biomechzoo 0.4.10__py3-none-any.whl → 0.5.0__py3-none-any.whl

biomechzoo/biomech_ops/filter_data.py

@@ -13,10 +13,10 @@ def filter_data(data, ch, filt=None):
         The name(s) of the channel(s) to filter.
     filt : dict, optional
         Dictionary specifying filter parameters. Keys may include:
-        - 'type': 'butter' (default)
+        - 'ftype': 'butter' (default)
         - 'order': filter order (default: 4)
         - 'cutoff': cutoff frequency or tuple (Hz)
-        - 'btype': 'low', 'high', 'bandpass', 'bandstop' (default: 'low')
+        - 'btype': 'low', 'high', 'bandpass', 'bandstop' (default: 'lowpass')
 
     Returns
     -------
@@ -25,32 +25,34 @@ def filter_data(data, ch, filt=None):
     """
 
     if filt is None:
-        filt = {}
+        filt = {'ftype': 'butter',
+                'order': 4,
+                'cutoff': 10,
+                'btype': 'lowpass',
+                'filtfilt': True}
 
     if isinstance(ch, str):
         ch = [ch]
 
-    analog_channels = data['zoosystem']['Analog']['Channels']
-    if analog_channels:
-        analog_freq = data['zoosystem']['Analog']['Freq']
-    video_channels = data['zoosystem']['Video']['Channels']
-    if video_channels:
-        video_freq = data['zoosystem']['Video']['Freq']
-
+    # loop through all channels and filter
     for c in ch:
         if c not in data:
             raise KeyError('Channel {} not found in data'.format(c))
 
         if 'fs' not in filt:
+
+            video_channels = data['zoosystem']['Video']['Channels']
+            analog_channels = data['zoosystem']['Analog']['Channels']
+
             if c in analog_channels:
-                filt['fs'] = analog_freq
-            elif c in video_freq:
-                filt['fs'] = video_freq
+                filt['fs'] = data['zoosystem']['Analog']['Freq']
+            elif c in video_channels:
+                filt['fs'] =  data['zoosystem']['Video']['Freq']
             else:
-                raise ValueError('frequency not provided and cannot be inferred from zoosystem for channel'.format(c))
+                raise ValueError('Channel not analog or video')
 
         signal_raw = data[c]['line']
-        signal_filtered = filter_line(signal_raw, filt)
+        signal_filtered = filter_line(signal_raw=signal_raw, filt=filt)
         data[c]['line'] = signal_filtered
 
     return data

biomechzoo/biomech_ops/filter_line.py

@@ -1,88 +1,85 @@
 import numpy as np
-from scipy.signal import butter, filtfilt
+import scipy.signal as sgl
 
 
-def filter_line(signal_raw, filt):
-    """ filter an array
+def filter_line(signal_raw, filt=None, fs=None):
+    """Filter an array using a Butterworth filter."""
+    #todo: verify that filter is working correctly
+    #todo add more filters
+    #todo: consider using kineticstoolkit
 
-    Arguments
-    ----------
-    signal_raw : n, or n x 3 array signal to be filtered
-    filt : dict, optional
-        Dictionary specifying filter parameters. Keys may include:
-        - 'type': 'butter' (default)
-        - 'order': filter order (default: 4)
-        - 'cutoff': cutoff frequency or tuple (Hz)
-        - 'btype': 'low', 'high', 'bandpass', 'bandstop' (default: 'low')
-        - 'fs' frequency
-
-    Returns
-    -------
-    signal_filtered: filtered version of signal_raw"""
-    # todo allow for missing frequency to be obtained from zoosystem metadata
     if filt is None:
-        filt = {}
-    if filt['type'] is 'butterworth':
-        filt['type'] = 'butter'
-    # Set default filter parameters
-    ftype = filt.get('type', 'butter')
-    order = filt.get('order', 4)
-    cutoff = filt.get('cutoff', None)
-    btype = filt.get('btype', 'low')
-    fs = filt.get('fs', None)
-
-    if ftype != 'butter':
-        raise NotImplementedError(f"Filter type '{ftype}' not implemented.")
-
-    if fs is None:
-        raise ValueError("Sampling frequency 'fs' must be specified in filt.")
-
-    if cutoff is None:
-        raise ValueError("Cutoff frequency 'cutoff' must be specified in filt.")
+        filt = {'ftype': 'butter',
+                'order': 4,
+                'cutoff': 10,
+                'btype': 'lowpass',
+                'filtfilt': True}
+        if fs is None:
+            raise ValueError('fs is required if no filt is specified')
 
+    else:
+        if 'fs' not in filt:
+            raise ValueError('fs is a required key of filt')
+
+    # Normalize filter type strings
+    if filt['ftype'] == 'butterworth':
+        filt['ftype'] = 'butter'
+    if filt['btype'] is 'low':
+        filt['btype'] = 'lowpass'
+    if filt['btype'] is 'high':
+        filt['btype'] = 'highpass'
+
+    # Extract parameters
+    ftype = filt['ftype']
+    order = filt['order']
+    cutoff = filt['cutoff']
+    btype = filt['btype']
+    filtfilt = filt['filtfilt']
+    fs = filt['fs']
+
+    # prepare normalized cutoff(s)
     nyq = 0.5 * fs
-    norm_cutoff = np.array(cutoff) / nyq
-
-    b, a = butter(order, norm_cutoff, btype=btype, analog=False)
+    norm_cutoff = np.atleast_1d(np.array(cutoff) / nyq)
 
-    if signal_raw.ndim == 1:
-        signal_filtered = filtfilt(b, a, signal_raw)
+    if ftype is 'butter':
+        signal_filtered = kt_butter(ts=signal_raw, fc=norm_cutoff, fs=fs, order=order, btype=btype, filtfilt=filtfilt)
     else:
-        # Apply filter to each column if multivariate
-        signal_filtered = np.array([filtfilt(b, a, signal_raw[:, i]) for i in range(signal_raw.shape[1])]).T
+        raise NotImplementedError(f"Filter type '{ftype}' not implemented.")
 
