halpe26.osim

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 <OpenSimDocument Version="40000">
-	<Model name="Pose2Sim_AlphaPose">
+	<Model name="Pose2Sim_RTMPose">
 		<!--The model's ground reference frame.-->
 		<Ground name="ground">
 			<!--The geometry used to display the axes of this Frame.-->
@@ -6808,7 +6808,7 @@
 					<!--Path to a Component that satisfies the Socket 'parent_frame' of type PhysicalFrame (description: The frame to which this station is fixed.).-->
 					<socket_parent_frame>/bodyset/pelvis</socket_parent_frame>
 					<!--The fixed location of the station expressed in its parent frame.-->
-					<location>-0.063927399999999995 0 0</location>
+					<location>-0.063927399999999995 -0.081343112945556642 0</location>
 				</Marker>
 				<Marker name="LHip">
 					<!--Path to a Component that satisfies the Socket 'parent_frame' of type PhysicalFrame (description: The frame to which this station is fixed.).-->

Pose2Sim/OpenSim_Setup/Model_Pose2Sim_Halpe68_136.osim

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 <OpenSimDocument Version="40000">
-	<Model name="Pose2Sim_AlphaPose">
+	<Model name="Pose2Sim_RTMPose">
 		<!--The model's ground reference frame.-->
 		<Ground name="ground">
 			<!--The geometry used to display the axes of this Frame.-->

Pose2Sim/Pose2Sim.py

@@ -539,7 +539,7 @@ def kinematics(config=None):
 
         end = time.time()
         elapsed = end - start
-        logging.info(f'\nOpenSim scaling and inverse kinematics took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')
+        logging.info(f'OpenSim scaling and inverse kinematics took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')
 
 
 def runAll(config=None, do_calibration=True, do_poseEstimation=True, do_synchronization=True, do_personAssociation=True, do_triangulation=True, do_filtering=True, do_markerAugmentation=True, do_kinematics=True):

Pose2Sim/common.py

@@ -219,11 +219,11 @@ def euclidean_distance(q1, q2):
     
     INPUTS:
     - q1: list of N_dimensional coordinates of point
+         or list of N points of N_dimensional coordinates
     - q2: idem
 
     OUTPUTS:
     - euc_dist: float. Euclidian distance between q1 and q2
-    
     '''
 
     q1 = np.array(q1)
@@ -233,11 +233,40 @@ def euclidean_distance(q1, q2):
         dist =  np.empty_like(dist)
         dist[...] = np.inf
 
-    euc_dist = np.sqrt(np.nansum( [d**2 for d in dist]))
+    if len(dist.shape)==1:
+        euc_dist = np.sqrt(np.nansum( [d**2 for d in dist]))
+    else:
+        euc_dist = np.sqrt(np.nansum( [d**2 for d in dist], axis=1))
 
     return euc_dist
 
 
+def trimmed_mean(arr, trimmed_percent=0.5):
+    '''
+    Trimmed mean calculation for an array.
+
+    INPUTS:
+    - arr (np.array): The input array.
+    - trimmed_percent (float): The percentage of values to be trimmed from both ends.
+
+    OUTPUTS:
+    - float: The trimmed mean of the array.
+    '''
+
+    # Sort the array
+    sorted_arr = np.sort(arr)
+
+    # Determine the indices for the 25th and 75th percentiles (if trimmed_percent = 0.5)
+    lower_idx = int(len(sorted_arr) * (trimmed_percent/2))
+    upper_idx = int(len(sorted_arr) * (1 - trimmed_percent/2))
+
+    # Slice the array to exclude the 25% lowest and highest values
+    trimmed_arr = sorted_arr[lower_idx:upper_idx]
+
+    # Return the mean of the remaining values
+    return np.mean(trimmed_arr)
+
+
 def world_to_camera_persp(r, t):
     '''
     Converts rotation R and translation T 
@@ -364,6 +393,7 @@ def natural_sort_key(s):
     Sorts list of strings with numbers in natural order (alphabetical and numerical)
     Example: ['item_1', 'item_2', 'item_10', 'stuff_1']
     '''
+    s=str(s)
     return [int(c) if c.isdigit() else c.lower() for c in re.split(r'(\d+)', s)]