biomechzoo 0.2.2__tar.gz → 0.4.0__tar.gz

{biomechzoo-0.2.2 → biomechzoo-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.2.2
+Version: 0.4.0
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo
@@ -9,7 +9,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: ezc3d>=1.5.19
 Requires-Dist: matplotlib>=3.10.6
-Requires-Dist: numpy>=2.3.3
+Requires-Dist: numpy==2.2.6
 Requires-Dist: pandas>=2.3.2
 Requires-Dist: scipy>=1.16.2
 Dynamic: license-file
@@ -25,4 +25,8 @@ This is a development version of the biomechzoo toolbox for python.
 - If you need to install a specific version, run ``pip install biomechzoo==x.x.x`` where x.x.x is the version number. 
 - If you need to update biomechzoo to the latest version in your env, run ``pip install biomechzoo --upgrade``
 
+## Dependencies notes
+- We use Python 3.11 for compatibility with https://github.com/stanfordnmbl/opencap-processing
+- We use Numpy 2.2.6 for compatibility with https://pypi.org/project/numba/
+
 See also http://www.github.com/mcgillmotionlab/biomechzoo or http://www.biomechzoo.com for more information

{biomechzoo-0.2.2 → biomechzoo-0.4.0}/README.md

@@ -9,4 +9,8 @@ This is a development version of the biomechzoo toolbox for python.
 - If you need to install a specific version, run ``pip install biomechzoo==x.x.x`` where x.x.x is the version number. 
 - If you need to update biomechzoo to the latest version in your env, run ``pip install biomechzoo --upgrade``
 
+## Dependencies notes
+- We use Python 3.11 for compatibility with https://github.com/stanfordnmbl/opencap-processing
+- We use Numpy 2.2.6 for compatibility with https://pypi.org/project/numba/
+
 See also http://www.github.com/mcgillmotionlab/biomechzoo or http://www.biomechzoo.com for more information

{biomechzoo-0.2.2 → biomechzoo-0.4.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "biomechzoo"
-version = "0.2.2"
+version = "0.4.0"
 description = "Python implementation of the biomechZoo toolbox"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -9,7 +9,7 @@ license-files = ["LICEN[CS]E*"]
 dependencies = [
     "ezc3d>=1.5.19",
     "matplotlib>=3.10.6",
-    "numpy>=2.3.3",
+    "numpy==2.2.6",
     "pandas>=2.3.2",
     "scipy>=1.16.2",
 ]

