biomechzoo 0.4.1__tar.gz → 0.4.5__tar.gz

{biomechzoo-0.4.1 → biomechzoo-0.4.5}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.4.1
+Version: 0.4.5
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo
-Requires-Python: >=3.11
+Requires-Python: <3.12,>=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: ezc3d>=1.5.19
@@ -12,6 +12,7 @@ Requires-Dist: matplotlib>=3.10.6
 Requires-Dist: numpy==2.2.6
 Requires-Dist: pandas>=2.3.2
 Requires-Dist: scipy>=1.16.2
+Requires-Dist: pyarrow>=19.0.0
 Dynamic: license-file
 
 # BiomechZoo for Python
@@ -30,3 +31,15 @@ This is a development version of the biomechzoo toolbox for python.
 - We use Numpy 2.2.6 for compatibility with https://pypi.org/project/numba/
 
 See also http://www.github.com/mcgillmotionlab/biomechzoo or http://www.biomechzoo.com for more information
+
+## Developer notes
+
+### Installing a dev environment
+conda create -n biomechzoo-dev python=3.11
+conda activate biomechzoo-dev
+pip install -e ".[dev]"
+
+### import issues
+if using PyCharm: 
+- Right-click on src/.
+- Select Mark Directory as → Sources Root.

{biomechzoo-0.4.1 → biomechzoo-0.4.5}/README.md

@@ -13,4 +13,16 @@ This is a development version of the biomechzoo toolbox for python.
 - We use Python 3.11 for compatibility with https://github.com/stanfordnmbl/opencap-processing
 - We use Numpy 2.2.6 for compatibility with https://pypi.org/project/numba/
 
-See also http://www.github.com/mcgillmotionlab/biomechzoo or http://www.biomechzoo.com for more information
+See also http://www.github.com/mcgillmotionlab/biomechzoo or http://www.biomechzoo.com for more information
+
+## Developer notes
+
+### Installing a dev environment
+conda create -n biomechzoo-dev python=3.11
+conda activate biomechzoo-dev
+pip install -e ".[dev]"
+
+### import issues
+if using PyCharm: 
+- Right-click on src/.
+- Select Mark Directory as → Sources Root.

{biomechzoo-0.4.1 → biomechzoo-0.4.5}/pyproject.toml

@@ -1,17 +1,18 @@
 [project]
 name = "biomechzoo"
-version = "0.4.1"
+version = "0.4.5"
 description = "Python implementation of the biomechZoo toolbox"
 readme = "README.md"
-requires-python = ">=3.11"
+requires-python = ">=3.11,<3.12"   # max version for opencap-process tools is 3.11
 license = "MIT"
 license-files = ["LICEN[CS]E*"]
 dependencies = [
-    "ezc3d>=1.5.19",
+    "ezc3d>=1.5.19",        # for reading c3d files
     "matplotlib>=3.10.6",
-    "numpy==2.2.6",
+    "numpy==2.2.6",         # max version for opencap-process tools
     "pandas>=2.3.2",
     "scipy>=1.16.2",
+    "pyarrow>=19.0.0",      # for parquet support
 ]
 
 [project.urls]

biomechzoo-0.4.5/src/__init__.py

@@ -0,0 +1,33 @@
+"""
+BiomechZoo: A Python toolbox for processing and analyzing human movement data.
+
+This package provides functions for converting, processing, analyzing,
+and visualizing biomechanical data (e.g., motion capture, EMG, kinetics).
+
+Example:
+    from biomechzoo import BiomechZoo
+    from biomechzoo.conversion import c3d2zoo
+
+    zoo = BiomechZoo()
+    zoo.conversion.c3d2zoo('path/to/data')
+"""
+
+# Import main class or entry point
+from .biomechzo import BiomechZoo
+
+# Import commonly used submodules
+from . import conversion
+from . import processing
+from . import plotting
+from . import utils
+
+# Define what gets exposed with "from biomechzoo import *"
+__all__ = [
+    "BiomechZoo",
+    "conversion",
+    "processing",
+    "plotting",
+    "utils",
+]
+
+__version__ = "0.4.4"