     return signal_filtered
 
 
-if __name__ == '__main__':
-    """ -------TESTING--------"""
-    import os
-    import matplotlib.pyplot as plt
-    from src.biomechzoo.utils.zload import zload
-    current_dir = os.path.dirname(os.path.abspath(__file__))
-    project_root = os.path.dirname(current_dir)
-    fl = os.path.join(project_root, 'data', 'other', 'HC030A05.zoo')
-    data = zload(fl)
-    data = data['data']
-    signal_raw = data['ForceFz1']['line']
-    filt = {'type': 'butterworth',
-            'order': 3,
-            'cutoff': 20,
-            'btype': 'low',
-            'fs': data['zoosystem']['Analog']['Freq']
-            }
-    signal_filtered = filter_line(signal_raw, filt)
-
-    # now plot
-    plt.figure(figsize=(10, 4))
-    plt.plot(signal_raw, label='Raw', alpha=0.6)
-    plt.plot(signal_filtered, label='Filtered', linewidth=2)
-    plt.xlabel('Frame')
-    plt.ylabel('Amplitude')
-    plt.title('Testing filter_line')
-    plt.legend()
-    plt.grid(True)
-    plt.tight_layout()
-    plt.show()
+def kt_butter(ts, fc, fs, order=2, btype='lowpass', filtfilt=True):
+    """
+    Apply a Butterworth filter to data.
+
+    Parameters
+    ----------
+    ts, ndarray, 1d.
+    fc, Cut-off frequency in Hz. This is a float for single-frequency filters
+        (lowpass, highpass), or a tuple of two floats (e.g., (10., 13.)
+        for two-frequency filters (bandpass, bandstop)).
+    order, Optional. Order of the filter. Default is 2.
+    btype, Optional. Can be either "lowpass", "highpass", "bandpass" or
+        "bandstop". Default is "lowpass".
+    filtfilt, Optional. If True, the filter is applied two times in reverse direction
+        to eliminate time lag. If False, the filter is applied only in forward
+        direction. Default is True.
+
+    Returns
+    -------
+    ts_f,  A copy of the input data which each data being filtered.
+    
+    Notes: 
+    - This code was adapted from kineticstoolkit Thanks @felxi
+    """
+
+    sos = sgl.butter(order, fc, btype, analog=False, output="sos", fs=fs)
 
+    # Filter
+    if filtfilt:
+        ts_f = sgl.sosfiltfilt(sos, ts, axis=0)
+    else:
+        ts_f = sgl.sosfilt(sos,ts, axis=0)
 
+    return ts_f

biomechzoo/biomech_ops/normalize_data.py

@@ -1,4 +1,5 @@
 import warnings
+import copy
 from biomechzoo.biomech_ops.normalize_line import normalize_line
 
 
@@ -14,14 +15,14 @@ def normalize_data(data, nlength=101):
     """
 
     # normalize channel length
-    data_new = data.copy()
+    data_new = copy.deepcopy(data)
     for ch_name, ch_data in data_new.items():
         if ch_name != 'zoosystem':
             ch_data_line = ch_data['line']
             ch_data_event = ch_data['event']
             ch_data_normalized = normalize_line(ch_data_line, nlength)
-    data_new[ch_name]['line'] = ch_data_normalized
-    data_new[ch_name]['event'] = ch_data_event
+            data_new[ch_name]['line'] = ch_data_normalized
+            data_new[ch_name]['event'] = ch_data_event
     warnings.warn('event data have not been normalized')
 
     # update zoosystem

biomechzoo/biomechzoo.py

@@ -12,6 +12,7 @@ from biomechzoo.conversion.table2zoo_data import table2zoo_data
 from biomechzoo.conversion.mvnx2zoo_data import mvnx2zoo_data
 from biomechzoo.processing.removechannel_data import removechannel_data
 from biomechzoo.processing.renamechannel_data import renamechannel_data
+from biomechzoo.processing.removeevent_data import removeevent_data
 from biomechzoo.processing.explodechannel_data import explodechannel_data
 from biomechzoo.processing.addevent_data import addevent_data
 from biomechzoo.processing.partition_data import partition_data
@@ -19,6 +20,7 @@ from biomechzoo.processing.renameevent_data import renameevent_data
 from biomechzoo.biomech_ops.normalize_data import normalize_data
 from biomechzoo.biomech_ops.phase_angle_data import phase_angle_data
 from biomechzoo.biomech_ops.continuous_relative_phase_data import continuous_relative_phase_data
+from biomechzoo.biomech_ops.filter_data import filter_data
 
 class BiomechZoo:
     def __init__(self, in_folder, inplace=False, subfolders=None, name_contains=None, verbose=0):
@@ -61,6 +63,8 @@ class BiomechZoo:
             in_folder_path = os.path.dirname(in_folder)
             self.in_folder = os.path.join(in_folder_path, out_folder)
 
+        batchdisp('all files saved to: {}'.format(self.in_folder ), level=1, verbose=self.verbose)
+
     def mvnx2zoo(self, out_folder=None, inplace=False):
         """ Converts all .mvnx files in the folder to .zoo format """
         start_time = time.time()
@@ -75,7 +79,7 @@ class BiomechZoo:
             f_zoo = f.replace('.mvnx', '.zoo')
             zsave(f_zoo, data, inplace=inplace, out_folder=out_folder, root_folder=in_folder)
         method_name = inspect.currentframe().f_code.co_name
-        batchdisp('{} conversion complete for {} files'.format(method_name, len(fl)), level=1, verbose=verbose)
+        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)
 
@@ -99,17 +103,21 @@ class BiomechZoo:
         # Update self.folder after  processing
         self._update_folder(out_folder, inplace, in_folder)
 