biomechzoo-0.4.0/src/biomechzoo/conversion/mvnx2zoo_data.py

@@ -0,0 +1,102 @@
+import numpy as np
+from src.biomechzoo.mvn.load_mvnx import load_mvnx
+from src.biomechzoo.mvn.mvn import JOINTS, SEGMENTS
+
+def mvnx2zoo_data(fl):
+    """ loads mvnx file from xsens"""
+
+    mvnx_file = load_mvnx(fl)
+
+    # create zoo data dict
+    data = {}
+
+    # extract joint angle data (All JOINTS may not exist in a given dataset)
+    for key, val in JOINTS.items():
+        try:
+            r = mvnx_file.get_joint_angle(joint=key)
+            data[val] = {
+                'line': r,
+                'event': {}
+            }
+        except KeyError:
+            print('joint {} does not exist, skipping'.format(val))
+
+    # extract segment orientations (All SEGMENTS may not exist in a given dataset)
+    for key, val in SEGMENTS.items():
+        try:
+            r = mvnx_file.get_sensor_ori(segment=key)
+            data[val] = {
+                'line': r,
+                'event': {}
+            }
+        except KeyError:
+            print('segment {} does not exist, skipping'.format(val))
+
+    # get foot strike events
+    data = _get_foot_strike_events(mvnx_file, data)
+
+    # add meta information
+    data = _get_meta_info(mvnx_file, data)
+
+    return data
+
+
+def _get_meta_info(mvnx_file, data):
+    # todo: add more, see mvnx_file object
+    data['zoosystem'] = {}
+    data['zoosystem']['Video'] = {}
+    data['zoosystem']['Video']['Freq'] = int(mvnx_file.frame_rate)
+    data['zoosystem']['Version'] = mvnx_file.version
+    data['zoosystem']['configuration'] = mvnx_file.configuration
+    data['zoosystem']['recording_date'] = mvnx_file.recording_date
+    data['zoosystem']['original_file_name'] = mvnx_file.original_file_name
+    data['zoosystem']['frame_count'] = mvnx_file.frame_count
+    data['zoosystem']['comments'] = mvnx_file.comments
+    return data
+
+
+def _get_foot_strike_events(mvnx_file, data):
+    RHeel = np.zeros(mvnx_file.frame_count)
+    LHeel = np.zeros(mvnx_file.frame_count)
+
+    for n in range(mvnx_file.frame_count):
+        list_contact = mvnx_file.get_foot_contacts(n)
+        for contact in list_contact:
+            if contact['segment_index'] == 17:
+                RHeel[n] = True
+            elif contact['segment_index'] == 21:
+                LHeel[n] = True
+
+    hs_r = []
+    hs_l = []
+    for i in range(1, len(LHeel)):  # Start from 1 to avoid i-1 out-of-range
+        if RHeel[i - 1] == 0 and RHeel[i] == 1:
+            hs_r.append(i)
+        if LHeel[i - 1] == 0 and LHeel[i] == 1:
+            hs_l.append(i)
+
+        # add to event branch of any channel
+    if 'jL5S1' in data:
+        ch = 'jL5S1'
+    else:
+        ch = next(iter(data))
+
+    if hs_r:
+        for i, rHS in enumerate(hs_r):
+            data[ch]['event']['R_FS' + str(i + 1)] = [rHS, 0, 0]
+    if hs_l:
+        for i, lHS in enumerate(hs_l):
+            data[ch]['event']['L_FS' + str(i + 1)] = [lHS, 0, 0]
+
+    return data
+
+
+if __name__ == '__main__':
+    """ testing """
+    import os
+    from src.biomechzoo.utils.zplot import zplot
+    # -------TESTING--------
+    project_root = os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))))
+    fl = os.path.join(project_root, 'data', 'other', 'Flat-001.mvnx')
+    data = mvnx2zoo_data(fl)
+    zplot(data, 'jRightKnee')

{biomechzoo-0.2.2 → biomechzoo-0.4.0}/src/biomechzoo/mvn/load_mvnx.py

@@ -6,8 +6,8 @@ Script to load an mvnx
 import xml.etree.ElementTree as ET
 import collections
 import numpy as np
-from biomechzoo.mvn.mvnx_file_accessor import MvnxFileAccessor
-from biomechzoo.mvn import mvn
+from src.biomechzoo.mvn.mvnx_file_accessor import MvnxFileAccessor
+from src.biomechzoo.mvn import mvn
 
 # Xml namespace for mvnx files
 ns = {'mvn': 'http://www.xsens.com/mvn/mvnx'}

{biomechzoo-0.2.2 → biomechzoo-0.4.0}/src/biomechzoo/mvn/main_mvnx.py

@@ -1,7 +1,7 @@
 import os
 import argparse
 import matplotlib.pyplot as plt
-from biomechzoo.mvn.load_mvnx import load_mvnx
+from src.biomechzoo.mvn.load_mvnx import load_mvnx
 
 
 # Convert mvnx file to python data

{biomechzoo-0.2.2 → biomechzoo-0.4.0}/src/biomechzoo/mvn/mvnx_file_accessor.py

@@ -1,4 +1,4 @@
-from biomechzoo.mvn import mvn
+from src.biomechzoo.mvn import mvn
 import warnings
 
 
@@ -405,9 +405,10 @@ class MvnxFileAccessor:
         :return: The contacts
         """
         frame, is_single_frame = self.frame_to_mapped_slice(frame)
-        return_values = self.file_data['frames']['footContacts'][frame]
+        return_values = self.file_data['frames']['contacts_data'][frame] #edited Phil Dixon
         return return_values[0] if is_single_frame else return_values
 
+
     def has_foot_contact(self, frame, foot_contact_flags=0):
         """
         Find out if the frame has a contact, optionally for a specific segment/point combo

{biomechzoo-0.2.2 → biomechzoo-0.4.0}/src/biomechzoo.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.2.2
+Version: 0.4.0
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo
@@ -9,7 +9,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: ezc3d>=1.5.19
 Requires-Dist: matplotlib>=3.10.6
-Requires-Dist: numpy>=2.3.3
+Requires-Dist: numpy==2.2.6
 Requires-Dist: pandas>=2.3.2
 Requires-Dist: scipy>=1.16.2
 Dynamic: license-file
@@ -25,4 +25,8 @@ This is a development version of the biomechzoo toolbox for python.
 - If you need to install a specific version, run ``pip install biomechzoo==x.x.x`` where x.x.x is the version number. 
 - If you need to update biomechzoo to the latest version in your env, run ``pip install biomechzoo --upgrade``
 