{biomechzoo-0.4.1 → biomechzoo-0.4.5}/src/biomechzoo/biomechzoo.py

@@ -1,4 +1,6 @@
 import os
+import inspect
+import time
 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
@@ -18,17 +20,28 @@ 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
 
-
 class BiomechZoo:
-    def __init__(self, in_folder, inplace=False, verbose=0):
+    def __init__(self, in_folder, inplace=False, subfolders=None, name_contains=None, verbose=0):
         self.verbose = verbose
         self.in_folder = in_folder
         self.verbose = verbose
-        self.inplace = inplace  # choice to save processed files to new folder
+        self.inplace = inplace               # choice to save processed files to new folder
+        self.subfolders = subfolders         # only run processes on list in subfolder
+        self.name_contains = name_contains   # only run processes on files with name_contains in file name
 
         batchdisp('BiomechZoo initialized', level=1, verbose=verbose)
         batchdisp('verbosity set to: {}'.format(verbose), level=1, verbose=verbose)
-        batchdisp('processing folder set to: {}'.format(self.in_folder), level=1, verbose=verbose)
+        batchdisp('root processing folder set to: {}'.format(self.in_folder), level=1, verbose=verbose)
+        if name_contains is not None:
+            batchdisp('only include files containing name_contains string: {}'.format(self.name_contains), level=1, verbose=verbose)
+        if subfolders is not None:
+            if type(subfolders) is list:
+                batchdisp('only process files in subfolder(s):', level=1, verbose=verbose)
+                for subfolder in self.subfolders:
+                    batchdisp('{}'.format(os.path.join(self.in_folder, subfolder)), level=1, verbose=verbose)
+            else:
+                batchdisp('only process files in subfolder(s): {}'.format(os.path.join(self.in_folder, self.subfolders)), level=1, verbose=verbose)
+
         if inplace:
             batchdisp('Processing mode: overwrite (inplace=True) (each step will be applied to same folder)', level=1, verbose=verbose)
         else:
@@ -50,57 +63,75 @@ class BiomechZoo:
 
     def mvnx2zoo(self, out_folder=None, inplace=False):
         """ Converts all .mvnx files 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='.mvnx')
+        fl = engine(in_folder, extension='.mvnx', name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
             batchdisp('converting mvnx to zoo for {}'.format(f), level=2, verbose=verbose)
             data = mvnx2zoo_data(f)
             f_zoo = f.replace('.mvnx', '.zoo')
             zsave(f_zoo, data, inplace=inplace, out_folder=out_folder, root_folder=in_folder)
-        batchdisp('mvnx to zoo conversion complete', level=1, verbose=verbose)
-
+        method_name = inspect.currentframe().f_code.co_name
+        batchdisp('{} conversion complete for {} files'.format(method_name, len(fl)), level=1, verbose=verbose)
         # Update self.folder after  processing
         self._update_folder(out_folder, inplace, in_folder)
 
     def c3d2zoo(self, out_folder=None, inplace=None):
         """ Converts all .c3d files in the folder to .zoo format """
+        start_time = time.time()
         from ezc3d import c3d
         verbose = self.verbose
         in_folder = self.in_folder
         if inplace is None:
             inplace = self.inplace
-
-        fl = engine(in_folder, extension='.c3d')
+        fl = engine(in_folder, extension='.c3d', name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
             batchdisp('converting c3d to zoo for {}'.format(f), level=2, verbose=verbose)
             c3d_obj = c3d(f)
             data = c3d2zoo_data(c3d_obj)
             f_zoo = f.replace('.c3d', '.zoo')
             zsave(f_zoo, data, inplace=inplace, out_folder=out_folder, root_folder=in_folder)
-        batchdisp('c3d to zoo conversion complete', level=1, verbose=verbose)
-
+        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 csv2zoo(self, out_folder=None, inplace=None):
+    def csv2zoo(self, out_folder=None, inplace=None, skip_rows=0):
         """ 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')
+        fl = engine(in_folder, extension='.csv', 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)
+            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)
-        batchdisp('csv to zoo conversion complete', level=1, verbose=verbose)
+        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')
+            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)
 