-    def table2zoo(self, out_folder=None, inplace=None, skip_rows=0, extension='csv'):
+    def table2zoo(self, extension, out_folder=None, inplace=None, skip_rows=0, freq=None):
         """ Converts generic .csv file in the folder to .zoo format """
         start_time = time.time()
         verbose = self.verbose
         in_folder = self.in_folder
+
+        if extension.startswith('.'):
+            extension = extension[1:]
+
         if inplace is None:
             inplace = self.inplace
         fl = engine(in_folder, extension=extension, name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
             batchdisp('converting {} to zoo for {}'.format(extension, f), level=2, verbose=verbose)
-            data = table2zoo_data(f, type=extension, skip_rows=skip_rows)
+            data = table2zoo_data(f, extension=extension, skip_rows=skip_rows, freq=freq)
             f_zoo = f.replace(extension, '.zoo')
             zsave(f_zoo, data, inplace=inplace, out_folder=out_folder, root_folder=in_folder)
         method_name = inspect.currentframe().f_code.co_name
@@ -118,8 +126,13 @@ class BiomechZoo:
         self._update_folder(out_folder, inplace, in_folder)
 
     def xls2zoo(self, out_folder=None, inplace=None):
-        """ Converts generic .xls file in the folder to .zoo format """
-        raise NotImplementedError
+        raise NotImplementedError('Use table2zoo instead')
+
+    def csv2zoo(self, out_folder=None, inplace=None):
+        raise NotImplementedError('Use table2zoo instead')
+
+    def parquet2zoo(self, out_folder=None, inplace=None):
+        raise NotImplementedError('Use table2zoo instead')
 
     def phase_angle(self, ch, out_folder=None, inplace=None):
         """ computes phase angles"""
@@ -184,7 +197,8 @@ class BiomechZoo:
                     batchdisp('splitting by gait cycle from {} to {} for {}'.format(start, end, f), level=2,
                               verbose=verbose)
                     data_new = split_trial(data, start, end)
-                    zsave(fl_new, data_new, inplace=inplace, out_folder=out_folder, root_folder=in_folder)
+                    if data_new is not None:
+                        zsave(fl_new, data_new, 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)
 
@@ -266,6 +280,27 @@ class BiomechZoo:
         # Update self.folder after  processing
         self._update_folder(out_folder, inplace, in_folder)
 
+
+    def removeevent(self, events, mode='remove', out_folder=None, inplace=None):
+        """ removes channels from zoo files """
+        start_time = time.time()
+        verbose = self.verbose
+        in_folder = self.in_folder
+        if inplace is None:
+            inplace = self.inplace
+        fl = engine(in_folder, extension='.zoo', name_contains=self.name_contains, subfolders=self.subfolders)
+        for f in fl:
+            batchdisp('removing events {} for {}'.format(events, f), level=2, verbose=verbose)
+            data = zload(f)
+            data = removeevent_data(data, events, mode)
+            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 explodechannel(self, out_folder=None, inplace=None):
         """ explodes all channels in a zoo file """
         start_time = time.time()
@@ -306,7 +341,7 @@ class BiomechZoo:
         # Update self.folder after  processing
         self._update_folder(out_folder, inplace, in_folder)
 
-    def addevent(self, ch, event_type, event_name, out_folder=None, inplace=None):
+    def addevent(self, ch, event_type, event_name, out_folder=None, inplace=None, constant=None):
         """ adds events of type evt_type with name evt_name to channel ch """
         start_time = time.time()
         verbose = self.verbose
@@ -318,7 +353,7 @@ class BiomechZoo:
             if verbose:
                 batchdisp('adding event {} to channel {} for {}'.format(event_type, ch, f), level=2, verbose=verbose)
             data = zload(f)
-            data = addevent_data(data, ch, event_type, event_name)
+            data = addevent_data(data, ch, event_type, event_name, constant)
             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)
@@ -346,28 +381,22 @@ class BiomechZoo:
         self._update_folder(out_folder, inplace, in_folder)
 
     def filter(self, ch, filt=None, out_folder=None, inplace=None):
-        raise NotImplementedError
-        # verbose = self.verbose
-        # in_folder = self.in_folder
-        # if inplace is None:
-        #     inplace = self.inplace
-        #
-        # # set filter type
-        # if filt is None:
-        #     filt = {'type': 'butterworth',
-        #             'order': 3,
-        #             'pass': 'lowpass'}
-        #
-        # fl = engine(in_folder)
-        # for f in fl:
-        #     batchdisp('filtering data in channels {} for {}'.format(ch, f), level=2, verbose=verbose)
-        #     data = zload(f)
-        #     data = filter_data(data, ch, filt)
-        #     zsave(f, data, inplace=inplace, root_folder=in_folder, out_folder=out_folder, verbose=verbose)
-        # method_name = inspect.currentframe().f_code.co_name
-        # batchdisp('{} computation complete for {} file(s)'.format(method_name, len(fl)), level=1, verbose=verbose)
-        #
-        # # Update self.folder after  processing
-        # self._update_folder(out_folder, inplace, in_folder)
-
+        """ filter 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:
+            if verbose:
+                batchdisp('filtering data for channel {} in {}'.format(ch, f), level=2, verbose=verbose)
+            data = zload(f)
+            data = filter_data(data, ch, filt)
+            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)
 

biomechzoo/conversion/c3d2zoo_data.py

@@ -8,10 +8,14 @@ def c3d2zoo_data(c3d_obj):
     - data (dict): Zoo dictionary with 'line' and 'event' fields per channel.
     """
     data = {}
-
+    data['zoosystem'] = set_zoosystem()
+    video_freq = None
+    analog_freq = None
+    # extract "video" data
     if 'points' in c3d_obj['data']:
         points = c3d_obj['data']['points']  # shape: (4, n_markers, n_frames)
-        labels = c3d_obj['parameters']['POINT']['LABELS']['value']
+        labels = list(c3d_obj['parameters']['POINT']['LABELS']['value'])
+        video_freq = int(c3d_obj['parameters']['POINT']['RATE']['value'][0])
         for i, label in enumerate(labels):
             line_data = points[:3, i, :].T  # shape: (frames, 3)
             data[label] = {
@@ -19,9 +23,32 @@ def c3d2zoo_data(c3d_obj):
                 'event': {}  # empty for now
             }
 
