biomechzoo 0.4.7__tar.gz → 0.4.9__tar.gz

{biomechzoo-0.4.7/src/biomechzoo.egg-info → biomechzoo-0.4.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.4.7
+Version: 0.4.9
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo

{biomechzoo-0.4.7 → biomechzoo-0.4.9}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "biomechzoo"
-version = "0.4.7"
+version = "0.4.9"
 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-0.4.7 → biomechzoo-0.4.9}/src/biomechzoo/biomechzoo.py

@@ -8,7 +8,7 @@ from biomechzoo.utils.batchdisp import batchdisp
 from biomechzoo.utils.get_split_events import get_split_events
 from biomechzoo.utils.split_trial import split_trial
 from biomechzoo.conversion.c3d2zoo_data import c3d2zoo_data
-from biomechzoo.conversion.csv2zoo_data import csv2zoo_data
+from biomechzoo.conversion.table2zoo 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
@@ -99,36 +99,18 @@ class BiomechZoo:
         # Update self.folder after  processing
         self._update_folder(out_folder, inplace, in_folder)
 
-    def csv2zoo(self, out_folder=None, inplace=None, skip_rows=0):
+    def table2zoo(self, out_folder=None, inplace=None, skip_rows=0, extension='csv'):
         """ Converts generic .csv file in the folder to .zoo format """
         start_time = time.time()
         verbose = self.verbose
         in_folder = self.in_folder
         if inplace is None:
             inplace = self.inplace
-        fl = engine(in_folder, extension='.csv', name_contains=self.name_contains, subfolders=self.subfolders)
+        fl = engine(in_folder, extension=extension, name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
-            batchdisp('converting csv to zoo for {}'.format(f), level=2, verbose=verbose)
-            data = csv2zoo_data(f, type='csv', skip_rows=skip_rows)
-            f_zoo = f.replace('.csv', '.zoo')
-            zsave(f_zoo, 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 parquet2zoo(self, out_folder=None, inplace=None):
-        """ Converts generic .csv file in the folder to .zoo format """
-        start_time = time.time()
-        verbose = self.verbose
-        in_folder = self.in_folder
-        if inplace is None:
-            inplace = self.inplace
-        fl = engine(in_folder, extension='.parquet', name_contains=self.name_contains, subfolders=self.subfolders)
-        for f in fl:
-            batchdisp('converting parquet to zoo for {}'.format(f), level=2, verbose=verbose)
-            data = csv2zoo_data(f, type='parquet')
-            f_zoo = f.replace('.parquet', '.zoo')
+            batchdisp('converting {} to zoo for {}'.format(extension, f), level=2, verbose=verbose)
+            data = table2zoo_data(f, type=extension, skip_rows=skip_rows)
+            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
         batchdisp('{} process complete for {} file(s) in {:.2f} secs'.format(method_name, len(fl), time.time() - start_time), level=1, verbose=verbose)

{biomechzoo-0.4.7 → biomechzoo-0.4.9}/src/biomechzoo/conversion/c3d2zoo_data.py

@@ -1,3 +1,5 @@
+from biomechzoo.utils.set_zoosystem import set_zoosystem
+
 def c3d2zoo_data(c3d_obj):
     """
     Converts an ezc3d C3D object to zoo format.
@@ -21,7 +23,7 @@ def c3d2zoo_data(c3d_obj):
         video_freq = c3d_obj['parameters']['POINT']['RATE']['value'][0]
         if 'EVENT' in params and 'TIMES' in params['EVENT']:
             times_array = params['EVENT']['TIMES']['value']
-            frames = times_array[1]  # second row = frames (or time, depending on C3D file)
+            frames = times_array[1]  # should be time depending on C3D file
 
             # Extract sides, types, subjects
             contexts = params['EVENT']['CONTEXTS']['value'] if 'CONTEXTS' in params['EVENT'] else ['']
@@ -55,11 +57,12 @@ def c3d2zoo_data(c3d_obj):
 
                     # Place in correct channel
                     if 'SACR' in data:
-                        data['SACR']['event'][key_name] = [frame, 0, 0]
+                        data['SACR']['event'][key_name] = [frame-1, 0, 0]       # remove 1 to follow python
                     else:
-                        data[labels[0]]['event'][key_name] = [frame, 0, 0]
+                        data[labels[0]]['event'][key_name] = [frame-1, 0, 0]    # remove 1 to follow python
 
     # todo add relevant meta data to zoosystem
-    data['zoosystem'] = params['EVENT']
+    data['zoosystem'] = set_zoosystem()
+    data['zoosystem']['Analog']['Freq'] = int(params['ANALOG']['RATE']['value'][0])
 
     return data

{biomechzoo-0.4.7 → biomechzoo-0.4.9}/src/biomechzoo/conversion/mvnx2zoo_data.py

@@ -1,6 +1,7 @@
 import numpy as np
 from biomechzoo.mvn.load_mvnx import load_mvnx
 from biomechzoo.mvn.mvn import JOINTS, SEGMENTS
+from biomechzoo.utils.set_zoosystem import set_zoosystem
 
 def mvnx2zoo_data(fl):
     """ loads mvnx file from xsens"""
@@ -37,10 +38,11 @@ def mvnx2zoo_data(fl):
     data = _get_foot_strike_events(mvnx_file, data)
 