@@ -110,67 +141,70 @@ class BiomechZoo:
 
     def phase_angle(self, ch, out_folder=None, inplace=None):
         """ computes phase angles"""
+        start_time = time.time()
         verbose = self.verbose
         in_folder = self.in_folder
         if inplace is None:
             inplace = self.inplace
-
-        fl = engine(in_folder)
+        fl = engine(in_folder, extension='.zoo', name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
             if verbose:
                 batchdisp('computing phase angles for {}'.format(f), level=2, verbose=verbose)
             data = zload(f)
             data = phase_angle_data(data, ch)
-            zsave(f, data, inplace=inplace, root_folder=in_folder, out_folder=out_folder)
-        batchdisp('phase angle computation complete', level=1, verbose=verbose)
+            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 continuous_relative_phase(self, ch_prox, ch_dist, out_folder=None, inplace=None):
         """ computes CRP angles"""
+        start_time = time.time()
         verbose = self.verbose
         in_folder = self.in_folder
         if inplace is None:
             inplace = self.inplace
-
-        fl = engine(in_folder)
+        fl = engine(in_folder, extension='.zoo', name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
             if verbose:
                 batchdisp('computing CRP angles between channel {} (prox) and {} (dist) for {}'.format(ch_prox, ch_dist, f), level=2, verbose=verbose)
             data = zload(f)
             data = continuous_relative_phase_data(data, ch_dist, ch_prox)
-            zsave(f, data, inplace=inplace, root_folder=in_folder, out_folder=out_folder)
-        batchdisp('CRP computation complete', level=1, verbose=verbose)
+            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 split_trial_by_gait_cycle(self, first_event_name, out_folder=None, inplace=None):
         """ split by gait cycle according to event_name"""
+        start_time = time.time()
         verbose = self.verbose
         in_folder = self.in_folder
         if inplace is None:
             inplace = self.inplace
-
-        fl = engine(in_folder)
+        fl = engine(in_folder, extension='.zoo', name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
             f_name = os.path.splitext(os.path.basename(f))[0]
-            batchdisp('splitting by gait cycle  for {} by {}'.format(f, first_event_name), level=2, verbose=verbose)
             data = zload(f)
             split_events = get_split_events(data, first_event_name)
             if split_events is None:
                 print('no event {} found, saving original file'.format(first_event_name))
-                zsave(f, data, inplace=inplace, root_folder=in_folder, out_folder=out_folder)
+                zsave(f, data, inplace=inplace, out_folder=out_folder, root_folder=in_folder)
             else:
                 for i, _ in enumerate(split_events[0:-1]):
                     fl_new = f.replace(f_name, f_name + '_' + str(i + 1))
                     start = split_events[i]
                     end = split_events[i + 1]
+                    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, root_folder=in_folder, out_folder=out_folder)
-
-        batchdisp('splitting by gait cycle complete', level=1, verbose=verbose)
+                    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)
 
