biomechzoo 0.5.1__tar.gz → 0.5.2__tar.gz

{biomechzoo-0.5.1/src/biomechzoo.egg-info → biomechzoo-0.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.5.1
+Version: 0.5.2
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo

{biomechzoo-0.5.1 → biomechzoo-0.5.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "biomechzoo"
-version = "0.5.1"
+version = "0.5.2"
 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-0.5.2/src/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-0.5.1 → biomechzoo-0.5.2}/src/biomechzoo/biomechzoo.py

@@ -2,7 +2,7 @@ import os
 import inspect
 import time
 
-from biomechzoo.imu.tilt_algoirthm import tilt_algorithm_data
+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
@@ -136,6 +136,8 @@ 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()

{biomechzoo-0.5.1 → biomechzoo-0.5.2}/src/biomechzoo/processing/addevent_data.py

@@ -1,6 +1,7 @@
 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
 
@@ -42,16 +43,16 @@ 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)
+            exd = movement_onset(yd, constant, etype=etype)
             eyd = yd[exd]
         elif etype == 'movement_offset':
-            exd = movement_onset(yd,constant)
+            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 ---
@@ -99,7 +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-0.5.1 → biomechzoo-0.5.2/src/biomechzoo.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.5.1
+Version: 0.5.2
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo

{biomechzoo-0.5.1 → biomechzoo-0.5.2}/src/biomechzoo.egg-info/SOURCES.txt

@@ -26,7 +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/imu/tilt_algorithm.py
 src/biomechzoo/mvn/__init__.py
 src/biomechzoo/mvn/load_mvnx.py
 src/biomechzoo/mvn/main_mvnx.py

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

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