add 5% margin in bboxes

* LSTM with wrist motion

* remove tab

Pose2Sim/OpenSim_Setup/IK_Setup_Pose2Sim_LSTM.xml

@@ -276,6 +276,42 @@
 					<!--Weight given to a marker or coordinate for solving inverse kinematics problems.-->
 					<weight>25</weight>
 				</IKMarkerTask>
+				<IKMarkerTask name="RThumb">
+					<!--Whether or not this task will be used during inverse kinematics solve, default is true.-->
+					<apply>true</apply>
+					<!--Weight given to the task when solving inverse kinematics problems, default is 0.-->
+					<weight>1</weight>
+				</IKMarkerTask>
+				<IKMarkerTask name="RIndex">
+					<!--Whether or not this task will be used during inverse kinematics solve, default is true.-->
+					<apply>true</apply>
+					<!--Weight given to the task when solving inverse kinematics problems, default is 0.-->
+					<weight>1</weight>
+				</IKMarkerTask>
+				<IKMarkerTask name="RPinky">
+					<!--Whether or not this task will be used during inverse kinematics solve, default is true.-->
+					<apply>true</apply>
+					<!--Weight given to the task when solving inverse kinematics problems, default is 0.-->
+					<weight>1</weight>
+				</IKMarkerTask>
+				<IKMarkerTask name="LThumb">
+					<!--Whether or not this task will be used during inverse kinematics solve, default is true.-->
+					<apply>true</apply>
+					<!--Weight given to the task when solving inverse kinematics problems, default is 0.-->
+					<weight>1</weight>
+				</IKMarkerTask>
+				<IKMarkerTask name="LIndex">
+					<!--Whether or not this task will be used during inverse kinematics solve, default is true.-->
+					<apply>true</apply>
+					<!--Weight given to the task when solving inverse kinematics problems, default is 0.-->
+					<weight>1</weight>
+				</IKMarkerTask>
+				<IKMarkerTask name="LPinky">
+					<!--Whether or not this task will be used during inverse kinematics solve, default is true.-->
+					<apply>true</apply>
+					<!--Weight given to the task when solving inverse kinematics problems, default is 0.-->
+					<weight>1</weight>
+				</IKMarkerTask>
 				<IKCoordinateTask name="sh_tx_l">
 					<!--Whether or not this task will be used during inverse kinematics solve, default is true.-->
 					<apply>true</apply>