+## Dependencies notes
+- We use Python 3.11 for compatibility with https://github.com/stanfordnmbl/opencap-processing
+- We use Numpy 2.2.6 for compatibility with https://pypi.org/project/numba/
+
 See also http://www.github.com/mcgillmotionlab/biomechzoo or http://www.biomechzoo.com for more information

{biomechzoo-0.2.2 → biomechzoo-0.4.0}/src/biomechzoo.egg-info/requires.txt

@@ -1,5 +1,5 @@
 ezc3d>=1.5.19
 matplotlib>=3.10.6
-numpy>=2.3.3
+numpy==2.2.6
 pandas>=2.3.2
 scipy>=1.16.2

biomechzoo-0.2.2/src/biomechzoo/conversion/mvnx2zoo_data.py

@@ -1,71 +0,0 @@
-import numpy as np
-from biomechzoo.mvn.load_mvnx import load_mvnx
-
-
-def mvnx2zoo_data(fl):
-    """ loads mvnx file from xsens"""
-    #todo: needs to be updated for the new version of mvnx direcly loaded in biomechzoo
-    mvnx_file = load_mvnx(fl)
-
-    # create zoo data dict
-    data = {}
-
-    # Accessing joint data :
-    joint_angle_data = mvnx_file.get_joint_angle()
-    joint_names = mvnx_file.joints
-    for i, joint in enumerate(joint_names):
-        start = i * 3
-        stop = start + 3
-        angles = joint_angle_data[:, start:stop]  # shape: (n_frames, 3)
-
-        data[joint] = {
-            'line': angles,
-            'event': {}
-        }
-    # get foot strike events
-    # Index 0: Left Heel contact (1 for contact, 0 for no contact)
-    # Index 1: Left Toe contact (1 for contact, 0 for no contact)
-    # Index 2: Right Heel contact (1 for contact, 0 for no contact)
-    # Index 3: Right Toe contact (1 for contact, 0 for no contact)
-    left_heel_contacts = np.array(mvnx_file.footContacts[:, 0])
-    right_heel_contacts = np.array(mvnx_file.footContacts[:, 2])
-
-    # Detect transitions from no contact (0) to contact (1)
-    left_contact_start = (left_heel_contacts[:-1] == 0) & (left_heel_contacts[1:] == 1)
-    right_contact_start = (right_heel_contacts[:-1] == 0) & (right_heel_contacts[1:] == 1)
-
-    # Get indices where these transitions occur (add 1 because we're checking between frames)
-    left_contact_frames = np.where(left_contact_start)[0] + 1
-    right_contact_frames = np.where(right_contact_start)[0] + 1
-
-    # add to zoo
-    data['jL5S1']['event'] = {}
-    for i, right_contact_frame in enumerate(right_contact_frames):
-        data['jL5S1']['event']['R_FS'+str(i+1)] = [right_contact_frame, 0, 0]
-    for i, left_contact_frame in enumerate(left_contact_frames):
-        data['jL5S1']['event']['L_FS' + str(i + 1)] = [left_contact_frame, 0, 0]
-
-    # add meta information
-    # todo: add more, see mvnx_file object
-    data['zoosystem'] = {}
-    data['zoosystem']['Video'] = {}
-    data['zoosystem']['Video']['Freq'] = int(mvnx_file.frame_rate)
-    data['zoosystem']['Version'] = mvnx_file.version
-    data['zoosystem']['configuration'] = mvnx_file.configuration
-    data['zoosystem']['recording_date'] = mvnx_file.recording_date
-    data['zoosystem']['original_file_name'] = mvnx_file.original_file_name
-    data['zoosystem']['frame_count'] = mvnx_file.frame_count
-    data['zoosystem']['comments'] = mvnx_file.comments
-
-    return data
-
-
-if __name__ == '__main__':
-    """ testing """
-    import os
-    from src.biomechzoo.utils.zplot import zplot
-    # -------TESTING--------
-    project_root = os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))))
-    fl = os.path.join(project_root, 'data', 'other', 'Flat-001.mvnx')
-    data = mvnx2zoo_data(fl)
-    zplot(data, 'jRightKnee')