         # Update self.folder after  processing
         self._update_folder(out_folder, inplace, in_folder)
@@ -195,130 +229,137 @@ class BiomechZoo:
     #     self._update_folder(out_folder, inplace, in_folder)
     def renameevent(self, evt, nevt, out_folder=None, inplace=None):
         """ renames event evt to nevt in all 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)
+        fl = engine(in_folder, extension='.zoo', name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
             batchdisp('renaming events from {} to {} for {}'.format(evt, nevt ,f), level=2, verbose=verbose)
             data = zload(f)
             data = renameevent_data(data, evt, nevt)
-            zsave(f, data, inplace=inplace, root_folder=in_folder, out_folder=out_folder)
-        batchdisp('rename event complete', level=1, verbose=verbose)
+            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 renamechannnel(self, ch, ch_new, out_folder=None, inplace=None):
         """ renames channels from ch to ch_new in all 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)
+        fl = engine(in_folder, extension='.zoo', name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
             batchdisp('renaming channels from {} to {} for {}'.format(ch, ch_new ,f), level=2, verbose=verbose)
             data = zload(f)
             data = renamechannel_data(data, ch, ch_new)
-            zsave(f, data, inplace=inplace, root_folder=in_folder, out_folder=out_folder)
-        batchdisp('rename channels complete', level=1, verbose=verbose)
+            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 removechannel(self, ch, 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)
+        fl = engine(in_folder, extension='.zoo', name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
             batchdisp('removing channels for {}'.format(f), level=2, verbose=verbose)
             data = zload(f)
             data = removechannel_data(data, ch, mode)
-            zsave(f, data, inplace=inplace, root_folder=in_folder, out_folder=out_folder)
-        batchdisp('remove channel complete', level=1, verbose=verbose)
+            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()
         verbose = self.verbose
         in_folder = self.in_folder
         if inplace is None:
             inplace = self.inplace
-
-        fl = engine(in_folder)
+        fl = engine(in_folder, extension='.zoo', name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
             if verbose:
                 batchdisp('removing channels for {}'.format(f), level=2, verbose=verbose)
             data = zload(f)
             data = explodechannel_data(data)
-            zsave(f, data, inplace=inplace, root_folder=in_folder, out_folder=out_folder)
-        batchdisp('explode channel complete', level=1, verbose=verbose)
+            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 normalize(self, nlen=101, out_folder=None, inplace=None):
         """ time normalizes all channels to length nlen """
+        start_time = time.time()
         verbose = self.verbose
         in_folder = self.in_folder
         if inplace is None:
             inplace = self.inplace
-
-        fl = engine(in_folder)
+        fl = engine(in_folder, extension='.zoo', name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
             if verbose:
                 batchdisp('normalizing channels to length {} for {}'.format(nlen, f), level=2, verbose=verbose)
             data = zload(f)
             data = normalize_data(data, nlen)
-            zsave(f, data, inplace=inplace, root_folder=in_folder, out_folder=out_folder)
-        batchdisp('normalization complete', level=1, verbose=verbose)
+            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 addevent(self, ch, evt_type, evt_name, out_folder=None, inplace=None):
         """ adds events of type evt_type with name evt_name to channel ch """
+        start_time = time.time()
         verbose = self.verbose
         in_folder = self.in_folder
         if inplace is None:
             inplace = self.inplace
-
-        fl = engine(in_folder)
+        fl = engine(in_folder, extension='.zoo', name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
             if verbose:
                 batchdisp('adding event {} to channel {} for {}'.format(evt_type, ch, f), level=2, verbose=verbose)
             data = zload(f)
             data = addevent_data(data, ch, evt_type, evt_name)
-            zsave(f, data, inplace=inplace, root_folder=in_folder, out_folder=out_folder)
-        batchdisp('add event complete', level=1, verbose=verbose)
+            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 partition(self, evt_start, evt_end, out_folder=None, inplace=None):
         """ partitions data between events evt_start and evt_end """
+        start_time = time.time()
         verbose = self.verbose
         in_folder = self.in_folder
         if inplace is None:
             inplace = self.inplace
-
-        fl = engine(in_folder)
+        fl = engine(in_folder, extension='.zoo', name_contains=self.name_contains, subfolders=self.subfolders)
         for f in fl:
             if verbose:
                 batchdisp('partitioning data between events {} and {} for {}'.format(evt_start, evt_end, f), level=2, verbose=verbose)
             data = zload(f)
             data = partition_data(data, evt_start, evt_end)
-            zsave(f, data, inplace=inplace, root_folder=in_folder, out_folder=out_folder)
-        batchdisp('partition complete', level=1, verbose=verbose)
+            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)
 