Pose2Sim/OpenSim_Setup/Model_Pose2Sim_LSTM.osim

@@ -6229,7 +6229,7 @@
 							<!--Flag indicating whether or not the values of the coordinates should be limited to the range, above.-->
 							<clamped>true</clamped>
 							<!--Flag indicating whether or not the values of the coordinates should be constrained to the current (e.g. default) value, above.-->
-							<locked>true</locked>
+							<locked>false</locked>
 							<!--If specified, the coordinate can be prescribed by a function of time. It can be any OpenSim Function with valid second order derivatives.-->
 							<prescribed_function />
 							<!--Flag indicating whether or not the values of the coordinates should be prescribed according to the function above. It is ignored if the no prescribed function is specified.-->
@@ -6245,7 +6245,7 @@
 							<!--Flag indicating whether or not the values of the coordinates should be limited to the range, above.-->
 							<clamped>true</clamped>
 							<!--Flag indicating whether or not the values of the coordinates should be constrained to the current (e.g. default) value, above.-->
-							<locked>true</locked>
+							<locked>false</locked>
 							<!--If specified, the coordinate can be prescribed by a function of time. It can be any OpenSim Function with valid second order derivatives.-->
 							<prescribed_function />
 							<!--Flag indicating whether or not the values of the coordinates should be prescribed according to the function above. It is ignored if the no prescribed function is specified.-->
@@ -6735,7 +6735,7 @@
 							<!--Flag indicating whether or not the values of the coordinates should be limited to the range, above.-->
 							<clamped>true</clamped>
 							<!--Flag indicating whether or not the values of the coordinates should be constrained to the current (e.g. default) value, above.-->
-							<locked>true</locked>
+							<locked>false</locked>
 							<!--If specified, the coordinate can be prescribed by a function of time. It can be any OpenSim Function with valid second order derivatives.-->
 							<prescribed_function />
 							<!--Flag indicating whether or not the values of the coordinates should be prescribed according to the function above. It is ignored if the no prescribed function is specified.-->
@@ -6751,7 +6751,7 @@
 							<!--Flag indicating whether or not the values of the coordinates should be limited to the range, above.-->
 							<clamped>true</clamped>
 							<!--Flag indicating whether or not the values of the coordinates should be constrained to the current (e.g. default) value, above.-->
-							<locked>true</locked>
+							<locked>false</locked>
 							<!--If specified, the coordinate can be prescribed by a function of time. It can be any OpenSim Function with valid second order derivatives.-->
 							<prescribed_function />
 							<!--Flag indicating whether or not the values of the coordinates should be prescribed according to the function above. It is ignored if the no prescribed function is specified.-->
@@ -7478,6 +7478,68 @@
 				<!--Flag (true or false) specifying whether the marker is fixed in its parent frame during the marker placement step of scaling.  If false, the marker is free to move within its parent Frame to match its experimental counterpart.-->
 				<fixed>false</fixed>
 			</Marker>
+			<Marker name="RThumb">
+				<!--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/hand_r</socket_parent_frame>
+				<!--The fixed location of the station expressed in its parent frame.-->
+				<location>0.015900600000000001 -0.053530099999999997 0.045219599999999999</location>
+			</Marker>
+			<Marker name="RIndex">
+				<!--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/hand_r</socket_parent_frame>
+				<!--The fixed location of the station expressed in its parent frame.-->
+				<location>0.0031182900000000001 -0.082610900000000001 0.0160293</location>
+			</Marker>
+			<Marker name="RPinky">
+				<!--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/hand_r</socket_parent_frame>
+				<!--The fixed location of the station expressed in its parent frame.-->
+				<location>0.00311312 -0.073810299999999995 -0.0325446</location>
+			</Marker>
+			<Marker name="LThumb">
+				<!--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/hand_l</socket_parent_frame>
+				<!--The fixed location of the station expressed in its parent frame.-->
+				<location>0.015900595366914239 -0.053530050744837965 -0.045219604622807212</location>
+			</Marker>
+			<Marker name="LIndex">
+				<!--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/hand_l</socket_parent_frame>
+				<!--The fixed location of the station expressed in its parent frame.-->
+				<location>0.0031182929587494357 -0.082610892492083754 -0.016029259621825068</location>
+			</Marker>
+			<Marker name="LPinky">
+				<!--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/hand_l</socket_parent_frame>
+				<!--The fixed location of the station expressed in its parent frame.-->
+				<location>0.0031131181410346542 -0.073810317144973658 0.032544599634169884</location>
+				<!--Flag (true or false) specifying whether the marker is fixed in its parent frame during the marker placement step of scaling.  If false, the marker is free to move within its parent Frame to match its experimental counterpart.-->
+				<fixed>false</fixed>		
+			</Marker>	
+			<Marker name="Nose">
+				<!--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/head</socket_parent_frame>
+				<!--The fixed location of the station expressed in its parent frame.-->
+				<location>0.107623784338859 0.54290490722614126 0.0001528854696219647</location>
+				<!--Flag (true or false) specifying whether the marker is fixed in its parent frame during the marker placement step of scaling.  If false, the marker is free to move within its parent Frame to match its experimental counterpart.-->
+				<fixed>true</fixed>
+			</Marker>
+			<Marker name="REye">
+				<!--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/head</socket_parent_frame>
+				<!--The fixed location of the station expressed in its parent frame.-->
+				<location>0.070157181776970542 0.55784285717609527 0.031106947145128013</location>
+				<!--Flag (true or false) specifying whether the marker is fixed in its parent frame during the marker placement step of scaling.  If false, the marker is free to move within its parent Frame to match its experimental counterpart.-->
+				<fixed>true</fixed>
+			</Marker>
+			<Marker name="LEye">
+				<!--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/head</socket_parent_frame>
+				<!--The fixed location of the station expressed in its parent frame.-->
+				<location>0.070157200000000003 0.55784299999999998 -0.0311069</location>
+				<!--Flag (true or false) specifying whether the marker is fixed in its parent frame during the marker placement step of scaling.  If false, the marker is free to move within its parent Frame to match its experimental counterpart.-->
+				<fixed>true</fixed>
+			</Marker>
 			</objects>
 			<groups />
 		</MarkerSet>

Pose2Sim/Utilities/bodykin_from_mot_osim.py

@@ -123,7 +123,8 @@ def bodykin_from_mot_osim_func(*args):
                 model.getCoordinateSet().get(coord).setValue(state, motion_data_np[n,c], enforceContraints=False)
             except:
                 pass
-        model.assemble(state)
+        # model.assemble(state)
+        model.realizePosition(state) # much faster (IK already done, no need to compute it again)
            
         # Use state of model to get body coordinates in ground
         loc_rot_frame = []

Pose2Sim/Utilities/reproj_from_trc_calib.py

@@ -56,7 +56,7 @@ biocvplus_markers = ['ACROM_R', 'ACROM_L', 'C7', 'T10', 'CLAV', 'XIP_PROC', 'UA_
 