-        params = c3d_obj['parameters']
-        video_freq = c3d_obj['parameters']['POINT']['RATE']['value'][0]
-        if 'EVENT' in params and 'TIMES' in params['EVENT']:
+        data['zoosystem']['Video']['Freq'] = video_freq
+        data['zoosystem']['Video']['Channels'] = labels
+
+    if 'analogs' in c3d_obj['data']:
+        analog_data = c3d_obj['data']['analogs']  # shape: (subframes, n_analog_channels, n_frames)
+        analog_labels = list(c3d_obj['parameters']['ANALOG']['LABELS']['value'])
+        analog_freq = int(c3d_obj['parameters']['ANALOG']['RATE']['value'][0])
+        # Flatten to 2D: (n_samples, n_channels)
+        # ezc3d stores analogs as subframes per frame, so we flatten across all
+        n_subframes, n_channels, n_frames = analog_data.shape
+        analog_data = analog_data.reshape(n_subframes * n_frames, n_channels)
+
+        for i, label in enumerate(analog_labels):
+            line_data = analog_data[:, i].reshape(-1, 1)  # shape: (samples, 1)
+            data[label] = {
+                'line': line_data,
+                'event': {},
+            }
+
+        data['zoosystem']['Analog']['Freq'] = analog_freq
+        data['zoosystem']['Analog']['Channels'] = analog_labels
+
+    # extract event information
+    params = c3d_obj['parameters']
+    if 'EVENT' in params and 'TIMES' in params['EVENT']:
+        if 'points' in c3d_obj['data']:
             times_array = params['EVENT']['TIMES']['value']
             frames = times_array[1]  # should be time depending on C3D file
 
@@ -61,8 +88,8 @@ def c3d2zoo_data(c3d_obj):
                     else:
                         data[labels[0]]['event'][key_name] = [frame-1, 0, 0]    # remove 1 to follow python
 
-    # todo add relevant meta data to zoosystem
-    data['zoosystem'] = set_zoosystem()
-    data['zoosystem']['Analog']['Freq'] = int(params['ANALOG']['RATE']['value'][0])
+    # add more zoosystem
+    if analog_freq is not None and video_freq is not None:
+        data['zoosystem']['AVR'] = analog_freq/video_freq
 
     return data

biomechzoo/conversion/mvnx2zoo_data.py

@@ -9,8 +9,7 @@ def mvnx2zoo_data(fl):
     mvnx_file = load_mvnx(fl)
 
     # create zoo data dict
-    data = {}
-
+    data = {'zoosystem': set_zoosystem()}
     # extract joint angle data (All JOINTS may not exist in a given dataset)
     for key, val in JOINTS.items():
         try:
@@ -58,7 +57,6 @@ def is_valid_for_zoo(val):
 
 def _get_meta_info(fl, mvnx_file, data):
     # todo: add more, see mvnx_file object
-    data['zoosystem'] = set_zoosystem(fl)
     data['zoosystem']['Video']['Freq'] = int(mvnx_file.frame_rate)
     data['zoosystem']['mvnx_version'] = mvnx_file.version
     data['zoosystem']['mvnx_configuration'] = mvnx_file.configuration

biomechzoo/conversion/table2zoo_data.py

@@ -6,42 +6,59 @@ from biomechzoo.utils.set_zoosystem import set_zoosystem
 from biomechzoo.utils.compute_sampling_rate_from_time import compute_sampling_rate_from_time
 
 
-def table2zoo_data(csv_path, type='csv', skip_rows=0, freq=None):
-    # todo: check calculation for sampling rate
+def table2zoo_data(fl, extension, skip_rows=0, freq=None):
 
-    if type not in ['csv', 'parquet']:
-        raise NotImplementedError('Only csv and parquet currently supported')
+    if extension == 'csv':
+        df, metadata, freq = _csv2zoo(fl, skip_rows=skip_rows, freq=freq)
 
-    # Read header lines until 'endheader'
-    metadata = {}
-    if type == 'csv' and skip_rows > 0:
-        header_lines = []
-        with open(csv_path, 'r') as f:
-            for line in f:
-                header_lines.append(line.strip())
-                if line.strip().lower() == 'endheader':
-                    break
-        # Parse metadata
-        metadata = _parse_metadata(header_lines)
-
-    if type == 'csv':
-        df = pd.read_csv(csv_path, skiprows=skip_rows)
-    elif type =='parquet':
-        df = pd.read_parquet(csv_path)
+    elif extension == 'parquet':
+        df, metadata, freq = _parquet2zoo(fl, skip_rows=skip_rows, freq=freq)
     else:
-        raise ValueError('type must be csv or parquet')
-
-    # Use all columns
-    data = df.iloc[:, 0:]
+        raise ValueError('extension {} not implemented'.format(extension))
 
     # assemble zoo data
-    zoo_data = {}
-    for ch in data.columns:
-        zoo_data[ch] = {
-            'line': data[ch].values,
+    data = {'zoosystem': set_zoosystem()}
+    for ch in df.columns:
+        data[ch] = {
+            'line': df[ch].values,
             'event': []
         }
 
+
+    # now try to calculate freq from a time column
+    if freq is None:
+        time_col = [col for col in df.columns if 'time' in col.lower()]
+        if time_col is not None and len(time_col) > 0:
+            time_data = df[time_col].to_numpy()[:, 0]
+            freq = compute_sampling_rate_from_time(time_data)
+        else:
+            raise ValueError('Unable to compute sampling rate for time column, please specify a sampling frequency'
+                             )
+    # add metadata
+    data['zoosystem']['Video']['Freq'] = freq
+    data['zoosystem']['Analog']['Freq'] = 'None'
+
+    if metadata is not None:
+        data['zoosystem']['Other'] = metadata
+
+    return data
+
+
+def _parquet2zoo(fl, skip_rows=0, freq=None):
+    df = pd.read_parquet(fl)
+    metadata = None
+    return df, metadata, freq
+
+def _csv2zoo(fl, skip_rows=0, freq=None):
+    header_lines = []
+    with open(fl, 'r') as f:
+        for line in f:
+            header_lines.append(line.strip())
+            if line.strip().lower() == 'endheader':
+                break
+    # Parse metadata
+    metadata = _parse_metadata(header_lines)
+
     # try to find frequency in metadata
     if freq is None:
         if 'freq' in metadata:
@@ -51,22 +68,12 @@ def table2zoo_data(csv_path, type='csv', skip_rows=0, freq=None):
         else:
             freq = None  # or raise an error
 
