fullproof until limb swapping solved

Pose2Sim/Demo/S00_Demo_Session/Config.toml

@@ -134,7 +134,7 @@ interpolation = 'cubic' #linear, slinear, quadratic, cubic, or none
                         # 'none' if you don't want to interpolate missing points
 interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
 show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
-handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
+handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
 undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
 make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
 

Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/Config.toml

@@ -135,7 +135,7 @@
 ## 'none' if you don't want to interpolate missing points
 # interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
 # show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
-# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
+# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
 # undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
 # make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
 

Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/Config.toml

@@ -135,7 +135,7 @@
 ## 'none' if you don't want to interpolate missing points
 # interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
 # show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
-# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
+# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
 # undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
 # make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
 

Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/Config.toml

@@ -135,7 +135,7 @@
 ## 'none' if you don't want to interpolate missing points
 # interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
 # show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
-# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
+# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
 # undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
 # make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
 

Pose2Sim/Demo/S01_Empty_Session/Config.toml

@@ -134,7 +134,7 @@ interpolation = 'cubic' #linear, slinear, quadratic, cubic, or none
 # 'none' if you don't want to interpolate missing points
 interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
 show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
-# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
+# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
 # undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
 # make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
 

Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/Config.toml

@@ -135,7 +135,7 @@
 ## 'none' if you don't want to interpolate missing points
 # interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
 # show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
-# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
+# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
 # undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
 # make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
 

Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T00_StaticTrial/Config.toml

@@ -134,7 +134,7 @@
 ## 'none' if you don't want to interpolate missing points
 # interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
 # show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
-# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
+# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
 # undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
 # make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
 

Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/Config.toml

@@ -134,7 +134,7 @@
 ## 'none' if you don't want to interpolate missing points
 # interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
 # show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
-# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
+# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
 # undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
 # make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
 

Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T02_MotionTrial2/Config.toml

@@ -134,7 +134,7 @@
 ## 'none' if you don't want to interpolate missing points
 # interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
 # show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
-# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
+# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
 # undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
 # make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
 

Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/Config.toml

@@ -135,7 +135,7 @@
 ## 'none' if you don't want to interpolate missing points
 # interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
 # show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
-# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
+# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
 # undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
 # make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
 

Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T00_StaticTrial/Config.toml

@@ -135,7 +135,7 @@
 ## 'none' if you don't want to interpolate missing points
 # interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
 # show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
-# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
+# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
 # undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
 # make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
 

Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T01_MotionTrial1/Config.toml

@@ -135,7 +135,7 @@
 ## 'none' if you don't want to interpolate missing points
 # interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
 # show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
-# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
+# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
 # undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
 # make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
 

Pose2Sim/Demo/S01_Empty_Session/S01_P01_Participant1/S01_P01_T02_MotionTrial2/Config.toml

@@ -135,7 +135,7 @@
 ## 'none' if you don't want to interpolate missing points
 # interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
 # show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
-# handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
+# handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
 # undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
 # make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon!
 

Pose2Sim/Utilities/bodykin_from_mot_osim.py

@@ -15,6 +15,9 @@
 
     Transforms from OpenSim's yup to Blender's zup unless you set direction = 'yup'
     
+    Beware, it can be quite slow depending on the ccomplexity 
+    of the model and on the number of frames.
+    
     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
@@ -74,11 +77,24 @@ def bodykin_from_mot_osim_func(*args):
     # Read model and motion files
     model = osim.Model(osim_path)
     motion_data = osim.TimeSeriesTable(motion_path)
+    
+    # # Degrees or radians
+    # with open(motion_path) as m_p:
+        # while True:
+            # line =  m_p.readline()
+            # if 'inDegrees' in line:
+                # break
+    # if 'yes' in line:
+        # in_degrees = True
+    # else:
+        # in_degrees = False
 
