biomechzoo 0.5.0__tar.gz → 0.5.1__tar.gz

{biomechzoo-0.5.0/src/biomechzoo.egg-info → biomechzoo-0.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.5.0
+Version: 0.5.1
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo

{biomechzoo-0.5.0 → biomechzoo-0.5.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "biomechzoo"
-version = "0.5.0"
+version = "0.5.1"
 description = "Python implementation of the biomechZoo toolbox"
 readme = "README.md"
 requires-python = ">=3.11,<3.12"   # max version for opencap-process tools is 3.11

biomechzoo-0.5.1/src/biomechzoo/biomech_ops/movement_onset.py

@@ -0,0 +1,2 @@
+def movement_onset():
+    raise NotImplementedError

{biomechzoo-0.5.0 → biomechzoo-0.5.1}/src/biomechzoo/biomechzoo.py

@@ -1,6 +1,8 @@
 import os
 import inspect
 import time
+
+from biomechzoo.imu.tilt_algoirthm import tilt_algorithm_data
 from biomechzoo.utils.engine import engine  # assumes this returns .zoo files in folder
 from biomechzoo.utils.zload import zload
 from biomechzoo.utils.zsave import zsave
@@ -134,6 +136,26 @@ class BiomechZoo:
     def parquet2zoo(self, out_folder=None, inplace=None):
         raise NotImplementedError('Use table2zoo instead')
 
+    def tilt_algorithm(self, chname_avert, chname_medlat, chname_antpost, out_folder=None, inplace=False):
+        """ tilt correction for acceleration data """
+        start_time = time.time()
+        verbose = self.verbose
+        in_folder = self.in_folder
+        if inplace is None:
+            inplace = self.inplace
+        fl = engine(in_folder, name_contains=self.name_contains, subfolders=self.subfolders)
+        for f in fl:
+            batchdisp('tilt correction of acceleration channels for {}'.format(f), level=2, verbose=verbose)
+            data = zload(f)
+            data = tilt_algorithm_data(data, chname_avert, chname_medlat, chname_antpost)
+            zsave(f, data, inplace=inplace, out_folder=out_folder, root_folder=in_folder)
+        method_name = inspect.currentframe().f_code.co_name
+        batchdisp(
+            '{} process complete for {} file(s) in {:.2f} secs'.format(method_name, len(fl), time.time() - start_time),
+            level=1, verbose=verbose)
+        # Update self.folder after  processing
+        self._update_folder(out_folder, inplace, in_folder)
+
     def phase_angle(self, ch, out_folder=None, inplace=None):
         """ computes phase angles"""
         start_time = time.time()

