Adding joint movements into the wholebody scaffold

src/scaffoldmaker/annotation/body_terms.py

@@ -10,8 +10,18 @@
     ("abdominopelvic cavity", "UBERON:0035819"),
     ("upper limb", "UBERON:0001460"),
     ("left upper limb", "UBERON:8300002", "FMA:7186"),
+    ("left shoulder", ""),
+    ("left brachium", ""),
+    ("left elbow", ""),
+    ("left antebrachium", ""),
+    ("left hand", ""),
     ("left upper limb skin epidermis outer surface", "ILX:0796504"),
     ("right upper limb", "UBERON:8300001", "FMA:7185"),
+    ("right shoulder", ""),
+    ("right brachium", ""),
+    ("right elbow", ""),
+    ("right antebrachium", ""),
+    ("right hand", ""),
     ("right upper limb skin epidermis outer surface", "ILX:0796503"),
     ("body", "UBERON:0000468", "ILX:0101370"),
     ("core", ""),
@@ -21,11 +31,18 @@
     ("head core", ""),
     ("diaphragm", "UBERON:0001103", "ILX:0103194"),
     ("hand", "ILX:0104885", "FMA:9712"),
+    ("hip", ""),
     ("left", ""),
     ("lower limb", "UBERON:0000978"),
     ("left lower limb", "UBERON:8300004", "FMA:24981"),
+    ("left upper leg", ""),
+    ("left lower leg", ""),
+    ("left foot", ""),
     ("left lower limb skin epidermis outer surface", "ILX:0796506"),
-    ("right lower limb ", "UBERON:8300003", "FMA:24980"),
+    ("right lower limb", "UBERON:8300003", "FMA:24980"),
+    ("right upper leg", ""),
+    ("right lower leg", ""),
+    ("right foot", ""),
     ("right lower limb skin epidermis outer surface", "ILX:0796505"),
     ("foot", "ILX:0745450", "FMA:9664"),
     ("neck", "UBERON:0000974", "ILX:0733967"),
@@ -38,7 +55,34 @@
     ("thoracic cavity", "UBERON:0002224"),
     ("thoracic cavity boundary surface", "ILX:0796508"),
     ("thorax", "ILX:0742178"),
-    ("ventral", "")
+    ("ventral", ""),
+    # kinematic tree markers
+    ('pelvis', ""), 
+    ('femur_r', ""), 
+    ('tibia_r', ""), 
+    ('talus_r', ""), 
+    ('calcn_r', ""), 
+    ('toes_r', ""), 
+    ('femur_l', ""), 
+    ('tibia_l', ""), 
+    ('talus_l', ""), 
+    ('calcn_l', ""), 
+    ('toes_l', ""), 
+    ('lumbar_body', ""), 
+    ('thorax_top', ""), 
+    ('head_marker', ""), 
+    ('scapula_r', ""), 
+    ('humerus_r', ""), 
+    ('ulna_r', ""), 
+    ('radius_r', ""), 
+    ('hand_r', ""), 
+    ('scapula_l', ""), 
+    ('humerus_l', ""), 
+    ('ulna_l', ""), 
+    ('radius_l', ""), 
+    ('hand_l', ""), 
+
+
     ]
 
 def get_body_term(name : str):
@@ -51,3 +95,12 @@ def get_body_term(name : str):
         if name in term:
             return ( term[0], term[1] )
     raise NameError("Body annotation term '" + name + "' not found.")
+
+def marker_name_in_terms(name: str):
+    """
+    Check if term exists in approved marker terms
+    """
+    for term in body_terms:
+        if name in term:
+            return True
+    return False