     # Model: get model coordinates and bodies
     model_coordSet = model.getCoordinateSet()
-    coordinates = [model_coordSet.get(i) for i in range(model_coordSet.getSize())]
+    # coordinates = [model_coordSet.get(i) for i in range(model_coordSet.getSize())]
-    coordinateNames = [c.getName() for c in coordinates]
+    # coordinates = [c for c in coordinates if '_beta' not in c.getName()]
+    # coordinateNames = [c.getName() for c in coordinates]
+    coordinateNames = motion_data.getColumnLabels()
     model_bodySet = model.getBodySet()
     bodies = [model_bodySet.get(i) for i in range(model_bodySet.getSize())]
     bodyNames = [b.getName() for b in bodies]
@@ -86,16 +102,21 @@ def bodykin_from_mot_osim_func(*args):
     # 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)):
+    for i, c in enumerate(coordinateNames):
-        if coordinates[i].getMotionType() == 1: # 1: rotation, 2: translation, 3: coupled
+        if model_coordSet.get(c).getMotionType() == 1: # 1: rotation, 2: translation, 3: coupled
-            motion_data_np[:,i] = motion_data_np[:,i] * np.pi/180 # if rotation, convert to radians
+            if  motion_data.getTableMetaDataAsString('inDegrees') == 'yes':
+    # if in_degrees:
+        # 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]])
+    print('Time frame:')
     for n in range(motion_data.getNumRows()):
-        
+        print(times[n], 's')
         # Set model struct in each time state
         for c, coord in enumerate(coordinateNames):
             model.getCoordinateSet().get(coord).setValue(state, motion_data_np[n,c])

Pose2Sim/Utilities/reproj_from_trc_calib

@@ -1 +0,0 @@
-

Pose2Sim/Utilities/trc_from_mot_osim.py

@@ -10,6 +10,9 @@
     Build a trc file which stores all real and virtual markers 
     calculated from a .mot motion file and a .osim model file.
     
+    Beware, it can be quite slow depending on the ccomplexity 
+    of the model and on the number of frames.
+    
     Usage: 
     from Pose2Sim.Utilities import trc_from_mot_osim; trc_from_mot_osim.trc_from_mot_osim_func(r'<input_mot_file>', r'<output_osim_file>', r'<output_trc_file>')
     python -m trc_from_mot_osim -m input_mot_file -o input_osim_file
@@ -37,7 +40,7 @@ __status__ = "Development"
 
 
 ## FUNCTIONS
-def get_marker_positions(motion_data, model):
+def get_marker_positions(motion_data, model, in_degrees=True):
     '''
     Get dataframe of marker positions
     
@@ -63,10 +66,12 @@ def get_marker_positions(motion_data, model):
     # Get marker positions at each state
     state = model.initSystem()
     marker_positions = []
+    print('Time frame:')
     for n,t in enumerate(times):
+        print(t, 's')
         # put the model in the right position
         for coord in joint_angle_set_names:
-            if not coord.endswith('_tx') and not coord.endswith('_ty') and not coord.endswith('_tz'):
+            if in_degrees and not coord.endswith('_tx') and not coord.endswith('_ty') and not coord.endswith('_tz'):
                 value = motion_data_pd.loc[n,coord]*np.pi/180
             else:
                 value = motion_data_pd.loc[n,coord]
@@ -109,7 +114,19 @@ def trc_from_mot_osim_func(*args):
     # Create dataframe with marker positions
     model = osim.Model(osim_path)
     motion_data = osim.TimeSeriesTable(motion_path)
-    marker_positions_pd = get_marker_positions(motion_data, model)
+    
+    # In degrees or radians
+    with open(motion_path) as m_p:
+        while True:
+            line =  m_p.readline()
+            if 'inDegrees' in line:
+                break
+    if 'yes' in line:
+        in_degrees = True
+    else:
+        in_degrees = False
+    
+    marker_positions_pd = get_marker_positions(motion_data, model, in_degrees=in_degrees)
     
     # Trc header
     times = motion_data.getIndependentColumn()