biomechzoo 0.5.0__py3-none-any.whl → 0.5.2__py3-none-any.whl

biomechzoo/biomech_ops/movement_onset.py

@@ -0,0 +1,51 @@
+def movement_onset(yd, constant, etype=etype):
+    """
+    Extracts movement onset based on the average and standard deviation of a sliding window
+    Standard thresholds for running are mean_thresh=1.2, std_thresh=0.2. For walking mean_thresh=0.6, std_thresh=0.2.
+
+    yd: 1d array of the vector
+    constants: [sample_frequency, mean_thresh, std_thresh]
+    """
+    acc_mag = yd.copy()
+
+    # ----extract the constants----
+    fs = constant[0]
+    mean_thresh = constant[1]
+    std_thresh = constant[2]
+
+    # ----sliding window features----
+    features = []
+    timestamps = []
+    window_size = 2 * fs  # windows van 2 seconds
+    step_size = 1 * fs  # with an overlap of 1 seconds
+
+    for start in range(0, len(acc_mag) - window_size, step_size):
+        segment = acc_mag[start:start + window_size]
+        mean_val = segment.mean()
+        std_val = segment.std()
+        # entropy = -np.sum((segment / np.sum(segment)) * np.log2(segment / np.sum(segment) + 1e-12))
+        timestamps.append(start)
+        features.append((mean_val, std_val))
+
+    features = np.array(features)
+    timestamps = np.array(timestamps)
+
+    # ----Check already moving else find start----
+    initial_window = features[:5]  # First few seconds
+    if np.all(initial_window[:, 0] > mean_thresh) and np.all(initial_window[:, 1] > std_thresh):
+        print("already moving")
+        if etype == 'movement_offset':
+            index = 0
+    else:
+        # features, timestamps = self.sliding_window_features(acc_mag)
+        movement_flags = (features[:, 0] > mean_thresh) & (features[:, 1] > std_thresh)
+        index = None
+        for i in range(len(movement_flags) - int(min_duration * self.fs / 50)):
+            if np.all(movement_flags[i:i + int(min_duration * self.fs / 50)]):
+                index = i
+                break
+
+    if etype == 'movement_offset':
+        index = len(yd) - end_time
+
+    return timestamps[index] if index is not None else timestamps[0]

biomechzoo/biomechzoo.py

@@ -1,6 +1,8 @@
 import os
 import inspect
 import time
+
+from biomechzoo.imu.tilt_algorithm 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 +136,28 @@ class BiomechZoo:
     def parquet2zoo(self, out_folder=None, inplace=None):
         raise NotImplementedError('Use table2zoo instead')
 
+    def rectify(self):
+        raise NotImplementedError
+    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/imu/tilt_algorithm.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/processing/addevent_data.py

@@ -1,7 +1,9 @@
 import numpy as np
 import copy
 import warnings
+from scipy.signal import find_peaks
 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):
 
@@ -41,11 +43,17 @@ def addevent_data(data, channels, ename, etype, constant=None):
         elif etype == 'rom':
             eyd = float(np.max(yd) - np.min(yd))
             exd = 0  # dummy index (like MATLAB version)
-        elif etype == 'max_stance':
+        elif etype == 'first peak':
             # special event for gait and running
-            exd = max_stance(yd)
-            eyd = float(yd[exd])
+            exd = find_first_peak(yd, constant)
             eyd = float(yd[exd])
+        elif etype == 'movement_onset':
+            exd = movement_onset(yd, constant, etype=etype)
+            eyd = yd[exd]
+        elif etype == 'movement_offset':
+            yd2 = yd[::-1].copy() # Reverse the time series.
+            exd = movement_onset(yd2, constant, etype=etype)
+            eyd = yd[exd]
         elif etype in ['fs_fp', 'fo_fp']:
             # --- Handle constant ---
             if constant is None:
@@ -92,7 +100,17 @@ def addevent_data(data, channels, ename, etype, constant=None):
 
     return data_new
 
-def max_stance(yd):
-    """ extracts max from first 40% of the gait cycle"""
-    raise NotImplementedError
+def find_first_peak(yd, constant):
+    """ extracts first peak from a series of 2 peaks """
+    # Find peaks above threshold
+    peaks, _ = find_peaks(yd, height=constant)
+
+    if len(peaks) == 0:
+        raise ValueError('No peaks found')
+    elif len(peaks) == 1:
+        raise ValueError('Only 1 peak found')
+    else:
+        # Take the first valid peak
+        exd = peaks[0]
+
     return exd