     # add meta information
-    data = _get_meta_info(mvnx_file, data)
+    data = _get_meta_info(fl, mvnx_file, data)
 
     return data
 
+
 def is_valid_for_zoo(val):
     """
     Returns True if the value is valid for a MATLAB-compatible zoo structure.
@@ -53,13 +55,13 @@ def is_valid_for_zoo(val):
         return False
     return True
 
-def _get_meta_info(mvnx_file, data):
+
+def _get_meta_info(fl, mvnx_file, data):
     # todo: add more, see mvnx_file object
-    data['zoosystem'] = {}
-    data['zoosystem']['Video'] = {}
+    data['zoosystem'] = set_zoosystem(fl)
     data['zoosystem']['Video']['Freq'] = int(mvnx_file.frame_rate)
-    data['zoosystem']['Version'] = mvnx_file.version
-    data['zoosystem']['configuration'] = mvnx_file.configuration
+    data['zoosystem']['mvnx_version'] = mvnx_file.version
+    data['zoosystem']['mvnx_configuration'] = mvnx_file.configuration
     data['zoosystem']['recording_date'] = mvnx_file.recording_date
     data['zoosystem']['original_file_name'] = mvnx_file.original_file_name
     data['zoosystem']['frame_count'] = mvnx_file.frame_count

biomechzoo-0.4.7/src/biomechzoo/conversion/csv2zoo_data.py → biomechzoo-0.4.9/src/biomechzoo/conversion/table2zoo_data.py

@@ -2,12 +2,16 @@ import pandas as pd
 import os
 import re
 
+from biomechzoo.utils.set_zoosystem import set_zoosystem
 from biomechzoo.utils.compute_sampling_rate_from_time import compute_sampling_rate_from_time
 
 
-def csv2zoo_data(csv_path, type='csv',skip_rows=0, freq=None):
+def table2zoo_data(csv_path, type='csv', skip_rows=0, freq=None):
     # todo: check calculation for sampling rate
 
+    if type not in ['csv', 'parquet']:
+        raise NotImplementedError('Only csv and parquet currently supported')
+
     # Read header lines until 'endheader'
     metadata = {}
     if type == 'csv' and skip_rows > 0:
@@ -51,13 +55,16 @@ def csv2zoo_data(csv_path, type='csv',skip_rows=0, freq=None):
     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]
+            time_data = df[time_col].to_numpy()[:, 0]
             freq = compute_sampling_rate_from_time(time_data)
 
     # add metadata
     # todo update zoosystem to match biomechzoo requirements
-    zoo_data['zoosystem'] = metadata
-    zoo_data['zoosystem']['Freq'] = freq
+    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
 
@@ -95,4 +102,4 @@ if __name__ == '__main__':
     project_root = os.path.dirname(current_dir)
     csv_file = os.path.join(project_root, 'data', 'other', 'opencap_walking1.csv')
 
-    data = csv2zoo_data(csv_file)
+    data = table2zoo_data(csv_file)

{biomechzoo-0.4.7 → biomechzoo-0.4.9}/src/biomechzoo/processing/partition_data.py

@@ -10,12 +10,16 @@ def partition_data(data, evt_start, evt_end):
     e1, _ = findfield(data, evt_start)
     e2, _ = findfield(data, 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}")
+
     data_new = copy.deepcopy(data)
     for ch_name, ch_data in data_new.items():
         if ch_name != 'zoosystem':
+            print(ch_name)
             line = ch_data['line']
             try:
-                if line.ndim ==1:
+                if line.ndim == 1:
                     data_new[ch_name]['line'] = line[e1[0]:e2[0]]
                 else:
                     data_new[ch_name]['line'] = line[e1[0]:e2[0], :]
@@ -28,9 +32,7 @@ def partition_data(data, evt_start, evt_end):
             events = ch_data['event']
             for event_name, value in events.items():
                 original_frame = value[0]
-                if original_frame == 1:
-                    continue  # leave index 1 as is (per MATLAB version)
-                elif original_frame == 999:
+                if original_frame == 999:
                     continue  # do not change outlier markers
                 else:
                     new_frame = original_frame - e1[0] + 1

{biomechzoo-0.4.7 → biomechzoo-0.4.9}/src/biomechzoo/utils/engine.py

@@ -22,7 +22,7 @@ def engine(root_folder, extension='.zoo', subfolders=None, name_contains=None, v
         subfolders (list or str, optional): List of folder names to restrict the search to.
             Only files inside these folders (or their subfolders) are included.
             If None, search all subfolders.
-        name_contains (str, optional): Substring that must be present in the filename
+        name_contains (str, or list; optional): Substring that must be present in the filename
             (case-insensitive). If None, no substring filtering is applied.
         verbose (bool, optional): If true, displays additional information to user
     Returns:
@@ -33,10 +33,14 @@ def engine(root_folder, extension='.zoo', subfolders=None, name_contains=None, v
         if type(subfolders) is str:
             subfolders = [subfolders]
 