-    # now try to calculate freq from a time column
-    if freq is None:
-        time_col = [col for col in df.columns if 'time' in col.lower()]
-        if time_col is not None:
-            time_data = df[time_col].to_numpy()[:, 0]
-            freq = compute_sampling_rate_from_time(time_data)
+    # read csv
+    df = pd.read_csv(fl, skiprows=skip_rows)
+
+    return df, metadata, freq
 
-    # add metadata
-    # todo update zoosystem to match biomechzoo requirements
-    zoo_data['zoosystem'] = set_zoosystem(csv_path)
-    zoo_data['zoosystem']['Video']['Freq'] = freq
-    zoo_data['zoosystem']['Analog']['Freq'] = 'None'
-    if 'version' in metadata:
-        zoo_data['zoosystem']['collection_system_version'] = metadata['version']
 
-    return zoo_data
 
 
 def _parse_metadata(header_lines):
@@ -96,6 +103,8 @@ def _parse_metadata(header_lines):
     return metadata
 
 
+
+
 if __name__ == '__main__':
     """ for unit testing"""
     current_dir = os.path.dirname(os.path.abspath(__file__))

biomechzoo/processing/addevent_data.py

@@ -1,23 +1,27 @@
 import numpy as np
+import copy
+import warnings
+from biomechzoo.utils.peak_sign import peak_sign
 
+def addevent_data(data, channels, ename, etype, constant=None):
 
-def addevent_data(data, ch, ename, etype):
-    if isinstance(ch, str):
-        ch = [ch]
+    data_new = copy.deepcopy(data)
 
-    if len(ch) == 1 and ch[0].lower() == 'all':
-        ch = [key for key in data if key != 'zoosystem']
+    if isinstance(channels, str):
+        channels = [channels]
 
-    for channel in ch:
+    if len(channels) == 1 and channels[0].lower() == 'all':
+        channels = [key for key in data if key != 'zoosystem']
+
+    for channel in channels:
         if ename == '':
             data[channel]['event'] = {}
             continue
 
         if channel not in data:
-            print(f'Channel {channel} does not exist')
-            continue
+            raise KeyError('Channel {} does not exist'.format(channel))
 
-        yd = data[channel]['line']  # 1D array
+        yd = data_new[channel]['line']  # 1D array
         etype = etype.lower()
         if etype == 'absmax':
             exd = int(np.argmax(np.abs(yd)))
@@ -42,13 +46,51 @@ def addevent_data(data, ch, ename, etype):
             exd = max_stance(yd)
             eyd = float(yd[exd])
             eyd = float(yd[exd])
+        elif etype in ['fs_fp', 'fo_fp']:
+            # --- Handle constant ---
+            if constant is None:
+                print('Warning: Force plate threshold not set, defaulting to 0.')
+                constant = 0.0
+
+            # --- Check sampling rates ---
+            AVR = data['zoosystem']['AVR']
+            if AVR != 1:
+                warnings.warn('Video and Analog channels must be at the same sampling rate or events will be incorrect.')
+
+            # --- Handle units ---
+            units = data['zoosystem']['Units']['Forces']
+            if units == 'N/kg':
+                m = data['zoosystem']['Anthro']['Bodymass']
+            else:
+                m = 1.0
+
+            # --- Extract force signal ---
+            if '_' not in channel:
+                yd = data_new[channel]['line'][:, 2]  # looking for GRF Z
+            else:
+                yd = data_new[channel]['line']
+
+            # --- Determine peak sign ---
+            peak = peak_sign(yd)  # user-defined function
+
+            # --- Find threshold crossing ---
+            threshold_signal = peak * yd * m
+            if 'fs' in etype:
+                exd_array = np.where(threshold_signal > constant)[0]
+                exd = exd_array[0] - 1  # MATLAB indexing correction
+                eyd = yd[exd]
+            else:  # 'FO' type
+                exd_array = np.where(threshold_signal > constant)[0]
+                exd = exd_array[-1] + 1
+                eyd = yd[exd]
+
         else:
             raise ValueError(f'Unknown event type: {etype}')
 
         # Add event to the channel's event dict
-        data[channel]['event'][ename] = [exd, eyd, 0]
+        data_new[channel]['event'][ename] = [exd, eyd, 0]
 
-    return data
+    return data_new
 
 def max_stance(yd):
     """ extracts max from first 40% of the gait cycle"""

biomechzoo/processing/explodechannel_data.py

@@ -1,4 +1,5 @@
 import copy
+import numpy as np
 
 def explodechannel_data(data, channels=None):
     """ Explodes 3D channels (n x 3 arrays) into separate X, Y, Z channels.
@@ -6,13 +7,23 @@ def explodechannel_data(data, channels=None):
     Arguments:
         data (dict): Zoo data loaded from a file
         channels (list of str or None): Channels to explode.
-        If None, explode all channels with 'line' shaped (n x 3).
+            If None, explode all channels with 'line' shaped (n x 3).
 
