biomechzoo 0.4.11__py3-none-any.whl → 0.5.1__py3-none-any.whl

biomechzoo/biomech_ops/movement_onset.py

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

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

@@ -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
@@ -12,6 +14,7 @@ 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
@@ -62,6 +65,8 @@ 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()
@@ -76,7 +81,7 @@ 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)
 
@@ -100,17 +105,21 @@ 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
@@ -119,8 +128,33 @@ 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 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"""
@@ -185,7 +219,8 @@ 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)
 
@@ -267,6 +302,27 @@ 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()
@@ -307,7 +363,7 @@ 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
@@ -319,7 +375,7 @@ 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)

biomechzoo/conversion/mvnx2zoo_data.py

@@ -9,9 +9,7 @@ def mvnx2zoo_data(fl):
     mvnx_file = load_mvnx(fl)
 
     # create zoo data dict
-    data = {}
-    data['zoosystem'] = set_zoosystem()
-
+    data = {'zoosystem': set_zoosystem()}
     # extract joint angle data (All JOINTS may not exist in a given dataset)
     for key, val in JOINTS.items():
         try:

biomechzoo/conversion/table2zoo_data.py

@@ -6,69 +6,76 @@ 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
-    df_data = df.iloc[:, 0:]
+        raise ValueError('extension {} not implemented'.format(extension))
 
     # assemble zoo data
-    data = {}
-    data['zoosystem'] = set_zoosystem()
-
-    for ch in df_data.columns:
+    data = {'zoosystem': set_zoosystem()}
+    for ch in df.columns:
         data[ch] = {
-            'line': df_data[ch].values,
+            'line': df[ch].values,
             'event': []
         }
 
-    # try to find frequency in metadata
-    if freq is None:
-        if 'freq' in metadata:
-            freq = metadata['freq']
-        elif 'sampling_rate' in metadata:
-            freq = metadata['sampling_rate']
-        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:
+        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 'version' in metadata:
-        data['zoosystem']['collection_system_version'] = metadata['version']
+
+    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:
+            freq = metadata['freq']
+        elif 'sampling_rate' in metadata:
+            freq = metadata['sampling_rate']
+        else:
+            freq = None  # or raise an error
+
+    # read csv
+    df = pd.read_csv(fl, skiprows=skip_rows)
+
+    return df, metadata, freq
+
+
+
+
 def _parse_metadata(header_lines):
     metadata = {}
     for line in 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/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/processing/addevent_data.py

@@ -1,23 +1,28 @@
 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):
 
-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 +47,57 @@ def addevent_data(data, ch, ename, etype):
             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:
+                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/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/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-0.4.11.dist-info → biomechzoo-0.5.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.4.11
+Version: 0.5.1
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo

{biomechzoo-0.4.11.dist-info → biomechzoo-0.5.1.dist-info}/RECORD

@@ -1,21 +1,23 @@
 __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=N2qqUJrSvWueB6TEOJjONdqGjy1pv1PmNXA177mvjGs,19772
+biomechzoo/biomechzoo.py,sha256=3PviTE-zv0TVp3pYayL2ZrMopj5LJtcSLjwxEsGMtxw,22515
 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/normalize_data.py,sha256=gpoUh6EpxpCprBdrSjmZ4UsAWgonJgD41XUJWD8Yo9Y,1299
+biomechzoo/biomech_ops/movement_onset.py,sha256=3VAoOp01P08BKMaOZW3CwbMdoSMOufDaoMkWeYRcPmo,51
+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=28JCj1Jpn7zsv2HjQdzH2F30jnGMwzmbBwYuRoWPJHo,4052
-biomechzoo/conversion/mvnx2zoo_data.py,sha256=fZBFFYHuTC0gsH4tjB0S8yszVtc5Ki7KosKN68-zTkU,3558
+biomechzoo/conversion/mvnx2zoo_data.py,sha256=uMAZ4pNSSZ7NToW1WnawrXeVP8D-xE3dNDnooPvALE4,3545
 biomechzoo/conversion/opencap2zoo_data.py,sha256=n4bLsrJI0wTSzG5bgJcmxj1dp2plnUKFNRzcTIbmV1o,608
-biomechzoo/conversion/table2zoo_data.py,sha256=H_r6RNt_MGwkOr4JH-M844DT_ivScQx_byc6DIZa5go,3210
+biomechzoo/conversion/table2zoo_data.py,sha256=rAP7OrKbVrb50NHJ6h8fgoMntV87-t9wT2xQ30AD96I,3330
+biomechzoo/imu/tilt_algoirthm.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
@@ -24,28 +26,30 @@ 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
-biomechzoo/processing/addevent_data.py,sha256=L9xaoP0yBvaGbseotxpGCVqjr-eSV-gpnQaeRTz4VKE,1631
+biomechzoo/processing/addevent_data.py,sha256=Z7vsHqhsn8byw4d9atinjGpvglwj6tu38uqZfXVvluQ,3573
 biomechzoo/processing/explodechannel_data.py,sha256=ceyXfcCmeNqj4p0zCksVdrnmsYR4t-JHLIyv3JlfNpU,2484
-biomechzoo/processing/partition_data.py,sha256=XF8dSqvHGpqsT-Q4i6qpoOajAT4LYjP-PJ6KbpoCfFc,2018
+biomechzoo/processing/partition_data.py,sha256=4wuKrnMmRMNobymYwZ0WuRvNGsvkhThZ2ZhoSkkhntg,1741
 biomechzoo/processing/removechannel_data.py,sha256=uO7jjuHapRr2CGLsrvYQ1eJLvb1y_8KR6Ct4M6TPALA,1740
+biomechzoo/processing/removeevent_data.py,sha256=DC1vBIwuo_mk5Oz0UGLK7Nx3BVqAeVDfT29XgUM_1Rc,1631
 biomechzoo/processing/renamechannel_data.py,sha256=5lEnWJknAwnJYXDlwO6cFe7C8ct5o42tTHW0Y4GeIL4,2210
-biomechzoo/processing/renameevent_data.py,sha256=9w7C_fQOsQ8XbdTr_hrg_iQe51oDczq2Rj7yJLyYG0M,2215
+biomechzoo/processing/renameevent_data.py,sha256=PRGHEs-t9qJMzDY1DCNgQz_h-aAOIII4ryQeCYBXwGo,1952
 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
+biomechzoo/utils/split_trial.py,sha256=0SNpKKkRoizRe9MCuMrQ6Ev6O5V51rN0D-e8FGlLlo4,1302
 biomechzoo/utils/version.py,sha256=JIXDUuOcaJiZv9ruMP6PtWvJBh4sP0D5kAvlqPiZK_I,130
 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-0.4.11.dist-info/licenses/LICENSE,sha256=Fsz62nrgRORre3A1wNXUDISaHoostodMvocRPDdXc9w,1076
-biomechzoo-0.4.11.dist-info/METADATA,sha256=IAMgsVbJdayIURX7FwWfT5XNsBy4JfvOnqbTu-jlbYE,1580
-biomechzoo-0.4.11.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-biomechzoo-0.4.11.dist-info/entry_points.txt,sha256=VdryUUiwwvx0WZxrgmMrsyfe5Z1jtyaxdXOi0zWHOqk,41
-biomechzoo-0.4.11.dist-info/top_level.txt,sha256=nJEtuEZ9UPoN3EOR-BJ6myevEu7B5quWsWhaM_YeQpw,20
-biomechzoo-0.4.11.dist-info/RECORD,,
+biomechzoo-0.5.1.dist-info/licenses/LICENSE,sha256=Fsz62nrgRORre3A1wNXUDISaHoostodMvocRPDdXc9w,1076
+biomechzoo-0.5.1.dist-info/METADATA,sha256=Jp2p2d6SsnirRpmQjUb91GyEX9sY5fRGG4jfVqRvwPA,1579
+biomechzoo-0.5.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+biomechzoo-0.5.1.dist-info/entry_points.txt,sha256=VdryUUiwwvx0WZxrgmMrsyfe5Z1jtyaxdXOi0zWHOqk,41
+biomechzoo-0.5.1.dist-info/top_level.txt,sha256=nJEtuEZ9UPoN3EOR-BJ6myevEu7B5quWsWhaM_YeQpw,20
+biomechzoo-0.5.1.dist-info/RECORD,,