 
 ## FUNCTIONS
-def str_to_id(string, length=8):
+def str_to_id(string, length=12):
     '''
     Convert a string to an integer id
     '''
@@ -285,12 +285,6 @@ def dataset_to_mmpose2d(coords_df, mmpose_json_file, img_size, markerset='custom
     - labels2d_json: saved json file
     '''
 
-    # transform first name in integer, and append other numbers from persons
-    persons = list(set(['_'.join(item.split('_')[:5]) for item in coords_df.columns.levels[1]]))
-    person_ids = [int(str(str_to_id(p.split('_')[1])) + ''.join(p.split('_')[3:])) if len(p.split('_'))>=3 
-                  else str_to_id(p.split('_')[0]) 
-                  for p in persons]
-    
     labels2d_json_data = {}
     labels2d_json_data['info'] = {'description': f'Bedlam Pose {markerset}', 
                                     'url': 'https://github.com/davidpagnon/bedlam_pose', 
@@ -303,14 +297,14 @@ def dataset_to_mmpose2d(coords_df, mmpose_json_file, img_size, markerset='custom
     labels2d_json_data['images'] = []
     labels2d_json_data['annotations'] = []
     labels2d_json_data['categories'] = [{'id': 1, 'name': 'person'}]
+    padding = 0.05
 
     # for each image
+    persons = list(set(['_'.join(item.split('_')[:5]) for item in coords_df.columns.levels[1]]))
     for i in range(len(coords_df)):
-        file_name = coords_df.index[i]
+        file_name = coords_df.index[i][0]
-        w, h = img_size
+        w, h = int(img_size[0]), int(img_size[1])
-        # id from concatenation of numbers from path
+        file_id = str_to_id(file_name, length=12)
-        # file_id = int(''.join(re.findall(r'\d+', str(file_name))))
-        file_id = int(hashlib.md5(file_name.encode()).hexdigest(), 16) % (10**12)  # Keep only 12 digits
 
         labels2d_json_data['images'] += [{'file_name': file_name, 
                                             'height': h, 
@@ -319,7 +313,8 @@ def dataset_to_mmpose2d(coords_df, mmpose_json_file, img_size, markerset='custom
                                             'license': 1}]
         
         # for each person
-        for p, person in enumerate(persons):
+        for person in persons:
+
             # store 2D keypoints and respect model keypoint order
             coords = coords_df.iloc[i, coords_df.columns.get_level_values(1)==person]
             coords_list = []
@@ -338,8 +333,13 @@ def dataset_to_mmpose2d(coords_df, mmpose_json_file, img_size, markerset='custom
             bbox_height = np.round(max_y - min_y, decimals=1)
             # bbox = [min_x, min_y, max_x, max_y]
             bbox = [min_x, min_y, bbox_width, bbox_height] # coco format
+            # add padding
+            bbox = [min(0, min_x-bbox_width*padding),
+                    min(0, min_y-bbox_height*padding),
+                    bbox_width*(1+padding*2) if max_x+bbox_width*padding < w else bbox_width*(1+padding),
+                    bbox_height*(1+padding*2) if max_y+bbox_height*padding < h else bbox_height*(1+padding)]
 
-            person_id = person_ids[p]
+            ann_id = str_to_id(person+file_name) 
             category_id = 1
             segmentation = [[min_x, min_y, min_x, max_y, max_x, max_y, max_x, min_y]] # no segmentation
             area = np.round(bbox_width * bbox_height, decimals=1)
@@ -349,7 +349,7 @@ def dataset_to_mmpose2d(coords_df, mmpose_json_file, img_size, markerset='custom
                 labels2d_json_data['annotations'] += [{ 'keypoints': coords_list, 
                                                         'num_keypoints': num_keypoints, 
                                                         'bbox': bbox, 
-                                                        'id': person_id, 
+                                                        'id': ann_id, 
                                                         'image_id': file_id, 
                                                         'category_id': category_id,
                                                         'segmentation': segmentation,

Pose2Sim/Utilities/trc_from_mot_osim.py

@@ -81,7 +81,8 @@ def get_marker_positions(motion_data, model, in_degrees=True, marker_list=[]):
             else:
                 value = motion_data_pd.loc[n,coord]
             model.getCoordinateSet().get(coord).setValue(state,value, enforceContraints=False)
-        model.assemble(state)
+        # model.assemble(state)
+        model.realizePosition(state) # much faster (IK already done, no need to compute it again)
         # get marker positions
         marker_positions += [np.array([marker_set.get(mk_name).findLocationInFrame(state, model.getGround()).to_numpy() for mk_name in marker_set_names]).flatten()]
     marker_positions_pd = pd.DataFrame(marker_positions, columns=marker_set_names_xyz)