     Returns:
         data_new (dict): Modified zoo dictionary with exploded channels.
     """
-
     data_new = copy.deepcopy(data)
+
+    # Ensure zoosystem channel lists are Python lists
+    for sys in ['Video', 'Analog']:
+        if sys in data_new.get('zoosystem', {}):
+            ch_list = data_new['zoosystem'][sys].get('Channels', [])
+            if isinstance(ch_list, np.ndarray):
+                ch_list = ch_list.tolist()
+            # strip whitespace
+            ch_list = [str(ch).strip() for ch in ch_list]
+            data_new['zoosystem'][sys]['Channels'] = ch_list
+
     # Find default channels if none provided
     if channels is None:
         channels = []
@@ -39,9 +50,20 @@ def explodechannel_data(data, channels=None):
             key = ch + axis
             data_new[key] = {
                 'line': line,
-                'event': data[ch]['event']}
+                'event': data_new[ch]['event']}
 
         # Remove original channel
         del data_new[ch]
 
+        # --- Update zoosystem lists ---
+        for sys in ['Video', 'Analog']:
+            if sys in data_new['zoosystem']:
+                ch_list = data_new['zoosystem'][sys]['Channels']
+                if ch in ch_list:
+                    # Remove original channel
+                    ch_list = [c for c in ch_list if c != ch]
+                    # Add exploded channels
+                    ch_list.extend([ch + '_x', ch + '_y', ch + '_z'])
+                    data_new['zoosystem'][sys]['Channels'] = ch_list
+
     return data_new

biomechzoo/processing/partition_data.py

@@ -1,6 +1,7 @@
 from biomechzoo.utils.findfield import findfield
 import warnings
 import copy
+import numpy as np
 
 
 def partition_data(data, evt_start, evt_end):
@@ -13,16 +14,19 @@ def partition_data(data, evt_start, evt_end):
     if e1 is None or e2 is None or len(e1) == 0 or len(e2) == 0:
         raise ValueError(f"Event not found: evt_start='{evt_start}' returned {e1}, evt_end='{evt_end}' returned {e2}")
 
+    # convert to int and get first value
+    e1 = int(e1[0])
+    e2 = int(e2[0])
+
     data_new = copy.deepcopy(data)
-    for ch_name, ch_data in data_new.items():
+    for ch_name, ch_data in sorted(data_new.items()):
         if ch_name != 'zoosystem':
-            print(ch_name)
-            line = ch_data['line']
+            r = ch_data['line']
             try:
-                if line.ndim == 1:
-                    data_new[ch_name]['line'] = line[e1[0]:e2[0]]
+                if r.ndim == 1:
+                    data_new[ch_name]['line'] = r[e1:e2]
                 else:
-                    data_new[ch_name]['line'] = line[e1[0]:e2[0], :]
+                    data_new[ch_name]['line'] = r[e1:e2, :]
             except (IndexError, ValueError) as e:
                 # IndexError: if e1[0]:e2[0] goes beyond the available indices
                 # ValueError: less likely, but may arise with shape mismatches
@@ -31,29 +35,12 @@ def partition_data(data, evt_start, evt_end):
             # partition events
             events = ch_data['event']
             for event_name, value in events.items():
-                original_frame = value[0]
+                original_frame = int(value[0])
                 if original_frame == 999:
                     continue  # do not change outlier markers
                 else:
-                    new_frame = original_frame - e1[0] + 1
-                    print(new_frame)
-                    data_new[ch_name]['event'][event_name][0] = new_frame
+                    arr = np.array(data_new[ch_name]['event'][event_name], dtype=np.int32)
+                    arr[0] = original_frame - e1
+                    data_new[ch_name]['event'][event_name] = arr
 
     return data_new
-
-
-def _partition_line(arr, evt_start, evt_end):
-    arr_new = arr[evt_start:evt_end, :]
-    return arr_new
-
-
-def _partition_event(event_dict, evt_start, evt_end, arr_len):
-    raise NotImplementedError
-    # event_dict_new = {}
-    # for event, event_val in event_dict:
-    #     event_val_new =
-    #     event_dict_new[event] =
-    #
-    #
-    #
-    # return event_dict_new

biomechzoo/processing/removechannel_data.py

@@ -13,7 +13,6 @@ def removechannel_data(data, channels, mode='remove'):
     if mode not in ['remove', 'keep']:
         raise ValueError("mode must be 'remove' or 'keep'.")
 
-    zoosystem = data.get('zoosystem', {})
     all_channels = [ch for ch in data if ch != 'zoosystem']
 
     # Check for missing channels
@@ -28,9 +27,20 @@ def removechannel_data(data, channels, mode='remove'):
     else:
         raise ValueError("Mode must be 'remove' or 'keep'.")
 
-    # Build new zoo dictionary
-    data_new = {'zoosystem': zoosystem}
-    for ch in keep_channels:
-        data_new[ch] = data[ch]
+    # --- Compute channels to remove ---
+    remove_channels = [ch for ch in all_channels if ch not in keep_channels]
 
-    return data_new
+    if remove_channels:
+        print('Removing channels: {}'.format(remove_channels))
+    else:
+        print('No channels to remove')
+
+    # Remove from main data dict ---
+    for ch in remove_channels:
+        data.pop(ch, None)
+        if ch in data['zoosystem']['Video']['Channels']:
+            data['zoosystem']['Video']['Channels'] = [c for c in data['zoosystem']['Video']['Channels'] if c != ch]
+        if ch in data['zoosystem']['Analog']['Channels']:
+            data['zoosystem']['Analog']['Channels'] = [c for c in data['zoosystem']['Analog']['Channels'] if c != ch]
+
+    return data

biomechzoo/processing/removeevent_data.py

@@ -0,0 +1,57 @@
+import copy
+import warnings
+from biomechzoo.utils.findfield import findfield
+
+def removeevent_data(data, events, mode='remove'):
+    """
+    Remove or keep specified events in all channels of a zoo dictionary.
+
+    Parameters
+    ----------
+    data : dict
+        Zoo data loaded from a file
+    events : list of str
+        Events to remove or keep
+    mode : str
+        'remove' or 'keep'
+
+    Returns
+    -------
+    dict
+        Modified zoo dictionary with events removed or kept
+    """
+    if mode not in ['remove', 'keep']:
+        raise ValueError("mode must be 'remove' or 'keep'.")
+
+    if isinstance(events, str):
+        events = [events]
+
+    # check if any events are not present
+    valid_events = []
+    for evt in events:
+        e, _ = findfield(data, evt)
+        if e is None:
+            warnings.warn('Could not find event {} in zoo file, skipping'.format(evt))
+        else:
+            valid_events.append(evt)
+    events = valid_events
+
+    data_new = copy.deepcopy(data)
+    channels = sorted([ch for ch in data_new if ch != 'zoosystem'])
+    for ch in channels:
+        event_dict = data_new[ch].get('event', {})
+        events_to_remove = []
+
+        for evt in list(event_dict.keys()):
+            if mode == 'remove' and evt in events:
+                events_to_remove.append(evt)
+            elif mode == 'keep' and evt not in events:
+                events_to_remove.append(evt)
+
+        for evt in events_to_remove:
+            event_dict.pop(evt, None)
+            # print('Removed event "{}" from channel "{}"'.format(evt, ch))
+
+        data_new[ch]['event'] = event_dict
+
+    return data_new

