biomechzoo 0.4.11__tar.gz → 0.5.0__tar.gz

{biomechzoo-0.4.11/src/biomechzoo.egg-info → biomechzoo-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.4.11
+Version: 0.5.0
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo

{biomechzoo-0.4.11 → biomechzoo-0.5.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "biomechzoo"
-version = "0.4.11"
+version = "0.5.0"
 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-0.4.11 → biomechzoo-0.5.0}/src/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-0.4.11 → biomechzoo-0.5.0}/src/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
@@ -62,6 +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()
@@ -76,7 +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)
 
@@ -100,17 +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
@@ -119,8 +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"""
@@ -185,7 +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)
 
@@ -267,6 +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()
@@ -307,7 +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
@@ -319,7 +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)

{biomechzoo-0.4.11 → biomechzoo-0.5.0}/src/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-0.4.11 → biomechzoo-0.5.0}/src/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-0.5.0/src/biomechzoo/processing/addevent_data.py

@@ -0,0 +1,98 @@
+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):
+
+    data_new = copy.deepcopy(data)
+
+    if isinstance(channels, str):
+        channels = [channels]
+
+    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:
+            raise KeyError('Channel {} does not exist'.format(channel))
+
+        yd = data_new[channel]['line']  # 1D array
+        etype = etype.lower()
+        if etype == 'absmax':
+            exd = int(np.argmax(np.abs(yd)))
+            eyd = float(yd[exd])
+        elif etype == 'first':
+            exd = 0
+            eyd = float(yd[exd])
+        elif etype == 'last':
+            exd = len(yd) - 1
+            eyd = float(yd[exd])
+        elif etype == 'max':
+            exd = int(np.argmax(yd))
+            eyd = float(yd[exd])
+        elif etype == 'min':
+            exd = int(np.argmin(yd))
+            eyd = float(yd[exd])
+        elif etype == 'rom':
+            eyd = float(np.max(yd) - np.min(yd))
+            exd = 0  # dummy index (like MATLAB version)
+        elif etype == 'max_stance':
+            # special event for gait and running
+            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_new[channel]['event'][ename] = [exd, eyd, 0]
+
+    return data_new
+
+def max_stance(yd):
+    """ extracts max from first 40% of the gait cycle"""
+    raise NotImplementedError
+    return exd

{biomechzoo-0.4.11 → biomechzoo-0.5.0}/src/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-0.5.0/src/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-0.4.11 → biomechzoo-0.5.0}/src/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-0.4.11 → biomechzoo-0.5.0}/src/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-0.5.0/src/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-0.5.0/src/biomechzoo/utils/split_trial.py

@@ -0,0 +1,35 @@
+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 = 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
+        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
+
+    return data_new

{biomechzoo-0.4.11 → biomechzoo-0.5.0/src/biomechzoo.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.4.11
+Version: 0.5.0
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo

{biomechzoo-0.4.11 → biomechzoo-0.5.0}/src/biomechzoo.egg-info/SOURCES.txt

@@ -37,6 +37,7 @@ src/biomechzoo/processing/addevent_data.py
 src/biomechzoo/processing/explodechannel_data.py
 src/biomechzoo/processing/partition_data.py
 src/biomechzoo/processing/removechannel_data.py
+src/biomechzoo/processing/removeevent_data.py
 src/biomechzoo/processing/renamechannel_data.py
 src/biomechzoo/processing/renameevent_data.py
 src/biomechzoo/processing/split_trial_by_gait_cycle.py
@@ -46,6 +47,7 @@ src/biomechzoo/utils/compute_sampling_rate_from_time.py
 src/biomechzoo/utils/engine.py
 src/biomechzoo/utils/findfield.py
 src/biomechzoo/utils/get_split_events.py
+src/biomechzoo/utils/peak_sign.py
 src/biomechzoo/utils/set_zoosystem.py
 src/biomechzoo/utils/split_trial.py
 src/biomechzoo/utils/version.py

biomechzoo-0.4.11/src/biomechzoo/processing/addevent_data.py

@@ -1,56 +0,0 @@
-import numpy as np
-
-
-def addevent_data(data, ch, ename, etype):
-    if isinstance(ch, str):
-        ch = [ch]
-
-    if len(ch) == 1 and ch[0].lower() == 'all':
-        ch = [key for key in data if key != 'zoosystem']
-
-    for channel in ch:
-        if ename == '':
-            data[channel]['event'] = {}
-            continue
-
-        if channel not in data:
-            print(f'Channel {channel} does not exist')
-            continue
-
-        yd = data[channel]['line']  # 1D array
-        etype = etype.lower()
-        if etype == 'absmax':
-            exd = int(np.argmax(np.abs(yd)))
-            eyd = float(yd[exd])
-        elif etype == 'first':
-            exd = 0
-            eyd = float(yd[exd])
-        elif etype == 'last':
-            exd = len(yd) - 1
-            eyd = float(yd[exd])
-        elif etype == 'max':
-            exd = int(np.argmax(yd))
-            eyd = float(yd[exd])
-        elif etype == 'min':
-            exd = int(np.argmin(yd))
-            eyd = float(yd[exd])
-        elif etype == 'rom':
-            eyd = float(np.max(yd) - np.min(yd))
-            exd = 0  # dummy index (like MATLAB version)
-        elif etype == 'max_stance':
-            # special event for gait and running
-            exd = max_stance(yd)
-            eyd = float(yd[exd])
-            eyd = float(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]
-
-    return data
-
-def max_stance(yd):
-    """ extracts max from first 40% of the gait cycle"""
-    raise NotImplementedError
-    return exd

biomechzoo-0.4.11/src/biomechzoo/utils/split_trial.py

@@ -1,23 +0,0 @@
-def split_trial(data, start_event_indx, end_event_indx):
-    # todo check index problem compared to matlab start at 0 or 1
-    data_new = data.copy()
-
-    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]
-
-        # 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
-
-    return data_new