+    # check format of name_contants (str or list)
+    if name_contains is not None:
+        if type(name_contains) is str:
+            name_contains = [name_contains]
+
     matched_files = []
 
     subfolders_set = set(subfolders) if subfolders else None
-
     for dirpath, _, filenames in os.walk(root_folder):
         if subfolders_set is not None:
             rel_path = os.path.relpath(dirpath, root_folder)
@@ -51,9 +55,16 @@ def engine(root_folder, extension='.zoo', subfolders=None, name_contains=None, v
         for file in filenames:
             if not file.lower().endswith(extension.lower()):
                 continue
-            if name_contains and name_contains.lower() not in file.lower():
-                continue
-            matched_files.append(os.path.join(dirpath, file))
+            full_path = os.path.join(dirpath, file)
+            if name_contains is not None:
+                match = False
+                for name_contain in name_contains:
+                    if name_contain and name_contain.lower() in full_path.lower():  # <-- check full path
+                        match = True
+                        break
+                if not match:
+                    continue
+            matched_files.append(full_path)
 
     if verbose:
         print("Found {} {} files in subfolders named {} with substring {}:".format(len(matched_files), extension, subfolders, name_contains))

biomechzoo-0.4.9/src/biomechzoo/utils/set_zoosystem.py

@@ -0,0 +1,66 @@
+import numpy as np
+from pathlib import Path
+from biomechzoo.utils.version import get_biomechzoo_version
+
+
+def set_zoosystem(fl=None):
+    """
+    Create the 'zoosystem' branch for data being imported to BiomechZoo.
+
+    Args:
+        fl: str
+            Path to the source file (e.g., C3D or CSV).
+
+    Returns:
+        zoosystem: dict
+            Dictionary containing default BiomechZoo system parameters.
+    """
+
+    # Default top-level fields
+    zch = ['Analog', 'Anthro', 'AVR', 'CompInfo', 'SourceFile',
+           'Units', 'Version', 'Video']
+
+    # Initialize top-level dict
+    zoosystem = {key: {} for key in zch}
+
+    # Section-specific defaults
+    section = ['Video', 'Analog']
+    for sec in section:
+        zoosystem[sec]['Channels'] = []
+        zoosystem[sec]['Freq'] = []
+        zoosystem[sec]['Indx'] = []
+        zoosystem[sec]['ORIGINAL_START_FRAME'] = []
+        zoosystem[sec]['ORIGINAL_END_FRAME'] = []
+        zoosystem[sec]['CURRENT_START_FRAME'] = []
+        zoosystem[sec]['CURRENT_END_FRAME'] = []
+
+    # Processing and AVR defaults
+    zoosystem['Processing'] = ''
+    zoosystem['AVR'] = 0
+
+    # Force plates defaults
+    zoosystem['Analog']['FPlates'] = {
+        'CORNERS': [],
+        'NUMUSED': 0,
+        'LOCALORIGIN': [],
+        'LABELS': []
+    }
+
+    # Version and source file
+    zoosystem['Version'] = get_biomechzoo_version()
+    if fl is None:
+        zoosystem['SourceFile'] = 'None'  # ensure string
+    else:
+        zoosystem['SourceFile'] = str(Path(fl))  # ensure string
+
+    # Units defaults
+    zoosystem['Units'] = {
+        'Markers': 'mm',
+        'Angles': 'deg',
+        'Forces': 'N',
+        'Moments': 'Nmm',
+        'Power': 'W/kg',
+        'Scalars': 'mm'
+    }
+
+    return zoosystem

biomechzoo-0.4.9/src/biomechzoo/utils/version.py

@@ -0,0 +1,5 @@
+from importlib.metadata import version as get_version
+
+
+def get_biomechzoo_version() -> str:
+    return get_version("biomechzoo")

{biomechzoo-0.4.7 → biomechzoo-0.4.9/src/biomechzoo.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.4.7
+Version: 0.4.9
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo

{biomechzoo-0.4.7 → biomechzoo-0.4.9}/src/biomechzoo.egg-info/SOURCES.txt

@@ -22,9 +22,9 @@ src/biomechzoo/biomech_ops/phase_angle_data.py
 src/biomechzoo/biomech_ops/phase_angle_line.py
 src/biomechzoo/conversion/__init__.py
 src/biomechzoo/conversion/c3d2zoo_data.py
-src/biomechzoo/conversion/csv2zoo_data.py
 src/biomechzoo/conversion/mvnx2zoo_data.py
 src/biomechzoo/conversion/opencap2zoo_data.py
+src/biomechzoo/conversion/table2zoo_data.py
 src/biomechzoo/mvn/__init__.py
 src/biomechzoo/mvn/load_mvnx.py
 src/biomechzoo/mvn/main_mvnx.py
@@ -46,7 +46,9 @@ 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/set_zoosystem.py
 src/biomechzoo/utils/split_trial.py
+src/biomechzoo/utils/version.py
 src/biomechzoo/utils/zload.py
 src/biomechzoo/utils/zplot.py
 src/biomechzoo/utils/zsave.py