biomechzoo-0.5.1/src/biomechzoo/imu/tilt_algoirthm.py

@@ -0,0 +1,112 @@
+import numpy as np
+import math
+import pandas as pd
+from biomechzoo.processing.add_channel_data import add_channel_data
+
+def tilt_algorithm_data(data,ch_vert, ch_medlat, ch_antpost, plot_or_not=None):
+
+    # extract channels from data
+    avert = data[ch_vert]['line']
+    amedlat = data[ch_medlat]['line']
+    aantpost = data[ch_antpost]['line']
+
+    _, avert_corr, amedlat_corr, aantpost_corr = tilt_algorithm_line(avert, amedlat, aantpost)
+
+    data = add_channel_data(data, ch_vert + '_tilt_corr', avert_corr)
+    data = add_channel_data(data, ch_medlat + '_tilt_corr', amedlat_corr)
+    data = add_channel_data(data, ch_antpost + '_tilt_corr', aantpost_corr)
+
+    return data
+
+
+def tilt_algorithm_line(avert, amedlat, aantpost, plot_or_not=None):
+    """
+    TiltAlgorithm - to account for gravity and improper tilt alignment of a tri-axial trunk accelerometer.
+    Step 1: Extract raw measured (mean) accelerations
+    Step 2: Calculate tilt angles
+    Step 3: Calculate horizontal dynamic accelerations vectors
+    Step 4: Calculate estimated provisional vertical vector
+    Step 5: Calculate vertical dynamic vector
+    step 6.1:  Calculate the contribution of static components
+    step 6.2 Transpose static component matrices
+    step 7: Remove the static components from the templates of pre and post
+
+    :param avert: signal predominantly in vertical direction
+    :param amedlat: signal predominantly in medio-lateral direction
+    :param aantpost: signal predominantly in anterior-posterior direction
+    :param plot_or_not: whether to plot the results
+    :return: dataframe of the tilt corrected and gravity subtracted vertical, medio-lateral and anterior-posterior
+    acceleration signals
+    """
+    #
+
+    a_vt = avert.mean()
+    a_ml = amedlat.mean()
+    a_ap = aantpost.mean()
+
+    # if avert is negative than turn the sensor around.
+    if a_vt < 0.5:
+        avert *= -1
+        amedlat *= -1
+        a_vt = avert.mean()
+        a_ml = amedlat.mean()
+
+    # Anterior tilt
+    TiltAngle_ap_rad = np.arcsin(a_ap)
+    TiltAngle_ap_deg = math.degrees(TiltAngle_ap_rad)
+
+    # mediolateral tilt
+    TiltAngle_ml_rad = np.arcsin(a_ml)
+    TiltAngle_ml_deg = math.degrees(TiltAngle_ml_rad)
+
+    # Anterior posterior
+    a_AP = (a_ap * np.cos(TiltAngle_ap_rad)) - (a_vt * np.sin(TiltAngle_ap_rad))
+    # AMediolateral
+    a_ML = (a_ml * np.cos(TiltAngle_ml_rad)) - (a_vt * np.sin(TiltAngle_ml_rad))
+
+    # a_vt_prov = a_ap*Sin(theta_ap) + a_vt*Cos(theta_ap)
+    a_vt_prov = (a_ap * np.sin(TiltAngle_ap_rad)) + (a_vt * np.cos(TiltAngle_ap_rad))
+
+    # a_VT = a_ml*sin(theta_ml) + a_vt_prov*cos(theta_ml) - 1
+    a_VT = (a_ml * np.sin(TiltAngle_ml_rad)) + (a_vt_prov * np.cos(TiltAngle_ml_rad)) - 1
+
+    a_AP_static = a_ap - a_AP
+    a_ML_static = a_ml - a_ML
+    a_VT_static = a_vt - a_VT
+
+    a_AP_static = np.transpose(a_AP_static)
+    a_ML_static = np.transpose(a_ML_static)
+    a_VT_static = np.transpose(a_VT_static)
+
+    amedlat2 = amedlat - a_ML_static
+    avert2 = avert - a_VT_static
+    aantpost2 = aantpost - a_AP_static
+
+    data = {'avert': avert2,
+            'amedlat': amedlat2,
+            'aantpost': aantpost2}
+    df_corrected = pd.DataFrame(data)
+
+    # if plot_or_not:
+    #     f, ax = plt.subplots(nrows=3, ncols=1, sharex=True, dpi=300)
+    #     sns.despine(offset=10)
+    #     f.tight_layout()
+    #     offset = 0.1
+    #     f.subplots_adjust(left=0.15, top=0.95)
+    #
+    #     sns.lineplot(avert, ax=ax[0], label='Raw')
+    #     sns.lineplot(avert2, ax=ax[0], label='tilt corrected')
+    #     ax[0].set_ylabel('vert acc (g)')
+    #     ax[0].set_title('Vertical acceleration corrected with {}'.format(np.round(a_VT_static, 2)))
+    #
+    #     sns.lineplot(amedlat, ax=ax[1], label='Raw')
+    #     sns.lineplot(amedlat2, ax=ax[1], label='Tilt corrected')
+    #     ax[1].set_ylabel('ml acc (g)')
+    #     ax[1].set_title('Medio-lateral tilt angle corrected with {} degrees'.format(np.round(TiltAngle_ml_deg, 2)))
+    #
+    #     sns.lineplot(aantpost, ax=ax[2], label='Raw')
+    #     sns.lineplot(aantpost2, ax=ax[2], label='Tilt corrected')
+    #     ax[2].set_ylabel('ap acc (g)')
+    #     ax[2].set_title('Anterior-posterior tilt angle corrected with {} degrees'.format(np.round(TiltAngle_ap_deg, 2)))
+
+    return df_corrected, avert2, amedlat2, aantpost2

{biomechzoo-0.5.0 → biomechzoo-0.5.1}/src/biomechzoo/processing/addevent_data.py

@@ -2,6 +2,7 @@ import numpy as np
 import copy
 import warnings
 from biomechzoo.utils.peak_sign import peak_sign
+from biomechzoo.biomech_ops.movement_onset import movement_onset
 
 def addevent_data(data, channels, ename, etype, constant=None):
 
@@ -46,6 +47,12 @@ def addevent_data(data, channels, ename, etype, constant=None):
             exd = max_stance(yd)
             eyd = float(yd[exd])
             eyd = float(yd[exd])
+        elif etype == 'movement_onset':
+            exd = movement_onset(yd, constant)
+            eyd = yd[exd]
+        elif etype == 'movement_offset':
+            exd = movement_onset(yd,constant)
+            eyd = yd[exd]
         elif etype in ['fs_fp', 'fo_fp']:
             # --- Handle constant ---
             if constant is None:

{biomechzoo-0.5.0 → biomechzoo-0.5.1/src/biomechzoo.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.5.0
+Version: 0.5.1
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo

{biomechzoo-0.5.0 → biomechzoo-0.5.1}/src/biomechzoo.egg-info/SOURCES.txt

@@ -16,6 +16,7 @@ src/biomechzoo/biomech_ops/continuous_relative_phase_data.py
 src/biomechzoo/biomech_ops/continuous_relative_phase_line.py
 src/biomechzoo/biomech_ops/filter_data.py
 src/biomechzoo/biomech_ops/filter_line.py
+src/biomechzoo/biomech_ops/movement_onset.py
 src/biomechzoo/biomech_ops/normalize_data.py
 src/biomechzoo/biomech_ops/normalize_line.py
 src/biomechzoo/biomech_ops/phase_angle_data.py
@@ -25,6 +26,7 @@ src/biomechzoo/conversion/c3d2zoo_data.py
 src/biomechzoo/conversion/mvnx2zoo_data.py
 src/biomechzoo/conversion/opencap2zoo_data.py
 src/biomechzoo/conversion/table2zoo_data.py
+src/biomechzoo/imu/tilt_algoirthm.py
 src/biomechzoo/mvn/__init__.py
 src/biomechzoo/mvn/load_mvnx.py
 src/biomechzoo/mvn/main_mvnx.py