@@ -340,8 +381,9 @@ class BiomechZoo:
         #     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)
-        # batchdisp('filter data complete', level=1, verbose=verbose)
+        #     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)

{biomechzoo-0.4.1 → biomechzoo-0.4.5}/src/biomechzoo/conversion/csv2zoo_data.py

@@ -5,25 +5,32 @@ import re
 from biomechzoo.utils.compute_sampling_rate_from_time import compute_sampling_rate_from_time
 
 
-def csv2zoo_data(csv_path, header_len=10):
+def csv2zoo_data(csv_path, type='csv',skip_rows=0, freq=None):
+    # todo: check calculation for sampling rate
 
     # Read header lines until 'endheader'
-    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)
-
-    # Step 3: Load data
-    df = pd.read_csv(csv_path, skiprows=header_len)
-    time = df.iloc[:, 0].values  # first column is Time
-    data = df.iloc[:, 1:]
-
-    # S Assemble zoo data
+    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)
+    else:
+        raise ValueError('type must be csv or parquet')
+
+    # Use all columns
+    data = df.iloc[:, 0:]
+
+    # assemble zoo data
     zoo_data = {}
     for ch in data.columns:
         zoo_data[ch] = {
@@ -31,13 +38,26 @@ def csv2zoo_data(csv_path, header_len=10):
             'event': []
         }
 
-    # compute sampling rate
-    fsamp = compute_sampling_rate_from_time(time)
+    # 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:
+            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'] = fsamp
+    zoo_data['zoosystem']['Freq'] = freq
 
     return zoo_data
 

{biomechzoo-0.4.1 → biomechzoo-0.4.5}/src/biomechzoo/processing/explodechannel_data.py

@@ -1,3 +1,5 @@
+import copy
+
 def explodechannel_data(data, channels=None):
     """ Explodes 3D channels (n x 3 arrays) into separate X, Y, Z channels.
 
@@ -10,8 +12,7 @@ def explodechannel_data(data, channels=None):
         data_new (dict): Modified zoo dictionary with exploded channels.
     """
 
-    data_new = data.copy()
-
+    data_new = copy.deepcopy(data)
     # Find default channels if none provided
     if channels is None:
         channels = []

{biomechzoo-0.4.1 → biomechzoo-0.4.5}/src/biomechzoo/processing/partition_data.py

@@ -1,19 +1,20 @@
 from biomechzoo.utils.findfield import findfield
 import warnings
+import copy
 
 
 def partition_data(data, evt_start, evt_end):
     """ partition data for all channels between events evt_start and evt_end"""
 
     # extract event values
-    e1, _ = findfield(data,evt_start)
-    e2, _ = findfield(data,evt_end)
+    e1, _ = findfield(data, evt_start)
+    e2, _ = findfield(data, evt_end)
 
-    data_new = data.copy()
+    data_new = copy.deepcopy(data)
     for ch_name, ch_data in data_new.items():
         if ch_name != 'zoosystem':
             try:
-                data_new[ch_name]['line'] = ch_data[e1[0]:e2[0], :]
+                data_new[ch_name]['line'] = ch_data[e1[0]:e2[0],]
             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
@@ -29,6 +30,7 @@ def partition_data(data, evt_start, evt_end):
                     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
 
     return data_new
@@ -48,4 +50,4 @@ def _partition_event(event_dict, evt_start, evt_end, arr_len):
     #
     #
     #
-    # return event_dict_new
+    # return event_dict_new