{biomechzoo-0.5.0.dist-info → biomechzoo-0.5.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.5.0
+Version: 0.5.2
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo

{biomechzoo-0.5.0.dist-info → biomechzoo-0.5.2.dist-info}/RECORD

@@ -1,12 +1,13 @@
 __init__.py,sha256=Uy3ykqw4l_lZKiUWSUFPRZpkZajYUfZLBaQLVhKzxdI,772
 biomechzoo/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biomechzoo/__main__.py,sha256=hSMHN1Rxn2367fSGTLHoOQ4_pocZw0IWI7HFxl-74oY,88
-biomechzoo/biomechzoo.py,sha256=EBh92xNnkYtQan1Q2vS2lnleoMUVEwoDJxw0YPD4FYA,21353
+biomechzoo/biomechzoo.py,sha256=Dma-eZNCud0pSD-OjNkAVlMrynOCysCQwUQXMS3GcQk,22572
 biomechzoo/biomech_ops/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biomechzoo/biomech_ops/continuous_relative_phase_data.py,sha256=RePbt6zyOI1iv74CWhxSrunIokTFYVfFmFnoW51781E,1300
 biomechzoo/biomech_ops/continuous_relative_phase_line.py,sha256=Fa1LFRuPlmGPLQLvln6HVnJy3zMSm9z5YeooHmTu0lc,1365
 biomechzoo/biomech_ops/filter_data.py,sha256=Q9knW23Ft_WeWVCBjaIQ5GkKU0NYV4SdGiDZV8Fm-hM,1805
 biomechzoo/biomech_ops/filter_line.py,sha256=XKUdRsxU5AO1gSldnwp3qNzsUUL8qpOpAMyQbEMo5uI,2600
+biomechzoo/biomech_ops/movement_onset.py,sha256=qKeNiVTDra_0wjjPTLfP_Gtoyz5cbHD2F_EDxOxo1oQ,1961
 biomechzoo/biomech_ops/normalize_data.py,sha256=ESdXeUkKdd0WpjP6FW2EYrOAd7NKWkX1JWUNn1SzDB4,1335
 biomechzoo/biomech_ops/normalize_line.py,sha256=KUE8gEkIolA-VDFCdUuaskk-waO8jjJ20ZMZaS8Qha8,854
 biomechzoo/biomech_ops/phase_angle_data.py,sha256=_ekUBW2v3iC4UawcDL38ZZLYJmQsAmyqA61Q6_AMtmQ,1435
@@ -16,6 +17,7 @@ biomechzoo/conversion/c3d2zoo_data.py,sha256=28JCj1Jpn7zsv2HjQdzH2F30jnGMwzmbBwY
 biomechzoo/conversion/mvnx2zoo_data.py,sha256=uMAZ4pNSSZ7NToW1WnawrXeVP8D-xE3dNDnooPvALE4,3545
 biomechzoo/conversion/opencap2zoo_data.py,sha256=n4bLsrJI0wTSzG5bgJcmxj1dp2plnUKFNRzcTIbmV1o,608
 biomechzoo/conversion/table2zoo_data.py,sha256=rAP7OrKbVrb50NHJ6h8fgoMntV87-t9wT2xQ30AD96I,3330
+biomechzoo/imu/tilt_algorithm.py,sha256=PYVErXHeY-Wgi0aXCQxDodohTDzirRXo8BEW3_Pskqo,4312
 biomechzoo/mvn/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biomechzoo/mvn/load_mvnx.py,sha256=B4VGuidQ-5G_5E1t5vpU51Nb_Lu85_EOS_FmGZYjfX8,22499
 biomechzoo/mvn/main_mvnx.py,sha256=e1LasJQ9icyzjWnRCEcAWQq_-L13-mIzf7PzYA3QYDg,2394