biomechzoo/processing/renameevent_data.py

@@ -28,17 +28,11 @@ def renameevent_data(data, evt, nevt):
     # Get all data channels except 'zoosystem'
     channels = [ch for ch in data if ch != 'zoosystem']
     for old_name, new_name in zip(evt, nevt):
-        eventsRenamed = False
         for ch in channels:
             events = data[ch].get('event', {})
             if old_name in events:
-                print('Renaming event {} in channel {} to {}'.format(old_name, ch, new_name))
                 data[ch]['event'][new_name] = events[old_name]
                 del data[ch]['event'][old_name]
-                eventsRenamed = True
-
-        if not eventsRenamed:
-            print('no event {} found in any channel'.format(old_name))
 
     return data
 

biomechzoo/utils/engine.py

@@ -1,4 +1,5 @@
 import os
+import numpy as np
 
 
 def engine(root_folder, extension='.zoo', subfolders=None, name_contains=None, verbose=False):
@@ -66,10 +67,13 @@ def engine(root_folder, extension='.zoo', subfolders=None, name_contains=None, v
                     continue
             matched_files.append(full_path)
 
+    # sort list
+    matched_files = np.sort(matched_files)
+
     if verbose:
-        print("Found {} {} files in subfolders named {} with substring {}:".format(len(matched_files), extension, subfolders, name_contains))
+        print("Found {} {} files in subfolder(s) named {} with substring {}:".format(len(matched_files), extension, subfolders, name_contains))
         for f in matched_files:
-            print(" - {}".format(f))
+            print('{}'.format(f))
 
     return matched_files
 
@@ -79,6 +83,6 @@ if __name__ == '__main__':
     with extension .c3d in the sample study folder (data)"""
     # -------TESTING--------
     current_dir = os.path.dirname(os.path.abspath(__file__))
-    project_root = os.path.dirname(current_dir)
+    project_root = os.path.dirname(os.path.dirname(os.path.dirname(current_dir)))
     sample_dir = os.path.join(project_root, 'data', 'sample_study', 'raw c3d files')
     c3d_files = engine(sample_dir, '.c3d', subfolders=['Straight'], name_contains='HC03', verbose=True)

biomechzoo/utils/peak_sign.py

@@ -0,0 +1,24 @@
+import numpy as np
+
+def peak_sign(r):
+    """
+    Determine whether the largest absolute peak in the signal is positive or negative.
+
+    Parameters
+    ----------
+    r : array-like
+        Signal vector.
+
+    Returns
+    -------
+    sign : int
+        1 if the maximum peak is positive, -1 if negative.
+    """
+    r = np.asarray(r)
+    max_val = np.max(r)
+    min_val = np.min(r)
+
+    if abs(max_val) > abs(min_val):
+        return 1
+    else:
+        return -1

biomechzoo/utils/split_trial.py

@@ -1,23 +1,35 @@
-def split_trial(data, start_event_indx, end_event_indx):
+import copy
+from biomechzoo.utils.findfield import findfield
+
+
+def split_trial(data, start_event, end_event):
     # todo check index problem compared to matlab start at 0 or 1
-    data_new = data.copy()
+    data_new = copy.deepcopy(data)
+
+    start_event_indx, _ = findfield(data_new, start_event)
+    end_event_indx, _ = findfield(data_new, end_event)
 
     for key, value in data_new.items():
         if key == 'zoosystem':
             continue
 
         # Slice the line data
-        data_new[key]['line'] = value['line'][start_event_indx:end_event_indx]
+        trial_length = len(data_new[key]['line'])
+        if trial_length > end_event_indx[0]:
+            data_new[key]['line'] = value['line'][start_event_indx[0]:end_event_indx[0]]
+        else:
+            print('skipping split trial since event is outside range of data')
+            return None
 
         # Update events if present
-        if 'event' in value:
-            new_events = {}
-            for evt_name, evt_val in value['event'].items():
-                event_frame = evt_val[0]
-                # Check if event falls within the new window
-                if start_event_indx <= event_frame < end_event_indx:
-                    # Adjust index relative to new start
-                    new_events[evt_name] = [event_frame - start_event_indx, 0, 0]
-            data_new[key]['event'] = new_events
+        # if 'event' in value:
+        #     new_events = {}
+        #     for evt_name, evt_val in value['event'].items():
+        #         event_frame = evt_val[0]
+        #         # Check if event falls within the new window
+        #         if start_event_indx <= event_frame < end_event_indx:
+        #             # Adjust index relative to new start
+        #             new_events[evt_name] = [event_frame - start_event_indx, 0, 0]
+        #     data_new[key]['event'] = new_events
 
     return data_new

biomechzoo/utils/zload.py

@@ -1,5 +1,6 @@
 from scipy.io import loadmat
 import os
+import numpy as np
 
 
 def zload(filepath):
@@ -29,6 +30,16 @@ def zload(filepath):
     if 'data' in data:
         data = data['data']
 
+    # Convert Video and Analog channel arrays to Python lists
+    for sys in ['Video', 'Analog']:
+        if 'zoosystem' in data and sys in data['zoosystem']:
+            channels = data['zoosystem'][sys].get('Channels', [])
+            # Convert to list and strip spaces
+            if isinstance(channels, np.ndarray):
+                channels = channels.tolist()
+            channels = [str(ch).strip() for ch in channels]
+            data['zoosystem'][sys]['Channels'] = channels
+
     return data
 
 

{biomechzoo-0.4.10.dist-info → biomechzoo-0.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.4.10
+Version: 0.5.0
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo

{biomechzoo-0.4.10.dist-info → biomechzoo-0.5.0.dist-info}/RECORD

@@ -1,21 +1,21 @@
 __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=A60kTUaMVWaKl-4ZUZpW8pOKLiZLEpbPYvHZe6urd5w,19800
+biomechzoo/biomechzoo.py,sha256=EBh92xNnkYtQan1Q2vS2lnleoMUVEwoDJxw0YPD4FYA,21353
 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=LZSlemUfbBTrqbo7miFubgTf9R4pr1kEgdmvljmNWdQ,1742
-biomechzoo/biomech_ops/filter_line.py,sha256=BuUFALIkmdFhmVocFaZ3aczy_efh2CY_qX9-5CoQZr0,2716
-biomechzoo/biomech_ops/normalize_data.py,sha256=gpoUh6EpxpCprBdrSjmZ4UsAWgonJgD41XUJWD8Yo9Y,1299
+biomechzoo/biomech_ops/filter_data.py,sha256=Q9knW23Ft_WeWVCBjaIQ5GkKU0NYV4SdGiDZV8Fm-hM,1805
+biomechzoo/biomech_ops/filter_line.py,sha256=XKUdRsxU5AO1gSldnwp3qNzsUUL8qpOpAMyQbEMo5uI,2600
+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
 biomechzoo/biomech_ops/phase_angle_line.py,sha256=p6osB17_3QQSyKLNojuc6nYhv-k0K6EUUH75EXu8ifc,1391
 biomechzoo/conversion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biomechzoo/conversion/c3d2zoo_data.py,sha256=gnSCw99Hg5JLdrGezZNVZ6EHqiD6i-mpsLRtWmEa-Mg,2855
-biomechzoo/conversion/mvnx2zoo_data.py,sha256=O6WuKe_5fZJfd1gUe3oP9rND_i5P4WGEuu2MDvI3ypY,3560
+biomechzoo/conversion/c3d2zoo_data.py,sha256=28JCj1Jpn7zsv2HjQdzH2F30jnGMwzmbBwYuRoWPJHo,4052
+biomechzoo/conversion/mvnx2zoo_data.py,sha256=uMAZ4pNSSZ7NToW1WnawrXeVP8D-xE3dNDnooPvALE4,3545
 biomechzoo/conversion/opencap2zoo_data.py,sha256=n4bLsrJI0wTSzG5bgJcmxj1dp2plnUKFNRzcTIbmV1o,608
-biomechzoo/conversion/table2zoo_data.py,sha256=OLiRlYB8GqOwv4MAlmwhIkGLxgAvmrgUjTb-Irev4lU,3297
+biomechzoo/conversion/table2zoo_data.py,sha256=rAP7OrKbVrb50NHJ6h8fgoMntV87-t9wT2xQ30AD96I,3330
 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
@@ -24,28 +24,30 @@ 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
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-biomechzoo/processing/explodechannel_data.py,sha256=AC2BOEw1tXcgJ1WuYWSE-yToS-q9XGdgkOHS4D3iUFo,1490
-biomechzoo/processing/partition_data.py,sha256=XF8dSqvHGpqsT-Q4i6qpoOajAT4LYjP-PJ6KbpoCfFc,2018
-biomechzoo/processing/removechannel_data.py,sha256=ndZcbWJRDvd7drlahGaq8MseT-rsxiu7pgdMtA1cTlo,1218
+biomechzoo/processing/addevent_data.py,sha256=T1l7u7cOuILO0mAk3Oac5FjOxH6VBKHHgXUgr8cnCTk,3282
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 biomechzoo/processing/renamechannel_data.py,sha256=5lEnWJknAwnJYXDlwO6cFe7C8ct5o42tTHW0Y4GeIL4,2210
-biomechzoo/processing/renameevent_data.py,sha256=9w7C_fQOsQ8XbdTr_hrg_iQe51oDczq2Rj7yJLyYG0M,2215
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 biomechzoo/processing/split_trial_by_gait_cycle.py,sha256=maMUwumSlFLFc5LHdNdBO9JCoT06aaLbpdp43dgowDA,1684
 biomechzoo/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biomechzoo/utils/batchdisp.py,sha256=Ke7yeZ4cYQvyf8bmgsiLaRElUeQm49TYIYzAcPWan9s,839
 biomechzoo/utils/compute_sampling_rate_from_time.py,sha256=iyHbN734vYe5bXEoAsHScJN7Qw--2quUgII7judSQDk,579
-biomechzoo/utils/engine.py,sha256=D91ZhevBnoWml_NztZP-1lzFoANy5TyIAnJg0FFZyUc,3859
+biomechzoo/utils/engine.py,sha256=tatGMBbgIe8DIHx2_z_JQwA9TJYCeVYqyWiKiMoRHw4,3971
 biomechzoo/utils/findfield.py,sha256=i7ewGQOMIiTC06tYFK-JctehHLCippkY9FoXIygx14w,381
 biomechzoo/utils/get_split_events.py,sha256=xNhEuG6Yqsr1bjWIBHLbepfX-fcqcCYIXZzS3eaDDHQ,911
+biomechzoo/utils/peak_sign.py,sha256=4XNqVIrAmpLw9C9RmWwIKkI1rluBTzeCXJE4-AHCzC4,465
 biomechzoo/utils/set_zoosystem.py,sha256=oubEc3fy0x6y-AlqQWL3v7QYJA951jU9CRnlJ9ikwQo,1750
-biomechzoo/utils/split_trial.py,sha256=Fumz_ZukNBNtPauUhCge5EAHkg05dYDhA1_njQw0lHE,886
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 biomechzoo/utils/version.py,sha256=JIXDUuOcaJiZv9ruMP6PtWvJBh4sP0D5kAvlqPiZK_I,130
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 biomechzoo/utils/zplot.py,sha256=WVA8aCy1Pqy_bo_HXab9AmW-cBd8J8MPX2LAOd6dznU,1512
 biomechzoo/utils/zsave.py,sha256=wnRNuDxQc8bwCji4UrfoGjYrSZmka4eaDxQ5rMa78pE,1759
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