{biomechzoo-0.4.1 → biomechzoo-0.4.5}/src/biomechzoo/utils/engine.py

@@ -19,7 +19,7 @@ def engine(root_folder, extension='.zoo', subfolders=None, name_contains=None, v
     Arguments:
         root_folder (str): The root directory path where the search begins.
         extension (str): File extension to search for (e.g., '.zoo', '.c3d'). Default .zoo
-        subfolders (list of str, optional): List of folder names to restrict the search to.
+        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
@@ -28,6 +28,11 @@ def engine(root_folder, extension='.zoo', subfolders=None, name_contains=None, v
     Returns:
         list of str: List of full file paths matching the criteria.
     """
+    # check format of subfolder (string or list)
+    if subfolders is not None:
+        if type(subfolders) is str:
+            subfolders = [subfolders]
+
     matched_files = []
 
     subfolders_set = set(subfolders) if subfolders else None

{biomechzoo-0.4.1 → biomechzoo-0.4.5}/src/biomechzoo/utils/zsave.py

@@ -2,8 +2,10 @@ from scipy.io import savemat
 import inspect
 import os
 
+from biomechzoo.utils.batchdisp import batchdisp
 
-def zsave(fl, data, inplace=True, out_folder=None, root_folder=None):
+
+def zsave(fl, data, inplace=True, out_folder=None, root_folder=None, verbose=False):
     """
     Save zoo data to .zoo file (MAT format)
 
@@ -28,9 +30,9 @@ def zsave(fl, data, inplace=True, out_folder=None, root_folder=None):
 
     # Determine save path
     if inplace:
-        save_path = fl
+        fl_new = fl
+        out_dir = os.path.dirname(fl)
     else:
-        filename = os.path.basename(fl)
         if out_folder is None:
             out_folder = 'processed'
 
@@ -47,4 +49,6 @@ def zsave(fl, data, inplace=True, out_folder=None, root_folder=None):
 
     # Save the .zoo file
     savemat(fl_new, data)
+    batchdisp('all files saved to ' + out_dir, level=1, verbose=verbose)
+
 

{biomechzoo-0.4.1 → biomechzoo-0.4.5}/src/biomechzoo.egg-info/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.4
 Name: biomechzoo
-Version: 0.4.1
+Version: 0.4.5
 Summary: Python implementation of the biomechZoo toolbox
 License-Expression: MIT
 Project-URL: Homepage, https://github.com/mcgillmotionlab/biomechzoo
-Requires-Python: >=3.11
+Requires-Python: <3.12,>=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: ezc3d>=1.5.19
@@ -12,6 +12,7 @@ Requires-Dist: matplotlib>=3.10.6
 Requires-Dist: numpy==2.2.6
 Requires-Dist: pandas>=2.3.2
 Requires-Dist: scipy>=1.16.2
+Requires-Dist: pyarrow>=19.0.0
 Dynamic: license-file
 
 # BiomechZoo for Python
@@ -30,3 +31,15 @@ This is a development version of the biomechzoo toolbox for python.
 - We use Numpy 2.2.6 for compatibility with https://pypi.org/project/numba/
 
 See also http://www.github.com/mcgillmotionlab/biomechzoo or http://www.biomechzoo.com for more information
+
+## Developer notes
+
+### Installing a dev environment
+conda create -n biomechzoo-dev python=3.11
+conda activate biomechzoo-dev
+pip install -e ".[dev]"
+
+### import issues
+if using PyCharm: 
+- Right-click on src/.
+- Select Mark Directory as → Sources Root.

{biomechzoo-0.4.1 → biomechzoo-0.4.5}/src/biomechzoo.egg-info/SOURCES.txt

@@ -1,6 +1,7 @@
 LICENSE
 README.md
 pyproject.toml
+src/__init__.py
 src/biomechzoo/__init__.py
 src/biomechzoo/__main__.py
 src/biomechzoo/biomechzoo.py

{biomechzoo-0.4.1 → biomechzoo-0.4.5}/src/biomechzoo.egg-info/requires.txt

@@ -3,3 +3,4 @@ matplotlib>=3.10.6
 numpy==2.2.6
 pandas>=2.3.2
 scipy>=1.16.2
+pyarrow>=19.0.0

{biomechzoo-0.4.1 → biomechzoo-0.4.5}/src/biomechzoo.egg-info/top_level.txt

@@ -1 +1,2 @@
+__init__
 biomechzoo