@@ -24,7 +26,7 @@ biomechzoo/mvn/mvnx_file_accessor.py,sha256=Gk2vKq9v_gPbnOS_12zgeJehjFz7v3ClTnN2
 biomechzoo/processing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biomechzoo/processing/add_channel_data.py,sha256=U1xLLBSnyJeeDWzgmHSxOz1hyguzuuDXxQCQ8IFoZkw,1955
 biomechzoo/processing/addchannel_data.py,sha256=rmnnlMRVkoMlQCR-nRg1jjh-hzMDt37Sx9fAmocrpqA,1953
-biomechzoo/processing/addevent_data.py,sha256=T1l7u7cOuILO0mAk3Oac5FjOxH6VBKHHgXUgr8cnCTk,3282
+biomechzoo/processing/addevent_data.py,sha256=GGzXSGNNpZFTEMh0l3awqeBf5jHaCdV84K2Nwjuhqkk,3955
 biomechzoo/processing/explodechannel_data.py,sha256=ceyXfcCmeNqj4p0zCksVdrnmsYR4t-JHLIyv3JlfNpU,2484
 biomechzoo/processing/partition_data.py,sha256=4wuKrnMmRMNobymYwZ0WuRvNGsvkhThZ2ZhoSkkhntg,1741
 biomechzoo/processing/removechannel_data.py,sha256=uO7jjuHapRr2CGLsrvYQ1eJLvb1y_8KR6Ct4M6TPALA,1740
@@ -45,9 +47,9 @@ biomechzoo/utils/version.py,sha256=JIXDUuOcaJiZv9ruMP6PtWvJBh4sP0D5kAvlqPiZK_I,1
 biomechzoo/utils/zload.py,sha256=_qmbQpiEwUNRcB86aS6dHiytOrz1ZXJVjYkk8h5fg8s,2039
 biomechzoo/utils/zplot.py,sha256=WVA8aCy1Pqy_bo_HXab9AmW-cBd8J8MPX2LAOd6dznU,1512
 biomechzoo/utils/zsave.py,sha256=wnRNuDxQc8bwCji4UrfoGjYrSZmka4eaDxQ5rMa78pE,1759
-biomechzoo-0.5.0.dist-info/licenses/LICENSE,sha256=Fsz62nrgRORre3A1wNXUDISaHoostodMvocRPDdXc9w,1076
-biomechzoo-0.5.0.dist-info/METADATA,sha256=GuXAmEs9sQ2uVq0SzUirvtKWzmWTGC-t6DMNKxWgkiI,1579
-biomechzoo-0.5.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-biomechzoo-0.5.0.dist-info/entry_points.txt,sha256=VdryUUiwwvx0WZxrgmMrsyfe5Z1jtyaxdXOi0zWHOqk,41
-biomechzoo-0.5.0.dist-info/top_level.txt,sha256=nJEtuEZ9UPoN3EOR-BJ6myevEu7B5quWsWhaM_YeQpw,20
-biomechzoo-0.5.0.dist-info/RECORD,,
+biomechzoo-0.5.2.dist-info/licenses/LICENSE,sha256=Fsz62nrgRORre3A1wNXUDISaHoostodMvocRPDdXc9w,1076
+biomechzoo-0.5.2.dist-info/METADATA,sha256=_2N7nddOIeDuoVCCXsD8aEggf84O21RBstPq4h3k7pM,1579
+biomechzoo-0.5.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+biomechzoo-0.5.2.dist-info/entry_points.txt,sha256=VdryUUiwwvx0WZxrgmMrsyfe5Z1jtyaxdXOi0zWHOqk,41
+biomechzoo-0.5.2.dist-info/top_level.txt,sha256=nJEtuEZ9UPoN3EOR-BJ6myevEu7B5quWsWhaM_YeQpw,20
+biomechzoo-0.5.2.dist-info/RECORD,,