Monocular integration

ActivityAnalyses/gait_analysis.py

@@ -19,7 +19,11 @@
 """
 
 import sys
-sys.path.append('../')
+import os
+# Add project root to path
+project_root = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+if project_root not in sys.path:
+    sys.path.insert(0, project_root)
 
 import numpy as np
 import copy
@@ -1046,5 +1050,4 @@ def detect_correct_order(rHS, rTO, lHS, lTO):
                       'eventNamesContralateral':['TO','HS'],
                       'ipsilateralLeg':leg}
 
-        return gaitEvents
-
+        return gaitEvents

marker_name_mapping.py

@@ -0,0 +1,99 @@
+"""
+Marker name mapping dictionary for converting from expected format (with '_study' suffix)
+to actual format (without '_study' suffix, lowercase).
+
+This mapping is used to rename markers in TRC files to match the expected format
+used by the gait_analysis class.
+
+Expected format: markers end with '_study' (e.g., 'r_calc_study', 'r.ASIS_study')
+Actual format: markers without '_study' suffix, lowercase (e.g., 'r_calc', 'r_ASIS')
+"""
+
+MARKER_NAME_MAPPING = {
+    # Pelvis markers
+    'r.ASIS_study': 'r_ASIS',
+    'L.ASIS_study': 'l_ASIS',
+    'r.PSIS_study': 'r_PSIS',
+    'L.PSIS_study': 'l_PSIS',
+
+    # Right leg markers
+    'r_knee_study': 'r_knee',
+    'r_mknee_study': 'r_mknee',
+    'r_ankle_study': 'r_ankle',
+    'r_mankle_study': 'r_mankle',
+    'r_toe_study': 'r_toe',
+    'r_5meta_study': 'r_5meta',
+    'r_calc_study': 'r_calc',
+
+    # Left leg markers
+    'L_knee_study': 'l_knee',
+    'L_mknee_study': 'l_mknee',
+    'L_ankle_study': 'l_ankle',
+    'L_mankle_study': 'l_mankle',
+    'L_toe_study': 'l_toe',
+    'L_calc_study': 'l_calc',
+    'L_5meta_study': 'l_5meta',
+
+    # Shoulder markers
+    'r_shoulder_study': 'r_shoulder',
+    'L_shoulder_study': 'l_shoulder',
+
+    # Spine markers
+    'C7_study': 'C7',
+
+    # Thigh markers (may not exist in all files)
+    # 'r_thigh1_study': 'r_thigh1',  # Check if exists in actual file
+    # 'r_thigh2_study': 'r_thigh2',  # Check if exists in actual file
+    # 'r_thigh3_study': 'r_thigh3',  # Check if exists in actual file
+    # 'L_thigh1_study': 'l_thigh1',  # Check if exists in actual file
+    # 'L_thigh2_study': 'l_thigh2',  # Check if exists in actual file
+    # 'L_thigh3_study': 'l_thigh3',  # Check if exists in actual file
+
+    # Shank markers (may not exist in all files)
+    # 'r_sh1_study': 'r_sh1',  # Check if exists in actual file
+    # 'r_sh2_study': 'r_sh2',  # Check if exists in actual file
+    # 'r_sh3_study': 'r_sh3',  # Check if exists in actual file
+    # 'L_sh1_study': 'l_sh1',  # Check if exists in actual file
+    # 'L_sh2_study': 'l_sh2',  # Check if exists in actual file
+    # 'L_sh3_study': 'l_sh3',  # Check if exists in actual file
+
+    # Hip joint centers
+    'RHJC_study': 'RHJC',  # Check if exists in actual file
+    'LHJC_study': 'LHJC',  # Check if exists in actual file
+
+    # Elbow markers
+    # 'r_lelbow_study': 'r_elbow',  # Approximate mapping
+    'r_melbow_study': 'r_melbow',
+    # 'L_lelbow_study': 'l_elbow',  # Approximate mapping
+    'L_melbow_study': 'l_melbow',
+
+    # Wrist markers
+    # 'r_lwrist_study': 'r_wrist_radius',  # Approximate mapping
+    # 'r_mwrist_study': 'r_wrist_ulna',  # Approximate mapping
+    # 'L_lwrist_study': 'l_wrist_radius',  # Approximate mapping
+    # 'L_mwrist_study': 'l_wrist_ulna',  # Approximate mapping
+}
+
+# Reverse mapping (actual -> expected) for renaming markers in TRC files
+REVERSE_MARKER_NAME_MAPPING = {v: k for k, v in MARKER_NAME_MAPPING.items()}
+
+# if __name__ == '__main__':
+#     """
+#     Print the mapping dictionary in a format suitable for use in cloud functions.
+#     """
+#     import json
+
+#     print("Marker name mapping (expected -> actual):")
+#     print("=" * 60)
+#     for expected, actual in sorted(MARKER_NAME_MAPPING.items()):
+#         print(f"  '{expected}' -> '{actual}'")
+
+#     print("\n\nReverse mapping (actual -> expected) for renaming:")
+#     print("=" * 60)
+#     for actual, expected in sorted(REVERSE_MARKER_NAME_MAPPING.items()):
+#         print(f"  '{actual}' -> '{expected}'")
+
+#     print("\n\nJSON format (for cloud function):")
+#     print("=" * 60)
+#     print(json.dumps(REVERSE_MARKER_NAME_MAPPING, indent=2))
+